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Sample records for microsatellite paternity analysis

  1. Paternity analysis using microsatellite markers to identify pollen donors in an olive grove.

    PubMed

    Mookerjee, Sonali; Guerin, Jenny; Collins, Graham; Ford, Chris; Sedgley, Margaret

    2005-10-01

    Olive (Olea europaea L.) is a wind-pollinated, allogamous species that is generally not considered to be self-compatible. In addition, cross-incompatibilities exist between cultivars that can result in low fruit set if compatible pollinisers are not planted nearby. In this study, microsatellite markers were used to identify 17 genotypes that were potential pollen donors in a commercial olive orchard. DNA typing with the same primers was also applied to 800 olive embryos collected from five cultivars in the grove over 2 years of study. Pollen donors for the cultivars Barnea, Corregiola, Kalamata, Koroneiki, and Mission were estimated by paternity analysis, based on the parental contribution of alleles in the genotypes of the embryos. The exclusion probability for the marker set was 0.998 and paternity was assigned on the basis of the 'most likely method'. Different pollen donors were identified for each of the maternal cultivars indicating that cross-compatibilities and incompatibilities varied between the genotypes studied. Cross-pollination was the principal method of fertilization, as selfing was only observed in two of the embryos studied and both of these were from the cultivar Mission. This is the first report where these techniques have been applied to survey the pollination patterns in an olive grove. The results indicate that careful planning in orchard design is required for efficient pollination between olive cultivars. PMID:16133312

  2. Paternity exclusion in koalas using hypervariable microsatellites.

    PubMed

    Houlden, B A; England, P; Sherwin, W B

    1996-01-01

    Koala microsatellite loci containing the dinucleotide motif (CA)n were isolated from a size-fractionated (250-500 bp) koala genomic library and sequenced. Six locus-specific primer pairs were designed and synthesized for DNA amplification using the polymerase chain reaction (PCR). Microsatellite genotyping of 12 individuals generated unique "fingerprints" for each koala. All six microsatellite loci were polymorphic, with a mean of 6.5 +/- 0.6 alleles/locus. This level of allelic diversity is capable of generating > 4 x 10(9) DNA profiles, making it the most powerful technology for fingerprinting koalas currently available. Observed heterozygosities (H(o)) in the eight unrelated individuals surveyed ranged from 0.25 to 0.75, with a mean of 0.54 +/- 0.06. Mendelian inheritance of the observed polymorphism was confirmed by family studies. We demonstrate that microsatellite loci are ideal genetic markers for paternity exclusion and pedigree analysis of koalas, which have shown little genetic variation using most other methods. PMID:8830092

  3. Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus).

    PubMed

    Worthington Wilmer, J; Allen, P J; Pomeroy, P P; Twiss, S D; Amos, W

    1999-09-01

    Microsatellites were used to conduct an extensive analysis of paternity of grey seals from two Scottish breeding colonies at North Rona (n = 1189) and the Isle of May (n = 694), spanning more than a decade. A maximum of 46% of pups at North Rona and 29% of pups at the Isle of May could be allocated a father, even though the majority of candidate males for specific study sites within each colony were believed to have been sampled. Based on the paternities which could be assigned, both colonies showed evidence of reproductive skew, apparently due to the presence of approximately five males who were exceptionally successful. Some males were assigned paternities at least 10 years before, and colleagues 10 years after, being sampled, implying a reproductive lifespan of at least 10 years, and there are indications that the real maximum lies in the range 15-20 years. Male grey seals appear to have at least two breeding strategies they can adopt. On land, some males benefit from a traditionally polygynous system. However, between 50 and 70% of grey seal pups born at a particular colony are not fathered by males who are likely to be sampled by us, implying that these males seldom venture ashore here. We conclude that aquatic mating may play a much larger role in the grey seal than has previously been thought. PMID:10564447

  4. Paternity Analysis of the Olive Variety “Istrska Belica” and Identification of Pollen Donors by Microsatellite Markers

    PubMed Central

    Jakše, Jernej

    2014-01-01

    The leading olive variety in Slovenia is “Istrska belica” (Olea europaea L.), which currently represents 70% of all olive trees in productive orchards. Paternity analysis based on microsatellite markers was used for genotyping and identification of the potential pollen donors of “Istrska belica” and for assessing the proportion of self-fertilization in monovarietal olive orchards in the Slovene Istria. Seven microsatellite loci were used for genotyping thirty-one olive embryos from “Istrska belica” trees and for all potential pollen donor varieties, which are grown in the region and could participate as pollinators. Genotyping results and allele identification were performed using the FaMoz software. The most probable pollen donor was assigned to 39% of all analyzed embryos. Among all analyzed embryos no single case of self-fertilization was confirmed. According to the present results, the variety “Istrska belica” was in all cases fertilized by foreign pollen. The results will contribute to defining the new guidelines for farmers regarding the proper management and growing practice in monovarietal olive groves. PMID:25097869

  5. Paternity determination of captive bottlenose dolphins (Tursiops truncatus) using microsatellite DNA analysis.

    PubMed

    Sumiyama, Daisuke; Kitamura, Shouichi; Terasawa, Fumio; Hori, Yukiko; Murata, Koichi; Kulski, Jerzy K; Inoko, Hidetoshi

    2008-07-01

    We applied previously published PCR primer pairs to amplify alleles at three polymorphic microsatellite loci to determine the genetic relationship of 6 bottlenose dolphins (Tursiops truncatus) that were living together in a Japanese aquarium. The three microsatellite loci were sufficient to determine the haplotype relationships of the six dolphins, which represented three different generations. It was confirmed that this genotyping method is simple and economical for assessing, establishing and maintaining genetic diversity in captive populations and will become a very effective technique for ex situ conservation in aquariums and zoos. PMID:18685244

  6. Extrapair paternity and maternity in the three-toed woodpecker, Picoides tridactylus: insights from microsatellite-based parentage analysis.

    PubMed

    Li, Meng-Hua; Välimäki, Kaisa; Piha, Markus; Pakkala, Timo; Merilä, Juha

    2009-01-01

    Molecular techniques have revealed that avian mating systems are more diverse and complex than previously thought. We used microsatellite markers to determine genetic parentage, the prevalence of extrapair paternity and quasi-parasitism (i.e. situations where a male's extrapair mate lay in his nest) in a socially monogamous population of three-toed woodpeckers (Picoides tridactylus) in southern Finland. A total of 129 adults and nestlings, representing 5-9 families annually from 2004-2007, were genotyped at up to ten microsatellite loci. The results of genetic assignment tests confirmed that monogamous parentage characterized the majority (84.6%, 22/26) of broods, and that most (93.8%, 75/80) nestlings were the offspring of their social parents. Two of 80 nestlings (2.5%) in two of 26 broods (7.7%) were sired by extrapair males and quasi-parasitism occurred in 3.8% (3/80) of nestlings and 7.7% (2/26) of broods. Hence, the levels of extrapair parentage were low, possibly because both genetic polygyny and polyandry are constrained by the high paternal effort required for parental care. The co-occurrence of low levels of extrapair paternity and quasi-parasitism are discussed in light of ecological and behavioural factors characterizing the species biology. PMID:19924300

  7. Paternity testing using microsatellite DNA markers in captive Adlie penguins (Pygoscelis adeliae).

    PubMed

    Sakaoka, Ken; Suzuki, Isao; Kasugai, Naeko; Fukumoto, Yohei

    2014-01-01

    We investigated the paternity of 39 Adlie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n?=?26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ?4 years old in the exhibit tank during each reproductive season; n?=?9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations. PMID:25157452

  8. Paternity identification in sugarcane polycrosses by using microsatellite markers.

    PubMed

    Xavier, M A; Pinto, L R; Fávero, T M; Perecin, D; Carlini-Garcia, L A; Landell, M G A

    2014-01-01

    Although polycrosses have been used to test the potential of cross-combination of a large number of sugarcane parents, the male parent of the half-sib progenies produced is unknown. The present study aimed to integrate the molecular marker technology to the sugarcane polycross approach by the application of microsatellite markers to identify the male parent of 41 elite clones derived from polycross families. Ten microsatellite [single sequence repeats (SSRs)] primer pairs were used to identify the most likely male parent considering markers present in the selected clone but absent in the female parent. The number of alleles generated by the 10 microsatellite primer pairs ranged from 102 (cross-pollination lantern 4) to 120 (cross-pollination lantern 2) with an average of 113.25 alleles per SSR. The average genetic similarity among the involved parents in the polycrosses was 45.9%. The results of the analysis of the SSR markers absent in the female parent and present only in the selected clone as well as the genetic similarity values allowed the identification of the most likely male parent in 73% of the total clones evaluated and also to detect probable contaminations. The obtained results highlight the importance of using molecular marker technology in the identification and confirmation of the male parent of high-performance clones derived from polycrosses in the sugarcane breeding programs. PMID:24737475

  9. Using rattlesnake microsatellites to determine paternity in captive bushmasters (Lachesis muta).

    PubMed

    Pozarowski, Krystyn; Ivy, Jamie; Herrmann, Hans-Werner

    2013-01-01

    We used 10 microsatellite DNA markers originally described for two Crotalus and one Sistrurus species to infer paternity in a captive-hatched clutch of Lachesis muta. Although the dam was known, records listed two potential sires, which prevented the inclusion of those offspring in a captive breeding program. Samples were collected from both possible sires, the presumed dam and two offspring. Five of the ten markers were paternity informative and either unambiguously identified one of the two males as the sire of the offspring or excluded the other male. A sixth marker identified the sire in one of the two offspring. These results reveal rattlesnake DNA markers as a useful tool in paternity testing and captive breeding management of Lachesis muta. It also indicates that, within the American crotalid radiation, a selection of microsatellite DNA markers cross-amplify and provide useful genotypic information across species and genera. PMID:23468376

  10. Mutation rate analysis at 19 autosomal microsatellites.

    PubMed

    Qian, Xiao-Qin; Yin, Cai-Yong; Ji, Qiang; Li, Kai; Fan, Han-Ting; Yu, Yan-Fang; Bu, Fan-Li; Hu, Ling-Li; Wang, Jian-Wen; Mu, Hao-Fang; Haigh, Steven; Chen, Feng

    2015-07-01

    Previous studies have demonstrated that a large sample size is needed to reliably estimate population- and locus-specific microsatellite mutation rates. Therefore, we conducted a long-term collaboration study and performed a comprehensive analysis on the mutation characteristics of 19 autosomal short tandem repeat (STR) loci. The STR loci located on 15 of 22 autosomal chromosomes were analyzed in a total of 21,106 samples (11,468 parent-child meioses) in a Chinese population. This provided 217,892 allele transfers at 19 STR loci. An overall mutation rate of 1.20 × 10(-3) (95% CI, 1.06-1.36 × 10(-3) ) was observed in the populations across 18 of 19 STR loci, except for the TH01 locus with no mutation found. Most STR mutations (97.7%) were single-step mutations, and only a few mutations (2.30%) comprised two and multiple steps. Interestingly, approximately 93% of mutation events occur in the male germline. The mutation ratios increased with the paternal age at child birth (r = 0.99, p<0.05), but not maternal age. Last, with the combination analysis of the data from the southern Chinese population, we drew a picture of 19 STR mutations in China. In conclusion, the data from this study will provide useful information in parentage testing, kinship analysis, and population genetics. PMID:25820688

  11. Genetic maternity and paternity in a local population of armadillos assessed by microsatellite DNA markers and field data.

    PubMed

    Prodhl, P A; Loughry, W J; McDonough, C M; Nelson, W S; Thompson, E A; Avise, J C

    1998-01-01

    Genetic data from polymorphic microsatellite loci were employed to estimate paternity and maternity in a local population of nine-banded armadillos (Dasypus novemcinctus) in northern Florida. The parentage assessments took advantage of maximum likelihood procedures developed expressly for situations when individuals of neither gender can be excluded a priori as candidate parents. The molecular data for 290 individuals, interpreted alone and in conjunction with detailed biological and spatial information for the population, demonstrate high exclusion probabilities and reasonably strong likelihoods of genetic parentage assignment in many cases; low mean probabilities of successful reproductive contribution to the local population by individual armadillo adults in a given year; and statistically significant microspatial associations of parents and their offspring. Results suggest that molecular assays of highly polymorphic genetic systems can add considerable power to assessments of biological parentage in natural populations even when neither parent is otherwise known. PMID:18811420

  12. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya.

    PubMed

    Oliveira, G A F; Dantas, J L L; Oliveira, E J

    2015-10-01

    The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used. PMID:26280323

  13. Establishing Paternity: An Analysis of Cases from Two Arizona Counties.

    ERIC Educational Resources Information Center

    Nichols-Casebolt, Ann

    1994-01-01

    Used data from sample of 877 child support paternity cases to determine what case characteristics influenced likelihood of successfully establishing paternity. Results indicated demographic differences between cases with and without paternity established but these differences were much less important to establishing paternity than obtaining

  14. A molecular analysis of African lion (Panthera leo) mating structure and extra-group paternity in Etosha National Park.

    PubMed

    Lyke, M M; Dubach, J; Briggs, M B

    2013-05-01

    The recent incorporation of molecular methods into analyses of social and mating systems has provided evidence that mating patterns often differ from those predicted by group social organization. Based on field studies and paternity analyses at a limited number of sites, African lions are predicted to exhibit a strict within-pride mating system. Extra-group paternity has not been previously reported in African lions; however, observations of extra-group associations among lions inhabiting Etosha National Park in Namibia suggest deviation from the predicted within-pride mating pattern. We analysed variation in 14 microsatellite loci in a population of 164 African lions in Etosha National Park. Genetic analysis was coupled with demographic and observational data to examine pride structure, relatedness and extra-group paternity (EGP). EGP was found to occur in 57% of prides where paternity was analysed (n = 7), and the overall rate of EGP in this population was 41% (n = 34). Group sex ratio had a significant effect on the occurrence of EGP (P < 0.05), indicating that variation in pride-level social structure may explain intergroup variation in EGP. Prides with a lower male-to-female ratio were significantly more likely to experience EGP in this population. The results of this study challenge the current models of African lion mating systems and provide evidence that social structure may not reflect breeding structure in some social mammals. PMID:23495802

  15. Comparative analysis of microsatellites and compound microsatellites in T4-like viruses.

    PubMed

    Zhou, Lan; Deng, Liang; Fu, Yongzhuo; Wu, Xiaolong; Zhao, Xiangyan; Chen, Yubao; Li, Mingfu; Tan, Zhongyang

    2016-01-10

    Microsatellites or simple sequence repeats (SSRs) are known to present ubiquitously in genomes of eukaryotes and prokaryotes, as well as viruses. A comprehensive analysis of microsatellites and compound microsatellites (CM) was performed for 67 T4-like bacteriophage genomes. We found that the number of repeats was generally proportional to the size of the genome. CM were more abundant in genic regions, while their relative abundance was higher in intergenic regions. Meanwhile, the number of CM rapidly decreased with the increase of complexity but gradually increased with higher dMAX (maximum distance between any two adjacent microsatellites). (A)n/(T)n, (AT)n/(TA)n and (AAG)n were the most abundant repeats of mono-, di- and trinucleotide microsatellites, respectively. The number of microsatellites in reference sequences was significantly lower than that in corresponding random sequences. This result was mainly attributed to mono- and dinucleotide repeats which hardly exceeded 6bp in T4-like viruses. These observations may be helpful to understand the distribution of microsatellites and viral genetic diversity in T4-like viruses. PMID:26410414

  16. Single cell analysis demonstrating somatic mosaicism involving 11p in a patient with paternal isodisomy and Beckwith-Wiedemann Syndrome

    SciTech Connect

    Bischoff, F.Z.; McCaskill, C.; Subramanian, S.

    1994-09-01

    Beckwith-Wiedemann Syndrome (BWS) is characterized by numerous growth abnormalities including exomphalos, macroglossia, gigantism, and hemihypertrophy or hemihyperplasia. The {open_quotes}BWS gene{close_quotes} appears to be maternally repressed and is suspected to function as a growth factor or regulator of somatic growth, since activation of this gene through a variety of mechanisms appears to result in somatic overgrowth and tumor development. Mosaic paternal isodisomy of 11p has been observed previously by others in patients with BWS by Southern blot analysis of genomic DNA. The interpretation of these results was primarily based on the intensities of the hybridization signals for the different alleles. In our study, we demonstrate somatic mosaicism directly through PCR and single cell analysis. Peripheral blood was obtained from a patient with BWS and initial genomic DNA analysis by PCR was suggestive of somatic mosaicism for paternal isodisomy of 11p. Through micromanipulation, single cells were isolated and subjected to primer extention preamplification. Locus-specific microsatellite marker analyses by PCR were performed to determine the chromosome 11 origins in the preamplified individual cells. Two populations of cells were detected, a population of cells with normal biparental inheritance and a population of cells with paternal isodisomy of 11p and biparental disomy of 11q. Using the powerful approach of single cell analysis, the detected somatic mosaicism provides evidence for a mitotic recombinational event that has resulted in loss of the maternal 11p region and gain of a second copy of paternal 11p in some cells. The direct demonstration of mosaicism may explain the variable phenotypes and hemihypertrophy often observed in BWS.

  17. Optimization of microsatellite analysis for genetic mapping

    SciTech Connect

    Hughes, A.E. )

    1993-02-01

    A method for typing microsatellite polymorphisms is described. It involves amplification using the polymerase chain reaction with one primer 5[prime] end-labeled with [sup 32]P. Alleles are separated by denaturing gel electrophoresis and detected by autoradiography. Standardized conditions allow accurate typing of almost all microsatellite polymorphisms, and results are usually obtained within 24 h. 4 refs., 1 fig.

  18. Establishing paternity in whooping cranes (Grus Americana) by DNA analysis

    USGS Publications Warehouse

    Longmire, J.L.; Gee, G.F.; Hardekopf, C.L.; Mark, G.A.

    1992-01-01

    DNA fingerprinting was used to study paternity and genetic variability within a captive flock of Whooping Cranes (Grus americana). Fingerprint patterns for 42 individuals were obtained by digesting genomic crane DNAs with HaeIII followed by electrophoresis, blotting, and hybridization to the M13 minisatellite probe. Despite finding reduced levels of genetic variation in the Whooping Crane due to a population 'bottleneck,' these polymorphisms were successfully used to determine paternity in six of seven cases of captive propagation where the maternal-offspring relationship was known, but where the sire was unknown. These determinations of paternity are required for effective genetic management of. the crane flock. These results also revealed a number of heterozygous minisatellite loci that will be valuable in future assessments of genetic variability in this endangered species.

  19. Microsatellite analysis of Saccharomyces uvarum diversity.

    PubMed

    Masneuf-Pomarede, Isabelle; Salin, Franck; Börlin, Marine; Coton, Emmanuel; Coton, Monika; Jeune, Christine Le; Legras, Jean-Luc

    2016-03-01

    Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities. PMID:26772797

  20. Prenatal and newborn paternity testing with DNA analysis.

    PubMed

    Csete, K; Beer, Zs; Varga, T

    2005-01-17

    In rape against youthful girls which yields pregnancy after the abortion DNA examinations can be performed from the aborted foetal material to provide evidence of paternity of the suspect. In our present work we demonstrate six cases: four of them are rape cases and two where the mother abandoned her newborn baby. These cases proved that DNA-STR profiles can be determined from foetus after the abortion and perpetrator of a rape can be found. Due to our result we suggest that not only placenta but also bloody vernix caseosa is useful tissue for identifying the putative mother because vernix caseosa can be the carrier of the mother's blood. PMID:15694732

  1. Mosaic Analysis with Double Markers Reveals Cell-Type Specific Paternal Growth Dominance

    PubMed Central

    Hippenmeyer, Simon; Johnson, Randy L.; Luo, Liqun

    2013-01-01

    SUMMARY Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used Mosaic Analysis with Double Markers (MADM) in mice to create uniparental chromosomal disomies (UPDs) and to visualize imprinting effects with unprecedented single cell resolution. While Chr.12 UPD did not produce detectable phenotypes, Chr.7 UPD caused highly significant paternal growth dominance in the liver and lung but not the brain or heart. A single gene on Chr.7, encoding the secreted Insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on Chr. 7 acting cell-autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects. PMID:23453967

  2. [Screening of peafowl microsatellite primers and analysis of genetic diversity].

    PubMed

    Bao, Wen-Bin; Chen, Guo-Hong; Shu, Jing-Ting; Xu, Qi; Li, Hui-Fang

    2006-10-01

    The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing. PMID:17035182

  3. Microsatellite Marker Analysis as a Typing System for Candida glabrata

    PubMed Central

    Foulet, F.; Nicolas, N.; Eloy, O.; Botterel, F.; Gantier, J.-C.; Costa, J.-M.; Bretagne, S.

    2005-01-01

    Candida glabrata is one of the most important causes of nosocomial fungal infection. We investigated, using a multiplex PCR, three polymorphic microsatellite markers, RPM2, MTI, and ERG3, in order to obtain a rapid genotyping method for C. glabrata. One set of primers was designed for each locus, and one primer of each set was dye labeled to read PCR signals using an automatic sequencer. Eight reference strains including other Candida species and 138 independent C. glabrata clinical isolates were tested. The clinical isolates were collected from different anatomical sites of adult patients either hospitalized in different wards of two different hospitals or not hospitalized. Since C. glabrata is haploid, one single PCR product for each PCR set was obtained and assigned to an allele. The numbers of different alleles were 5, 7, and 15 for the RPM2, MTI, and ERG3 loci, respectively. The number of allelic associations was 21, leading to a discriminatory power of 0.84. The markers were stable after 25 subcultures, and the amplifications were specific for C. glabrata. A factorial correspondence analysis did not indicate any correlation between the 21 multilocus genotypes and the clinical data (source, sex, ward, anatomical sites). Microsatellite marker analysis is a rapid and reliable technique to investigate clinical issues concerning C. glabrata. However, its discriminatory power should be improved by testing other polymorphic microsatellite loci. PMID:16145109

  4. Analysis of new microsatellite markers developed from reported sequences of Japanese flounder Paralichthys olivaceus

    NASA Astrophysics Data System (ADS)

    Yu, Haiyang; Jiang, Liming; Chen, Wei; Wang, Xubo; Wang, Zhigang; Zhang, Quanqi

    2010-12-01

    The expressed sequence tags (ESTs) of Japanese flounder, Paralichthys olivaceus, were selected from GenBank to identify simple sequence repeats (SSRs) or microsatellites. A bioinformatic analysis of 11111 ESTs identified 751 SSR-containing ESTs, including 440 dinucleotide, 254 trinucleotide, 53 tetranucleotide, 95 pentanucleotide and 40 hexanucleotide microsatellites respectively. The CA/TG and GA/TC repeats were the most abundant microsatellites. AT-rich types were predominant among trinucleotide and tetranucleotide microsatellites. PCR primers were designed to amplify 10 identified microsatellites loci. The PCR results from eight pairs of primers showed polymorphisms in wild populations. In 30 wild individuals, the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average PIC value was 0.8. These microsatellite markers should prove to be a useful addition to the microsatellite markers that are now available for this species.

  5. Microsatellite data analysis for population genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  6. Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale.

    PubMed Central

    Nielsen, R; Mattila, D K; Clapham, P J; Palsbll, P J

    2001-01-01

    We present a new method for paternity analysis in natural populations that is based on genotypic data that can take the sampling fraction of putative parents into account. The method allows paternity assignment to be performed in a decision theoretic framework. Simulations are performed to evaluate the utility and robustness of the method and to assess how many loci are necessary for reliable paternity inference. In addition we present a method for testing hypotheses regarding relative reproductive success of different ecologically or behaviorally defined groups as well as a new method for estimating the current population size of males from genotypic data. This method is an extension of the fractional paternity method to the case where only a proportion of all putative fathers have been sampled. It can also be applied to provide abundance estimates of the number of breeding males from genetic data. Throughout, the methods were applied to genotypic data collected from North Atlantic humpback whales (Megaptera novaeangliae) to test if the males that appear dominant during the mating season have a higher reproductive success than the subdominant males. PMID:11290722

  7. Microsatellite (simple sequence repeat) marker-based paternity analysis of a seven-parent sugarcane polycross

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is not feasible to make all possible cross combinations among elite parents used in sugarcane (Saccharum spp.) breeding programs, particularly within a single year. Hence, the polycross approach has been used to maximize the number of cross combinations that can be represented among progeny. Th...

  8. MICROSATELLITE-BASED PATERNITY ANALYSIS OF A SEVEN-PARENT SUGARCANE POLYCROSS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is virtually impossible to make all cross combinations among even the most elite parents used in breeding programs. Hence, the polycross approach has been used in sugarcane breeding to maximize the number of cross combinations that could be represented among progeny at the seedling stage of test...

  9. Paternity and relatedness in wild chimpanzee communities

    PubMed Central

    Vigilant, Linda; Hofreiter, Michael; Siedel, Heike; Boesch, Christophe

    2001-01-01

    The genetic structure of three contiguous wild chimpanzee communities in West Africa was examined to determine the extent to which the community, the mixed-sex social unit of chimpanzees, represents a closed reproductive unit. An analysis of paternity for 41 offspring resulted in 34 cases of paternity assignment to an adult male belonging to the same community. Among the 14 offspring for which all potential within-community fathers have been tested, one likely case of extra-group paternity (EGP) has been identified, suggesting an incidence of EGP of 7%. This more extensive analysis contradicts a previous genetic study of the Taï chimpanzees that inferred 50% extra-group fathers. We suggest, based on direct comparison of results for 33 individuals at 1 microsatellite locus and direct comparison of paternity assignments for 11 offspring, that the error rate in the previous study was too high to produce accurate genotypes and assignments of paternity and hence caused the false inference of a high rate of EGP. Thus, the community is the primary but not exclusive unit for reproduction in wild chimpanzees, and females do not typically reproduce with outside males. Despite the inferred low level of gene flow from extra-community males, relatedness levels among the community males are not significantly higher than among community females, and the distribution of genetic relationships within the group suggests that, rather than a primarily male-bonded social structure, the group is bonded through relationships between males and females. Kinship may explain cooperative behaviors directed against other communities, but is unlikely to explain the high levels of affiliation and cooperation seen for male within-community interactions. PMID:11606765

  10. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    PubMed Central

    Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

    2013-01-01

    Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73?kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

  11. Multiple paternity and hybridization in two smooth-hound sharks

    PubMed Central

    Marino, Ilaria A. M.; Riginella, Emilio; Gristina, Michele; Rasotto, Maria B.; Zane, Lorenzo; Mazzoldi, Carlotta

    2015-01-01

    Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations. PMID:26257113

  12. Multiple paternity and hybridization in two smooth-hound sharks.

    PubMed

    Marino, Ilaria A M; Riginella, Emilio; Gristina, Michele; Rasotto, Maria B; Zane, Lorenzo; Mazzoldi, Carlotta

    2015-01-01

    Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations. PMID:26257113

  13. Challenges in analysis and interpretation of microsatellite data for population genetic studies

    PubMed Central

    Putman, Alexander I; Carbone, Ignazio

    2014-01-01

    Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics. PMID:25540699

  14. Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis.

    PubMed

    George, B; Alam, Ch Mashhood; Kumar, R Vinoth; Gnanasekaran, Prabu; Chakraborty, S

    2015-08-01

    The compound microsatellites consist of two or more individual microsatellites, originate from mutation or imperfection in simple repeat sequences. The reports on systematic analysis of the occurrence, size and density of compound microsatellite (cSSR) types are very rare. Our study indicates that cSSRs are clustered at specific regions in the begomovirus genomes. cSSRs were overrepresented in majority of begomovirus genomes indicating that they might have some functional significance. Further, non-random distribution pattern of cSSR in begomovirus genomes was significantly correlated with the recombination breakpoint positions in the genome. The analysis of cSSR regions in the viral genome indicates the presence of stem loop (hairpin) secondary structure. The significance of these findings in biology of geminiviruses is discussed based on our present understanding of recombination and repetitive DNA. To our knowledge, this is the first analysis suggesting the possible association between recombination and microsatellites in any viral genome. PMID:25817404

  15. Genetic variation analysis of the Bali street dog using microsatellites

    PubMed Central

    Irion, Dawn N; Schaffer, Alison L; Grant, Sherry; Wilton, Alan N; Pedersen, Niels C

    2005-01-01

    Background Approximately 800,000 primarily feral dogs live on the small island of Bali. To analyze the genetic diversity in this population, forty samples were collected at random from dogs in the Denpasar, Bali region and tested using 31 polymorphic microsatellites. Australian dingoes and 28 American Kennel Club breeds were compared to the Bali Street Dog (BSD) for allelic diversity, heterozygosities, F-statistics, GST estimates, Nei's DA distance and phylogenetic relationships. Results The BSD proved to be the most heterogeneous, exhibiting 239 of the 366 total alleles observed across all groups and breeds and had an observed heterozygosity of 0.692. Thirteen private alleles were observed in the BSD with an additional three alleles observed only in the BSD and the Australian dingo. The BSD was related most closely to the Chow Chow with a FST of 0.088 and also with high bootstrap support to the Australian dingo and Akita in the phylogenetic analysis. Conclusions This preliminary study into the diversity and relationship of the BSD to other domestic and feral dog populations shows the BSD to be highly heterogeneous and related to populations of East Asian origin. These results indicate that a viable and diverse population of dogs existed on the island of Bali prior to its geographic isolation approximately 12,000 years ago and has been little influenced by domesticated European dogs since that time. PMID:15701179

  16. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

  17. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about how SSR markers are being transmitted into reproductive and zygotic cells. To illustrate this, a high-throughput molecular genotyping experiment was conducted on 964 individ...

  18. Paternal Child Care and Relationship Quality: A Longitudinal Analysis of Reciprocal Associations

    ERIC Educational Resources Information Center

    Schober, Pia S.

    2012-01-01

    This study explored reciprocal associations between paternal child-care involvement and relationship quality by following British couples from the birth of a child until he or she reached school age. It extends the literature by distinguishing between paternal engagement in absolute terms and relative to the mother and by considering relationship…

  19. Paternalism modernised.

    PubMed Central

    Weiss, G B

    1985-01-01

    The practice of paternalism has changed along with developments in medicine, philosophy, law, sociology and psychology. Physicians have learned that a patient's values are a factor in determining what is best for that patient. Modern paternalism continues to be guided by the principle that the physician decides what is best for the patient and pursues that course of action, taking into account the values and interests of the patient. In the autonomy model of the doctor-patient relationship, patient values are decisive. In the paternalistic model, they are but one among several factors the physician must consider in making a medical decision. Although difficult to practise because of limitations in empathising with another person, modern paternalism remains a way to achieve maximum patient benefit. PMID:4078856

  20. Comparative analysis of microsatellite variability in five macaw species (Psittaciformes, Psittacidae): Application for conservation

    PubMed Central

    Presti, Flavia T.; Oliveira-Marques, Adriana R.; Caparroz, Renato; Biondo, Cibele; Miyaki, Cristina Y.

    2011-01-01

    Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots) compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable]), and two unthreatened red macaws (Ara chloropterus and Ara macao). Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus) to 0.85 (A. macao). As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation. PMID:21734841

  1. Multiplexed systems of microsatellite markers for genetic analysis of mahogany, Swietenia macrophylla King (Meliaceae), a threatened neotropical timber species.

    PubMed

    Lemes, M R; Brondani, R P V; Grattapaglia, D

    2002-01-01

    Mahogany (Swietenia macrophylla King [Meliaceae]) is the most valuable hardwood species in the neotropics. Its conservation status has been the subject of increasing concern due to overexploitation and habitat destruction. In this work we report the development and characterization of 10 highly variable microsatellite loci for S. macrophylla. Twenty-nine percent of the 126 sequenced mahogany clones yielded useful microsatellite loci. Three high-throughput genotyping systems were developed based on polymerase chain reaction (PCR) multiplexing of these mahogany loci. We identified a total of 158 alleles in 121 adult individuals of S. macrophylla, with an average of 15.8 alleles (range 11-25) per locus. All loci showed Mendelian inheritance in open-pollinated half-sib families. The mean expected heterozygosity was 0.84 and the mean observed heterozygosity was 0.73. The combined probability of identity-the probability that two individuals selected at random from a population would have identical genotypes--was 7.0 x 10(-15), and combined probability of paternity exclusion was 0.999998 overall loci. These microsatellite loci permit precise estimates of parameters such as gene flow, mating system, and paternity, thus providing important insights into the population genetics and conservation of S. macrophylla. PMID:12407218

  2. Single-male paternity in coelacanths.

    PubMed

    Lampert, Kathrin P; Blassmann, Katrin; Hissmann, Karen; Schauer, Jürgen; Shunula, Peter; el Kharousy, Zahor; Ngatunga, Benjamin P; Fricke, Hans; Schartl, Manfred

    2013-01-01

    Latimeria chalumnae, a 'living fossil,' is of great scientific interest, as it is closely related to the aquatic ancestors of land-living tetrapods. Latimeria show internal fertilization and bear live young, but their reproductive behaviour is poorly known. Here we present for the first time a paternity analysis of the only available material from gravid females and their offspring. We genotype two L. chalumnae females and their unborn brood for 14 microsatellite loci. We find that the embryos are closely related to each other and never show more than three different alleles per locus, providing evidence for a single father siring all of the offspring. We reconstruct the father's genotype but cannot identify it in the population. These data suggest that coelacanths have a monogamous mating system and that individual relatedness is not important for mate choice. PMID:24048316

  3. [Analysis of genetic diversity of population of Northern Eurasia from autosomal microsatellite loci].

    PubMed

    Stepanov, V A; Spiridonova, M G; Tadinova, V N; Puzyrev, V P

    2003-10-01

    The paper presents the results of analysis of the gene pools of several North Eurasian ethnic groups (Buryats, Evenks, Altaians, Russians, Kyrgyzes, Tuvinians, Tatars, and Ukrainians) examined using a panel of autosomal microsatellite markers (D4S397, D5S393, D7S640, D8S514, D9S161, D10S197, D11S1358, D12S364, and D13S173) mapped on different chromosomes and represented by the (CA)n dinucleotide repeats. In the group of populations examined the proportion of genetic variability at microsatellite loci explained by interpopulation differences was about 2.5%, while genetic differences between the individuals within a population accounted for 97.5% of this variability. Analysis of genetic relationships among the populations revealed substantial differences between the populations belonging to the Indo-European and Altaic linguistic families in gene diversity at microsatellite loci. PMID:14658343

  4. Mosaic paternal genome-wide uniparental isodisomy with down syndrome.

    PubMed

    Darcy, Diana; Atwal, Paldeep Singh; Angell, Cathy; Gadi, Inder; Wallerstein, Robert

    2015-10-01

    We report on a 6-month-old girl with two apparent cell lines; one with trisomy 21, and the other with paternal genome-wide uniparental isodisomy (GWUPiD), identified using single nucleotide polymorphism (SNP) based microarray and microsatellite analysis of polymorphic loci. The patient has Beckwith-Wiedemann syndrome (BWS) due to paternal uniparental disomy (UPD) at chromosome location 11p15 (UPD 11p15), which was confirmed through methylation analysis. Hyperinsulinemic hypoglycemia is present, which is associated with paternal UPD 11p15.5; and she likely has medullary nephrocalcinosis, which is associated with paternal UPD 20, although this was not biochemically confirmed. Angelman syndrome (AS) analysis was negative but this testing is not completely informative; she has no specific features of AS. Clinical features of this patient include: dysmorphic features consistent with trisomy 21, tetralogy of Fallot, hemihypertrophy, swirled skin hyperpigmentation, hepatoblastoma, and Wilms tumor. Her karyotype is 47,XX,+21[19]/46,XX[4], and microarray results suggest that the cell line with trisomy 21 is biparentally inherited and represents 40-50% of the genomic material in the tested specimen. The difference in the level of cytogenetically detected mosaicism versus the level of mosaicism observed via microarray analysis is likely caused by differences in the test methodologies. While a handful of cases of mosaic paternal GWUPiD have been reported, this patient is the only reported case that also involves trisomy 21. Other GWUPiD patients have presented with features associated with multiple imprinted regions, as does our patient. PMID:26219535

  5. Microsatellite analysis in the genome of Acanthaceae: An in silico approach

    PubMed Central

    Kaliswamy, Priyadharsini; Vellingiri, Srividhya; Nathan, Bharathi; Selvaraj, Saravanakumar

    2015-01-01

    Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future. PMID:25709226

  6. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants.

    PubMed

    George, Biju; Bhatt, Bhavin S; Awasthi, Mayur; George, Binu; Singh, Achuit K

    2015-11-01

    Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distributionof SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2)=0.5, P<0.05) and relative abundance (R (2)=0.6, P<0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants. PMID:25999216

  7. Meta-analysis of microsatellite data from US and Brazil sheep breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this study was to adapt a methodology for merging independent microsatellite data sets and exploring the differences between Brazilian (BZ) and US hair breeds of sheep. Eleven markers were in common for the US-BZ dataset and were merged for analysis of genetic structure and diversity. It ...

  8. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    PubMed Central

    Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies. PMID:26697878

  9. [Extrapair paternity in Parus major].

    PubMed

    Yin, Li-Xian; Zhang, Lei; Chang, Peng; Li, Jing; Wan, Dong-Mei

    2013-02-01

    Mating systems, as an evolutionary stable strategy, play an important role in animal reproductive process and result from an animal's adaption to their environment, including their inter-specific environment. In the 1980s, extrapair paternity (EPP) was first noted in the eurychoric species, the Great Tit, Parus major. As earlier studies indicated, morphology, physiology, behavior, ecological characteristics and mating systems of eurychoric species differ greatly between areas or populations. Accordingly, we analyzed the mating system of the Great Tit (P.m.minor) in Fairy Cave National Nature Reserve, Liaoning, China. We collected total parent-offspring blood samples from 22 broods. We used 8 hypervariable loci, which were selected from 11 reported microsatellite loci for paternity test. In conjunction with the known genetic pattern of the female parent, the accuracy of the paternity testing reached 99.98% with this genetic data. Results of paternity testing showed that 7 of 22 broods (31.8%) had extra-pair nestling, with 16 of 197 nestlings (8.12%) a result of extra-pair fertilizations. The EPP rate of the Great Tit we noted in Liaoning is obviously lower than those in other passerine forest birds (less than 10%). Though between 55.6% and 9.1% extrapair offspring were found among the different nests, we were, however, unable to find any explanatory rule. PMID:23389978

  10. Do Paternal Arrest and Imprisonment Lead to Child Behaviour Problems and Substance Use? A Longitudinal Analysis

    ERIC Educational Resources Information Center

    Kinner, Stuart A.; Alati, Rosa; Najman, Jake M.; Williams, Gail M.

    2007-01-01

    Background: Children of prisoners are at increased risk of impaired health, behavioural problems and substance misuse; however, the causal pathways to these problems are unclear. Under some circumstances, parental imprisonment may result in improved outcomes for the child. This study investigates the impact of paternal arrest and imprisonment on

  11. Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)

    PubMed Central

    Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Loureno; Buso, Glucia Salles Cortopassi; Buso, Jos Amauri; Ferreira, Mrcio Elias

    2004-01-01

    Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker development in melon. One-hundred and forty-four new markers were developed from Tsp-AG/TC genomic library. This is the first reported attempt of successfully using enriched library for microsatellite marker development in the species. A sample of the microsatellite markers tested proved efficient for genetic analysis of melon, including genetic distance estimates and identity tests. Linkage analysis indicated that the markers developed are dispersed throughout the genome and should be very useful for genetic analysis of melon. PMID:15149552

  12. Microsatellite analysis of population structure in Canadian polar bears.

    PubMed

    Paetkau, D; Calvert, W; Stirling, I; Strobeck, C

    1995-06-01

    Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait-Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long-distance seasonal movements undertaken by polar bears. PMID:7663752

  13. Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

    PubMed Central

    Matute, Daniel R.; Sepulveda, Victoria E.; Quesada, Lina M.; Goldman, Gustavo H.; Taylor, John W.; Restrepo, Angela; McEwen, Juan G.

    2006-01-01

    Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an important human systemic mycosis in Latin America. Recently, the existence of three different phylogenetic species (S1, PS2, and PS3) of P. brasiliensis was demonstrated. Despite being genetically isolated, all three species were capable of inducing disease in both humans and animals, although lower virulence has been found with the PS2 species. The available molecular methods developed to characterize and type strains have not been useful for assigning isolates to the described species, creating the need for molecular markers capable of distinguishing genetically isolated groups. Here, we describe a PCR and sequencing-based microsatellite marker system that is stable, easy to assay, adaptable to large series of isolates, and discriminatory enough to be used as a typing system in identifying the three proposed species of P. brasiliensis. In addition, this system provides an unambiguous tool for strain discrimination between two (S1 and PS2) of the three phylogenetic species. PMID:16757613

  14. [Identification and analysis of a novel microsatellite marker flanking porcine myostatin gene (MSTN)].

    PubMed

    Jiang, Yun-Liang; Li, Ning; Zhao, Xing-Bo; Hu, Xiao-Xiang; Liu, Zhao-Liang; Deng, Xue-Mei; Wu, Chang-Xin; Du, Li-Xin; Cao, Ji-Sheng

    2004-05-01

    In animal breeding, microsatellite marker plays an important role in constructing genetic maps, QTL mapping and function analysis of structural genes. Myostatin, also known as GDF8, is a negative regulator of skeletal muscle mass and, in swine, it is evidenced to be related to birth weight and average daily gain from 60 kg to 100 kg of body weight. In present study, by subcloning and sequencing,we identified a novel microsatellite marker which is useful for fine QTL mapping for meat traits. A BAC clone containing porcine MSTN was extracted and digested with EcoR I to recover the fragment of > 4 kb for subcloning in pGEM-3zf (+). Sequencing and alignment results showed that this subcloned fragment was not from porcine MSTN, but included a tandem repeat of (TG) 13, which is a novel microsatellite marker (GenBank accession number: AF454400) flanking MSTN. To exclude its vector origin we designed specific primers flanking this marker and successfully amplified this fragment from porcine genome. Through a pedigree analysis of a double-muscled Yorshire strain, we found that it is inherited in a co-dominant manner. We also checked the gene frequencies of this locus in 381 unrelated individuals of 7 pig breeds, namely Laiwu,Landrace, Yorkshire,Duroc, Peterian, Min and Erhualian. Only two alleles were detected, the repeating number of which are 13 (allele A) and 19 (allele B) respectively, which indicated that it is a low poly morphic microsatellite marker. In addition, the frequencies of the two alleles are different between the two types of pig breeds, while allele A is dominant in Chinese local breeds, allele B is dominant in imported breeds. Alignment with AY208121 indicate that this locus is located 42 kb downstream of porcine MSTN. We speculate that this microsatellite DNA is an important marker both in fine QTL mapping for meat traits and in the expression study of porcine MSTN. PMID:15478608

  15. Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae).

    PubMed

    Viruel, M A; Hormaza, J I

    2004-03-01

    We report 12 microsatellites enriched in CT repeats obtained from a genomic library of the lychee ( Litchi chinensis Sonn.) cultivar Mauritius. The polymorphisms revealed by these microsatellites were evaluated in a collection of 21 lychee cultivars. A total of 59 fragments were detected with these 12 SSRs, with an average of 4.9 bands/SSR. Three primer pairs seem to amplify more than a single locus. The mean expected and observed heterozygosities over the 9 single-locus SSRs averaged 0.571 (range: 0.137-0.864) and 0.558 (range: 0.169-0.779) respectively. The total value for the probability of identity was 7.53 x 10(-5). In addition, the selected SSRs were used to amplify DNA from four longan cultivars. Eleven of the 12 SSRs produced amplification fragments in longan, and eight of these fragments were polymorphic. All except two of the products amplified from longan were the same size as those amplified from lychee, suggesting a close genetic proximity between the two species. The SSRs studied produced 22 different patterns, allowing the unambiguous identification of 16 lychee and the 4 longan cultivars studied. Discrimination was possible with just four selected microsatellites. Two groups with two and three undistinguishable cultivars were obtained, reflecting probable synonymies. Unweighted pair-group method of artimetic averages (UPGMA) cluster analysis divided the lychee cultivars studied into two main groups, one consisting of ancient cultivars and the other with more diverse recent cultivars. This is the first report of microsatellite development in the Sapindaceae, and the results demonstrate the usefulness of microsatellites for identification, similarity studies and germplasm conservation in lychee and related species. PMID:14605809

  16. Mechanical Aspects of Design, Analysis, and Testing for the NORSAT-1 Microsatellite

    NASA Astrophysics Data System (ADS)

    Kanji, Shahil

    NORSAT-1 is a multi-payload microsatellite mission funded by the Norwegian Space Center, with three overall objectives: investigating solar radiation, space plasma research, and developing improved methods for detection and management of ship traffic. The successful development of the NORSAT-1 platform aims to lay the groundwork for additional low-cost microsatellites in the NORSAT series, and expand the Norwegian presence in space and space-based ship tracking technologies. This thesis provides some insight into the NORSAT-1 satellite platform design, and focuses heavily on the mechanical aspects of design, analysis, and testing. The structural design is detailed from the early conceptual design phases, and follows the development to the manufacturing, integration, and testing of the flight spacecraft. Validation of the design through finite element modeling is presented, along with the development and design of two honeycomb composite solar panels, and two deployable whip antennas.

  17. Mosaic analysis and tumor induction in zebrafish by microsatellite instability-mediated stochastic gene expression

    PubMed Central

    Koole, Wouter; Tijsterman, Marcel

    2014-01-01

    Mosaic analysis, in which two or more populations of cells with differing genotypes are studied in a single animal, is a powerful approach to study developmental mechanisms and gene function in vivo. Over recent years, several genetic methods have been developed to achieve mosaicism in zebrafish, but despite their advances, limitations remain and different approaches and further refinements are warranted. Here, we describe an alternative approach for creating somatic mosaicism in zebrafish that relies on the instability of microsatellite sequences during replication. We placed the coding sequences of various marker proteins downstream of a microsatellite and out-of-frame; in vivo frameshifting into the proper reading frame results in expression of the protein in random individual cells that are surrounded by wild-type cells. We optimized this approach for the binary Gal4-UAS expression system by generating a driver line and effector lines that stochastically express Gal4-VP16 or UAS:H2A-EGFP and self-maintaining UAS:H2A-EGFP-Kaloop, respectively. To demonstrate the utility of this system, we stochastically expressed a constitutively active form of the human oncogene H-RAS and show the occurrence of hyperpigmentation and sporadic tumors within 5 days. Our data demonstrate that inducing somatic mosaicism through microsatellite instability can be a valuable approach for mosaic analysis and tumor induction in Danio rerio. PMID:24487406

  18. Analysis of population genetic structure of Indian Anopheles culicifacies species A using microsatellite markers

    PubMed Central

    2013-01-01

    Background Anopheles culicifacies sensu lato is an important vector of malaria in Southeast Asia contributing to almost 70% of malaria cases in India. It exists as morphologically similar sibling species A, B, C, D and E with varied geographical distribution patterns. Vector control measures have been difficult for this important vector as the sibling species have developed varying levels of resistance to the currently used insecticides. In view of the importance of this vector, we developed and validated a set of microsatellite markers and the same were used to analyze the population genetic structure of five different geographical populations of An. culicifacies A. Methods Anopheles culicifacies A samples were collected from different localities across India, and genotyping was performed using eight microsatellite markers on ABI Prism 310 Genetic Analyzer. Several statistical analyses were performed to ascertain the genetic diversity that exists within and between the populations. Results The markers were found to be moderately polymorphic in the populations. Genetic analysis indicated significant genetic differentiation between the majority of the population pairs analyzed and was not found to be related to the geographical distances between populations. Conclusion This is the first and successful attempt to test the microsatellite markers developed for population genetic analysis of An. culicifacies A. Host feeding and breeding habits of species A suggest that factors other than ecological and geographical barriers were responsible for the genetic differentiation that has been observed between the populations. PMID:23742032

  19. Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses.

    PubMed

    Alam, Chaudhary Mashhood; Singh, Avadhesh Kumar; Sharfuddin, Choudhary; Ali, Safdar

    2014-01-01

    An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences. PMID:24291012

  20. Mosaic analysis and tumor induction in zebrafish by microsatellite instability-mediated stochastic gene expression.

    PubMed

    Koole, Wouter; Tijsterman, Marcel

    2014-07-01

    Mosaic analysis, in which two or more populations of cells with differing genotypes are studied in a single animal, is a powerful approach to study developmental mechanisms and gene function in vivo. Over recent years, several genetic methods have been developed to achieve mosaicism in zebrafish, but despite their advances, limitations remain and different approaches and further refinements are warranted. Here, we describe an alternative approach for creating somatic mosaicism in zebrafish that relies on the instability of microsatellite sequences during replication. We placed the coding sequences of various marker proteins downstream of a microsatellite and out-of-frame; in vivo frameshifting into the proper reading frame results in expression of the protein in random individual cells that are surrounded by wild-type cells. We optimized this approach for the binary Gal4-UAS expression system by generating a driver line and effector lines that stochastically express Gal4-VP16 or UAS:H2A-EGFP and self-maintaining UAS:H2A-EGFP-Kaloop, respectively. To demonstrate the utility of this system, we stochastically expressed a constitutively active form of the human oncogene H-RAS and show the occurrence of hyperpigmentation and sporadic tumors within 5 days. Our data demonstrate that inducing somatic mosaicism through microsatellite instability can be a valuable approach for mosaic analysis and tumor induction in Danio rerio. PMID:24487406

  1. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Qi, Haigang; Li, Li; Zhang, Guofan

    2014-01-01

    Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (?24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

  2. Early diagnosis and monitoring of superficial transitional cell carcinoma by microsatellite analysis on urine sediment.

    PubMed

    Bartoletti, Riccardo; Dal Canto, Maurizio; Cai, Tommaso; Piazzini, Mauro; Travaglini, Fabrizio; Gavazzi, Andrea; Rizzo, Michelangelo

    2005-03-01

    It has recently been shown that allelic abnormalities, detected by microsatellite analysis of the DNA extracted from urine sediment, can be successfully used for the detection of transitional cell carcinoma (TCC) of the bladder. The diagnostic accuracy of urinary cytology, urinary bladder cancer (UBC) marker, bladder tumor antigen (BTA) and microsatellite sequence alterations was compared in 42 patients who were recruited for the study. Of them, 30 had been diagnosed with TCC at cystoscopy plus biopsy (group A). Seven patients without any apparent lesions after trans-urethral resection (TUR) and 6 subsequent weeks of endovesical administration of bacillus Calmette-Guerin (BCG), had irritative symptoms. None of them had positive cytology or TCC bladder mucosa biopsies (group B). In the control group were 5 other subjects who were affected by benign prostatic hypertrophy and candidates for prostatectomy (group C). Urine and blood samples were obtained from all of the patients before surgery. Tumor tissue and normal mucosa samples were taken from groups A and C during surgery. Different urinary sediment analyses were performed by using both nuclear medicine and molecular tests. UBC and BTA-t analyses were carried out using monoclonal antibody tests while microsatellite analyses were performed using extracted DNA and electrophoresis of polymerase chain reaction (PCR) products on 13 different primers. Urinary cytological examinations were carried out using the Autocyte Preparation System(R). Urinary cytology confirmed the presence of TCC in 13.3% of patients. The BTA-t marker allowed the identification of 73.3% of cancers with 50% specificity; the UBC marker identified 63.3% of the cases with 41.6% specificity. Microsatellite analysis permitted the identification of 83.3% of the tumors with 100% specificity. DNA analysis demonstrated high sensitivity in patients affected by superficial (81.4%) or G1 (80%) tumors, even when cytological studies demonstrated little or no sensitivity. Microsatellite analysis is a highly-sensitive and specific marker for TCC diagnosis and its monitoring, especially in patients with low-stage and low-grade tumors. Other testing procedures failed to increase urinary cytological diagnostic significance. PMID:15706429

  3. Identification of geographically distributed sub-populations of Leishmania (Leishmania) major by microsatellite analysis

    PubMed Central

    2008-01-01

    Background Leishmania (Leishmania) major, one of the agents causing cutaneous leishmaniasis (CL) in humans, is widely distributed in the Old World where different species of wild rodent and phlebotomine sand fly serve as animal reservoir hosts and vectors, respectively. Despite this, strains of L. (L.) major isolated from many different sources over many years have proved to be relatively uniform. To investigate the population structure of the species highly polymorphic microsatellite markers were employed for greater discrimination among it's otherwise closely related strains, an approach applied successfully to other species of Leishmania. Results Multilocus Microsatellite Typing (MLMT) based on 10 different microsatellite markers was applied to 106 strains of L. (L.) major from different regions where it is endemic. On applying a Bayesian model-based approach, three main populations were identified, corresponding to three separate geographical regions: Central Asia (CA); the Middle East (ME); and Africa (AF). This was congruent with phylogenetic reconstructions based on genetic distances. Re-analysis separated each of the populations into two sub-populations. The two African sub-populations did not correlate well with strains' geographical origin. Strains falling into the sub-populations CA and ME did mostly group according to their place of isolation although some anomalies were seen, probably, owing to human migration. Conclusion The model- and distance-based analyses of the microsatellite data exposed three main populations of L. (L.) major, Central Asia, the Middle East and Africa, each of which separated into two sub-populations. This probably correlates with the different species of rodent host. PMID:18577226

  4. Autosomal microsatellite and mtDNA genetic analysis in Sicily (Italy).

    PubMed

    Romano, V; Cal, F; Ragalmuto, A; D'Anna, R P; Flugy, A; De Leo, G; Giambalvo, O; Lisa, A; Fiorani, O; Di Gaetano, C; Salerno, A; Tamouza, R; Charron, D; Zei, G; Matullo, G; Piazza, A

    2003-01-01

    DNA samples from 465 blood donors living in 7 towns of Sicily, the largest island of Italy, have been collected according to well defined criteria, and their genetic heterogeneity tested on the basis of 9 autosomal microsatellite and mitochondrial DNA polymorphisms for a total of 85 microsatellite allele and 10 mtDNA haplogroup frequencies. A preliminary account of the results shows that: a) the samples are genetically heterogeneous; b) the first principal coordinates of the samples are correlated more with their longitude than with their latitude, and this result is even more remarkable when one outlier sample (Butera) is not considered; c) distances among samples calculated from allele and haplogroup frequencies and from the isonymy matrix are weakly correlated (r = 0.43, P = 0.06) but such correlation disappears (r = 0.16) if the mtDNA haplogroups alone are taken into account; d) mtDNA haplogroups and microsatellite distances suggest settlements of people occurred at different times: divergence times inferred from microsatellite data seem to describe a genetic composition of the town of Sciacca mainly derived from settlements after the Roman conquest of Sicily (First Punic war, 246 BC), while all other divergence times take root from the second to the first millennium BC, and therefore seem to backdate to the pre-Hellenistic period. A more reliable association of these diachronic genetic strata to different historical populations (e.g. Sicani, Elymi, Siculi), if possible, must be postponed to the analysis of more samples and hopefully more informative uniparental DNA markers such as the recently available DHPLC-SNP polymorphisms of the Y chromosome. PMID:12556234

  5. Male mating success in an aquatically mating pinniped, the harbour seal (Phoca vitulina), assessed by microsatellite DNA markers.

    PubMed

    Coltman, D W; Bowen, W D; Wright, J M

    1998-05-01

    Similar to many other pinniped species, harbour seals (Phoca vitulina) mate exclusively at sea. Here we present the first attempt to measure male mating success in an aquatically mating pinniped. Male mating success was estimated by paternity analysis in two cohorts of pups born at Sable Island, Nova Scotia, Canada, using microsatellite DNA markers. The genotypes of 275 pups born in 1994 and 1995 were compared to those of 90 candidate males at six microsatellite loci using a likelihood approach to resolve paternity. Paternity could be assigned for two, 22, 40 and 85 pups at confidence levels of 95, 80, 65 and 50%, respectively. Most successful males were assigned the paternity of a single offspring, suggesting a low variance in male mating success relative to most pinniped species. The proportion of paternal half sibs within cohorts and between maternally related sibs estimated by maximum likelihood were not significantly different from zero. It is thus unlikely that most offspring were sired by a small number of highly successful unsampled males, and that female harbour seals do not usually exhibit fidelity to the same male in sequential breeding seasons. A low level of polygyny in Sable Island harbour seals is consistent with predictions based on their breeding ecology, as females are highly mobile and widely dispersed in the aquatic mating environment at Sable Island. PMID:9633104

  6. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    PubMed Central

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  7. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness

    PubMed Central

    Telfer, Emily J.; Stovold, Grahame T.; Li, Yongjun; Silva-Junior, Orzenil B.; Grattapaglia, Dario G.; Dungey, Heidi S.

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource available with the EuCHIP60k, opens a whole new array of opportunities for high-throughput, genome-wide or targeted genotyping in species of Eucalyptus. PMID:26158446

  8. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids.

    PubMed

    Lu, X; Zhou, H; Pan, Y-B; Chen, C Y; Zhu, J R; Chen, P H; Li, Y-R; Cai, Q; Chen, R K

    2015-01-01

    No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis- and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S1) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S1 populations. Within the S1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S1 population. PIC values of the five SSR markers were greater in pollen than S1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders. PMID:26782486

  9. Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

    PubMed Central

    Regidor-Cerrillo, Javier; Dez-Fuertes, Francisco; Garca-Culebras, Alicia; Moore, Dadn P.; Gonzlez-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Daz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

    2013-01-01

    The cyst-forming protozoan parasite Neosporacaninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N. caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N. caninum, which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N. caninum-derived reference isolates from around the world and 96 N. caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N. caninum. Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N. caninum samples. Geographic sub-structuring was present in the country populations according to pairwise FST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N. caninum MLGs in cattle. PMID:23940816

  10. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    PubMed Central

    2012-01-01

    Background Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD) was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop. PMID:22305491

  11. Evaluation of bull prolificacy on commercial beef cattle ranches using DNA paternity analysis.

    PubMed

    Van Eenennaam, A L; Weber, K L; Drake, D J

    2014-06-01

    SNP-based DNA testing was used to assign paternity to 5,052 calves conceived in natural service multisire breeding pastures from 3 commercial ranches in northern California representing 15 calf crops over 3 yr. Bulls present for 60 to 120 d at a 25:1 cow to bull ratio in both fall and spring breeding seasons in ∼40 ha or smaller fenced breeding pastures sired a highly variable (P < 0.001) number of calves (Ncalf), ranging from 0 (4.4% of bulls present in any given breeding season) to 64 calves per bull per breeding season, with an average of 18.9 ± 13.1. There was little variation in Ncalf among ranches (P = 0.90), years (P = 0.96), and seasons (P = 0.94). Bulls varied widely (P < 0.01) in the average individual 205-d adjusted weaning weight (I205) of progeny, and I205 varied between years (P < 0.01) and seasons (P < 0.01) but not ranches (P = 0.29). The pattern for cumulative total 205-d adjusted weaning weight of all progeny sired by a bull (T205) was highly correlated to Ncalf, with small differences between ranches (P = 0.35), years (P = 0.66), and seasons (P = 0.20) but large differences (P < 0.01) between bulls, ranging from an average of 676 to 8,838 kg per bull per calf crop. The peak Ncalf occurred at about 5 yr of age for bulls ranging from 2 to 11 yr of age. Weekly conception rates as assessed by date of calving varied significantly and peaked at wk 3 of the calving season. The distribution of calves born early in the calving season was disproportionately skewed toward the highly prolific bulls. The DNA paternity testing of the subset of those calves born in wk 3 of the calving season was highly predictive of overall bull prolificacy and may offer a reduced-cost DNA-based option for assessing prolificacy. Prolificacy of young bulls in their first breeding season was positively linearly related (P < 0.05) to subsequent breeding seasons, explaining about 20% of the subsequent variation. Prolificacy was also positively linearly related (P < 0.05) to scrotal circumference (SC) EPD for Angus bulls that had SC EPD Beef Improvement Federation accuracies greater than 0.05. Varying prolificacy of herd bulls has implications for the genetic composition of replacement heifers, with the genetics of those bulls siring an increased number of calves being disproportionately represented in the early-born replacement heifer pool. PMID:24753384

  12. Microsatellite and Mitochondrial Diversity Analysis of Native Pigs of Indo-Burma Biodiversity Hotspot.

    PubMed

    Sahoo, Nihar Ranjan; Nesa, Nashimun; Naskar, Soumen; Banik, Santanu; Pankaj, Prabhat Kumar; Sahoo, Monalisa

    2016-01-01

    Assessment of genetic diversity in indigenous animals is an important and essential task for animal genetic improvement studies as well as conservation decision-making. The genetic diversity and evolutionary relationships among geographically and phenotypically distinct three pig breeds/types native to Indo-Burma and Eastern Himalayan global biodiversity hotspots were determined by genotyping with a panel of 22 ISAG recommended microsatellite loci as well as sequencing partial MTRNR1gene. The mean number of alleles per locus, effective number of alleles and observed heterozygosity were found to be 11.27 0.85, 5.29 0.34, and 0.795 0.01, respectively. The moderate FST value (0.115 0.01) indicated a fair degree of genetic differentiation among the native breeds. The Nei's unbiased genetic identity estimates indicated less genetic distance (0.2909) between Niang Megha and Tenyi Vo pigs than the both individually with Ghoongroo breed. The divergence time was also estimated from the microsatellite analysis. Analysis of MTRNR1gene revealed distinct clustering of native Indian pigs with Chinese pigs over European pigs. The study revealed the abundance of genetic variation within native Indian pigs and their relationships as well as genetic distances. PMID:26695527

  13. Selection of an effective microsatellite marker system for genetic control and analysis of gerbil populations in China.

    PubMed

    Du, X Y; Li, W; Sa, X Y; Li, C L; Lu, J; Wang, Y Z; Chen, Z W

    2015-01-01

    Although gerbils have been widely used in many areas of biological research over many years, there is currently no effective genetic quality control system available. In the present study, we sought to establish a microsatellite marker system for quality control and con-ducted an optimized analysis of 137 microsatellite loci in two labora-tory gerbil populations and one wild population. Independent sample t-tests on the mean effective allele number, mean of Shannon's infor-mation index, and mean HE suggested that 28 of the 137 microsatellite markers were informative for gerbil genetic control. Analysis of 4 labo-ratory gerbil populations and 1 wild population using the 28 microsatel-lite loci indicated that allele numbers varied from 1.9639 (Guangzhou, GZ) to 6.6071 (North-West wild, NW). The average of HO versus HE was 0.6236/0.3802, 0.6671/0.4159, 0.4185/0.3464, 0.4592/0.3821, and 0.3972/0.4167 for the Beijing, NW, Hangzhou, Dalian, and GZ popula-tions, respectively. The GZ population showed the greatest differentia-tion, having higher RST and Nei's standard genetic distances. An AMO-VA revealed high genetic differentiation among the five populations (FST = 0.296). The microsatellite system established here is effective and will be important in future studies for genetic quality control and monitoring of gerbil breeds. PMID:26400333

  14. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

    PubMed Central

    2012-01-01

    Background Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited ?- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L. asiaticus' in Florida were not clearly understood, the less-pervasive groups may have been introduced directly from Asia or via Brazil. Notably, the recent outbreak of HLB in Florida probably occurred through multiple introductions. Microsatellite markers developed in this study provide adequate discriminatory power for the identification and differentiation of closely-related isolates, as well as for genetic studies of 'Ca. L. asiaticus'. PMID:22433492

  15. Genotype Reconstruction of Paternity in European Lobsters (Homarus gammarus).

    PubMed

    Ellis, Charlie D; Hodgson, David J; Andr, Carl; Srdalen, Tonje K; Knutsen, Halvor; Griffiths, Amber G F

    2015-01-01

    Decapod crustaceans exhibit considerable variation in fertilisation strategies, ranging from pervasive single paternity to the near-ubiquitous presence of multiple paternity, and such knowledge of mating systems and behaviour are required for the informed management of commercially-exploited marine fisheries. We used genetic markers to assess the paternity of individual broods in the European lobster, Homarus gammarus, a species for which paternity structure is unknown. Using 13 multiplexed microsatellite loci, three of which are newly described in this study, we genotyped 10 eggs from each of 34 females collected from an Atlantic peninsula in the south-western United Kingdom. Single reconstructed paternal genotypes explained all observed progeny genotypes in each of the 34 egg clutches, and each clutch was fertilised by a different male. Simulations indicated that the probability of detecting multiple paternity was in excess of 95% if secondary sires account for at least a quarter of the brood, and in excess of 99% where additional sire success was approximately equal. Our results show that multiple paternal fertilisations are either absent, unusual, or highly skewed in favour of a single male among H. gammarus in this area. Potential mechanisms upholding single paternal fertilisation are discussed, along with the prospective utility of parentage assignments in evaluations of hatchery stocking and other fishery conservation approaches in light of this finding. PMID:26566271

  16. Genotype Reconstruction of Paternity in European Lobsters (Homarus gammarus)

    PubMed Central

    Ellis, Charlie D.; Hodgson, David J.; André, Carl; Sørdalen, Tonje K.; Knutsen, Halvor; Griffiths, Amber G. F.

    2015-01-01

    Decapod crustaceans exhibit considerable variation in fertilisation strategies, ranging from pervasive single paternity to the near-ubiquitous presence of multiple paternity, and such knowledge of mating systems and behaviour are required for the informed management of commercially-exploited marine fisheries. We used genetic markers to assess the paternity of individual broods in the European lobster, Homarus gammarus, a species for which paternity structure is unknown. Using 13 multiplexed microsatellite loci, three of which are newly described in this study, we genotyped 10 eggs from each of 34 females collected from an Atlantic peninsula in the south-western United Kingdom. Single reconstructed paternal genotypes explained all observed progeny genotypes in each of the 34 egg clutches, and each clutch was fertilised by a different male. Simulations indicated that the probability of detecting multiple paternity was in excess of 95% if secondary sires account for at least a quarter of the brood, and in excess of 99% where additional sire success was approximately equal. Our results show that multiple paternal fertilisations are either absent, unusual, or highly skewed in favour of a single male among H. gammarus in this area. Potential mechanisms upholding single paternal fertilisation are discussed, along with the prospective utility of parentage assignments in evaluations of hatchery stocking and other fishery conservation approaches in light of this finding. PMID:26566271

  17. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    NASA Astrophysics Data System (ADS)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  18. Analysis of olive fly invasion in California based on microsatellite markers.

    PubMed

    Zygouridis, N E; Augustinos, A A; Zalom, F G; Mathiopoulos, K D

    2009-04-01

    The olive fruit fly, Bactrocera oleae, is the main pest of the olive fruit and its expansion is exclusively restricted to the cultivation zone of the olive tree. Even though olive production has a century-old history in California, the olive fly was first detected in the Los Angeles area in 1998. Within 5 years of the first observation, the insect was reported from all olive cultivation areas of the state. Field-collected flies from five locations in California and another from Israel were analyzed on the basis of microsatellite polymorphisms in 10 microsatellite loci. These results were integrated with those of a previous study of olive fly populations around the European part of the Mediterranean basin. The analysis pointed to the eastern part of the Mediterranean as the putative source of the observed invasion. Moreover, samples from California were quite different from Mediterranean samples implying the participation of phenomena such as genetic drift during the invasion and expansion of the olive fly in California. PMID:19107137

  19. Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry.

    PubMed

    Ardalan, Arman; Oskarsson, Mattias; Natanaelsson, Christian; Wilton, Alan N; Ahmadian, Afshin; Savolainen, Peter

    2012-03-01

    The dingo (Canis lupus dingo) is an iconic animal in the native culture of Australia, but archaeological and molecular records indicate a relatively recent history on the continent. Studies of mitochondrial DNA (mtDNA) imply that the current dingo population was founded by a small population of already tamed dogs from Southeast Asia. However, the maternal genetic data might give a unilateral picture, and the gene pool has yet to be screened for paternal ancestry. We sequenced 14,437bp of the Y-chromosome (Y-chr) from two dingoes and one New Guinea Singing Dog (NGSD). This positioned dingo and NGSD within the domestic dog Y-chr phylogeny, and produced one haplotype not detected before. With this data, we characterized 47 male dingoes in 30 Y-chr single-nucleotide polymorphism sites using protease-mediated allele-specific extension technology. Only two haplotypes, H3 and H60, were found among the dingoes, at frequencies of 68.1 and 31.9%, respectively, compared to 27 haplotypes previously established in the domestic dog. While H3 is common among Southeast Asian dogs, H60 was specifically found in dingoes and the NGSD, but was related to Southeast Asian dog Y-chr haplotypes. H3 and H60 were observed exclusively in the western and eastern parts of Australia, respectively, but had a common range in Southeast. Thus, the Y-chr diversity was very low, similar to previous observations for d-loop mtDNA. Overall genetic evidence suggests a very restricted introduction of the first dingoes into Australia, possibly from New Guinea. This study further confirms the dingo as an isolated feral dog. PMID:22618967

  20. [Analysis of microsatellite loci of the chloroplast genome in the genus Capsicum (Pepper)].

    PubMed

    Ryzhova, N N; Kochieva, E Z

    2004-08-01

    Six plastome microsatellites were examined in 43 accessions of the genus Capsicum. In total, 33 allelic variants were detected. A specific haplotype of chloroplast DNA was identified for each Capsicum species. Species-specific allelic variants were found for most wild Capsicum species. The highest intraspecific variation was observed for the C. baccatum plastome. Low cpDNA polymorphism was characteristic of C. annuum: the cpSSRs were either monomorphic or dimorphic. The vast majority of C. annuum accessions each had alleles of one type. Another allele type was rare and occurred only in wild accessions. The results testified again to genetic conservation of C. annuum and especially its cultivated forms. The phylogenetic relationships established for the Capsicum species on the basis of plastome analysis were similar to those inferred from the morphological traits, isozyme patterns, and molecular analysis of the nuclear genome. PMID:15523848

  1. Isolation and characterization of microsatellite markers for Bertholletia excelsa (Lecythidaceae) population genetic analysis.

    PubMed

    Sujii, P S; Inglis, P W; Ciampi, A Y; Solferini, V N; Azevedo, V C R

    2013-01-01

    Seven polymorphic microsatellite markers were developed and validated for Bertholletia excelsa (Brazil nut tree) population genetic studies. This species is a widespread monotypic Amazonian tree with high non-timber economic value. Unfortunately, Brazil nut production is currently less than 25% of historical production levels, because of extensive deforestation. All pairs of primers produced clearly interpretable and polymorphic bands. No linkage disequilibrium was observed in an analysis of 46 individuals from one population, three to seven alleles per locus were observed; the expected heterozygosity ranged from 0.378 to 0.978, with significant heterozygote excess for four loci. An analysis of individuals from two populations showed private alleles at all loci. These primer pairs will be useful for population studies, especially for comparing samples from different parts of the Amazon forest. PMID:24301788

  2. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    PubMed

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-01-01

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy. PMID:20486088

  3. Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis.

    PubMed

    Parida, Swarup K; Yadava, Devendra K; Mohapatra, Trilochan

    2010-01-01

    Microsatellites present in the transcribed regions of the genome have the potential to reveal functional diversity. Unigene sequence databases are the sources of such genic microsatellites with unique flanking sequences and genomic locations even in complex polyploids. The present study was designed to assay the unigenes of Brassica napus and B. rapa for various microsatellite repeats, and to design markers and use them in comparative genome analysis and study of evolution. The average frequency of microsatellites in Brassica unigenes was one in every 7.25 kb of sequence, as compared with one in every 8.57 kb of sequence in Arabidopsis thaliana. Trinucleotide motifs coding for serine and the dinucleotide motif GA were most abundant. We designed 2374 and 347 unigene-based microsatellite (UGMS) markers including 541 and 58 class I types in B. napus and B. rapa, respectively, and evaluated their use across diverse species and genera. Most of these markers (93.3%) gave successful amplification of target microsatellite motifs, which was confirmed by sequencing. Interspecific polymorphism between B. napus and B. rapa detected in silico for the UGMS markers was 4.16 times higher in 5' untranslated regions than in coding sequences. Physical anchoring of Brassica UGMS markers on the A. thaliana genome indicated their significance in studying the evolutionary history of A. thaliana genomic duplications in relation to speciation. Comparative physical mapping identified 85% of Brassica unigenes as single copy and gave clues for the presence of conserved primordial gene order. Complex chromosomal rearrangements such as inversions, tandem and segmental duplications, and insertions/deletions were evident between A. thaliana and B. rapa genomes. The results obtained have encouraging implications for the use of UGMS markers in comparative genome analysis and for understanding evolutionary complexities in the family Brassicaceae. PMID:20130749

  4. The impact of extensive clonal growth on fine-scale mating patterns: a full paternity analysis of a lily-of-the-valley population (Convallaria majalis)

    PubMed Central

    Vandepitte, Katrien; De Meyer, Tim; Jacquemyn, Hans; Roldán-Ruiz, Isabel; Honnay, Olivier

    2013-01-01

    Background and Aims The combination of clonality and a mating system promoting outcrossing is considered advantageous because outcrossing avoids the fitness costs of selfing within clones (geitonogamy) while clonality assures local persistence and increases floral display. The spatial spread of genetically identical plants (ramets) may, however, also decrease paternal diversity (the number of sires fertilizing a given dam) and fertility, particularly towards the centre of large clumped clones. This study aimed to quantify the impact of extensive clonal growth on fine-scale paternity patterns in a population of the allogamous Convallaria majalis. Methods A full analysis of paternity was performed by genotyping all flowering individuals and all viable seeds produced during a single season using AFLP. Mating patterns were examined and the spatial position of ramets was related to the extent of multiple paternity, fruiting success and seed production. Key Results The overall outcrossing rate was high (91 %) and pollen flow into the population was considerable (27 %). Despite extensive clonal growth, multiple paternity was relatively common (the fraction of siblings sharing the same father was 0·53 within ramets). The diversity of offspring collected from reproductive ramets surrounded by genetically identical inflorescences was as high as among offspring collected from ramets surrounded by distinct genets. There was no significant relationship between the similarity of the pollen load received by two ramets and the distance between them. Neither the distance of ramets with respect to distinct genets nor the distance to the genet centre significantly affected fruiting success or seed production. Conclusions Random mating and considerable pollen inflow most probably implied that pollen dispersal distances were sufficiently high to mitigate local mate scarcity despite extensive clonal spread. The data provide no evidence for the intrusion of clonal growth on fine-scale plant mating patterns. PMID:23439847

  5. Multiple paternity in the freshwater snail, Potamopyrgus antipodarum

    PubMed Central

    Soper, Deanna M; Delph, Lynda F; Lively, Curt M

    2012-01-01

    Mating multiply may incur costs, such as exposure to predators and to sexually transmitted diseases. Nevertheless, it may be favored, in spite of these costs, as a way to increase the genetic diversity of offspring through fertilization by multiple males. Here, we tested for multiple paternity in a freshwater snail (Potamopyrgus antipodarum), which is host to several species of sterilizing trematode worms. Using microsatellites markers, we found multiple paternity in two different snail populations, with as many as seven males fertilizing a single female. In addition, high evenness of sire fertilization was found within individual broods. Multiple paternity can occur for a variety of reasons; however, given that these populations experience high risk of infection by a sterilizing trematode, one potential explanation may be that multiple paternity and high evenness of sire fertilizations increase the chances of the production of parasite-resistant offspring. PMID:23301182

  6. Phylogenetic analysis and species allocation of individual equids using microsatellite data.

    PubMed

    Krger, K; Gaillard, C; Stranzinger, G; Rieder, S

    2005-04-01

    The taxonomic status of all equid species is not completely unravelled. This is of practical relevance for conservation initiatives of endangered, fragmented equid populations, such as the Asiatic wild asses (in particular Equus hemionus onager and E. hemionus kulan). In this study, a marker panel consisting of 31 microsatellite loci was used to assess species demarcation and phylogeny, as well as allocation of individuals (n = 120) to specific populations of origin (n = 11). Phylogenetic analysis revealed coalescence times comparable with those previously published from fossil records and mtDNA data. Using Bayesian approaches, it was possible to distinguish between the studied equids, although individual assignment levels varied. The observed results support the maintenance of separate captive conservation herds for E. hemionus onager and E. hemionus kulan. The first molecular genetic results for E. hemionus luteus remained contradictory, as they unexpectedly indicated a closer genetic relationship between E. hemionus luteus and E. kiang holderi compared with the other hemiones. PMID:16130461

  7. System Performance Analysis of Three Dimensional Reaction Wheel for the Attitude Control of Microsatellites

    NASA Astrophysics Data System (ADS)

    Shirasawa, Yoji; Tsuda, Yuichi

    This paper presents a novel attitude control device which is called three dimensional reaction wheel (3DRW). 3DRW consists of only one levitated spherical mass which can rotate around arbitrary axes. This leads to the reduction of the weight and volume of the device as compared to existing reaction wheel. Furthermore, this device has no mechanical contact between rotor and stator, so the failure caused by the mechanical contact would be reduced. In this paper, the results of the analysis and experiment on the dynamics and control of 3DRW are shown. In the experiments of the rotation control, the air bearing system is used. Using this device, the characteristics of rotation of the spherical mass are obtained. To verify the feasibility of the concept of 3DRW, the experiments of angular velocity feedback control are carried out. The results of experiments are applied to the numerical simulation of the attitude control for microsatellites, and the feasibility of 3DRW is verified.

  8. Genetic Variation Between Two Cucumber Genotypes Inferred from Genome-wide Microsatellite Polymorphism Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability at microsatellite loci has been used widely to infer the extent of genetic diversity among related plant taxa. However, typically, only the most polymorphic loci in the genome were analyzed that may result in a biased, and generally overestimated picture of genome-wide microsatellite div...

  9. Paternal obesity negatively affects male fertility and assisted reproduction outcomes: a systematic review and meta-analysis.

    PubMed

    Campbell, Jared M; Lane, Michelle; Owens, Julie A; Bakos, Hassan W

    2015-11-01

    This systematic review investigated the effect of paternal obesity on reproductive potential. Databases searched were Pubmed, Ovid, Web of Science, Scopus, Cinahl and Embase. Papers were critically appraised by two reviewers, and data were extracted using a standardized tool. Outcomes were: likelihood of infertility, embryo development, clinical pregnancy, live birth, pregnancy viability, infant development, sperm; concentration, morphology, motility, volume, DNA fragmentation, chromatin condensation, mitochondrial membrane potential (MMP), and seminal plasma factors. Thirty papers were included, with a total participant number of 115,158. Obese men were more likely to experience infertility (OR = 1.66, 95% CI 1.53-1.79), their rate of live birth per cycle of assisted reproduction technology (ART) was reduced (OR = 0.65, 95% CI 0.44-0.97) and they had a 10% absolute risk increase of pregnancy non-viability. Additionally, obese men had an increased percentage of sperm with low MMP, DNA fragmentation, and abnormal morphology. Clinically significant differences were not found for conventional semen parameters. From these findings it can be concluded that male obesity is associated with reduced reproductive potential. Furthermore, it may be informative to incorporate DNA fragmentation analysis and MMP assessment into semen testing, especially for obese men whose results suggest they should have normal fertility. PMID:26380863

  10. Microsatellite-Based Fingerprinting of Western Blackberries from Plants, IQF Berries and Puree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The blackberry industry needs a reliable method to ensure trueness-to-type of blackberry products. Microsatellite markers or simple sequence repeats (SSRs) are ideal for cultivar fingerprinting, paternity testing and identity certification. Fingerprinting is valuable for variety identification, qual...

  11. Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers

    SciTech Connect

    Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr.

    1994-05-15

    Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

  12. Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps.

    PubMed

    Goossens, B; Chikhi, L; Taberlet, P; Waits, L P; Allain, D

    2001-01-01

    The genetic structure of the Alpine marmot, Marmota marmota, was studied by an analysis of five polymorphic microsatellite loci. Eight locations were sampled in the French Alps, one from Les Ecrins valley (n = 160), another from La Sassire valley (n = 289) and the six others from the Maurienne valley (n = 139). Information on social group structure was available for both Les Ecrins and La Sassire but not for the other samples. The high levels of genetic diversity observed are at odds with the results obtained using microsatellites, minisatellites and allozymes on Alpine marmots from Germany, Austria and Switzerland. Strong deficits in heterozygotes were found in Les Ecrins and La Sassire. They are caused by a Wahlund effect due to the family structure (i.e. differentiation between the family groups). The family groups exhibit excess of heterozygotes rather than deficits. This may be caused by outbreeding and this is compatible with recent results from the genetics of related social species when information on the social structure is taken into account. The observed outbreeding could be the result of females mating with transient males or males coming from neighbouring colonies. Both indicate that the species may not be as monogamous as is usually believed. The results are also compatible with a male-biased dispersal but do not allow us to exclude some female migration. We also found a significant correlation between geographical and genetic distance indicating that isolation by distance could be an issue in marmots. This study is the first that analysed populations of marmots taking into account the social structure within populations and assessing inbreeding at different levels (region, valley, population, and family groups). Our study clearly demonstrated that the sampling strategy and behavioural information can have dramatic effects on both the results and interpretation of the genetic data. PMID:11251786

  13. Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes

    PubMed Central

    Babaei, Alireza; Tabaei-Aghdaei, Seyed Reza; Khosh-Khui, Morteza; Omidbaigi, Reza; Naghavi, Mohammad Reza; Esselink, Gerhard D; Smulders, Marinus JM

    2007-01-01

    Background Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran. Results All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus). Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions). It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions) were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran. Conclusion This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding. PMID:17346330

  14. Population genetic structure and phylogeography of cyprinid fish, Labeo dero (Hamilton, 1822) inferred from allozyme and microsatellite DNA marker analysis.

    PubMed

    Chaturvedi, Anshumala; Mohindra, Vindhya; Singh, Rajeev K; Lal, Kuldeep K; Punia, Peyush; Bhaskar, Ranjana; Mandal, Anup; Narain, Lalit; Lakra, W S

    2011-06-01

    We examined population structure of Labeo dero (Hamilton, 1822) from different riverine locations in India using 10 polymorphic allozyme and eight microsatellite loci. For analysis, 591 different tissue samples were obtained from commercial catches covering a wide geographic range. Allozyme variability (An = 1.28-1.43, Ho = 0.029-0.071) was much lower than for microsatellites (An = 4.625-6.125, Ho = 0.538-0.633). Existence of rare alleles was found at three allozyme (MDH-2, GPI and PGDH) and at two microsatellite loci (R-3 and MFW-15). Deviation from Hardy-Weinberg equilibrium (P < 0.05, after the critical probability levels were adjusted for sequential Bonferroni adjustment) could be detected at three loci (EST-1, -2 and XDH) whereas, after correction for null alleles, two microsatellite loci (MFW-1,-15) deviated from HWE in the river Yamuna. Fst for all the samples combined over all allozyme loci was found to be 0.059 suggesting that 5.9% of the total variation was due to genetic differentiation while microsatellite analysis yielded 0.019 which was concordant to mean Rst (0.02). Hierarchical partition of genetic diversity (AMOVA) showed that greater variability (approx. 95%) was due to within population component than between geographical regions. Based on distribution of genetic differentiation detected by both markers, at least five different genetic stocks of L. dero across its natural distribution could be identified. These results are useful for the evaluation and conservation of L. dero in natural water bodies. PMID:21132388

  15. Limiting dilution analysis of the allo-MHC anti-paternal cytotoxic T cell response. I: Normal primigravid and multiparous pregnancies.

    PubMed Central

    Manyonda, I T; Pereira, R S; Pearce, J M; Sharrock, C E

    1993-01-01

    Anti-paternal cytotoxic T lymphocyte precursor frequencies (CTLpF) were determined by limiting dilution analysis (LDA) in the peripheral blood of eight primigravid and seven multiparous women during the three trimesters of pregnancy. In five of these women the responses to cord blood lymphocytes (CBL) and paternal lymphocytes were also determined at the time of delivery and at 6 weeks post delivery. As controls, CTLpF against unrelated third party donors were determined. A wide range of CTLpF against all three groups of targets was found in both the primigravid and multiparous women, reflecting the wide range of frequencies found in random populations. These frequencies remained fairly constant during and 6 weeks after the pregnancy. Splitwell analysis demonstrated that the responses generated in our culture system were specific to the stimulator. The LDA data conform to single-hit kinetics, indicating that only cytotoxic T cells were limiting in the assay. Proliferative responses of maternal lymphocytes to paternal, cord blood and third party MHC antigens also remained unchanged as determined by time-course mixed lymphocyte reactions (MLR). Our data suggest that there is no significant allo-stimulation or suppression of the maternal immune system during normal pregnancy. The mother remains immunocompetent and is capable of both cytotoxic and proliferative responses to paternally-derived fetal MHC antigens. Our findings confirm that in normal pregnancy the trophoblast, which is devoid of classical MHC antigens, forms an effective immune barrier which prevents interaction of the maternal and fetal immune systems. PMID:8324898

  16. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi).

    PubMed

    Gupta, S K; Gopalakrishna, T

    2009-02-01

    Genetic diversity in 20 elite blackgram (Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies. PMID:19234560

  17. Microsatellite markers for an endemic Atlantic Forest tree, Manilkara multifida (Sapotaceae).

    PubMed

    Moraes, Ramiris C S; Vivas, Caio V; Oliveira, Fernanda A; Menezes, Ivandilson P P; van den Berg, Cassio; Gaiotto, Fernanda A

    2013-01-01

    Manilkara multifida is a tropical tree that is endemic to the Atlantic forests of southern Bahia, Brazil. Currently, populations of this species are restricted to fragmented landscapes that are susceptible to anthropogenic disturbances. Considering this issue, and that there is no genetic information available for this endangered species, we developed microsatellite markers for M. multifida to provide resources for future conservation genetics studies. Using an enriched genomic library, we isolated eight polymorphic microsatellite loci and optimized the amplification conditions for M. multifida. For each locus, we estimated the number of alleles, H E and H O, paternity exclusion Q, individual identity I and fixation index F, and examined the presence of null alleles. The mean number of alleles was 11.9, and the heterozygosity was high at all loci (average H E = 0.809 and H O = 0.777). The combined values for both paternity exclusion and individual identity were Q = 0.9959 and I = 5.45 × 10(-11), respectively. No evidence of null alleles was detected. The results of our analysis indicated that all eight microsatellites are promising for assessing questions involving inbreeding, gene flow, co-ancestry and mating patterns in M. multifida. PMID:23487575

  18. Microsatellite markers for an endemic Atlantic Forest tree, Manilkara multifida (Sapotaceae)

    PubMed Central

    Moraes, Ramiris C. S.; Vivas, Caio V.; Oliveira, Fernanda A.; Menezes, Ivandilson P. P.; van den Berg, Cassio; Gaiotto, Fernanda A.

    2013-01-01

    Manilkara multifida is a tropical tree that is endemic to the Atlantic forests of southern Bahia, Brazil. Currently, populations of this species are restricted to fragmented landscapes that are susceptible to anthropogenic disturbances. Considering this issue, and that there is no genetic information available for this endangered species, we developed microsatellite markers for M. multifida to provide resources for future conservation genetics studies. Using an enriched genomic library, we isolated eight polymorphic microsatellite loci and optimized the amplification conditions for M. multifida. For each locus, we estimated the number of alleles, HE and HO, paternity exclusion Q, individual identity I and fixation index F, and examined the presence of null alleles. The mean number of alleles was 11.9, and the heterozygosity was high at all loci (average HE = 0.809 and HO = 0.777). The combined values for both paternity exclusion and individual identity were Q = 0.9959 and I = 5.45 1011, respectively. No evidence of null alleles was detected. The results of our analysis indicated that all eight microsatellites are promising for assessing questions involving inbreeding, gene flow, co-ancestry and mating patterns in M. multifida. PMID:23487575

  19. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  20. Longtime analysis of floating potential and electron temperature by TPMU - PROBA II microsatellite instrument

    NASA Astrophysics Data System (ADS)

    Podolska, Katerina; Hruska, Frantisek; Truhlik, Vladimir

    2015-04-01

    This study is a next step of our previous conference paper. We use methods of multivariate time-series analysis to study seasonal and geographical variations of the floating potential and the electron temperature measured by TPMU - PROBA II microsatellite instrument. The device is working with limitations of scientific measurements caused by installed onboard software. This brings lower data volume as it was planned. Thus affected are ion measurement and partially also electron temperature measurement. This limited function of the instrument is stable and lasts since the beginning of the mission. The data from the period 2010-2014 are joined with orbital parameters. The analysis is then performed separately for Equatorial region, and North and South hemispheres. We implement the time-series decomposition to recognize seasonal and non-periodic components. The annual seasonal changes in the floating potential and electron temperature are observed in this analysis. Changes of the floating potential in the beginning, the end and duration of seasons over a period of years also reflect changes of Kp and Dst indices.

  1. High resolution melt-curve analysis to fine map a locus controlling the paternal sorting of mitochondria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondria are required for normal growth and development and play an important role in programmed cell death and aging. The mitochondrial DNA is maternally transmitted in the vast majority of eukaryotes. One exception is cucumber (Cucumis sativus), whose mitochondrial DNA is paternally transmit...

  2. An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

    PubMed Central

    Kayser, Manfred; Krawczak, Michael; Excoffier, Laurent; Dieltjes, Patrick; Corach, Daniel; Pascali, Vincente; Gehrig, Christian; Bernini, Luigi F.; Jespersen, Jrgen; Bakker, Egbert; Roewer, Lutz; deKnijff, Peter

    2001-01-01

    The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were .86.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, ?ST statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure. PMID:11254455

  3. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    PubMed Central

    Seo, Dongwon; Bhuiyan, Md. Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-01-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  4. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  5. Spatio-temporal Genetic Structuring of Leishmania major in Tunisia by Microsatellite Analysis

    PubMed Central

    Harrabi, Myriam; Bettaieb, Jihène; Ghawar, Wissem; Toumi, Amine; Zaâtour, Amor; Yazidi, Rihab; Chaâbane, Sana; Chalghaf, Bilel; Hide, Mallorie; Bañuls, Anne-Laure; Ben Salah, Afif

    2015-01-01

    In Tunisia, cases of zoonotic cutaneous leishmaniasis caused by Leishmania major are increasing and spreading from the south-west to new areas in the center. To improve the current knowledge on L. major evolution and population dynamics, we performed multi-locus microsatellite typing of human isolates from Tunisian governorates where the disease is endemic (Gafsa, Kairouan and Sidi Bouzid governorates) and collected during two periods: 1991–1992 and 2008–2012. Analysis (F-statistics and Bayesian model-based approach) of the genotyping results of isolates collected in Sidi Bouzid in 1991–1992 and 2008–2012 shows that, over two decades, in the same area, Leishmania parasites evolved by generating genetically differentiated populations. The genetic patterns of 2008–2012 isolates from the three governorates indicate that L. major populations did not spread gradually from the south to the center of Tunisia, according to a geographical gradient, suggesting that human activities might be the source of the disease expansion. The genotype analysis also suggests previous (Bayesian model-based approach) and current (F-statistics) flows of genotypes between governorates and districts. Human activities as well as reservoir dynamics and the effects of environmental changes could explain how the disease progresses. This study provides new insights into the evolution and spread of L. major in Tunisia that might improve our understanding of the parasite flow between geographically and temporally distinct populations. PMID:26302440

  6. Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle.

    PubMed

    Heaton, Michael P; Harhay, Gregory P; Bennett, Gary L; Stone, Roger T; Grosse, W Michael; Casas, Eduardo; Keele, John W; Smith, Timothy P L; Chitko-McKown, Carol G; Laegreid, William W

    2002-05-01

    DNA marker technology represents a promising means for determining the genetic identity and kinship of an animal. Compared with other types of DNA markers, single nucleotide polymorphisms (SNPs) are attractive because they are abundant, genetically stable, and amenable to high-throughput automated analysis. In cattle, the challenge has been to identify a minimal set of SNPs with sufficient power for use in a variety of popular breeds and crossbred populations. This report describes a set of 32 highly informative SNP markers distributed among 18 autosomes and both sex chromosomes. Informativity of these SNPs in U.S. beef cattle populations was estimated from the distribution of allele and genotype frequencies in two panels: one consisting of 96 purebred sires representing 17 popular breeds, and another with 154 purebred American Angus from six herds in four Midwestern states. Based on frequency data from these panels, the estimated probability that two randomly selected, unrelated individuals will possess identical genotypes for all 32 loci was 2.0 x 10(-13) for multi-breed composite populations and 1.9 x 10(-10) for purebred Angus populations. The probability that a randomly chosen candidate sire will be excluded from paternity was estimated to be 99.9% and 99.4% for the same respective populations. The DNA immediately surrounding the 32 target SNPs was sequenced in the 96 sires of the multi-breed panel and found to contain an additional 183 polymorphic sites. Knowledge of these additional sites, together with the 32 target SNPs, allows the design of robust, accurate genotype assays on a variety of high-throughput SNP genotyping platforms. PMID:12016516

  7. Noninvasive genotyping and Mendelian analysis of microsatellites in African savannah elephants.

    PubMed

    Okello, J B A; Wittemyer, G; Rasmussen, H B; Douglas-Hamilton, I; Nyakaana, S; Arctander, P; Siegismund, H R

    2005-01-01

    We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu, Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n = 46) and 0.9% (n = 37) of heterozygous and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing. Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000-0.042) and below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates. PMID:16251516

  8. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  9. Genetic diversity analysis of the Uruguayan Creole cattle breed using microsatellites and mtDNA markers.

    PubMed

    Armstrong, E; Iriarte, A; Martnez, A M; Feijoo, M; Vega-Pla, J L; Delgado, J V; Postiglioni, A

    2013-01-01

    The Uruguayan Creole cattle population (N = 600) is located in a native habitat in south-east Uruguay. We analyzed its genetic diversity and compared it to other populations of American Creole cattle. A random sample of 64 animals was genotyped for a set of 17 microsatellite loci, and the D-loop hyper-variable region of mtDNA was sequenced for 28 calves of the same generation. We identified an average of 5.59 alleles per locus, with expected heterozygosities between 0.466 and 0.850 and an expected mean heterozygosity of 0.664. The polymorphic information content ranged from 0.360 to 0.820, and the global FIS index was 0.037. The D-loop analysis revealed three haplotypes (UY1, UY2 and UY3), belonging to the European matriline group, with a haplotype diversity of 0.532. The history of the population, changes in the effective population size, bottlenecks, and genetic drift are possible causes of the genetic variability patterns that we detected. PMID:23661437

  10. [MICROSATELLITE ANALYSIS OF HOMOEOLOGOUS CHROMOSOME GROUP 5 OF INTROGRESSIVE WHEAT LINES TRITICUM AESTIVUM/AMBLYOPYRUM MUTICUM].

    PubMed

    Iefimenko, T S; Fedak, Yu G; Antonyuk, M Z; Ternovska, T K

    2015-01-01

    Introgressive hybridization of common wheat is still one of the most effective way of wheat genome enrichment with resistance genes to stresses. In this context, T genome of Amblyopyrum muticum is a promising one for such wheat improvement. Genome substitution amphidiploid Aurotica (AABBTT) with A and B subgenomes from common wheat cultivar Aurora and with T subgenome from Amblyopyrum muticum is characterized by high level of cold resistance. In wheat, this characteristic associated with chromosomes of the homoeologous group 5. Comparative microsatellite analysis of Aurora and Aurotica identified 9 SSR loci specific to D genome which produced other amplicons with Aurotica DNA spectrum. Primers for these loci were used for screening (Aurora x Aurotica)F5 progeny (234 plants) in purpose to find those individuals, which carry 5T chromosome or its fragments in their genomes. In this study were detected 24 plants with disomic substitutions 5D/5T. All of them were offspring of five F4 plants, which in turn derived from two F2 individuals. A significant number of plants contain recombinant chromosome 5D/5T. The recombination event could occur in any generation since F2. PMID:26214905

  11. [Microsatellite markers for parentage identification in Jian Carp (Cyprinus carpio var. Jian)].

    PubMed

    Gu, Ying; Li, Chao; Lu, Cui-Yun; Zheng, Xian-Hu; Yu, Ju-Hua; Sun, Xiao-Wen

    2012-11-01

    Using 16 microsatellite loci we estimated the parentage of 647 progeny in 10 Jian Carp full-sib families. Cervus 3.0 analysis showed that mean PIC value of 16 microsatellites, mean number of allele, and mean expected heterozygosity were 0.7025, 6.63, and 0.7405, respectively. The combined probability of exclusion was 0.99922456 when both parents were unknown and the combined probability of exclusion was 0.99999557 when only one of the parental genotype was known, with the confidence level of 95%. Further simulations based on allele frequencies suggested that to achieve the requirements of paternity test usually took 8 to 12 microsatellite loci when both parents were unknown and 5 to 8 microsatellite loci when one parent was known. Out of 647 progenies, 94.6% were assigned to their parental pairs without the information of both parents in parentage analysis, which were lower than the theoretical assignment rates predicted by the Cervus simulations. This could be explained by the relationship between the candidate parents or existence of null and by typing errors. The identification of 9 families was useful for linkage analysis of Jian Carp and QTL location, also for marker assisted selection for economical traits. PMID:23208142

  12. Design and performance analysis of the electric power sub-system for a multi-mission microsatellite

    NASA Astrophysics Data System (ADS)

    Pastena, Massimiliano; Grassi, Michele

    1999-04-01

    This paper deals with the design and performance analysis of the electric power sub-system of a microsatellite for multi-mission applications. The solar array and battery design has been performed in order to have the required power on different sun-synchronous orbits without configuration adjustments. To effectively manage the power provided by the solar arrays and batteries a power control unit has been designed which controls the bus voltage and regulates the battery charge and discharge phases. A numerical code has been then developed to test the performance of the proposed electric power sub-system. The code integrates the microsatellite orbital motion with the power sub-system operations. Numerical results show that the proposed power sub-system is able to provide and control the required power on a large range of sun-synchronous orbits.

  13. Molecular tracking of mountain lions in the Yosemite valley region in California: genetic analysis using microsatellites and faecal DNA.

    PubMed

    Ernest, H B; Penedo, M C; May, B P; Syvanen, M; Boyce, W M

    2000-04-01

    Twelve microsatellite loci were characterized in California mountain lions (Puma concolor) and sufficient polymorphism was found to uniquely genotype 62 animals sampled at necropsy. Microsatellite genotypes obtained using mountain lion faecal DNA matched those from muscle for all of 15 individuals examined. DNA from potential prey species and animals whose faeces could be misidentified as mountain lion faeces were reliably distinguished from mountain lions using this microsatellite panel. In a field application of this technique, 32 faecal samples were collected from hiking trails in the Yosemite Valley region where seven mountain lions previously had been captured, sampled, and released. Twelve samples yielded characteristic mountain lion genotypes, three displayed bobcat-type genotypes, and 17 did not amplify. The genotype of one of the 12 mountain lion faecal samples was identical to one of the mountain lions that previously had been captured. Three of the 12 faecal samples yielded identical genotypes, and eight new genotypes were detected in the remaining samples. This analysis provided a minimum estimate of 16 mountain lions (seven identified by capture and nine identified by faecal DNA) living in or travelling through Yosemite Valley from March 1997 to August 1998. Match probabilities (probabilities that identical DNA genotypes would be drawn at random a second time from the population) indicated that the samples with identical genotypes probably came from the same mountain lion. Our results demonstrate that faecal DNA analysis is an effective method for detecting and identifying individual mountain lions. PMID:10736046

  14. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

    PubMed Central

    Moges, Asmare D.; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R.

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

  15. Map and Analysis of Microsatellites in Genome of Populus: the First Sequenced Perennial Plant

    SciTech Connect

    Li, Shuxian; Yin, Tongming

    2007-01-01

    We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri- and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di- and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

  16. Analysis and injury paterns of walnut tree falls in central anatolia of turkey

    PubMed Central

    2014-01-01

    Introduction Falls are the second most common cause of injury-associated mortality worldwide. This study aimed to analysis the injuries caused by falls from walnut tree and assess their mortality and morbidity risk. Methods This is a retrospective hospital-based study of patients presenting to emergency department (ED) of Ahi Evran Univercity between September and October 2012. For each casualty, we computed the ISS (defined as the sum of the squares of the highest Abbreviated Injury Scale (AIS) score in each of the three most severely injured body regions). Severe injury was defined as ISS???16. The duration of hospital stay and final outcome were recorded. Statistical comparisons were carried out with Chi-Square test for categorical data and non-parametric spearman correlation tests were used to test the association between variables. A p value less than 0.05 was considered to be statistically significant. Results Fifty-four patients admitted to our emergency department with fall from walnut tree. Fifty (92.6%) patients were male. The mean age was 48??14 years. Spinal region (44.4%) and particularly lumbar area (25.9%) sustained the most of the injuries among all body parts. Wedge compression fractures ranked first among all spinal injuries. Extremities injuries were the second most common injury. None of the patients died. Morbidity rate was 9.25%. Conclussion Falls from walnut trees are a significant health problem. Preventive measures including education of farmers and agricultural workers and using mechanized methods for harvesting walnut will lead to a dramatic decrease in mortality and morbidity caused by falls from walnut trees. PMID:25006346

  17. Development of microsatellite markers for, and a preliminary population genetic analysis of, the white-backed planthopper.

    PubMed

    Sun, J-T; Jiang, X-Y; Wang, M-M; Hong, X-Y

    2014-12-01

    For a better understanding of the population structure and dispersal rates of Sogatella furcifera, we developed 21 novel polymorphic expressed sequence tags (EST) derived microsatellites, which were successfully amplified in four multiplex polymerase chain reaction sets. These new microsatellites were firstly assessed in 20 individuals sampled from Wenshan in China. The results showed that all 21 loci were highly polymorphic; the number of alleles ranged from 3 to 9, with an average of 4.8 alleles per locus. The observed and expected heterozygosity ranged from 0.200 to 0.900 and from 0.184 to 0.799, respectively. Nineteen of the 21 microsatellites without null allele, were subsequently used for population genetic structure analyses of five S. furcifera populations sampled in south region of China (sites up to 1314 kilometers apart). The observed and expected heterozygosity for each population ranged from 0.436 to 0.494 and from 0.454 to 0.482, respectively. The level of population differentiation was very low, with an average pairwise F ST of 0.002. Bayesian cluster analysis result suggested that the five S. furcifera populations formed one genetic cluster. Discriminant analysis of principle components detected three genetic clusters. The spread of the three clusters across the five populations explained the lack of population differentiation and the Bayesian cluster result. All the results indicated that long-distance migration of this pest allowed genetic mixing between populations from remote geographical origins. These new microsatellites will be powerful tools for population genetics studies of S. furcifera. PMID:25208970

  18. Paternal and Maternal Genetic Analysis of a Desert Keriyan Population: Keriyans Are Not the Descendants of Guge Tibetans

    PubMed Central

    Chen, Kaixu; Ablimit, Abdurahman; Ling, Fengjun; Wu, Weiwei; Shan, Wenjuan; Qin, Wenbei; Keweier, Tuerhong; Zuo, Hongli; Zhang, Fuchun; Ma, Zhenghai; Zheng, Xiufen

    2014-01-01

    The Keriyan people live in an isolated village in the Taklimakan Desert in Xinjiang, Western China. The origin and migration of the Keriyans remains unclear. We studied paternal and maternal genetic variance through typing Y-STR loci and sequencing the complete control region of the mtDNA and compared them with other adjacent populations. Data show that the Keriyan have relatively low genetic diversity on both the paternal and maternal lineages and possess both European and Asian specific haplogroups, indicating Keriyan is an admixture population of West and East. There is a gender-bias in the extent of contribution from Europe vs. Asia to the Keriyan gene pool. Keriyans have more genetic affinity to Uyghurs than to Tibetans. The Keriyan are not the descendants of the Guge Tibetans. PMID:24968299

  19. A battery of 12 microsatellite markers for genetic analysis of the Leishmania (Viannia) guyanensis complex.

    PubMed

    Rougeron, V; De Mees, T; Hide, M; Waleckx, E; Dereure, J; Arevalo, J; Llanos-Cuentas, A; Bauls, A L

    2010-11-01

    We used 12 microsatellite markers developed for Leishmania braziliensis to genotype 28 strains of the main species of the Leishmania guyanensis complex (i.e. L. guyanensis and L. panamensis) collected in Ecuador and Peru. The important heterozygote deficits observed in these populations are similar with the previous data obtained in L. braziliensis and raise again the debate on the reproductive mode of these protozoan parasites. The data showed genetic polymorphism and geographical differentiation giving information on population structure of the L. guyanensis complex. Regarding the two species, this study enhances again the debate on the taxonomic status of the different isolates belonging to L. guyanensis s.l. since the results showed substantial heterogeneity within this species complex. In conclusion, this study increases the number of available microsatellite loci for L. guyanensis species complex and raises fundamental biological questions. It confirms that microsatellite markers constitute good tools for population genetic studies on parasites of this complex. PMID:20609264

  20. Analysis of microsatellite instability and loss of heterozygosity in ovarian cancer: a study in the population of Esprito Santo, Brazil.

    PubMed

    Alves, L N R; Wolfgramm, E V; de Castro Neto, A K; Louro, I D

    2013-01-01

    Ovarian cancer is currently the most lethal gynecological malignancy in women. It is a heterogeneous and cytogenetically complex disease previously associated with genomic instability. Our purpose was to analyze microsatellite markers to determine patterns and levels of instability as well as possible correlations with histopathological parameters. Polymerase chain reaction was used to characterize microsatellite instability (MSI) and loss of heterozygosity (LOH) in 24 ovarian tumors at 12 microsatellite loci. A total of 11 samples displayed MSI or LOH. Only low-level MSI was found. Markers D5S346 and CYP11 showed the highest MSI and LOH frequencies. D17S250 LOH was significantly associated with tumor histological type (P = 0.0003), and estrogen receptor ? was also associated with tumor histological type (P = 0.048) when a combined analysis of LOH and MSI was performed. Furthermore, LOH was observed in a greater number of markers compared with those displaying MSI. Thus, our results support that MSI is less common than LOH in ovarian cancers. PMID:23913383

  1. Multiple Mating, Paternity and Complex Fertilisation Patterns in the Chokka Squid Loligo reynaudii

    PubMed Central

    Naud, Marie-Jose; Sauer, Warwick H. H.; McKeown, Niall J.; Shaw, Paul W.

    2016-01-01

    Polyandry is widespread and influences patterns of sexual selection, with implications for sexual conflict over mating. Assessing sperm precedence patterns is a first step towards understanding sperm competition within a female and elucidating the roles of male- and female-controlled factors. In this study behavioural field data and genetic data were combined to investigate polyandry in the chokka squid Loligo reynaudii. Microsatellite DNA-based paternity analysis revealed multiple paternity to be the norm, with 79% of broods sired by at least two males. Genetic data also determined that the male who was guarding the female at the moment of sampling was a sire in 81% of the families tested, highlighting mate guarding as a successful male tactic with postcopulatory benefits linked to sperm deposition site giving privileged access to extruded egg strings. As females lay multiple eggs in capsules (egg strings) wherein their position is not altered during maturation it is possible to describe the spatial / temporal sequence of fertilisation / sperm precedence There were four different patterns of fertilisation found among the tested egg strings: 1) unique sire; 2) dominant sire, with one or more rare sires; 3) randomly mixed paternity (two or more sires); and 4) a distinct switch in paternity occurring along the egg string. The latter pattern cannot be explained by a random use of stored sperm, and suggests postcopulatory female sperm choice. Collectively the data indicate multiple levels of male- and female-controlled influences on sperm precedence, and highlights squid as interesting models to study the interplay between sexual and natural selection. PMID:26872354

  2. Multiple Mating, Paternity and Complex Fertilisation Patterns in the Chokka Squid Loligo reynaudii.

    PubMed

    Naud, Marie-Jose; Sauer, Warwick H H; McKeown, Niall J; Shaw, Paul W

    2016-01-01

    Polyandry is widespread and influences patterns of sexual selection, with implications for sexual conflict over mating. Assessing sperm precedence patterns is a first step towards understanding sperm competition within a female and elucidating the roles of male- and female-controlled factors. In this study behavioural field data and genetic data were combined to investigate polyandry in the chokka squid Loligo reynaudii. Microsatellite DNA-based paternity analysis revealed multiple paternity to be the norm, with 79% of broods sired by at least two males. Genetic data also determined that the male who was guarding the female at the moment of sampling was a sire in 81% of the families tested, highlighting mate guarding as a successful male tactic with postcopulatory benefits linked to sperm deposition site giving privileged access to extruded egg strings. As females lay multiple eggs in capsules (egg strings) wherein their position is not altered during maturation it is possible to describe the spatial / temporal sequence of fertilisation / sperm precedence There were four different patterns of fertilisation found among the tested egg strings: 1) unique sire; 2) dominant sire, with one or more rare sires; 3) randomly mixed paternity (two or more sires); and 4) a distinct switch in paternity occurring along the egg string. The latter pattern cannot be explained by a random use of stored sperm, and suggests postcopulatory female sperm choice. Collectively the data indicate multiple levels of male- and female-controlled influences on sperm precedence, and highlights squid as interesting models to study the interplay between sexual and natural selection. PMID:26872354

  3. Population genetic analysis and origin discrimination of snow crab (Chionoecetes opilio) using microsatellite markers.

    PubMed

    Kang, Jung-Ha; Park, Jung-Youn; Kim, Eun-Mi; Ko, Hyun-Sook

    2013-10-01

    Major habitats for the snow crab Chionoecetes opilio are mostly found within the northwest Atlantic and North Pacific Oceans. However, the East Sea populations of C. opilio, along with its relative the red snow crab (C. japonicas), are two of the most important commercial crustacean species for fisheries on the east coast of the Korean Peninsula. The East Sea populations of C. opilio are facing declining resources due to overfishing and global climate change. Thus, an analysis of population structure is necessary for future management. Five Korean and one Russian group of C. opilio were analyzed using nine microsatellite markers that were recently developed using next-generation sequencing. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The number of alleles per locus varied from 4 to 18 with a mean of 12, and allelic richness per locus ranged from 4.0 to 17.1 across all populations with a mean of 9.7. The Hardy-Weinberg equilibrium test revealed significant deviation in three out of nine loci in some populations after sequential Bonferroni correction and all of them had higher expected heterozygosity than observed heterozygosity. Null alleles were presumed in four loci, which explained the homozygosity in three loci. The pairwise fixation index (F ST ) values among the five Korean snow crab populations did not differ significantly, but all of the pairwise F ST values between each of the Korean snow crab populations and the Russian snow crab population differed significantly. An UPGMA dendrogram revealed clear separation of the Russian snow crab population from the Korean snow crab populations. Assignment tests based on the allele distribution discriminated between Korean and Russian origins with 93 % accuracy. Therefore, the snow crab populations around the Korean Peninsula need to be managed separately from the populations in Bering Sea in global scale resource management. Also, this information can be used for identification of snow crab origin which is problematic in worldwide crab trade. PMID:24022521

  4. New carrot microsatellites – linkage mapping, diversity analysis and transferability to other apiaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nearly 300 new microsatellite, or simple sequence repeat (SSR) markers were developed from genomic sequences of carrot. Efforts to map these markers and evaluate their usefulness in diversity studies are underway. In one F2 carrot population, a total of 51 polymorphic markers, including 37 codominan...

  5. Analysis of genetic diversity of flowering dogwood natural stands using microsatellites the effects of dogwood anthracnose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flowering dogwood (Cornus florida) populations recently have experienced severe declines caused by dogwood anthracnose. Mortality ranged from 48-98%, raising the concern that genetic diversity has been reduced significantly. Microsatellite data was used to evaluate the level and distribution of ge...

  6. Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 1...

  7. Non-invasive prenatal diagnosis for cystic fibrosis: detection of paternal mutations, exploration of patient preferences and cost analysis

    PubMed Central

    Hill, Melissa; Twiss, Philip; Verhoef, Talitha I; Drury, Suzanne; McKay, Fiona; Mason, Sarah; Jenkins, Lucy; Morris, Stephen; Chitty, Lyn S

    2015-01-01

    Abstract Objectives We aim to develop non-invasive prenatal diagnosis (NIPD) for cystic fibrosis (CF) and determine costs and implications for implementation. Methods A next-generation sequencing assay was developed to detect ten common CF mutations for exclusion of the paternal mutation in maternal plasma. Using uptake data from a study exploring views on NIPD for CF, total test-related costs were estimated for the current care pathway and compared with those incorporating NIPD. Results The assay reliably predicted mutation status in all control and maternal plasma samples. Of carrier or affected adults with CF (n?=?142) surveyed, only 43.5% reported willingness to have invasive testing for CF with 94.4% saying they would have NIPD. Using these potential uptake data, the incremental costs of NIPD over invasive testing per 100 pregnancies at risk of CF are 9025 for paternal mutation exclusion, and 26?510 for direct diagnosis. Conclusions We have developed NIPD for risk stratification in around a third of CF families. There are economic implications due to potential increased test demand to inform postnatal management rather than to inform decisions around termination of an affected pregnancy. 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. PMID:25708280

  8. Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

    PubMed Central

    Gerloff, U; Hartung, B; Fruth, B; Hohmann, G; Tautz, D

    1999-01-01

    Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community. PMID:10406131

  9. Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

    PubMed

    Gerloff, U; Hartung, B; Fruth, B; Hohmann, G; Tautz, D

    1999-06-01

    Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community. PMID:10406131

  10. Taxonomy of the Rhizopogon vinicolor species complex based on analysis of ITS sequences and microsatellite loci.

    PubMed

    Kretzer, Annette M; Luoma, Daniel L; Molina, Randy; Spatafora, Joseph W

    2003-01-01

    We are re-addressing species concepts in the Rhizopogon vinicolor species complex (Boletales, Basidiomycota) using sequence data from the internal-transcribed spacer (ITS) region of the nuclear ribosomal repeat, as well as genotypic data from five microsatellite loci. The R. vinicolor species complex by our definition includes, but is not limited to, collections referred to as R. vinicolor Smith, R. diabolicus Smith, R. ochraceisporus Smith, R. parvulus Smith or R. vesiculosus Smith. Holo- and/or paratype material for the named species is included. Analyses of both ITS sequences and microsatellite loci separate collections of the R. vinicolor species complex into two distinct clades or clusters, suggestive of two biological species that subsequently are referred to as R. vinicolor sensu Kretzer et al and R. vesiculosus sensu Kretzer et al. Choice of the latter names, as well as morphological characters, are discussed. PMID:21156637

  11. Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

    PubMed Central

    2013-01-01

    Background Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions. Methods A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity. Results Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds. Conclusions Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival. PMID:24079454

  12. Genetic diversity and structure in Leishmania infantum populations from southeastern Europe revealed by microsatellite analysis

    PubMed Central

    2013-01-01

    Background The dynamic re-emergence of visceral leishmaniasis (VL) in south Europe and the northward shift to Leishmania-free European countries are well-documented. However, the epidemiology of VL due to Leishmania infantum in southeastern (SE) Europe and the Balkans is inadequately examined. Herein, we aim to re-evaluate and compare the population structure of L. infantum in SE and southwestern (SW) Europe. Methods Leishmania strains collected from humans and canines in Turkey, Cyprus, Bulgaria, Greece, Albania and Croatia, were characterized by the K26-PCR assay and multilocus enzyme electrophoresis (MLEE). Genetic diversity was assessed by multilocus microsatellite typing (MLMT) and MLM Types were analyzed by model- and distance- based algorithms to infer the population structure of 128 L. infantum strains. Results L. infantum MON-1 was found predominant in SE Europe, whilst 16.8% of strains were MON-98. Distinct genetic populations revealed clear differentiation between SE and SW European strains. Interestingly, Cypriot canine isolates were genetically isolated and formed a monophyletic group, suggesting the constitution of a clonal MON-1 population circulating among dogs. In contrast, two highly heterogeneous populations enclosed all MON-1 and MON-98 strains from the other SE European countries. Structure sub-clustering, phylogenetic and Splitstree analysis also revealed two distinct Croatian subpopulations. A mosaic of evolutionary effects resulted in consecutive sub-structuring, which indicated substantial differentiation and gene flow among strains of both zymodemes. Conclusions This is the first population genetic study of L. infantum in SE Europe and the Balkans. Our findings demonstrate the differentiation between SE and SW European strains; revealing the partition of Croatian strains between these populations and the genetic isolation of Cypriot strains. This mirrors the geographic position of Croatia located in central Europe and the natural isolation of the island of Cyprus. We have analysed the largest number of MON-98 strains so far. Our results indicate extensive gene flow, recombination and no differentiation between MON-1 and MON-98 zymodemes. No correlation either to host specificity or place and year of strain isolation was identified. Our findings may be associated with intensive host migration and common eco-epidemiological characteristics in these countries and give valuable insight into the dynamics of VL. PMID:24308691

  13. Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

    PubMed Central

    Qi, Wen-Hua; Jiang, Xue-Mei; Du, Lian-Ming; Xiao, Guo-Sheng; Hu, Ting-Zhang; Yue, Bi-Song; Quan, Qiu-Mei

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same nucleotide SSR type showed great similarity among different chromosomes of B. taurus, O. aries, and C. hircus. PMID:26196922

  14. Analysis of Microsatellite Polymorphisms in South Indian Patients with Non Syndromic Cleft Lip and Palate

    PubMed Central

    Xavier, DL; Arif, YA; Murali, RV; Kishore Kumar, S; Vipin Kumar, S; Tamang, R; Thangaraj, K; Bhaskar, LVKS

    Non syndromic cleft lip and/or palate (NSCLP) is a complex congenital anomaly with varying incidence among patients of different geographical origins. Multiple contributing factors are known to trigger the cleft formation. There are several genes involved in the aetiology of NSCLP and they are different in different populations. The genetic components of clefts that underlie the susceptibility to respond to the environment still remain unclear. In this study, five microsatellite polymorphisms from five candidate genes were employed to analyze the association between these genes and NSCLP in 83 patients and 90 controls. Genotyping was performed by separating and visualizing the fluorescently-labeled polymerase chain reaction (PCR) products. The association of the five microsatellite polymorphisms with NSCLP was tested by using the CLUMP v1.9 program that uses the Monte Carlo method. The genotypic distribution is in Hardy-Weinberg equilibrium in the control group for only the MSX1 and DLX3 genes. The RARA microsatellite was significantly associated with NSCLP. Our results suggest that the RARA gene is involved in pathogenesis of cleft lip and palate in South Indians. PMID:24265584

  15. Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum

    PubMed Central

    Mallick, Prashant K.; Sutton, Patrick L.; Singh, Ruchi; Singh, Om P.; Dash, Aditya P.; Singh, Ashok K.; Carlton, Jane M.; Bhasin, Virendra K.

    2013-01-01

    Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasites acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST = 0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r = 0.49, P=0.003, N = 83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India. PMID:23871774

  16. Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum.

    PubMed

    Mallick, Prashant K; Sutton, Patrick L; Singh, Ruchi; Singh, Om P; Dash, Aditya P; Singh, Ashok K; Carlton, Jane M; Bhasin, Virendra K

    2013-10-01

    Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite's acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST=0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r=0.49, P=0.003, N=83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India. PMID:23871774

  17. [HLA-DRB1 typing by PCR-sequence specific primers for paternity determination].

    PubMed

    Liu, L M; Liang, J; Wang, B J; Ding, M; Li, J P; Li, C M; Xiao, Y Z; Jia, J T

    1999-11-01

    HLA-DRB1 typing by PCR-SSP technique was first used for paternity testing. The analysis of 42 paternity cases shows that this identification method is simple, fast and reliable and has high exclusion probability of paternity (66.3%). This method can also be applied to the study of transplantation, HLA associated disease and anthropogenesis. PMID:12536433

  18. Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population.

    PubMed

    Ford, Michael J; Hanson, M Bradley; Hempelmann, Jennifer A; Ayres, Katherine L; Emmons, Candice K; Schorr, Gregory S; Baird, Robin W; Balcomb, Kenneth C; Wasser, Samuel K; Parsons, Kim M; Balcomb-Bartok, Kelly

    2011-01-01

    We used data from 78 individuals at 26 microsatellite loci to infer parental and sibling relationships within a community of fish-eating ("resident") eastern North Pacific killer whales (Orcinus orca). Paternity analysis involving 15 mother/calf pairs and 8 potential fathers and whole-pedigree analysis of the entire sample produced consistent results. The variance in male reproductive success was greater than expected by chance and similar to that of other aquatic mammals. Although the number of confirmed paternities was small, reproductive success appeared to increase with male age and size. We found no evidence that males from outside this small population sired any of the sampled individuals. In contrast to previous results in a different population, many offspring were the result of matings within the same "pod" (long-term social group). Despite this pattern of breeding within social groups, we found no evidence of offspring produced by matings between close relatives, and the average internal relatedness of individuals was significantly less than expected if mating were random. The population's estimated effective size was <30 or about 1/3 of the current census size. Patterns of allele frequency variation were consistent with a population bottleneck. PMID:21757487

  19. Paternal occupation and anencephaly

    SciTech Connect

    Brender, J.D.; Suarez, L. )

    1990-03-01

    It has been suggested that paternal occupational exposures to pesticides and solvents increase the risk of neural tube defects in offspring. With the use of Texas livebirth, fetal death, and linked livebirth-death records, the authors conducted a population-based case-control study among 1981-1986 Texas births to examine the association between paternal occupation and anencephalic births. Fathers employed in occupations associated with solvent exposure were more likely to have offspring with anencephaly (odds ratio (OR) = 2.53), with painters having the highest risk (OR = 3.43). A lesser association was found for fathers employed in occupations involving pesticide exposure (OR = 1.28). Further studies are indicated to clarify these associations.

  20. Paternal programming in sticklebacks

    PubMed Central

    Stein, Laura R.; Bell, Alison M.

    2015-01-01

    In a wide range of organisms, including humans, mothers can influence offspring via the care they provide. Comparatively little is known about the effects of fathering on offspring. Here, we test the hypothesis that fathers are capable of programming their offspring for the type of environment they are likely to encounter. Male threespine sticklebacks, Gasterosteus aculeatus, were either exposed to predation risk while fathering or not. Fathers altered their paternal behaviour when exposed to predation risk, and consequently produced adult offspring with phenotypes associated with strong predation pressure (smaller size, reduced body condition, reduced behavioural activity). Moreover, more attentive fathers produced offspring that showed stronger antipredator responses. These results are consistent with behaviourally mediated paternal programming: fathers can alter offspring phenotypes to match their future environment and influence offspring traits well into adulthood.

  1. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand.

    PubMed

    Seilsuth, Somkiat; Seo, Joo Hee; Kong, Hong Sik; Jeon, Gwang Joo

    2016-03-01

    The genetic relationships between different populations and breeds of exotic dairy goats in Thailand were studied using 12 microsatellite markers. Blood samples were obtained from 211 goats from Department of Livestock Development breeding and research farms: 29 Anglonubian (AN), 21 Alpine (AP), 23 Jamunapari (JAM), 50 Saanen (SN), and 88 Toggenburg (TG). Five of the 12 microsatellite markers were found to be polymorphic. A mean of 7.40 alleles per locus was found, with a range from 5 (SPS115 and ETH225) to 11 (TGLA122). We found 24, 27, 19, 32, and 24 alleles in the AN, AP, JAM, SN, and TG breeds, respectively; 37 alleles were present in all breeds. The mean number of alleles in each population ranged from 3.2 (ETH225 locus) to 7.6 (TGLA122 locus). Genetic variability within the breeds was moderate as evidenced by the mean expected heterozygosity of 0.539. The average observed heterozygosity across the 5 markers in all breeds was 0.529 with the maximum observed at the BM1818 locus (0.772) and the minimum at the ETH225 locus (0.248). The observed and expected heterozygosity for all breeds for the 5 microsatellite markers ranged from 0.419 to 0.772 and 0.227 to 0.792, respectively. On the basis of their means, the TGLA122 and BM1818 loci were the most suitable markers for distinguishing genetic diversity among the goats. The estimated average F is value for the breeds ranged from -0.044 (ETH225) to 0.180 (SPS115), while the estimated average F st value ranged from 0.021 (SPS115) to 0.104 (ETH10). These results indicated that TGLA122 and BM1818 markers are suitable to be used for aiding conservation and breeding improvement strategies of dairy. PMID:26950862

  2. An intelligent maintenance system for earth-based failure analysis and self-repairing of microsatellites

    NASA Astrophysics Data System (ADS)

    Sierra, Enrique A.; Quiroga, Juan J.; Fernndez, Roberto; Monte, Gustavo E.

    2004-07-01

    This paper describes a recently developed maintenance system for a microsatellite, which is being constructed and it is expected to be launched shortly. The autonomous maintenance system is going to be installed on a personal computer located in an earth-based control room. As this place will most likely be staffed 24 h a day, 7 days a week, there is a good deal of interest in the use of increased automation in maintenance tasks in order to improve the efficiency with which personnel are used and as a way to reduce costs. The system described here is a good example of emerging automation technology that is intended to replace human operators responsible for system maintenance. The structure of the automation system is based upon an architecture of collaborative intelligent agents designed to detect failure in any of the microsatellites components. The multiagent system consists of a set of different agents devoted to failure detection, prevention and correction. Regarding correction, specific agents for each constitutive part of the microsatellite have been developed that take over the necessary actions to solve any given problem in its operation. The detection agent decides which correction agent control should be transferred, based upon inference obtained from its knowledge base made up of rules for testing and diagnosis. Actions for correction may imply the use of redundant systems, which can reconfigure themselves to avoid defective circuits, among other repairing strategies. The prevention agent uses predictive models that have been developed for each significant failure mode. Statistical models are also used by this agent to determine the shape of the distribution of times to failure. The prevention agent selects the corresponding correction agent to which control is going to be transferred and this agent carries out the necessary actions to prevent the system failure. The overall intelligent system employs a blackboard architecture for communication and collaboration among agents. Several simulations with specially designed test cases used to evaluate the system performance suggest that in order for maintenance automation to be effective, it must be designed in close relationship with human operators who will occasionally troubleshoot, maintain and repair the microsatellite from earth. This human-centered approach of the design implies assigning particular importance to the effectiveness achieved in the process of knowledge acquisition when the intelligent agents are being designed.

  3. Microsatellite analysis to estimate genetic relationships among five bulgarian sheep breeds

    PubMed Central

    2010-01-01

    Herein, genetic relationships among five breeds of Bulgarian sheep were estimated using microsatellite markers. The total number of alleles identified was 226 at the 16 loci examined. DA distance values were used for phylogenetic tree construction with the UPGMA algorithm. The two Tsigai and two Maritza populations were found to be geneticallvery closely related to each other y (0.198, and 0.258 respectively). The Pleven Black Head population was distinct from the other four. These results could be useful for preserving genes in these breeds, thereby ensuring their preservation in Bulgaria. PMID:21637604

  4. Paternal age bioethics.

    PubMed

    Smith, Kevin R

    2015-09-01

    Modern genetic sequencing studies have confirmed that the sperm of older men contain a greater number of de novo germline mutations than the sperm of younger men. Although most of these mutations are neutral or of minimal phenotypic impact, a minority of them present a risk to the health of future children. If demographic trends towards later fatherhood continue, this will likely lead to a more children suffering from genetic disorders. A trend of later fatherhood will accelerate the accumulation of paternal-origin de novo mutations in the gene pool, gradually reducing human fitness in the long term. These risks suggest that paternal age is of ethical importance. Children affected by de novo mutations arising from delayed fatherhood can be said to be harmed, in the sense of 'impersonal' harm or 'non-comparative' harm. Various strategies are open at societal and individual levels towards reducing deleterious paternal age effects. Options include health education to promote earlier fatherhood, incentives for young sperm donors and state-supported universal sperm banking. The latter approach would likely be of the greatest benefit and could in principle be implemented immediately. More futuristically, human germline genetic modification offers the potential to repair heritable mutational damage. PMID:26037282

  5. Population structure of the predatory mite Neoseiulus womersleyi in a tea field based on an analysis of microsatellite DNA markers

    PubMed Central

    Todokoro, Yasuhiro; Higaki, Tomomi

    2010-01-01

    The predatory mite Neoseiulus womersleyi (Schicha) (Acari: Phytoseiidae) is an important natural enemy of the Kanzawa spider mite, Tetranychus kanzawaki Kishida (Acari: Tetranychidae), in tea fields. Attraction and preservation of natural enemies by habitat management to reduce the need for acaricide sprays is thought to enhance the activity of N. womersleyi. To better conserve N. womersleyi in the field, however, it is essential to elucidate the population genetic structure of this species. To this end, we developed ten microsatellite DNA markers for N. womersleyi. We then evaluated population structure of N. womersleyi collected from a tea field, where Mexican sunflower, Tithonia rotundifolia (Mill.), was planted to preserve N. womersleyi. Seventy-seven adult females were collected from four sites within 200 m. The fixation indexes FST among subpopulations were not significantly different. The kinship coefficients between individuals did not differ significantly within a site as a function of the sampling dates, but the coefficients gradually decreased with increasing distance. Bayesian clustering analysis revealed that the population consisted of three genetic clusters, and that subpopulations within 100 m, including those collected on T. rotundifolia, were genetically similar to each other. Given the previously observed population dynamics of N. womersleyi, it appears that the area inhabited by a given cluster of the mite did not exceed 100 m. The estimation of population structure using microsatellite markers will provide valuable information in conservation biological control. PMID:20625919

  6. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    PubMed

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-01-01

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis. PMID:23884768

  7. Population genetic structure of Myzus persicae nicotianae (Hemiptera: Aphididae) in China by microsatellite analysis.

    PubMed

    Zhao, C; Yang, X M; Tang, S H; Xu, P J; Bian, W J; Wang, X F; Wang, X W; Ren, G W

    2015-01-01

    The tobacco aphid, Myzus persicae nicotianae (Hemiptera: Aphididae), is an important agricultural pest that feeds on host plants and transmits plant viruses in China. To effectively control this pest, we investigated the genetic variation and genetic structure of 54 populations of tobacco aphids collected in China, using five microsatellite loci. An average of 7 alleles with effective number ranging from 1.5 to 6.6 was detected using these five loci, and the average polymorphic information content (PIC) was 0.652, suggesting that the five selected microsatellite loci were polymorphic and suitable for the study of population genetics. The expected heterozygosities in the populations studied ranged from 0.128 and 0.653, with an average value of 0.464. However, the observed heterozygosities ranged from 0.250 and 0.942 (average = 0.735), revealing a high genetic variability and heterozygosity excess in the Chinese tobacco aphid populations. The global fixation index (FST) and mean gene flow (Nm) were 0.34 (P < 0.0001) and 0.50, respectively, suggesting the high genetic differentiation among Chinese populations. The 54 populations of tobacco aphids were classified into two groups. The populations did not cluster geographically, as populations from the same provinces were usually present in different clusters. This was also confirmed by the Mantel test, which showed no significant correlation between the genetic distance and geographical distance or altitude. Long distance migration might be responsible for the lack of distance-related isolation. PMID:26681063

  8. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis.

    PubMed

    Novick, Rachel Roth; Dick, Christopher W; Lemes, Maristerra R; Navarro, Carlos; Caccone, Adalgisa; Bermingham, Eldredge

    2003-11-01

    While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation. PMID:14629370

  9. A new source of polymorphic DNA markers for sperm typing: analysis of microsatellite repeats in single cells.

    PubMed Central

    Hubert, R; Weber, J L; Schmitt, K; Zhang, L; Arnheim, N

    1992-01-01

    We show that dinucleotide and tetranucleotide repeat polymorphisms can be analyzed in single cells without using radioactivity or denaturing gels. This provides a rich new source of DNA polymorphisms for genetic mapping by sperm typing. The recombination fraction between two CA repeat polymorphisms was determined after whole genome amplification of single sperm, followed by typing of two different aliquots, one aliquot for each polymorphic locus. Single-cell analysis of microsatellites may also be valuable both for preimplantation genetic disease diagnosis based on single-blastomere or polar-body analysis and for the typing of forensic or ancient DNA samples containing very small amounts of nucleic acid. Images Figure 2 Figure 3 PMID:1415267

  10. Molecular and genomic characterisation of cryptic chromosomal alterations leading to paternal duplication of the 11p15.5 Beckwith‐Wiedemann region

    PubMed Central

    Russo, S; Finelli, P; Recalcati, M P; Ferraiuolo, S; Cogliati, F; Bernardina, B Dalla; Tibiletti, M G; Agosti, M; Sala, M; Bonati, M T; Larizza, L

    2006-01-01

    Background Beckwith‐Wiedemann syndrome (BWS) is an overgrowth disorder with increased risk of paediatric tumours. The aetiology involves epigenetic and genetic alterations affecting the 11p15 region, methylation of the differentially methylated DMR2 region being the most common defect, while less frequent aetiologies include mosaic paternal 11p uniparental disomy (11patUPD), maternally inherited mutations of the CDKN1C gene, and hypermethylation of DMR1. A few patients have cytogenetic abnormalities involving 11p15.5. Methods Screening of 70 trios of BWS probands for 11p mosaic paternal UPD and for cryptic cytogenetic rearrangements using microsatellite segregation analysis identified a profile compatible with paternal 11p15 duplication in two patients. Results Fluorescence in situ hybridisation analysis revealed in one case the unbalanced translocation der(21)t(11;21)(p15.4;q22.3) originated from missegregation of a cryptic paternal balanced translocation. The second patient, trisomic for D11S1318, carried a small de novo dup(11)(p15.5p15.5), resulting from unequal recombination at paternal meiosis I. The duplicated region involves only IC1 and spares IC2/LIT1, as shown by fluorescent in situ hybridisation (FISH) mapping of the proximal duplication breakpoint within the amino‐terminal part of KvLQT1. Conclusions An additional patient with Wolf‐Hirschorn syndrome was shown by FISH studies to carry a der(4)t(4;11)(p16.3;p15.4), contributed by a balanced translocation father. Interestingly, refined breakpoint mapping on 11p and the critical regions on the partner 21q and 4p chromosomal regions suggested that both translocations affecting 11p15.4 are mediated by segmental duplications. These findings of chromosomal rearrangements affecting 11p15.5–15.4 provide a tool to further dissect the genomics of the BWS region and the pathogenesis of this imprinting disorder. PMID:16882733

  11. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    NASA Astrophysics Data System (ADS)

    Li, Li; Guo, Ximing; Zhang, Guofan

    2009-02-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  12. ANALYSIS OF GENETIC DIVERSITY AND POPULATION STRUCTURE WITHIN FLORIDA COCONUT (COCOS NUCIFERA L.) GERMPLASM USING MICROSATELLITE DNA, WITH SPECIAL EMPHASIS ON THE FIJI DWARF CULTIVAR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using fifteen simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at bo...

  13. Development of 304 new microsatellite markers for carrot. Analysis of their potential for linkage mapping, assessment of genetic diversity and cross-taxa utilization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two different approaches were used to isolate carrot SSRs: 1) Construction and analysis of a genomic DNA library enriched for SSR loci (GSSRs) and 2) Bioinformatic mining for SSR motifs in a 1.7 Mb BAC-end sequence database (BSSR). The SSR-enriched library yielded microsatellites with more repeats b...

  14. Multiplex automated analysis of microsatellite loci for linkage analysis of the entire human genome

    SciTech Connect

    Freas-Lutz, D.L.; Walczak, C.A.; Gillanders, E.M.

    1994-09-01

    We are evaluating 29 panels of fluorescently labeled markers located at approximately 10 cM intervals. Each chromosome is covered at this marker density in 1-4 panels (11-17 loci/panel). Individual markers are labeled with 1 of 3 different fluorescent dyes, combined after PCR and run in a single gel lane. Genotypes are obtained for each locus using Applied Biosystems automated DNA sequencers and GENESCAN analysis and Genotyper allele scoring software. These programs automate the identification of alleles by distinguishing major peaks from PCR artifacts and facilitate export of data in a format suitable for standard genetic analysis programs. To verify the reported genetic relationships among individuals involved in gene mapping studies, we developed software to determine the number of alleles shared among individuals within a family. We use these statistics to distinguish full and half sibs and parent-child relations from unrelated individuals. Finally, we are developing a database using Fourth Dimension software so that the tremendous amounts of data generated can be processed efficiently in an integrated suite of specialized computer programs for linkage/association studies.

  15. A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.

    PubMed

    Mahfooz, Sahil; Srivastava, Arpita; Srivastava, Alok K; Arora, Dilip K

    2015-09-01

    We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents <1%. Among all classes of repeats, 36.5% motifs were found conserved within Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium. PMID:26269381

  16. Are clownfish groups composed of close relatives? An analysis of microsatellite DNA variation in Amphiprion percula.

    PubMed

    Buston, Peter M; Bogdanowicz, Steven M; Wong, Alex; Harrison, Richard G

    2007-09-01

    A central question of evolutionary ecology is: why do animals live in groups? Answering this question requires that the costs and benefits of group living are measured from the perspective of each individual in the group. This, in turn, requires that the group's genetic structure is elucidated, because genetic relatedness can modulate the individuals' costs and benefits. The clown anemonefish, Amphiprion percula, lives in groups composed of a breeding pair and zero to four nonbreeders. Both breeders and nonbreeders stand to gain by associating with relatives: breeders might prefer to tolerate nonbreeders that are relatives because there is little chance that relatives will survive to breed elsewhere; nonbreeders might prefer to associate with breeders that are relatives because of the potential to accrue indirect genetic benefits by enhancing anemone and, consequently, breeder fitness. Given the potential benefits of associating with relatives, we use microsatellite loci to investigate whether or not individuals within groups of A. percula are related. We develop seven polymorphic microsatellite loci, with a number of alleles (range 2-24) and an observed level of heterozygosity (mean = 0.5936) sufficient to assess fine-scale genetic structure. The mean coefficient of relatedness among group members is 0.00 +/- 0.10 (n = 9 groups), and there are no surprising patterns in the distribution of pairwise relatedness. We conclude that A. percula live in groups of unrelated individuals. This study lays the foundation for further investigations of behavioural, population and community ecology of anemonefishes which are emerging as model systems for evolutionary ecology in the marine environment. PMID:17845439

  17. Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci.

    PubMed

    Roy, M S; Geffen, E; Smith, D; Ostrander, E A; Wayne, R K

    1994-07-01

    Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf. PMID:8078397

  18. Microsatellite and Mini-Exon Analysis of Mexican Human DTU I Trypanosoma cruzi Strains and Their Susceptibility to Nifurtimox and Benznidazole

    PubMed Central

    Martínez, Ignacio; Nogueda, Benjamín; Martínez-Hernández, Fernando

    2013-01-01

    Abstract Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, and it affects as many as 10 million people in North and South America, where it represents a major public health problem. T. cruzi is a parasite with high genetic diversity, and it has been grouped into 6 discrete typing units (DTUs), designated as T. cruzi I (TcI) to T. cruzi VI (TcVI). Mexican isolates from humans and from vector insects have been primarily found to be TcI, and these isolates are likely to be the strains that cause the clinical manifestations observed in Mexico. However, genetic characterization and drug susceptibility assays are limited in Mexican TcI strains. In this work, 24 Mexican T. cruzi strains, obtained primarily from humans, were studied with 7 locus microsatellites and mini-exon gene by PCR. Also, drug susceptibility was evaluated by growth and mobility assays. All of the human strains belonged to TcI, and they could be further grouped through microsatellite analysis into 2 subgroups (microsatellite genotypes 1 and 2), which were not related to the host clinical status or biological origin of the strain. Two strains, both from wild mammals, belonged to the TcII–TcVI groups; these strains and the CL Brener strain constituted microsatellite genotype 3. The number of alleles in each locus was lower than reported for South American strains, and a departure from the Hardy–Weinberg equilibrium was observed. The susceptibility of these strains to nifurtimox and benznidazole was heterogeneous. T. cruzi strains characterized as microsatellite genotypes 2 and 3 were significantly more susceptible to benznidazole than strains of microsatellite genotype 1. Only 1 Mexican strain resistant to both drugs was found in this study. PMID:23421890

  19. Microsatellite and mini-exon analysis of Mexican human DTU I Trypanosoma cruzi strains and their susceptibility to nifurtimox and benznidazole.

    PubMed

    Martnez, Ignacio; Nogueda, Benjamn; Martnez-Hernndez, Fernando; Espinoza, Bertha

    2013-03-01

    Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, and it affects as many as 10 million people in North and South America, where it represents a major public health problem. T. cruzi is a parasite with high genetic diversity, and it has been grouped into 6 discrete typing units (DTUs), designated as T. cruzi I (TcI) to T. cruzi VI (TcVI). Mexican isolates from humans and from vector insects have been primarily found to be TcI, and these isolates are likely to be the strains that cause the clinical manifestations observed in Mexico. However, genetic characterization and drug susceptibility assays are limited in Mexican TcI strains. In this work, 24 Mexican T. cruzi strains, obtained primarily from humans, were studied with 7 locus microsatellites and mini-exon gene by PCR. Also, drug susceptibility was evaluated by growth and mobility assays. All of the human strains belonged to TcI, and they could be further grouped through microsatellite analysis into 2 subgroups (microsatellite genotypes 1 and 2), which were not related to the host clinical status or biological origin of the strain. Two strains, both from wild mammals, belonged to the TcII-TcVI groups; these strains and the CL Brener strain constituted microsatellite genotype 3. The number of alleles in each locus was lower than reported for South American strains, and a departure from the Hardy-Weinberg equilibrium was observed. The susceptibility of these strains to nifurtimox and benznidazole was heterogeneous. T. cruzi strains characterized as microsatellite genotypes 2 and 3 were significantly more susceptible to benznidazole than strains of microsatellite genotype 1. Only 1 Mexican strain resistant to both drugs was found in this study. PMID:23421890

  20. Genetic components of grey cattle in Estonia as revealed by microsatellite analysis using two Bayesian clustering methods

    PubMed Central

    2011-01-01

    Background It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock. Genotypes at 17 microsatellite loci from a total of 243 cattle from North European breeds and 11 grey cattle in Estonia were used in an attempt to clarify the genetic composition of the grey cattle. Findings We characterize the genetic components of 11 examples of the grey cattle in Estonia at the population and individual levels. Our results show that the grey cattle in Estonia are most genetically similar to the Holstein-Friesian breed and secondarily to the Estonian Red cattle. Conclusions Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components. This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds. PMID:21314923

  1. Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

    PubMed

    Schueler, Silvio; Tusch, Alexandra; Scholz, Florian

    2006-10-01

    Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus. PMID:16968267

  2. Allele frequencies of microsatellite loci for genetic characterization of a Sicilian bovine population.

    PubMed

    Cosenza, M; Reale, S; Lupo, T; Vitale, F; Caracappa, S

    2015-01-01

    Short tandem repeats are used as an effective method to trace DNA markers in genotyping. Using a standardized kit, we tested 11 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) in a sample of 495 Sicilian cattle. The aim of this study was to investigate the allele frequencies in the Sicilian cattle population to provide a reference database and at the same time to assess the use of the ISAG microsatellite panel for pedigree analysis. DNA samples were collected from blood and amplified in an 11-plex polymerase chain reaction (PCR); PCR products were injected in a 3130 Genetic Analyzer. All loci showed high mean polymorphism information content (0.768), and the observed mean heterozygosity was less than the expected value (0.732 vs 0.794, respectively). The exact test for Hardy-Weinberg proportions, allele number, and inbreeding coefficient were calculated. Our results indicated that equilibrium was not always maintained. The observed mean homozygote value exceeded the expected value (132.81 vs 102.14), but no evidence for allele dropout was found. These results could be explained by a non-random mating; further studies using a larger number of animals could confirm or invalidate this hypothesis. The probability of identity and exclusion of a locus were also estimated and proved to be useful in paternity testing. The ISAG microsatellite panel is useful to screen the Sicilian bovine kinship. Currently, an allele frequency database is being constructed. PMID:25730006

  3. Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus.

    PubMed

    Sousa-Santos, Carla; Fonseca, Paulo J; Amorim, Maria Clara P

    2015-01-01

    The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy-Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. PMID:25653909

  4. Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

    PubMed Central

    Fonseca, Paulo J.; Amorim, Maria Clara P.

    2015-01-01

    The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from HardyWeinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. PMID:25653909

  5. Multiyear multiple paternity and mate fidelity in the American alligator, Alligator mississippiensis.

    PubMed

    Lance, S L; Tuberville, T D; Dueck, L; Holz-Schietinger, C; Trosclair, P L; Elsey, R M; Glenn, T C

    2009-11-01

    We examined multiple paternity during eight breeding events within a 10-year period (1995-2005) for a total of 114 wild American alligator nests in Rockefeller Wildlife Refuge in south-west Louisiana. Our goals included examining (i) within population variation in multiple paternity among years, (ii) variation in multiple paternity in individual females and (iii) the potential for mate fidelity. To accomplish this, in the current study, eggs were sampled from 92 nests over 6 years and analysed along with 22 nests from a previous 2-year study. Genotypes at five microsatellite loci were generated for 1802 alligator hatchlings. Multiple paternity was found in 51% of clutches and paternal contributions to these clutches were highly skewed. Rates of multiple paternity varied widely among years and were consistently higher in the current study than previously reported for the same population. Larger females have larger clutches, but are not more likely to have multiply sired nests. However, small females are unlikely to have clutches with more than two sires. For 10 females, nests from multiple years were examined. Seven (70%) of these females exhibited long-term mate fidelity, with one female mating with the same male in 1997, 2002 and 2005. Five females exhibiting partial mate fidelity (71%) had at least one multiple paternity nest and thus mated with the same male, but not exclusively. These patterns of mate fidelity suggest a potential role for mate choice in alligators. PMID:19804377

  6. Sad dads: paternal postpartum depression.

    PubMed

    Kim, Pilyoung; Swain, James E

    2007-02-01

    The postpartum period is associated with many adjustments to fathers that pose risks for depression. Estimates of the prevalence of paternal postpartum depression (PPD) in the first two months postpartum vary in the postpartum period from 4 to 25 percent. Paternal PPD has high comorbidity with maternal PPD and might also be associated with other postpartum psychiatric disorders. Studies so far have only used diagnostic criteria for maternal PPD to investigate paternal PPD, so there is an urgent need to study the validity of these scales for men and develop accurate diagnostic tools for paternal PPD. Paternal PPD has negative impacts on family, including increasing emotional and behavioral problems among their children (either directly or through the mother) and increasing conflicts in the marital relationship. Changes in hormones, including testosterone, estrogen, cortisol, vasopressin, and prolactin, during the postpartum period in fathers may be biological risk factors in paternal PPD. Fathers who have ecological risk factors, such as excessive stress from becoming a parent, lack of social supports for parenting, and feeling excluded from mother-infant bonding, may be more likely to develop paternal PPD. Support from their partner, educational programs, policy for paid paternal leave, as well as consideration of psychiatric care may help fathers cope with stressful experiences during the postpartum period. PMID:20805898

  7. Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis.

    PubMed

    Kim, Yung-Kun; Hong, Yoon-Jee; Min, Mi-Sook; Kim, Kyung Seok; Kim, Young-Jun; Voloshina, Inna; Myslenkov, Alexander; Smith, Gavin J D; Cuong, Nguyen Dinh; Tho, Huynh Huu; Han, Sang-Hoon; Yang, Doo-Ha; Kim, Chang-Bae; Lee, Hang

    2011-01-01

    The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed. PMID:21325020

  8. Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers.

    PubMed

    Zuccaro, A; Bordonaro, S; Criscione, A; Guastella, A M; Perrotta, G; Blasi, M; D'Urso, G; Marletta, D

    2008-07-01

    Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategies of the Sanfratellano horse. The whole sample included 384 horses (238 Sanfratellano, 50 Sicilian Oriental Purebred, 30 Sicilian Indigenous and 66 Maremmano), chosen avoiding closely related animals. A total of 111 alleles from 11 microsatellite loci were detected, from four at HTG7 to 15 at ASB2 locus. The mean number of alleles was the lowest in Oriental Purebred (6.7), the highest in Sanfratellano (8.3). All the breeds showed a high level of gene diversity (He) ranging from 0.71 0.04 in Sicilian Oriental Purebred to 0.81 0.02 in Sicilian Indigenous. The genetic differentiation index was low; only about 6% of the diversity was found among breeds. Nei's standards (DS) and Reynolds' (DR) genetic distances reproduced the same population ranking. Individual genetic distances and admixture analysis revealed that: (a) nowadays Maremmano breed does not significantly influence the current Sanfratellano breed; (b) within Sanfratellano breed, it is possible to distinguish two well-defined groups with different proportions of Indigenous blood. PMID:22443698

  9. Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).

    PubMed

    Thvenon, S; Thuy, L T; Ly, L V; Maudet, F; Bonnet, A; Jarne, P; Maillard, J-C

    2004-01-01

    The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam. PMID:14757725

  10. A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States.

    PubMed

    Conant, E K; Juras, R; Cothran, E G

    2012-02-01

    The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear. PMID:22221025

  11. [Analysis of microsatellite loci from Bactrocera dorsalis based on transcriptome dataset].

    PubMed

    Wei, Dan-Dan; Shi, Jun-Xia; Zhang, Xia-Xuan; Chen, Shi-Chun; Wei, Dong; Wang, Jin-Jun

    2014-06-01

    The transcriptome database of the oriental fruit fly, Bactrocera dorsalis (Hendel), was used to identify the functional gene-microsatellite (EST-SSR) markers and to analyze the SSR loci information. In total, 1890 EST-SSR loci were identified, of which, 1296 SSR sequences could be used for primer design. The average distribution frequency of the transcriptomic SSRs was 1/10. 21 kb. However, these distribution frequencies varied considerably among different types of repeat SSRs. The tri-nucleotide repeat SSRs were found to have the highest frequency among the different types of repeat SSRs in the EST-SSR of B. dorsalis. Combining with other literatures, we inferred that the tri-nucleotide repeat SSRs were the most abundant EST-SSR in all of insects. In this study, 42 pairs of EST-SSR primers were designed and 18 pairs produced amplification bands of expected sizes. According to the results of other related literatures, the practices and challenges of strategy for SSR isolation from insect transcriptome databases were discussed, and the problems which should be considered in the screening of insect transcriptomic EST-SSR were put forward. PMID:25223041

  12. Short communication: development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon.

    PubMed

    Luo, C; Zhang, Q L; Luo, Z R

    2014-01-01

    Oriental persimmon (Diospyros kaki Thunb.) (2n = 6x = 90) is a major commercial and deciduous fruit tree that is believed to have originated in China. However, rare transcriptomic and genomic information on persimmon is available. Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed. A total of 1,250,893 reads were generated and 83,898 unigenes were assembled. A total of 42,711 SSR loci were identified from 23,494 unigenes and 289 polymerase chain reaction primer pairs were designed. Of these 289 primers, 155 (53.6%) showed robust PCR amplification and 98 revealed polymorphism between 15 persimmon genotypes, indicating a polymorphic rate of 63.23% of the productive primers for characterization and genotyping of the genus Diospyros. Transcriptome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no genomic sequence information available. PMID:24782136

  13. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

    PubMed

    Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

    2016-01-01

    Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates. PMID:26712623

  14. Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis.

    PubMed

    Ciofi, C; Bruford, M W

    1999-12-01

    A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted. PMID:10703549

  15. Mating behaviour of Rhytidoponera sp. 12 ants inferred from microsatellite analysis.

    PubMed

    Tay, W T; Crozier, R H

    2001-01-01

    In the queenless ponerine ant Rhytidoponera sp. 12, all workers have a spermatheca and functional ovaries and are potentially able to mate and reproduce. Within a colony gamergates may either be full sisters to each other (Type 1 colony), or they may not be full sisters but still be significantly related to each other (Type 2 colony) due to daughter gamergates reproducing in their natal colonies after mating. Despite many studies the mating behaviour of R. sp. 12 has been poorly understood. In this study, we used microsatellite markers to investigate intracolony relatednesses of male mates to the gamergates (bmq) and between male mates (bmm), and mating frequencies and mating patterns, using gamergate DNA and sperm DNA isolated from the spermathecae of gamergates from five colonies. Average bmm and bmq estimates for all five colonies studied were not significantly different from zero, suggesting that on average, within colonies, mating males were unrelated both to each other and to the gamergates. A low frequency (3%) of multiple mating by gamergates was detected. Multiple mating by individual males with sister gamergates within Type 1 colonies was also detected at 3% and could give rise to half-sister nestmate workers. Polygamy in R. sp. 12 might indicate local female-biased operational sex ratios despite the expectation of overall male biases. Our results concur with previous reports that gamergates mate within the colony or nearby, but indicate more diversity in mating patterns than previously indicated for this polygynous ponerine ant species. PMID:11251795

  16. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    PubMed Central

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-01-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parentoffspring relationships in natural populations, with over 99.6% accuracy in parentoffspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 2896% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. PMID:25360247

  17. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

    PubMed

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-06-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. PMID:25360247

  18. Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci.

    PubMed

    Ciofi, Claudio; Tzika, Athanasia C; Natali, Chiara; Watts, Phillip C; Sulandari, Sri; Zein, Moch S A; Milinkovitch, Michel C

    2011-05-01

    Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions. PMID:21481213

  19. Obesity, paternalism and fairness.

    PubMed

    Kniess, Johannes

    2015-11-01

    Many liberal theories are committed to the promotion of population health, and the principle of non-interference in individual life plans. Public health interventions often bring out a tension between these two values. In this paper, I examine this tension by assessing the justifiability of liberty-restricting policies in the field of obesity prevention. As I want to show, a 'soft' form of paternalism, which interferes with people's choices to safeguard their true interests, goes some way in justifying such policies, but it leaves unaddressed the problem of limiting the liberty of those whose true interest is in pursuing an unhealthy lifestyle. I argue that in this latter case, the key to reconcile the promotion of population health with the respect for individual liberty is distributive justice: when we cannot help those who care about their health without doing the same for those who do not, fairness will often require us to do so. PMID:26282279

  20. Microsatellite Marker Analysis Reveals the Complex Phylogeographic History of Rhododendron ferrugineum (Ericaceae) in the Pyrenees

    PubMed Central

    Charrier, Olivia; Dupont, Pierre; Pornon, André; Escaravage, Nathalie

    2014-01-01

    Genetic variation within plant species is determined by a number of factors such as reproductive mode, breeding system, life history traits and climatic events. In alpine regions, plants experience heterogenic abiotic conditions that influence the population's genetic structure. The aim of this study was to investigate the genetic structure and phylogeographic history of the subalpine shrub Rhododendron ferrugineum across the Pyrenees and the links between the populations in the Pyrenees, the Alps and Jura Mountains. We used 27 microsatellite markers to genotype 645 samples from 29 Pyrenean populations, three from the Alps and one from the Jura Mountains. These data were used to estimate population genetics statistics such as allelic richness, observed heterozygosity, expected heterozygosity, fixation index, inbreeding coefficient and number of migrants. Genetic diversity was found to be higher in the Alps than in the Pyrenees suggesting colonization waves from the Alps to the Pyrenees. Two separate genetic lineages were found in both the Alps and Pyrenees, with a substructure of five genetic clusters in the Pyrenees where a loss of genetic diversity was noted. The strong differentiation among clusters is maintained by low gene flow across populations. Moreover, some populations showed higher genetic diversity than others and presented rare alleles that may indicate the presence of alpine refugia. Two lineages of R. ferrugineum have colonized the Pyrenees from the Alps. Then, during glaciation events R. ferrugineum survived in the Pyrenees in different refugia such as lowland refugia at the eastern part of the chain and nunataks at high elevations leading to a clustered genetic pattern. PMID:24667824

  1. Haplotype analysis of DNA microsatellites tightly linked to the locus of Usher syndrome type I on chromosome 11q

    SciTech Connect

    Korostishevsky, M.; Kalinsky, H.; Seroussi, E.

    1994-09-01

    Usher syndrome type I (USHI), an autosomal recessive disorder associated with congenital sensorineural deafness and progressive visual loss, is closely linked to the D11S533 locus. The availability of 7 other polymorphic markers within few centimorgans spanning the disease locus allowed us to identify a unique and single haplotype among all carriers of USHI gene in the Samaritan kindred. Occurrence of recombination in this small chromosomal interval is rare, hindering the detection of the mitotic recombination events needed for analysis by traditional linkage methods. Attempts to order the eight loci by linkage disequilibrium models proved to be problematic. However, our haplotype analysis implied that recombinations which had arisen in past generations may be utilized in fine mapping of the USHI gene and in resolving the conflicting linkage maps previously obtained for this region. We have developed a simple algorithm for predicting the order of the microsatellites on the basis of haplotype resemblance. The following chromosomal map in which the USHI gene is closest to D11S533 (location score of 31.0 by multipoint analysis) is suggested: D11S916, GARP, D11S527, D11S533, OMP, D11S906, D11S911, D11S937. Physical mapping efforts are currently directed to verify and to detail the map of this chromosomal region.

  2. 32 CFR 584.3 - Paternity claims.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 3 2014-07-01 2014-07-01 false Paternity claims. 584.3 Section 584.3 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY PERSONNEL FAMILY SUPPORT, CHILD CUSTODY, AND PATERNITY § 584.3 Paternity claims. (a) General. (1) This chapter sets policy and procedures to process paternity claims against male...

  3. 32 CFR 584.3 - Paternity claims.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 3 2012-07-01 2009-07-01 true Paternity claims. 584.3 Section 584.3 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY PERSONNEL FAMILY SUPPORT, CHILD CUSTODY, AND PATERNITY § 584.3 Paternity claims. (a) General. (1) This chapter sets policy and procedures to process paternity claims against male...

  4. Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

    PubMed Central

    Alexander, Michelle; Ho, Simon Y. W.; Molak, Martyna; Barnett, Ross; Carlborg, rjan; Dorshorst, Ben; Honaker, Christa; Besnier, Francois; Wahlberg, Per; Dobney, Keith; Siegel, Paul; Andersson, Leif; Larson, Greger

    2015-01-01

    Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 10?7 mutations/site/year (95% confidence interval 3.75 10?81.12 10?6). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods. PMID:26510672

  5. Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.

    PubMed

    Alexander, Michelle; Ho, Simon Y W; Molak, Martyna; Barnett, Ross; Carlborg, rjan; Dorshorst, Ben; Honaker, Christa; Besnier, Francois; Wahlberg, Per; Dobney, Keith; Siegel, Paul; Andersson, Leif; Larson, Greger

    2015-10-01

    Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 10(-7) mutations/site/year (95% confidence interval 3.75 10(-8)-1.12 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods. PMID:26510672

  6. Paternal exposure not to blame.

    PubMed

    Doll, R; Evans, H J; Darby, S C

    1994-02-24

    The "Gardner hypothesis" suggests that an excess of childhood leukaemia near a nuclear reprocessing plant is caused by paternal exposure to ionizing radiation. But the evidence shows that this explanation is wrong. PMID:8107860

  7. Advances in understanding paternally transmitted Chromosomal Abnormalities

    SciTech Connect

    Marchetti, F; Sloter, E; Wyrobek, A J

    2001-03-01

    Multicolor FISH has been adapted for detecting the major types of chromosomal abnormalities in human sperm including aneuploidies for clinically-relevant chromosomes, chromosomal aberrations including breaks and rearrangements, and other numerical abnormalities. The various sperm FISH assays have been used to evaluate healthy men, men of advanced age, and men who have received mutagenic cancer therapy. The mouse has also been used as a model to investigate the mechanism of paternally transmitted genetic damage. Sperm FISH for the mouse has been used to detect chromosomally abnormal mouse sperm, while the PAINT/DAPI analysis of mouse zygotes has been used to evaluate the types of chromosomal defects that can be paternally transmitted to the embryo and their effects on embryonic development.

  8. Higher levels of multiple paternities increase seedling survival in the long-lived tree Eucalyptus gracilis.

    PubMed

    Breed, Martin F; Christmas, Matthew J; Lowe, Andrew J

    2014-01-01

    Studying associations between mating system parameters and fitness in natural populations of trees advances our understanding of how local environments affect seed quality, and thereby helps to predict when inbreeding or multiple paternities should impact on fitness. Indeed, for species that demonstrate inbreeding avoidance, multiple paternities (i.e. the number of male parents per half-sib family) should still vary and regulate fitness more than inbreeding--named here as the 'constrained inbreeding hypothesis'. We test this hypothesis in Eucalyptus gracilis, a predominantly insect-pollinated tree. Fifty-eight open-pollinated progeny arrays were collected from trees in three populations. Progeny were planted in a reciprocal transplant trial. Fitness was measured by family establishment rates. We genotyped all trees and their progeny at eight microsatellite loci. Planting site had a strong effect on fitness, but seed provenance and seed provenance planting site did not. Populations had comparable mating system parameters and were generally outcrossed, experienced low biparental inbreeding and high levels of multiple paternity. As predicted, seed families that had more multiple paternities also had higher fitness, and no fitness-inbreeding correlations were detected. Demonstrating that fitness was most affected by multiple paternities rather than inbreeding, we provide evidence supporting the constrained inbreeding hypothesis; i.e. that multiple paternity may impact on fitness over and above that of inbreeding, particularly for preferentially outcrossing trees at life stages beyond seed development. PMID:24587373

  9. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    NASA Astrophysics Data System (ADS)

    Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin

    2012-03-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation. To better understand the genetic relationships of different gametophyte cultures isolated from different sources, 20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U. pinnatifida isolated from wild sporophytes in Vladivostok, Russia and from cultivated sporophytes from Dalian and Qingdao, China. One locus was abandoned because of poor amplification. At the sex-linked locus of Up-AC-2A8, 3 alleles were detected in 25 female gametophyte clones, with sizes ranging from 307 to 316 bp. At other loci, 3 to 7 alleles were detected with an average of 4.5 alleles per locus. The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones, respectively. The average gene diversity for Russian, Chinese, and for the combined total of gametophyte clones was 0.1, 0.4, and 0.5, respectively. Russian gametophyte clones had unique alleles at 7 out of the 19 loci. In cluster analysis, Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance. Overall, high genetic diversity was detected in gametophyte clones isolated from the two countries. These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  10. Male-Biased Sexual Size Dimorphism, Resource Defense Polygyny, and Multiple Paternity in the Emei Moustache Toad (Leptobrachium boringii)

    PubMed Central

    Hudson, Cameron M.; Fu, Jinzhong

    2013-01-01

    We tested the hypotheses that the Emei moustache toad (Leptobrachium boringii) exhibits resource defense polygyny and that combat led to the evolution of male-biased sexual size dimorphism. Between February and March of 2011 and 2012, 26 female and 55 male L. boringii from Mount Emei UNESCO World Heritage Site, Sichuan, China, were observed throughout the breeding season. Prior to the breeding season, males grow 1016 keratinized maxillary nuptial spines, which fall off once the season has ended. Throughout this time, males construct and defend aquatic nests where they produce advertisement calls to attract females. In a natural setting, we documented 14 cases involving a total of 22 males where males used their moustaches for aggressive interaction, and nest takeover was observed on seven occasions. Males were also observed to possess injuries resulting from combat. Genetic analysis using microsatellite DNA markers revealed several cases of multiple paternity, both within nest and within clutch. This observation indicated that some alternative male reproductive strategy, such as satellite behaviour, is occurring, which may have led to the multiple paternity. Larger males were observed to mate more frequently, and in multiple nests, suggesting that females are selecting for larger males, or that larger males are more capable of defending high quality territories. PMID:23840725

  11. The impact of paternity leave on fathers' future earnings.

    PubMed

    Rege, Mari; Solli, Ingeborg F

    2013-12-01

    Using Norwegian registry data, we investigate the effect of paternity leave on fathers' long-term earnings. If the paternity leave increased long-term father involvement, then we should expect a reduction in fathers' long-term earnings as they shift time and effort from market to home production. For identification, we use the Norwegian introduction of a paternity-leave quota in 1993, reserving four weeks of the total of 42 weeks of paid parental leave exclusively for the father. The introduction of the paternity-leave quota led to a sharp increase in rates of leave-taking for fathers. We estimate a difference-in-differences model that exploits differences in fathers' exposure to the paternity-leave quota by the child's age and year of observation. Our analysis suggests that four weeks of paternity leave during the child's first year decreases fathers' future earnings, an effect that persists through our last point of observation, when the child is 5 years old. A battery of robustness tests supports our results. PMID:24135861

  12. Strong male-biased operational sex ratio in a breeding population of loggerhead turtles (Caretta caretta) inferred by paternal genotype reconstruction analysis

    PubMed Central

    Lasala, Jacob A; Harrison, J Scott; Williams, Kris L; Rostal, David C

    2013-01-01

    Characterization of a species mating systems is fundamental for understanding the natural history and evolution of that species. Polyandry can result in the multiple paternity of progeny arrays. The only previous study of the loggerhead turtle (Caretta caretta) in the USA showed that within the large peninsular Florida subpopulation, multiple paternity occurs in approximately 30% of clutches. Our study tested clutches from the smaller northern subpopulation for the presence of multiple paternal contributions. We examined mothers and up to 20 offspring from 19.5% of clutches laid across three nesting seasons (20082010) on the small nesting beach on Wassaw Island, Georgia, USA. We found that 75% of clutches sampled had multiple fathers with an average of 2.65 fathers per nest (17 fathers found). The average number of fathers per clutch varied among years and increased with female size. There was no relationship between number of fathers and hatching success. Finally, we found 195 individual paternal genotypes and determined that each male contributed to no more than a single clutch over the 3-year sampling period. Together these results suggest that the operational sex ratio is male-biased at this site. PMID:24363901

  13. Strong male-biased operational sex ratio in a breeding population of loggerhead turtles (Caretta caretta) inferred by paternal genotype reconstruction analysis.

    PubMed

    Lasala, Jacob A; Harrison, J Scott; Williams, Kris L; Rostal, David C

    2013-11-01

    Characterization of a species mating systems is fundamental for understanding the natural history and evolution of that species. Polyandry can result in the multiple paternity of progeny arrays. The only previous study of the loggerhead turtle (Caretta caretta) in the USA showed that within the large peninsular Florida subpopulation, multiple paternity occurs in approximately 30% of clutches. Our study tested clutches from the smaller northern subpopulation for the presence of multiple paternal contributions. We examined mothers and up to 20 offspring from 19.5% of clutches laid across three nesting seasons (2008-2010) on the small nesting beach on Wassaw Island, Georgia, USA. We found that 75% of clutches sampled had multiple fathers with an average of 2.65 fathers per nest (1-7 fathers found). The average number of fathers per clutch varied among years and increased with female size. There was no relationship between number of fathers and hatching success. Finally, we found 195 individual paternal genotypes and determined that each male contributed to no more than a single clutch over the 3-year sampling period. Together these results suggest that the operational sex ratio is male-biased at this site. PMID:24363901

  14. Paternal Uniparental Isodisomy of Chromosome 11p15.5 within the Pancreas Causes Isolated Hyperinsulinemic Hypoglycemia

    PubMed Central

    Flanagan, S. E.; Kapoor, R. R.; Smith, V. V.; Hussain, K.; Ellard, Sian

    2011-01-01

    Background: Loss of function mutations in the genes encoding the pancreatic ?-cell ATP-sensitive potassium (KATP) channel are identified in approximately 80% of patients with diazoxide unresponsive hyperinsulinemic hypoglycemia (HH). For a small number of patients HH can occur as part of a multisystem disease such as BeckwithWiedemann syndrome (BWS). In approximately 20% of patients, BWS results from chromosome 11 paternal uniparental disomy (UPD), which causes dysregulation of imprinted growth regulation genes at 11p15.5. There is a considerable range in the clinical features and phenotypic severity associated with BWS which is likely to be due to somatic mosaicism. The cause of HH in these patients is not known. Research Design and Methods: We undertook microsatellite analysis of 12 markers spanning chromosome 11p in two patients with severe HH and diffuse disease requiring a pancreatectomy. In both patients mutations in the KATP channel genes had not been identified. Results: We identified segmental paternal UPD in DNA extracted from pancreatic tissue in both patients. UPD was not observed in DNA extracted from the patients leukocytes or buccal samples. In both cases the UPD encompassed the differentially methylated region at chromosome 11p15.5. Despite this neither patient had any further features of BWS. Conclusion: Paternal UPD of the chromosome 11p15.5 differentially methylated region limited to the pancreatic tissue may represent a novel cause of isolated diazoxide unresponsive HH. Loss of heterozygosity studies should therefore be considered in all patients with severe HH who have undergone pancreatic surgery when KATP channel mutation(s) have not been identified. PMID:22654821

  15. Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18, and MYT1L genes

    PubMed Central

    Doco-Fenzy, Martine; Leroy, Camille; Schneider, Anouck; Petit, Florence; Delrue, Marie-Ange; Andrieux, Joris; Perrin-Sabourin, Laurence; Landais, Emilie; Aboura, Azzedine; Puechberty, Jacques; Girard, Manon; Tournaire, Magali; Sanchez, Elodie; Rooryck, Caroline; Ameil, Agnès; Goossens, Michel; Jonveaux, Philippe; Lefort, Geneviève; Taine, Laurence; Cailley, Dorothée; Gaillard, Dominique; Leheup, Bruno; Sarda, Pierre; Geneviève, David

    2014-01-01

    Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader–Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early-onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. Paternal origin of the deletion was determined by genotyping using microsatellite markers. Analysis of the genes encompassed in the deleted region led us to speculate that the ACP1, TMEM18, and/or MYT1L genes might be involved in early-onset obesity. In addition, intellectual deficiency and behavioural troubles can be explained by the heterozygous loss of the SNTG2 and MYT1L genes. Finally, we discuss the parent-of-origin of the deletion. PMID:24129437

  16. Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18, and MYT1L genes.

    PubMed

    Doco-Fenzy, Martine; Leroy, Camille; Schneider, Anouck; Petit, Florence; Delrue, Marie-Ange; Andrieux, Joris; Perrin-Sabourin, Laurence; Landais, Emilie; Aboura, Azzedine; Puechberty, Jacques; Girard, Manon; Tournaire, Magali; Sanchez, Elodie; Rooryck, Caroline; Ameil, Agnès; Goossens, Michel; Jonveaux, Philippe; Lefort, Geneviève; Taine, Laurence; Cailley, Dorothée; Gaillard, Dominique; Leheup, Bruno; Sarda, Pierre; Geneviève, David

    2014-04-01

    Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader-Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early-onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. Paternal origin of the deletion was determined by genotyping using microsatellite markers. Analysis of the genes encompassed in the deleted region led us to speculate that the ACP1, TMEM18, and/or MYT1L genes might be involved in early-onset obesity. In addition, intellectual deficiency and behavioural troubles can be explained by the heterozygous loss of the SNTG2 and MYT1L genes. Finally, we discuss the parent-of-origin of the deletion. PMID:24129437

  17. A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird.

    PubMed

    Weinman, Lucia R; Solomon, Joseph W; Rubenstein, Dustin R

    2015-05-01

    The development of genetic markers has revolutionized molecular studies within and among populations. Although poly-allelic microsatellites are the most commonly used genetic marker for within-population studies of free-living animals, biallelic single nucleotide polymorphisms, or SNPs, have also emerged as a viable option for use in nonmodel systems. We describe a robust method of SNP discovery from the transcriptome of a nonmodel organism that resulted in more than 99% of the markers working successfully during genotyping. We then compare the use of 102 novel SNPs with 15 previously developed microsatellites for studies of parentage and kinship in cooperatively breeding superb starlings (Lamprotornis superbus) that live in highly kin-structured groups. For 95% of the offspring surveyed, SNPs and microsatellites identified the same genetic father, but only when behavioural information about the likely parents at a nest was included to aid in assignment. Moreover, when such behavioural information was available, the number of SNPs necessary for successful parentage assignment was reduced by half. However, in a few cases where candidate fathers were highly related, SNPs did a better job at assigning fathers than microsatellites. Despite high variation between individual pairwise relatedness values, microsatellites and SNPs performed equally well in kinship analyses. This study is the first to compare SNPs and microsatellites for analyses of parentage and relatedness in a species that lives in groups with a complex social and kin structure. It should also prove informative for those interested in developing SNP loci from transcriptome data when published genomes are unavailable. PMID:25224810

  18. Microsatellite based ovine parentage testing to identify the source responsible for the killing of an endangered species.

    PubMed

    Rendo, Fernando; Iriondo, Mikel; Manzano, Carmen; Estonba, Andone

    2011-08-01

    In this study, we present an animal forensic genetics case in which we applied ovine microsatellite based parentage testing to the resolution of an act against protected wildlife. The aim was to identify the origin of the animal responsible for the death of an Egyptian vulture (Neophron percnopterus) that had been poisoned through consumption of a Latxa Blond Face breed lamb. Thus, we carried out a 22 microsatellite based parentage test in order to identify the parents of the lamb in the flock which grazes in the same place where the vulture's remains were found. Multiple parentage analysis revealed two possible parents, one ewe and one ram, with a combined paternity/maternity index (PI) higher than 9.09E9 and a likelihood (W) value of 99.9999%, assuming 50% probability a priori. This result confirmed the flock of origin of the poisoned lamb and shows that the microsatellite panel described herein is a potentially useful tool for the resolution of animal forensic cases. PMID:20952265

  19. Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

    PubMed Central

    Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

    2015-01-01

    Background Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Principal Findings Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a distinct cluster. The cluster analysis also distinguished diploid and tetraploid wild species of safflower. Conclusion Next generation sequencing of safflower genome generated a large set of microsatellite markers. The novel markers developed in this study will add to the existing repertoire of markers and can be used for diversity analysis, synteny studies, construction of linkage maps and marker-assisted selection. PMID:26287743

  20. Facilitating co-existence by tracking gene dispersal in conventional potato systems with microsatellite markers.

    PubMed

    Petti, Carloalberto; Meade, Conor; Downes, Martin; Mullins, Ewen

    2007-01-01

    Based on international findings, Irish co-existence guidelines for the cultivation of GM potato stipulate that an isolation distance of 20 m is required to minimize the spread of transgenic pollen in accordance with required labeling thresholds. As potato tolerant to Phytophthora infestans is the most applicable GM crop from an Irish context, we tested the efficacy of this isolation distance under Irish environmental conditions using the conventional variety Dsire as a pollen donor and the male-sterile variety British Queen as a pollen receptor. Gene flow was determined by scoring for berry presence on receptor plants and confirmed using a microsatellite marker system designed to assess paternity in F(1) seedlings. 99.1% of seedlings recovered were identified as having Dsire paternity. Whereas 19.9% (140/708) of total berries formed on receptor plants occurred at a distance of 21 m from the pollen source, only 4 of these berries bore viable true potato seed (TPS), from which 23 TPS germinated. TPS-bearing berry formation was negatively correlated with distance from the pollen source, and although overall distribution of berries and seeds was non-random across the plot, no significant correlation was evident with respect to wind direction. Microsatellite markers were also used to confirm that the foraging beetle Meligethes aeneus is a vector for the transmission of potato pollen, but a more detailed statistical analysis of this dataset was limited by inclement weather during the trial. To conclude, we recommend that a two-tiered system be established in regard to establishing isolation distances for the experimental trial and commercial cultivation of GM potato in Ireland, and that responsible crop management be adopted to minimize the establishment of TPS-derived volunteers, which we have noted will emerge through a rotation as a result of pollen-mediated gene flow. PMID:18289498

  1. Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications

    PubMed Central

    2014-01-01

    Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

  2. Inheritance pattern of microsatellite loci and their use for kinship analysis in the Japanese scallop Patinopecten yessoensis

    NASA Astrophysics Data System (ADS)

    Xu, Kefeng; Li, Qi

    2009-06-01

    The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four controlled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four families were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.

  3. Inheritance mode of microsatellite loci and their use for kinship analysis in the Pacific oyster ( Crassostrea gigas)

    NASA Astrophysics Data System (ADS)

    Li, Qi; Zheng, Xiaodong; Yu, Ruihai

    2008-08-01

    Five full-sib families of the Pacific oyster ( Crassostrea gigas) larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.

  4. An induced mass spawn of the hermaphroditic lion-paw scallop, Nodipecten subnodosus: genetic assignment of maternal and paternal parentage.

    PubMed

    Petersen, Jessica L; Ibarra, Ana M; Ramirez, Jos L; May, Bernie

    2008-01-01

    The Pacific lion-paw scallop is commonly propagated for aquaculture by induced mass spawns of few individuals. Parentage of a mass spawn of this species has not been evaluated nor has the maternal and paternal contribution of each of these functional hermaphrodites to the progeny. Genotypes of 6 spawners and 374 resulting progeny at 6 microsatellite loci were coupled with mitochondrial DNA sequencing to assign maternal and paternal parentage. After the identification of a high proportion of null alleles (9.7%), microsatellite data revealed that 51.7% of the progenies were full siblings, with a significant, unequal contribution of the 6 spawners to the progeny. Three progenies were the result of self-fertilization. All spawners contributed paternally (though unequally); however, 2 spawners were the maternal parents of all but 7 progenies resulting in a variance effective population size of 3.52. DNA sequencing confirmed 4 microsatellite mutations within 4476 alleles scored, all in the paternal germ line. With minor exception, the loci conformed to Mendelian rules of segregation when null alleles were accounted for, and 2 loci were found to be linked. These results lend insight to the genetic composition of induced mass spawns and provide a basis for the development of more effective spawning techniques. PMID:18334505

  5. Hospital Based Paternity Establishment in Colorado.

    ERIC Educational Resources Information Center

    Pearson, Jessica; Thoennes, Nancy

    1997-01-01

    Describes the impact of the Colorado's Child Support Improvement Project on voluntary paternity acknowledgment rate, which increased almost 24% from 1991 to 1994. Program activities include simplifying voluntary acknowledgment procedures and training hospital personnel on paternity. Voluntary paternity acknowledgment is associated with the

  6. Microsatellites: evolution and contribution.

    PubMed

    Madesis, Panagiotis; Ganopoulos, Ioannis; Tsaftaris, Athanasios

    2013-01-01

    Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed. PMID:23546780

  7. Immunohistochemistry and microsatellite instability analysis in molecular subtyping of colorectal carcinoma based on mismatch repair competency

    PubMed Central

    Yuan, Lin; Chi, Yayun; Chen, Weixiang; Chen, Xiaochen; Wei, Ping; Sheng, Weiqi; Zhou, Xiaoyan; Shi, Daren

    2015-01-01

    Mismatch repair defective (MMRd) colorectal carcinoma (CRC) is a distinct molecular phenotype of colorectal cancer, including 12% of sporadic CRC and 3% of Lynch Syndrome. In order to investigate the clinicopathological characteristics of MMRd colorectal carcinoma, and to find the most effective method for preliminary screening, 296 CRC fulfilled revised Bethesda Guideline (RB) were selected from 1450 CRCs to perform both IHC staining for MLH1, MSH2, MSH6, PMS2 and MSI analysis. Sixty-eight tumors were classified as MSI-H by MSI test. Colorectal carcinomas with MSI-H were prone to be proximal located, poorly differentiated, and relatively early staged, with infrequent metastasis to lymph node as well as to distant organs, compared with MSS ones. All of the 68 MMRd CRCs presented abnormal expression of at least one mismatch repair protein (MMRP), with 48 concurrent negative of MLH1 and PMS2, 14 concurrent negative of MSH2 and MSH6, 4 isolated negative of MSH6, 1 isolated negative of PMS2, and 1 concurrent negative of 4 MMRPs. All of the MLH1 negative tumors also showed abnormal expression of PMS2. All of the MSH2 negative cases also presented negative expression of MSH6. The sensitivity and specificity of the 2-antibody IHC test contained only PMS2 and MSH6 for screening for MMRd CRC were 100% and 98.2% respectively, exactly the same as that of the 4-antibody IHC test with all of the 4 MMRPs. The diagnostic accordance rate of the 2-antibody approach and MSI analysis was 98.6%. In conclusion, MMRd CRC has characteristic clinicopathological features different from MSS CRCs. The 2-antibody IHC approach containing MSH6 and PMS2 is the most easy and effective way to detecting MMR deficiency in CRC. PMID:26885030

  8. Molecular evidence for multiple paternity in a population of the Viviparous Tule Perch Hysterocarpus traski.

    PubMed

    Liu, Jin-Xian; Tatarenkov, Andrey; O'Rear, Teejay A; Moyle, Peter B; Avise, John C

    2013-03-01

    Population density might be an important variable in determining the degree of multiple paternity. In a previous study, a high level of multiple paternity was detected in the shiner perch Cymatogaster aggregata, a species with high population density and a high mate encounter rate. The tule perch Hysterocarpus traski is phylogenetically closely related to C. aggregata, but it has relatively lower population density, which may result in distinct patterns of multiple paternity in these 2 species. To test the hypothesis that mate encounter rate may affect the rate of successful mating, we used polymorphic microsatellite markers to identify multiple paternity in the progeny arrays of 12 pregnant females from a natural population of tule perch. Multiple paternity was detected in 11 (92%) of the 12 broods. The number of sires per brood ranged from 1 to 4 (mean 2.5) but with no correlation between sire number and brood size. Although the brood size of tule perch is considerably larger than that of shiner perch (40.7 vs. 12.9, respectively), the average number of sires per brood in tule perch is much lower than that in shiner perch (2.5 vs. 4.6, respectively). These results are consistent with the hypothesis that mate encounter rate is an important factor affecting multiple mating. PMID:23267018

  9. Paternal UPD15: further genetic and clinical studies in four Angelman syndrome patients.

    PubMed

    Fridman, C; Varela, M C; Kok, F; Diament, A; Koiffmann, C P

    2000-06-19

    Among 25 patients diagnosed with Angelman syndrome, we detected 21 with deletion and 4 with paternal uniparental disomy (UPD), 2 isodisomies originating by postzygotic error, and 1 MII nondisjunction event. The diagnosis was obtained by molecular techniques, including methylation pattern analysis of exon 1 of SNRPN and microsatellite analysis of loci within and outside the 15q11-q13 region. Most manifestations present in deletion patients are those previously reported. Comparing the clinical data from our and published UPD patients with those with deletions we observed the following: the age of diagnosis is higher in UPD group (average 7 3/12 years), microcephaly is more frequent among deletion patients, UPD children start walking earlier (average age 2 9/12 years), whereas in deletion patients the average is 4 (1/2) years, epilepsy started later in UPD patients (average 5 10/12 years) than in deletion patients (average 1 11/12 years), weight above the 75th centile is reported mainly in UPD patients, complete absence of speech is more common in the deleted (88.9%) than in the UPD patients because half of the children are able to say few words. Thus, besides the abnormalities already described, the UPD patients have somewhat better verbal development, a weight above the 75th centile, and OFC in the upper normal range. PMID:10861661

  10. [Development of microsatellites and genetic diversity analysis of Scutellaria baicalensis Georgi using genomic-SSR markers].

    PubMed

    Qi, Lin-jie; Long, Ping; Jiang, Chao; Yuan, Yuan; Huang, Lu-qi

    2015-04-01

    A total of 12 775 SSRs were identified from Scutellaria baicalensis Georgi genomic database, accounting for 2.56% of the total genomic sequences. The result showed that S. baicalensis SSRs were based on 68.32% dinucleotide and 18.63% trinucleotide repeats; CT/GA and TTC/GAA were predominant in the dinucleotide motifs and the trinucleotide motifs respectively. Nine primers were selected to produce highly reproducible SSR bands and were used in studying the genetic diversity of S. baicalensis, 50 individuals from ten populations. 68 SSR polymorphic loci were detected, these loci were polymorphic and displayed 4 to 12 alleles per locus with a mean number of 7; the effect number of alleles was 3. Expected heterozygosities were 0.6 and were far more greater than the average in dicotyledonous plants. PIC (polymorphism information content) was 0.72, Shannon's information index was 1.32, these all proved that S. baicalensis had a high genetic diversity in general. Genetic differentiation among population Gst was 0.131, genetic variation among population accounted for 13.1% and genetic variation within population accounted for 86.9%. The cluster analysis showed that 10 populations S. Baicalensis were classified into 2 groups, but it was not associated with geographical distribution. PMID:26223135

  11. Quantification of the paternal allele bias for new germline mutations in the retinoblastoma gene

    SciTech Connect

    Morrow, J.F.; Rapaport, J.M.; Dryia, T.P.

    1994-09-01

    New germline mutations in the human retinoblastoma gene preferentially arise on a paternally derived allele. In nonhereditary retinoblastoma, the initial somatic mutation seems to have no such bias. The few previous reports of these phenomena included relatively few cases (less than a dozen new germline or initial somatic mutations), so that the magnitude of the paternal allele bias for new germline mutations is not known. Knowledge of the magnitude of the bias is valuable for genetic counseling, since, for example, patients with new germline mutations who reproduce transmit risk for retinoblastoma according to the risk that the transmitted allele has a germline mutation. We sought to quantitate the paternal allele bias and to determine whether paternal age is a factor possibly accounting for it. We studied 311 families with retinoblastoma (261 simplex, 50 multiplex) that underwent clinical genetic testing and 5 informative families recruited from earlier research. Using RFLPs and polymorphic microsatellites in the retinoblastoma gene, we could determine the parental origin of 45 new germline mutations and 44 probable initial somatic mutations. Thirty-seven of the 45 new germline mutations, or 82%, arose on a paternal allele while only 24 of the 44 initial somatic mutations (55%) did so. Increased paternal age does not appear to account for the excess of new paternal germline mutations, since the average age of fathers of children with new germline mutations (29.4 years, n=26, incomplete records on 11) was not significantly different from the average age of fathers of children with maternal germline mutations or somatic initial mutations (29.8 years, n=35, incomplete records on 17).

  12. Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm?

    PubMed

    Kuijper, B; Lane, N; Pomiankowski, A

    2015-02-01

    A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males - 'mother's curse'. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. 'reverse dominance') are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why 'mother's curse' is less pervasive than predicted by earlier work. PMID:25653025

  13. Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm?

    PubMed Central

    Kuijper, B; Lane, N; Pomiankowski, A

    2015-01-01

    A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males mother's curse. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. reverse dominance) are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why mother's curse is less pervasive than predicted by earlier work. PMID:25653025

  14. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)

    PubMed Central

    Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants. PMID:26536014

  15. [Variation of mini- and microsatellite DNA repeats in parthenogenetic lizard Darevskia armeniaca as revealed by DNA fingerprinting analysis].

    PubMed

    Martirosian, I A; Kan, N G; Petrosian, V G; Malysheva, D N; Trofimova, A A; Danielian, F D; Darevski?, I S; Korochkin, L I; Ryskov, A P; Tokarskaia, O N

    2003-02-01

    Population and family samples of two morphological forms (mutant and normal with respect to dorsal color) of pathogenetic lizard Darevskia armeniaca were examined by means of DNA fingerprinting using M13 mini- and (GATA)n and (TCC)n microsatellite DNA markers. The morphological forms examined were characterized by clonally inherited, species-specific patterns of the DNA markers, which were different from the species-specific DNA fingerprints of the other parthenogenetic species of the genus Darevskia (D. dahli. D. unisexualis, and D. rostombekovi). The mean index of similarity (S) obtained for a sample of 36 individuals from three isolated populations using three types of DNA markers was 0.966. This was similar to the variability level observed in D. dahli (0.962) (P > 0.05), but higher than that in D. unisexualis (0.950) (P < 0.05) and D. rostombekovi (0.875) (P < 0.01). Inheritance of M13 minisatellite and (TCC)n microsatellite DNA markers in the F1 offspring of parthenogenetic lizards was examined. It was shown that variability and clonal diversity of the fingerprint phenotypes observed in the populations and families of D. armeniaca could be at least partly explained by RFLP mutations in microsatellite repeats. PMID:12669417

  16. Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites.

    PubMed

    Haponski, A E; Bollin, T L; Jedlicka, M A; Stepien, C A

    2009-12-01

    Catchment population structure and divergence patterns of the rainbow darter Etheostoma caeruleum (Percidae: Teleostei), an eastern North American benthic fish, are tested using a landscape genetics approach. Allelic variation at eight nuclear DNA microsatellite loci and two mitochondrial DNA regions [cytochrome (cyt) b gene and control region; 2056 aligned base pairs (bp)] is analysed from 89 individuals and six sites in the Lake Erie catchment (Blanchard, Chagrin, Cuyahoga and Grand Rivers) v. the Ohio River catchment (Big Darby Creek and Little Miami River). Genetic and geographic patterning is assessed using phylogenetic trees, pair-wise F(ST) analogues, AMOVA partitioning, Mantel regression, Bayesian assignment, 3D factorial correspondence and barrier analyses. Results identify 34 cyt b haplotypes, 22 control region haplotypes and 137 microsatellite alleles whose distributions demonstrate marked genetic divergence between populations from the Lake Erie and Ohio River catchments. Etheostoma caeruleum populations in the Lake Erie and Ohio River catchments diverged c. 1.6 mya during the Pleistocene glaciations. Greater genetic separations characterize the Ohio River populations, reflecting their older habitat age and less recent connectivity. Divergence levels within the Lake Erie catchment denote more recent post-glacial origins. Notably, the western Lake Erie Blanchard River population markedly differs from the three central basin tributary samples, which are each genetically distinguishable using microsatellites. Overall relationships among the Lake Erie sites refute a genetic isolation by geographic distance hypothesis. Etheostoma caeruleum populations thus exchange few genes and have low migration among tributaries and catchments. PMID:20738685

  17. [Genetic variation analysis of two silver carp populations in the middle and upper Yangtze River by microsatellite.

    PubMed

    Wang, Chang-Zhong; Liang, Hong-Wei; Zou, Gui-Wei; Luo, Xiang-Zhong; Li, Zhong; Tian, Hua1; Hu, Guang-Fu

    2008-10-01

    Thirty nine microsatellite markers were applied to analyze the genetic diversity of two silver carp populations in the middle and upper reaches of the Yangtze River. The following parameters were calculated: average observed number of alleles, average effective number of alleles, genetic heterozygosity, polymorphism information content (PIC), genetic similarity coefficient, genetic distance, Hardy-Weinberg balance deflection index. These results indicated that the average observed number of alleles in each microsatellite locus of the Wanzhou population and Jianli populations is 6.128 and 4.974, respectively; the average effective number of alleles is 4.107 and 3.395, respectively; and the number of total alleles of these 39 microsatellite loci is 259. The PIC of polymorphic loci varies between 0.077-0.865, and the average PIC is 0.617. The average observed heterozygosity (Ho) of two populations is 0.834 and 0.775, respectively, and the average expective heterzygosity (He) is 0.713 and 0.623, respectively. The genetic similarity coefficient of two populations is 0.618 and the genetic distance of these populations is 0.482. These results indicated that the two populations belong to different popula-tions for the obvious genetic differentiation. PMID:18930896

  18. Analysis of transferability of microsatellite primers (SSR) in wild Passiflora species and intraspecific genetic diversity in Passiflora alata.

    PubMed

    Silva, M A A; Souza, M M; Silva, G S; Melo, C A F; Corra, R X; Arajo, I S; Conceio, L D H C S

    2014-01-01

    The genus Passiflora L. is the most representative of Passifloraceae, with over 500 known species, among which 150-200 originated from Brazil. In addition to the great commercial importance of this genus for the fruit market, many of the species have exotic flowers with a huge diversity of colors and can thereby be exploited as ornamental plants. This study was aimed at investigating the transferability of microsatellite primers in wild Passiflora species (P. cacao, P. cincinnata, P. glandulosa, P. gibertii, and P. mucronata) and characterizing 29 P. alata accessions using microsatellite primers that were previously developed in a library enriched with microsatellites from P. edulis f. flavicarpa for P. alata. The interspecies cross-amplification rate varied, and P. cacao exhibited the highest rate of amplification, suggesting a greater degree of proximity to P. edulis. The study of intraspecific accessions in P. alata found genetic similarity, with values ranging from 0.47 to 1.00 and an average similarity of 0.74. Hence, this study revealed the intraspecific genetic variability of P. alata in the Universidade Estadual de Santa Cruz's Active Germplasm Bank and will lead to the adoption of mating strategies between accessions; thus making their use more suitable for breeding purposes. PMID:25117349

  19. Characterization of microsatellites in wild and sweet cherry (Prunus avium L.)--markers for individual identification and reproductive processes.

    PubMed

    Schueler, Silvio; Tusch, Alexandra; Schuster, Mirko; Ziegenhagen, Birgit

    2003-02-01

    Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry. PMID:12669801

  20. New softwares for automated microsatellite marker development.

    PubMed

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimares, Patrcia; Moretzsohn, Marcio; Bertioli, David

    2006-01-01

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut. PMID:16493138

  1. Genetic Diversity and Differentiation of the Orange-Spotted Grouper (Epinephelus coioides) Between and Within Cultured Stocks and Wild Populations Inferred from Microsatellite DNA Analysis

    PubMed Central

    Wang, Le; Meng, Zining; Liu, Xiaochun; Zhang, Yong; Lin, Haoran

    2011-01-01

    In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise Fst, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper. PMID:21845084

  2. The physical and genomic organization of microsatellites in sugar beet.

    PubMed Central

    Schmidt, T; Heslop-Harrison, J S

    1996-01-01

    Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis. Images Fig. 1 Fig. 2 Fig. 3 PMID:8710945

  3. Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single Nucleotide Polymorphism (SNP) markers are increasingly being used in crop breeding programs, slowly replacing microsatellites and other markers. SNPs provide many benefits over microsatellites, including ease of analysis and unambiguous results across various platforms. We compare SNPs to m...

  4. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  5. Paternity testing in an autotetraploid alfalfa breeding polycross

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining unknown parentage in autotetraploid alfalfa (Medicago sativa L.) (2n = 4x = 32) can improve breeding gains. Exclusion analysis based paternity testing SAS code is presented, amenable to genotyping errors, for autotetraploid species utilizing co-dominant molecular markers with ambiguous d...

  6. Rapid and inexpensive analysis of genetic variability in Arapaima gigas by PCR multiplex panel of eight microsatellites.

    PubMed

    Hamoy, I G; Santos, E J M; Santos, S E B

    2008-01-01

    The aim of the present study was the development of a multiplex genotyping panel of eight microsatellite markers of Arapaima gigas, previously described. Specific primer pairs were developed, each one of them marked with either FAM-6, HEX or NED. The amplification conditions using the new primers were standardized for a single reaction. The results obtained demonstrate high heterozygosity (average of 0.69) in a Lower Amazon population. The multiplex system described can thus be considered a fast, efficient and inexpensive method for the investigation of genetic variability in Arapaima populations. PMID:18273816

  7. Analysis of four microsatellite markers on the long arm of chromosome 9 by meiotic recombination in flow-sorted single sperm

    SciTech Connect

    Furlong, R.A.; Goudie, D.R.; Carter, N.P.; Lyall, J.E.W.; Affara, N.A.; Ferguson-Smith, M.A. )

    1993-06-01

    Meiotic recombination in flow-sorted single sperm was used to analyze four highly polymorphic microsatellite markers on the long arm of chromosome 9. The microsatellites comprised three tightly linked markers: 9CMP1 (D9S109), 9CMP2 (D9S127), and D9S53, which map to 9q31, and a reference marker, ASS, which is located in 9q34.1. Haplotypes of single sperm were assessed by using PCR in a single-step multiplex reaction to amplify each locus. Recombinant haplotypes were identified by their relative infrequency and were analyzed using THREELOC, a maximum-likelihood-analysis program, and an adaptation of CRI-MAP. The most likely order of these markers was cen-D9S109-D9S127-D9S53-ASS-tel with D9S109, D9S127, and D9S53 being separated by a genetic distance of approximately 3%. The order of the latter three markers did not however achieve statistical significance using the THREELOC program. 21 refs., 2 figs., 4 tabs.

  8. Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae)

    PubMed Central

    Politov, Dmitry V.; Belokon, Maryana M.; Belokon, Yuri S.; Polyakova, Tatyana A.; Shatokhina, Anna V.; Mudrik, Elena A.; Azarova, Anna B.; Filippov, Mikhail V.; Shestibratov, Konstantin A.

    2015-01-01

    Testing systems for molecular identification of micropropagated elite aspen (Populus tremula L.) genotypes were developed on the base on microsatellite (SSR) loci. Out of 33 tested microsatellite loci, 14 were selected due to sustainable PCR amplification and substantial variability in elite clones of aspen aimed for establishment of fast-rotated forest plantations. All eight tested clones had different multilocus genotypes. Among 114 trees from three reference native stands located near the established plantations, 80 haplotypes were identified while some repeated genotypes were attributed to natural clones which appeared as a result of sprouting. The selected set of SSR markers showed reliable individual identification with low probability of appearance of identical aspen genotypes (a minimum of 4.8 · 10−10 and 1 × 10−4 for unrelated and related individuals, resp.). Case studies demonstrating practical applications of the test system are described including analysis of clonal structure and levels of genetic diversity in three natural aspen stands growing in the regions where plantations made of elite clones were established. PMID:26823661

  9. Multiple paternity and sperm storage in captive Hermann's tortoises, Testudo hermanni boettgeri determined from amniotic fluid adhering to the eggshell.

    PubMed

    Farke, C M; Olek, K; Gerding, W M; Distler, C

    2015-08-01

    We identified multiple paternity in 52.9% of the clutches of Hermann's tortoise Testudo hermanni boettgeri using polymorphic microsatellite markers. In addition we demonstrated sperm storage across seasons. DNA was extracted from the amniotic fluid adhering to the eggshell's inner surface, a procedure suitable for easy, non-invasive DNA sampling in conservation and breeding programs. To improve the informative value of monomorphic single tandem repeat (STR) markers we additionally analyzed single nucleotide polymorphism (SNP) variability. PMID:26003400

  10. Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability.

    PubMed

    Liu, Qi; Zhang, Bing

    2016-03-01

    Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers. PMID:26680540

  11. Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability

    PubMed Central

    2015-01-01

    Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers. PMID:26680540

  12. Density drives polyandry and relatedness influences paternal success in the Pacific gooseneck barnacle, Pollicipes elegans

    PubMed Central

    2014-01-01

    Background Polyandry is a common mating strategy in animals, increasing female fitness through direct (material) and indirect (genetic) benefits. Most theories about the benefits of polyandry come from studies of terrestrial animals, which have relatively complex mating systems and behaviors; less is known about the potential benefits of polyandry in sessile marine animals, for which potential mates may be scarce and females have less control over pre-copulatory mate choice. Here, we used microsatellite markers to examine multiple paternity in natural aggregations of the Pacific gooseneck barnacle Pollicipes elegans, testing the effect of density on paternity and mate relatedness on male reproductive success. Results We found that multiple paternity was very common (79% of broods), with up to five fathers contributing to a brood, though power was relatively low to detect more than four fathers. Density had a significant and positive linear effect on the number of fathers siring a brood, though this relationship leveled off at high numbers of fathers, which may reflect a lack of power and/or an upper limit to polyandry in this species. Significant skew in male reproductive contribution in multiply-sired broods was observed and we found a positive and significant relationship between the proportion of offspring sired and the genetic similarity between mates, suggesting that genetic compatibility may influence reproductive success in this species. Conclusions To our knowledge, this is the first study to show high levels of multiple paternity in a barnacle, and overall, patterns of paternity in P. elegans appear to be driven primarily by mate availability. Evidence of paternity bias for males with higher relatedness suggests some form of post-copulatory sexual selection is taking place, but more work is needed to determine whether it operates during or post-fertilization. Overall, our results suggest that while polyandry in P. elegans is driven by mate availability, it may also provide a mechanism for females to ensure fertilization by compatible gametes and increase reproductive success in this sessile species. PMID:24739102

  13. Characterization of microsatellite loci and repeat density in the gooseneck barnacle, Pollicipes elegans, using next generation sequencing.

    PubMed

    Plough, Louis V; Marko, Peter B

    2014-01-01

    Pollicipes elegans is a commercially important and biogeographically significant rocky-shore gooseneck barnacle found along the eastern Pacific coasts of Peru, El Salvador, and Mexico. Little is known about its reproductive biology, and no genetic resources exist despite its growing importance as a fisheries species in the region. Next generation sequencing methods can provide rapid and cost-effective development of molecular markers such as microsatellites, which can be applied to studies of paternity, parentage, and population structure in this understudied species. Here, we used Roche 454 pyrosequencing to develop microsatellite markers in P. elegans and made genomic comparisons of repeat density and repeat class frequency with other arthropods and more distantly related taxa. We identified 13 809 repeats of 1-6 bp, or a density of 9744 bp of repeat per megabase queried, which was intermediate in the range of taxonomic groups compared. Comparison of repeat class frequency distributions revealed that P. elegans was most similar to Drosophila melanogaster rather than the more closely related crustacean Daphnia pulex. We successfully isolated 15 polymorphic markers with an average of 9.4 alleles per locus and average observed and expected heterozygosities of 0.501 and 0.597, respectively. Four loci were found to be out of Hardy-Weinberg equilibrium, likely due to the presence of null alleles. A preliminary population genetic analysis revealed low but significant differentiation between a Peruvian (n = 47) and Mexican (n = 48) population (F(ST) = 0.039) and markedly reduced genetic diversity in Peru. These markers should facilitate future studies of paternity, parentage, and population structure in this species. PMID:24115106

  14. Toward the authentication of varietal wines by the analysis of grape (Vitis vinifera L.) residual DNA in must and wine using microsatellite markers.

    PubMed

    Siret, R; Boursiquot, J M; Merle, M H; Cabanis, J C; This, P

    2000-10-01

    In an attempt to develop a technique for the identification of grape cultivars in commercial wines, a method for the extraction of DNA from must and experimental wines was adapted and optimal PCR conditions for the amplification of this DNA were established. DNA was analyzed during the fermentation process for six cultivars (Chardonnay, Clairette blanche, Grenache noir, Merlot, Muscat blanc petits grains, and Syrah). The extractions were performed on solid parts in suspension as well as on the aqueous fraction. Expected profiles for these cultivars were obtained with DNA extracted from the solid parts during all of the fermentation process and for the wine. The analysis of DNA extracted from aqueous fractions was less reproducible, and microsatellite amplifications were obtained only in the case of Clairette blanche, Merlot, and Syrah wines. Results demonstrate that the purification process is adequate for the analysis but that the DNA concentration represents the main limiting factor. Technical improvements of the method are discussed. PMID:11052774

  15. Decrease in the CGG{sub n} trinucleotide repeat mutation of the fragile X syndrome to normal size range during paternal transmission

    SciTech Connect

    Vaeisaenen, M.L.; Haataja, R.; Leisti, J.

    1996-09-01

    The fragile X syndrome, the most common inherited form of mental retardation, is caused by the expansion of a CGG{sub n} trinucleotide repeat in the FMR-1 gene. Although the repeat number usually increases during transmission, few cases with reduction of an expanded CGG{sub n} repeat back to the normal size range have been reported. We describe for the first time a family in which such reduction has occurred in the paternal transmission. The paternal premutation ({Delta} = 300 hp) was not detected in one of the five daughters or in the son of this daughter, although he had the grandpaternal RFLP haplotype. Instead, fragments indicating the normal CGG{sub n} repeat size were seen on a Southern blot probed with StB12.3. PCR analysis of the CGG{sub n} repeat confirmed this; in addition to a maternal allele of 30 repeats, an allele of 34 repeats was detected in the daughter and, further, in her son. Sequencing of this new allele revealed a pure CGG{sub n} repeat configuration without AGG interruptions. No evidence for a somatic mosaicism of a premutation allele in the daughter or a normal allele in her father was detected when investigating DNA derived from blood lymphocytes and skin fibroblasts. Another unusual finding in this family was lack of the PCR product of the microsatellite marker RS46 (DXS548) in one of the grandmaternal X chromosomes, detected as incompatible inheritance of RS46 alleles. The results suggest an intergenerational reduction in the CGG{sub n} repeat from premutation size to the normal size range and stable transmission of the contracted repeat to the next generation. However, paternal germ-line mosaicism could not be excluded as an alternative explanation for the reverse mutation. 37 refs., 4 figs.

  16. Male dominance, paternity, and relatedness in the Jamaican fruit-eating bat (Artibeus jamaicensis).

    PubMed

    Ortega, Jorge; Maldonado, Jess E; Wilkinson, Gerald S; Arita, Hctor T; Fleischer, Robert C

    2003-09-01

    We analysed variation at 14 nuclear microsatellite loci to assess the genetic structure, relatedness, and paternity of polygynous Jamaican fruit-eating bats. A total of 84 adults captured in two caves exhibited little genetic differentiation between caves (FST = 0.008). Average relatedness among adult females in 10 harem groups was very low (R = 0.014 +/- 0.011), providing no evidence of harem structure. Dominant and subordinate males shared paternity in large groups, while dominant and satellite males shared paternity in smaller groups. However, our results suggest that male rank influences paternity. Dominant males fathered 69% of 40 offspring, followed by satellite (22%) and subordinate males (9%). Overall adult male bats are not closely related, however, in large harem groups we found that subordinate and dominant males exhibited relatedness values consistent with a father-offspring relationship. Because dominant and subordinate males also sired all the pups in large groups, we propose that their association provides inclusive fitness to them. PMID:12919478

  17. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

    PubMed Central

    2011-01-01

    Background The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae. PMID:21806822

  18. Analysis of microsatellite polymorphisms within the GLC1F locus in Japanese patients with normal tension glaucoma

    PubMed Central

    Murakami, Kaori; Ota, Masao; Shiota, Tomoko; Nomura, Naoko; Kashiwagi, Kenji; Mabuchi, Fumihiko; Iijima, Hiroyuki; Kawase, Kazuhide; Yamamoto, Tetsuya; Nakamura, Makoto; Negi, Akira; Sagara, Takeshi; Nishida, Teruo; Inatani, Masaru; Tanihara, Hidenobu; Aihara, Makoto; Araie, Makoto; Fukuchi, Takeo; Abe, Haruki; Higashide, Tomomi; Sugiyama, Kazuhisa; Kanamoto, Takashi; Kiuchi, Yoshiaki; Iwase, Aiko; Ohno, Shigeaki; Inoko, Hidetoshi; Mizuki, Nobuhisa

    2010-01-01

    Purpose To investigate whether the GLC1F locus is associated with normal tension glaucoma (NTG) in Japanese patients. Methods We recruited 242 unrelated Japanese subjects, including, 141 NTG patients and 101 healthy controls. The patients exhibiting a comparatively early onset were selected as they suggest that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 11 highly polymorphic microsatellite markers in and around the GLC1F locus. Results Individuals carrying the 163 allele of D7S1277i had a statistically significant increased risk of NTG (p=0.0013, pc=0.016, OR=2.47, 95%CI=1.42–4.30). None of the other markers identified significant loci (pc>0.05) after Bonferroni’s correction. Conclusions These findings suggested that the genes in the GLC1F locus may be associated with the pathogenesis of NTG. PMID:20309402

  19. CERISE microsatellite system

    NASA Astrophysics Data System (ADS)

    Kaced, J.

    1993-01-01

    The main CERISE objective is measurement and characterization of the radioelectrical environment onboard a low orbit satellite in a wide frequency band. It involves a microsatellite with a mass less than 50 kg, microsatellite command/control, a ground station for telemetry scientific exploitation. Mission design and constraints are reviewed: satellite orbit in terms of the launch opportunity, no orbit control, simplified attitude control, onboard data storage capacity, short life time, low cost, launch opportunities. CERISE system is built from the UoSAT-5 concept improved as regards electrical power, flight software, telemetry/telecommand frequency modifications. Details of the CERISE payload (computer, hyperfrequency sensor, onboard testing and qualification) and groundstation (microsatellite position acquisition, orbital acceptance, telemetry exploiting unit) are dealt with.

  20. A measure of population subdivision based on microsatellite allele frequencies

    SciTech Connect

    Slatkin, M.

    1995-01-01

    Microsatellite loci, loci that vary in the number of repeats of a simple DNA sequence, are becoming commonly used in the analysis of natural populations. Microsatellite loci are often highly polymorphic and relatively easy to survey and hence offer the hope of greater understanding of population structure. The question is how to make the best use of allele frequencies at microsatellite loci. This paper, like the accompanying paper by Goldstein et al. (1995), discusses how information about the mutation process at microsatellite loci can suggest statistics that are more appropriate for the analysis of microsatellite loci than are existing statistics. In this paper, I will introduce a new statistic analogous to Wright`s (1951) F{sub ST} that can be used to estimate effective migration rates or times since population divergence. This statistic is closely related to the distance measures introduced by Goldstein et al. (1995). 15 refs., 15 figs., 1 tab.

  1. Risk Factors for Paternal Physical Child Abuse

    ERIC Educational Resources Information Center

    Lee, Shawna J.; Guterman, Neil B.; Lee, Yookyong

    2008-01-01

    Objective: This study uses the developmental-ecological framework to examine a comprehensive set of paternal factors hypothesized to be linked to risk for paternal child abuse (PCA) among a diverse sample of fathers. Attention was given to fathers' marital status and their race/ethnicity (White, African American, and Hispanic). Methods: Interviews

  2. Epigenetics and the Origins of Paternal Effects

    PubMed Central

    Curley, James P.; Mashoodh, Rahia; Champagne, Frances A.

    2010-01-01

    Though there are multiple routes through which parents can influence their offspring, recent studies of environmentally induced epigenetic variation have highlighted the role of non-genomic pathways. In addition to the experience-dependent modification of DNA methylation that can be achieved via mother-infant interactions, there has been increasing interest in the epigenetic mechanisms through which paternal influences on offspring development can be achieved. Epidemiological and laboratory studies suggest that paternal nutritional and toxicological exposures as well as paternal age and phenotypic variation can lead to variations in offspring and, in some cases, grand-offspring development. These findings suggest a potential epigenetic germline inheritance of paternal effects. However, it may be important to consider the interplay between maternal and paternal influences as well as the experimental dissociation between experience-dependent and germline transmission when exploring the role of epigenetic variation within the germline as a mediator of these effects. In this review, we will explore these issues, with a particular focus on the potential role of paternally-induced maternal investment, highlight the literature illustrating the transgenerational impact of paternal experiences, and discuss the evidence supporting the role of epigenetic mechanisms in maintaining paternal effects both within and across generations. PMID:20620140

  3. Teenage Paternity, Child Support, and Crime.

    ERIC Educational Resources Information Center

    Pirog-Good, Maureen A.

    1988-01-01

    Examines the relationship between teenage premarital paternity, child support enforcement, and delinquency. The non-random data were gathered from the Marian County, Indiana District Attorney's Office and Juvenile Court. Suggests that the early establishment of paternity should be pursued and that child support enforcement strategies should

  4. Risk Factors for Paternal Physical Child Abuse

    ERIC Educational Resources Information Center

    Lee, Shawna J.; Guterman, Neil B.; Lee, Yookyong

    2008-01-01

    Objective: This study uses the developmental-ecological framework to examine a comprehensive set of paternal factors hypothesized to be linked to risk for paternal child abuse (PCA) among a diverse sample of fathers. Attention was given to fathers' marital status and their race/ethnicity (White, African American, and Hispanic). Methods: Interviews…

  5. Paternal inheritance in mealybugs (Hemiptera: Coccoidea: Pseudococcidae)

    NASA Astrophysics Data System (ADS)

    Kol-Maimon, Hofit; Mendel, Zvi; Franco, José Carlos; Ghanim, Murad

    2014-10-01

    Mealybugs have a haplodiploid reproduction system, with paternal genome elimination (PGE); the males are diploid soon after fertilization, but during embryogenesis, the male paternal set of chromosomes becomes heterochromatic (HC) and therefore inactive. Previous studies have suggested that paternal genes can be passed on from mealybug males to their sons, but not necessarily by any son, to the next generation. We employed crosses between two mealybug species— Planococcus ficus (Signoret) and Planococcus citri (Risso)—and between two populations of P. ficus, which differ in their mode of pheromone attraction, in order to demonstrate paternal inheritance from males to F2 through F1 male hybrids. Two traits were monitored through three generations: mode of male pheromone attraction (pherotype) and sequences of the internal transcribed spacer 2 (ITS2) gene segment (genotype). Our results demonstrate that paternal inheritance in mealybugs can occur from males to their F2 offspring, through F1 males (paternal line). F2 backcrossed hybrid males expressed paternal pherotypes and ITS2 genotypes although their mother originated through a maternal population. Further results revealed other, hitherto unknown, aspects of inheritance in mealybugs, such as that hybridization between the two species caused absence of paternal traits in F2 hybrid females produced by F1 hybrid females. Furthermore, hybridization between the two species raised the question of whether unattracted males have any role in the interactions between P. ficus and P. citri.

  6. A New Electrophoresis Technique to Seperate Microsatellite Alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional agarose and polyacrylamide gel electrophoresis have been used commonly for microsatellite (simple sequence repeats, SSRs) analysis, but they are labor- intensive and not always able to provide accurate sizes for different alleles. Capillary sequencers provide automated analysis and accur...

  7. Power of exclusion of 19 microsatellite markers for parentage testing in river buffalo (Bubalus bubalis).

    PubMed

    Kathiravan, P; Kataria, R S; Mishra, B P

    2012-08-01

    In the present study, 19 microsatellite markers were assessed for their power of exclusion to test parentage in river buffalo. Microsatellite genotypes of 216 unrelated buffaloes belonging to five different breeds were utilized for the study. The probabilities of exclusion were calculated for three hypothetical situations viz. paternity testing (PE1), one parental genotype unavailable (PE2) and exclusion of both parents i.e. substituted offspring (PE3). The mean probability of exclusion across 19 investigated markers in buffalo was 0.578 (PE1), 0.405 (PE2) and 0.764 (PE3) respectively. The probability of exclusion for paternity (PE1) ranged between 0.297 and 0.814 across different markers. The exclusion probability for the cases one parent unavailable (PE2) and substituted offspring (PE3) varied from 0.143 to 0.688 and 0.465 to 0.946 respectively. Polymorphism information content and expected heterozygosity were found to have significantly high correlation with probability of exclusion of microsatellite markers. The cumulative PE1 of nine marker loci was estimated to be 0.9999 while in case of absence of one of the parental genotypes, a minimum of 11 markers were required to achieve a cumulative PE2 of 0.999. In conclusion, the present study proposes two multiplex sets with four and five markers respectively for routine parentage testing in buffalo and an additional set of four markers for doubtful cases of paternity. PMID:22555978

  8. The Effect of Paternal Age on Relapse in First-Episode Schizophrenia

    PubMed Central

    Hui, Christy L M; Chiu, Cindy P Y; Li, Yuet-Keung; Law, Chi-Wing; Chang, Wing-Chung; Chan, Sherry K W; Lee, Edwin H M; Sham, Pak; Chen, Eric Y H

    2015-01-01

    Objective: Multiple etiological and prognostic factors have been implied in schizophrenia and its outcome. Advanced paternal age has been reported as a risk factor in schizophrenia. Whether this may affect schizophrenia outcome was not previously studied. We hypothesized that advanced paternal age may have a negative effect on the outcome of relapse in schizophrenia. Method: We interviewed 191 patients with first-episode schizophrenia and their relatives for parental ages, sociodemographic factors at birth, birth rank, family history of psychotic disorders, and obstetric complications. The outcome measure was the presence of relapse at the end of the first year of treatment. Results: In the 1-year follow-up period, 42 (22%) patients experienced 1 or more relapses. The mean paternal age was 34.62 years (SD 7.69). Patients who relapsed had significantly higher paternal age, poorer medication adherence, were female, and were hospitalized at onset, compared with patients who did not relapse. A multivariate regression analysis showed that advanced paternal age (OR 1.05, 95% CI 1.01 to 1.10), medication nonadherence (OR 2.37, 95% CI 1.12 to 4.99), and female sex (OR 2.44, 95% CI 1.14 to 5.24) independently contributed to a higher risk of relapse. Analysis between different paternal age groups found a significantly higher relapse rate with paternal age over 40. Conclusions: Advanced paternal age is found to be modestly but significantly related to more relapses, and such an effect is the strongest at a cut-off of paternal age of 40 years or older. The effect is less likely to be mediated through less effective parental supervision or nonadherence to medication. Other possible biological mechanisms need further explorations. PMID:26454556

  9. Measuring Microsatellite Conservation in Mammalian Evolution with a Phylogenetic Birth–Death Model

    PubMed Central

    Sawaya, Sterling M.; Lennon, Dustin; Buschiazzo, Emmanuel; Gemmell, Neil; Minin, Vladimir N.

    2012-01-01

    Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites. PMID:22593552

  10. Novel microsatellite control system

    SciTech Connect

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1996-12-31

    The authors are developing extremely simple yet quite capable analog pulse-coded neural networks for smaller-faster-cheaper spacecraft attitude and control systems. They will demonstrate a prototype microsatellite that uses the novel control system to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source.

  11. Paternal isodisomy for chromosome 7 and normal growth and development in a patient with congenital chloride diarrhea

    SciTech Connect

    Hoeglund, P.; de la Chapelle, A.; Kere, J.

    1994-09-01

    Uniparental disomy (UPD) has been reported in an increasing number of patients, occasionally ascertained because of concomitant autosomal recessive disorders. In some cases, additional signs such as growth alteration, mental retardation or minor anomalies are present, suggesting an imprinting effect. For maternal chromosome 7, UPD has been described in three patients with recessive disorders. Severe growth retardation diagnosed in all these patients has been explained by the effect of imprinting of growth related genes on maternal chromosome 7. No cases of paternally derived disomy from chromosome 7 were previously known. Here we report paternal isodisomy for chromosome 7 and normal growth in a patient with a recessive disorder, congenital chloride diarrhea (CLD; MIM 214700). Ten informative microsatellite markers on chromosome 7 demonstrated that the proband did not have any maternal contribution to her genotype for that chromosome. Maternal and paternal alleles could not be distinguished for another 10 markers tested for chromosome 7, but the proband was always homozygous. As most uniparental paternal disomies appear to have a postzygotic origin, the primary event might have been a maternal meiotic nondisjunction. A thorough clinical evaluation with a view to additional signs of imprinted genes localized in chromosome 7 was performed. The physical status and laboratory tests were normal except for a mild high-frequency sensorineural hearing loss. As the patient has normal stature, it is likely that the paternal chromosome 7 lacks the suggested maternal imprinting effect on growth. The origin of the hearing loss remains speculative.

  12. Non-Density Dependent Pollen Dispersal of Shorea maxwelliana (Dipterocarpaceae) Revealed by a Bayesian Mating Model Based on Paternity Analysis in Two Synchronized Flowering Seasons

    PubMed Central

    Masuda, Shinsuke; Tani, Naoki; Ueno, Saneyoshi; Lee, Soon Leong; Muhammad, Norwati; Kondo, Toshiaki; Numata, Shinya; Tsumura, Yoshihiko

    2013-01-01

    Pollinator syndrome is one of the most important determinants regulating pollen dispersal in tropical tree species. It has been widely accepted that the reproduction of tropical forest species, especially dipterocarps that rely on insects with weak flight for their pollination, is positively density-dependent. However differences in pollinator syndrome should affect pollen dispersal patterns and, consequently, influence genetic diversity via the mating process. We examined the pollen dispersal pattern and mating system of Shorea maxwelliana, the flowers of which are larger than those of Shorea species belonging to section Mutica which are thought to be pollinated by thrips (weak flyers). A Bayesian mating model based on the paternity of seeds collected from mother trees during sporadic and mass flowering events revealed that the estimated pollen dispersal kernel and average pollen dispersal distance were similar for both flowering events. This evidence suggests that the putative pollinators – small beetles and weevils – effectively contribute to pollen dispersal and help to maintain a high outcrossing rate even during sporadic flowering events. However, the reduction in pollen donors during a sporadic event results in a reduction in effective pollen donors, which should lead to lower genetic diversity in the next generation derived from seeds produced during such an event. Although sporadic flowering has been considered less effective for outcrossing in Shorea species that depend on thrips for their pollination, effective pollen dispersal by the small beetles and weevils ensures outcrossing during periods of low flowering tree density, as occurs in a sporadic flowering event. PMID:24391712

  13. Monosomy 1p36.31-33{yields}pter due to a paternal reciprocal translocation: Prognostic significance of FISH analysis

    SciTech Connect

    Blennow, E.; Bui, The-Hung; Wallin, A.

    1996-10-02

    A rare monosomy 1p36.31-33{r_arrow}pter was found in a child with physical anomalies, psycho-motor retardation, and seizures. Cytogenetic investigation suggested an unbalanced translocation between 1p and an acrocentric chromosome, but the rearrangement was difficult to assess accurately using conventional chromosome banding techniques. The half-cryptic translocation was further characterized using fluorescence in situ hybridization, and the aberrant chromosome 1 was shown to be a derivate of a paternal reciprocal translocation t(1;15)(p36.31-33;p11.2-12). The breakpoints on chromosome 1 and 15 were defined in detail using locus specific probes. The rearrangement did not include the region on chromosome 1p which previously has been suggested to predispose to the development of neuroblastoma in a case with a constitutional translocation. At 3 6/12 years, the patient has no clinical signs of this disease, which illustrates the prognostic significance of this investigation. 30 refs., 4 figs., 1 tab.

  14. Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC.

    PubMed

    Nybom, H; Esselink, G D; Werlemark, G; Vosman, B

    2004-03-01

    According to previous cytological evidence, the hemisexual dog-rose species, Rosa sect. Caninae, transmit only seven chromosomes (derived from seven bivalents) through their pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on ploidy level. Two sets of reciprocal pairwise interspecific crosses involving the pentaploid species pair R. dumalis and R. rubiginosa, and the pentaploid/tetraploid species pair R. sherardii and R. villosa, were analysed for 13 and 12 microsatellite DNA loci, respectively. Single loci were represented by a maximum of three simultaneously occurring alleles in R. villosa, and four alleles in the other three parental plants. In the experimentally derived offspring, the theoretical maximum of five alleles was found for only one locus in the pentaploid progenies. Microsatellite DNA allele composition was identical with that of the maternal parent in 10 offspring plants, which were probably derived through apomixis. Almost all microsatellite DNA alleles were shared with the maternal parent also in the remaining offspring, but 1-4 alleles shared only with the paternal parent, indicating sexual seed formation. Analysis of quantitative peak differences allowed a tentative estimation of allelic configuration in the individual plants, and suggested that bivalent formation preferentially takes place between chromosomes that consistently share the same microsatellite alleles and therefore appear to be highly homologous. Moreover, alleles that were shared between the species in each cross combination comparatively often appear to reside on the bivalent-forming chromosomes, whereas species-specific alleles instead occur comparatively often on the univalent-forming chromosomes and are therefore inherited through the maternal parent only. Recombination then takes place between very similar genomes also in interspecific crosses, resulting in a reproduction system that is essentially a mixture between apomixis and selfing. PMID:14981531

  15. [Genetic analysis of 32 microsatellite loci in 13 families of Wuzhishan pig by multiplex PCR and gene scanning technique].

    PubMed

    Huang, Li-Guang; Wang, Xi-Long; Ou, Jiang-Tao; Guo, Chun-Hua; Li, Xiao-Cheng; Wang, Feng; Zheng, Xin-Li

    2005-01-01

    Wuzhishan pig is one of the rare and endangered breeds in china. They have the following characteristics such as :light body weight and small size, early sexually maturity, high meat quality and genetic identification with 6 approximately 8 pares litter size,body weight of born 0.3 approximately 0.4 kg, 15 approximately 16 kg at 6 month old, 35 kg at 2 years old, and so on. They may be used for laboratory utilization, comparative studies on human medical model, embryonic engineering, nutrition metabolism, sensitivity test on virus and bacteria, skin brut and tranfer, removing lipid, teeth and mouth cavity diseases, studies on cardiovascular model and evaluation of new medicine products. The polymorphisms of 32 microsatellites in 13 families of Wuzhishan pig in Hainan were Analysed. Number of alleles in each family was counted, mean heterozygosity and polymorphism Information content(PIC) were calculated. The results showed that number of alleles was 13.66, mean heterozygosity was 0.559 while polymorphism information content was 0.731. This revealed that genetic diversity is abundant in Wuzhishan pig in Hainan. These results have instructional significance for preserving breeds, selection and breeding, development and utilization of Wuzhishan pig in Hainan. PMID:15730963

  16. Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species

    PubMed Central

    Maebe, Kevin; Meeus, Ivan; Ganne, Maarten; De Meulemeester, Thibaut; Biesmeijer, Koos; Smagghe, Guy

    2015-01-01

    Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949–1955 and 1975–1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline. PMID:26061732

  17. Microsatellite analysis of genetic diversity and genetic structure in five consecutive breeding generations of mandarin fish Siniperca chuatsi (Basilewsky).

    PubMed

    Yi, T L; Guo, W J; Liang, X F; Yang, M; Lv, L Y; Tian, C X; Song, Y; Zhao, C; Sun, J

    2015-01-01

    In this report, 10 polymorphic microsatellites were applied to assess the genetic diversity and genetic differentiation of 5 consecutive breeding generations of mandarin fish, Siniperca chuatsi (Basilewsky). The results from total number of alleles, average polymorphism information content, and average homozygosity and heterozygosity showed that the genetic diversity of the breeding population was decreasing. The genetic identity between F1 and its descendant generations (F2, F3, F4, F5) decreased (from 0.9248 to 0.8803), while the genetic distance (from 0.0782 to 0.1275) and fixation index (from 0.03796 to 0.07393) increased. The allele frequency of SS181-235 and SS211-246 changed regularly in the 5 breeding generations, and they may be negatively associated with the selected trait, which needs to be confirmed by further research. Our study indicated that selective breeding was an efficient strategy for mandarin fish. In the process of breeding, some deleterious genes were phased out, and the genetic structure of the breeding populations became stable. PMID:25867407

  18. Genetic evidence for polygynandry in the black-striped pipefish Syngnathus abaster: a microsatellite-based parentage analysis.

    PubMed

    Hübner, Kerstin; Gonzalez-Wanguemert, Mercedes; Diekmann, Onno E; Serrão, Ester A

    2013-01-01

    Sexual selection theory predicts that, in organisms with reversed sex roles, more polyandrous species exhibit higher levels of sexual dimorphism. In the family Syngnathidae (pipefish, seahorses, and seadragons), males provide all parental care by carrying developing embryos on their ventral surfaces, and females develop secondary sex characters. Syngnathids exhibit a variety of genetic mating patterns, making them an ideal group to test predictions of sexual selection theory. Here, we describe the mating system of the black-striped pipefish Syngnathus abaster, using 4 highly variable microsatellites to analyze parentage of 102 embryos. Results revealed that 1) both sexes mate multiple times over the course of a pregnancy (polygynandrous mating system), 2) eggs are spatially segregated by maternity within each brood pouch, and 3) larger females have higher mating success (Kolmogorov-Smirnov test; P < 0.05). Together with similar studies of other syngnathid species, our results support the hypothesis that the mating system is related to the intensity of sexual dimorphism. PMID:23975836

  19. Multiplex PCR panel of microsatellite markers for the tambaqui, Colossoma macropomum, developed as a tool for use in conservation and broodstock management.

    PubMed

    Hamoy, I G; Santos, S

    2012-01-01

    The tambaqui, Colossoma macropomum, native to Brazil, is widely used in aquaculture systems. We developed a multiplex PCR panel for this species, comprising 12 microsatellite loci. This panel was used to genotype 73 specimens collected from Juruti, a city in the Brazilian Amazon. The mean number of alleles per locus was 8.8, the mean observed heterozygosity was 0.76, and the combined power of discrimination and the combined power of exclusion were 0.99999999999999993 and 0.999991762, respectively. We observed no significant deviation from Hardy-Weinberg equilibrium in this population. All amplified alleles were clearly typed, and easily interpretable results were obtained. This method will be useful for paternity analysis, population genetics and conservation studies, as well as for selective breeding programs for C. macropomum. PMID:22370880

  20. Molecular Evidence for High Frequency of Multiple Paternity in a Freshwater Shrimp Species Caridina ensifera

    PubMed Central

    Yue, Gen Hua; Chang, Alex

    2010-01-01

    Background Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. Methodology/Principal Findings In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. Conclusions/Significance Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species. PMID:20856862

  1. Analysis of the population structure of Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) in the Palaearctic region using microsatellite markers

    PubMed Central

    Sanchez, Juan Antonio; Spina, Michelangelo La; Perera, Omaththage P

    2012-01-01

    Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) is widely distributed throughout the Palaearctic region. The aim was to explain the current geographic distribution of the species by investigating its genetic population structure. Samples of M. pygmaeus were collected in 15 localities through its range of distribution. A sample from a commercial producer was also analyzed. A total of 367 M. pygmaeus were genotyped for nine microsatellite loci. Isolation by distance was tested by Mantel's test. The molecular structure of M. pygmaeus populations was inferred by UPGMA, AMOVA, Principal component and Bayesian analyses. The average number of alleles per locus per population was 5.5 (range: 3.1–7.8). Istanbul (Turkey) and Nimes (France) had the lowest (0.291) and the highest (0.626) expected heterozygosity (He), respectively. There was an increase in He from the Canary Islands to Nimes, and a progressive decrease thereafter. A significant negative correlation was found between allelic richness and He, and the distance of each population to the easternmost locality (Canary Islands). Significant linkage disequilibrium was observed in the populations from Turkey. FST (0.004–0.334) indicated a high population differentiation, with isolation by distance supported by a high correlation. Bayesian analyses, PCA, and UPGMA pointed to three main clusters: (1) Greece and Turkey, (2) Italy and France, and (3) southern Iberia and the Canary Islands. The recent evolutionary history of M. pygmaeus is inferred from the data as follows: (1) the reduction in the geographic distribution of the species to the Iberian, Italian, and Balkan peninsulas, and possibly southern France, during glaciations and re-colonization of northern Europe from its southern refuges; (2) the maintenance of high diversity in Iberia and Italy (and possibly southern France) during contraction periods, and bottlenecks in the Balkans; (3) introgression of the Italian–French lineage in northern Spain, naturally or through trade. PMID:23301179

  2. Molecular phylogenetics and microsatellite analysis reveal cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon's Great Basin.

    PubMed

    Hoekzema, Kendra; Sidlauskas, Brian L

    2014-08-01

    Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs throughout western North America and is the most commonly occurring fish in Oregon. Because of the high genetic and morphological variation in this species across its range, it has been referred to as a species complex; however, no revision to its taxonomy has occurred since 1984. Here, the phylogenetics and population genetics of speckled dace are examined throughout Oregon's Great Basin to describe genetic variation and infer the geographic boundaries between distinct taxonomic entities and populations. We tested the validity of a putative subspecies, Foskett Spring speckled dace, that occurs in a single spring within Warner Valley in Southeast Oregon and is listed Federally as threatened. Dace were collected from Foskett Spring and all surrounding basins containing speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur), created phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data, and genotyped eight microsatellite loci for population-level analyses. Three highly divergent clades warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins combined. Although Foskett Spring dace were not monophyletic, substantial population structure occurs at the basin-level and separates Foskett Spring dace from other dace in the surrounding Warner Valley. Thus, we recommend ESU status for the isolated population of speckled dace in Foskett Spring. The high, previously unrecognized, taxonomic diversity within this region indicates a need for a range-wide phylogeographic study of speckled dace and an investigation of the morphological distinctiveness of the putative new species. PMID:24795214

  3. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    SciTech Connect

    Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle; Le Tacon, F; Martin, Francis

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  4. Microsatellite deletion mapping on chromosome 10q and mutation analysis of MMAC1, FAS, and MXI1 in human glioblastoma multiforme.

    PubMed

    Fults, D; Pedone, C A; Thompson, G E; Uchiyama, C M; Gumpper, K L; Iliev, D; Vinson, V L; Tavtigian, S V; Perry, W L

    1998-04-01

    Glioblastoma multiforme (GBM) is an end-stage brain tumor of glial origin. Allelic deletions encompassing all or part of chromosome 10q occur frequently in GBMs, indicating that loss of one or more tumor suppressor genes on 10q plays a role in GBM formation. One of these genes is MMAC1 (PTEN), a gene on 10q23 which encodes a dual-specificity protein phosphatase. We carried out a loss of heterozygosity (LOH) analysis of 66 GBM patients using microsatellite markers for 27 loci on 10q. Overall, LOH was detected in 70% of cases, most showing LOH with every informative marker. Eleven patients showed partial 10q deletions, the smallest spanning a 35 cM region distal to D10S187. Sequence analysis of the MMAC1 gene in 45 of these tumors revealed mutations in eleven cases (24%), all with LOH on 10q. None of these mutations was present in normal DNA from the same patients. In addition, we utilized SSCP analysis to test two other candidate genes on 10q: FAS, a cell surface receptor which transduces an apoptotic, cell death signal and MXI1, a transcriptional repressor. The absence of mutations in these genes suggested that FAS and MXI1 are not likely to be tumor suppressor genes physiologically relevant to GBM. These data do support a significant role for MMAC1 in GBM. PMID:9499454

  5. Brief Report: Phenotypic Differences and their Relationship to Paternal Age and Gender in Autism Spectrum Disorder.

    PubMed

    Vierck, Esther; Silverman, Jeremy M

    2015-06-01

    Two modes of inheritance have been proposed in autism spectrum disorder, transmission though pre-existing variants and de novo mutations. Different modes may lead to different symptom expressions in affected individuals. De novo mutations become more likely with advancing paternal age suggesting that paternal age may predict phenotypic differences. To test this possibility we measured IQ, adaptive behavior, and autistic symptoms in 830 probands from simplex families. We conducted multiple linear regression analysis to estimate the predictive value of paternal age, maternal age, and gender on behavioral measures and IQ. We found a differential effect of parental age and sex on repetitive and restricted behaviors. Findings suggest effects of paternal age on phenotypic differences in simplex families with ASD. PMID:25526953

  6. Paternal environmental exposures and gene expression during spermatogenesis: research review to research framework.

    PubMed

    Hansen, Deborah A

    2008-06-01

    The primary objective is to review Dioxin toxicity, the potential impact on spermatogenesis, what is known and unknown about paternal exposures, and the potential mechanisms whereby paternal preconception exposures result in neural tube defects (NTD). The secondary goal is to suggest a versatile research framework utilizing gene expression microarray to evaluate the impact of acute, intermittent, and chronic paternal exposures to environmental agents on gene expression during the stages of spermatogenesis. There are multiple barriers to establishing a paradigm whereby paternal environmental exposures result in adverse birth outcomes. Microarray expression studies are unique in their ability to detect transcription dysregulation, thereby facilitating the identification of molecular and developmental pathways through hierarchical and pathway analysis. To date there are no studies of gene expression during spermatogenesis following exposure to environmental agents. PMID:18546338

  7. THE DEVELOPMENT OF MICROSATELLITE MARKERS FOR PERSEA AMERICANA (AVOCADO).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of their relative abundance, distribution across the genome, hypervariability and co-dominance, microsatellites, or simple sequence repeats are considered to be cost effective and efficient molecular genetic markers for parentage analysis, linkage mapping, association studies, and genetic fi...

  8. Paternal age and mental health of offspring.

    PubMed

    Malaspina, Dolores; Gilman, Caitlin; Kranz, Thorsten Manfred

    2015-06-01

    The influence of paternal age on the risk for sporadic forms of Mendelian disorders is well known, but a burgeoning recent literature demonstrates, in addition, a paternal age effect for complex neuropsychiatric conditions, including schizophrenia, autism, bipolar disorder, and even for learning potential, expressed as intelligence. Mental illness is costly to patients, their family, and the public health system, accounting for the largest portion of disability costs in our economy. The delayed onset of neuropsychiatric conditions and lack of physical manifestations at birth are common frequencies in the population that have obscured the recognition that a portion of the risks for mental conditions is associated with paternal age. Identification of these risk pathways may be leveraged for knowledge about mental function and for future screening tests. However, only a small minority of at-risk offspring are likely to have such a psychiatric or learning disorder attributable to paternal age, including the children of older fathers. PMID:25956369

  9. Contribution of Lidia cattle breed historical castes to the paternal genetic stock of Spain.

    PubMed

    Pelayo, R; Valera, M; Molina, A; Royo, L J

    2015-06-01

    The main objective of this work was to determine whether the five founding castes defined in the Lidia cattle breed actually have an important contribution to the Spanish paternal genetic stock as well as to the paternal genetic origin support. A total of 1300 Bos taurus male individuals were genotyped for five microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1) and one indel (ZFY10). Microsatellite and indel alleles were combined into haplotypes, identifying a total of 38 haplotypes, 11 of them belonging to haplogroup Y1 and 27 to haplogroup Y2. Ten different haplotypes were found in the Lidia cattle breed, with five being exclusive to this breed. Our results agree with different male genetic stocks in the Lidia breed: one hypothetically representing the ancient Iberian bovine genetic stock (Gallardo, Navarra and Cabrera castes and some encastes from Vistahermosa) and a second one that is the result of the more recent breeding strategy of choosing the most aggressive individuals from traditional herds (including some Vistahermosa encastes and the Vazqueña caste). In terms of conservation, it would be better to not consider this breed as a unit but to consider the caste, or even better the encaste, as the target of putative conservation efforts. PMID:25728408

  10. Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species.

    PubMed

    Hale, Marie L; Borland, Anne M; Gustafsson, Mats H G; Wolff, Kirsten

    2004-02-01

    Chloroplast DNA sequences and microsatellites are useful tools for phylogenetic as well as population genetic analyses of plants. Chloroplast microsatellites tend to be less variable than nuclear microsatellites and therefore they may not be as powerful as nuclear microsatellites for within-species population analysis. However, chloroplast microsatellites may be useful for phylogenetic analysis between closely related taxa when more conventional loci, such as ITS or chloroplast sequence data, are not variable enough to resolve phylogenetic relationships in all clades. To determine the limits of chloroplast microsatellites as tools in phylogenetic analyses, we need to understand their evolution. Thus, we examined and compared phylogenetic relationships of species within the genus Clusia, using both chloroplast sequence data and variation at seven chloroplast microsatellite loci. Neither ITS nor chloroplast sequences were variable enough to resolve relationships within some sections of the genus, yet chloroplast microsatellite loci were too variable to provide any useful phylogenetic information. Size homoplasy was apparent, caused by base substitutions within the microsatellite, base substitutions in the flanking regions, indels in the flanking regions, multiple microsatellites within a fragment, and forward/reverse mutations of repeat length resulting in microsatellites of identical base composition that were not identical by descent. PMID:15042338

  11. Effect of Paternal Age on Reproductive Outcomes of In Vitro Fertilization

    PubMed Central

    Zheng, Haiyan; Liu, Haiying; Liu, Jianqiao

    2015-01-01

    Although the adverse effects of maternal aging on reproductive outcomes have been investigated widely, there is no consensus on the impact of paternal age. Therefore, we investigated the effect of paternal age on reproductive outcomes in a retrospective analysis of 9,991 in vitro fertilization (IVF) cycles performed at the Reproductive Medicine Center of the Third Affiliated Hospital of Guangzhou Medical University (China) between January 2007 and October 2013. Samples were grouped according to maternal age [<30 (3,327 cycles), 30–34 (4,587 cycles), and 35–38 (2,077 cycles)] and then subgrouped according to paternal age (<30, 30–32, 33–35, 36–38, 39–41, and ≥42). The groups did not differ in terms of fertilization rate, numbers of viable and high-quality embryos and miscarriage rate when controlling maternal age (P >0.05). Chi-squared analysis revealed that there were no differences in implantation and pregnancy rates among the different paternal age groups when maternal age was <30 and 35–38 years (P >0.05). However, implantation and pregnancy rates decreased with paternal age in the 31–34 y maternal age group (P <0.05). Our study indicates that paternal age has no impact on fertilization rate, embryo quality at the cleavage stage and miscarriage rate. For the 30–34 y maternal age group, the implantation rate decreased with increased paternal age, with the pregnancy rate in this group being significantly higher in the paternal <30 y and 30–32 y age groups, compared with those in the 36–38 y and 39–41 y groups. PMID:26352861

  12. Energetic Neutral Atom Imaging at Low Altitudes from the Swedish Microsatellite Astrid: Images and Spectral Analysis. Paper 1

    NASA Technical Reports Server (NTRS)

    Brandt, Pontus C:son; Barabash, Stas; Norberg, Olle; Lundin, Rickard; Roelof, Rdmond C.; Chase, Christopher J.

    1999-01-01

    Observations of energetic neutral atoms (ENA) in the energy range 26- 52 keV are reported from four occasions during geomagnetically disturbed periods. The data were acquired by the ENA imager flown on the Swedish microsatellite Astrid in a 1000 km circular orbit with 83 deg inclination. The ENA imager separates charged particles from neutrals through an electrostatic deflection system in the energy range between 0.1 and 114 keV. ENA images obtained from vantage points in the polar cap and in the afternoon magnetic local time (MLT) hours looking into the antisunward hemisphere show intense ENA fluxes (approx. 10(exp 4)/sq cm sr s over 26-37 keV) coming from the dusk region and low altitudes (approx. 300 km). The morphology shows no relation to local magnetic field excluding the possibility of charged particle detection. It is concluded that the source of these ENAs are precipitating/mirroring ions from the ring current/trapped radiation interacting with the exobase on auroral L-shells and in the dusk region. The observed ENA fluxes show a relation with Kp and Dst geomagnetic indices. The observed ENA spectrum from a geomagnetic storm on February 8, 1995, is investigated in more detail and compared to the parent ion spectrum obtained by the Defense Meteorological Satellite Project (DMSP) satellite, Fl2, during the same period on L = 6 +/- 2 around dusk. The observed ENA spectral slope is used to derive the parent ion spectral temperature. The derived ion temperatures range is 3.0 - 6.0 keV for H and 4.5 - 8.5 keV for O. The higher of these ion temperatures comes closest in agreement to the extrapolated DMSP spectrum leading us to favor O over H as the species of the detected ENAS. It is shown that the detected ENAs must have been produced at L greater than or equal to 6 to reach the detector without atmospheric attenuation and that the main energy dependence of the ENA spectrum, apart from the parent ion spectrum, is governed by the energy dependence of the charge exchange cross section between ions and exospheric oxygen.

  13. Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila.

    PubMed

    Tran, Ngoc Tuan; Gao, Ze-Xia; Zhao, Hong-Hao; Yi, Shao-Kui; Chen, Bo-Xiang; Zhao, Yu-Hua; Lin, Li; Liu, Xue-Qin; Wang, Wei-Min

    2015-07-01

    The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription-quantitative PCR (RT-qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species. PMID:25681750

  14. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers.

    PubMed

    Selkoe, Kimberly A; Toonen, Robert J

    2006-05-01

    Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists' ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike. PMID:16643306

  15. Paternal isodisomy of chromosome 6 in association with a maternal supernumerary marker chromosome (6)

    SciTech Connect

    James, R.S.; Crolla, J.A.; Sitch, F.L.

    1994-09-01

    Uniparental disomy may arise by a number of different mechanisms of aneuploidy correction. A population that has been identified as being at increased risk of aneuploidy are those individuals bearing supernumerary marker chromosomes (SMCs). There have been a number of cases reported of trisomy 21 in association with bi-satellited marker chromosomes have described two individuals with small inv dup (15) markers. One had paternal isodisomy of chromosome 15 and Angelman syndrome. The other had maternal heterodisomy (15) and Prader-Willi syndrome. At the Wessex Regional Genetics Laboratory we have conducted a search for uniparental disomy of the normal homologues of the chromosomes from which SMCs originated. Our study population consists of 39 probands with SMCs originating from a number of different autosomes, including 17 with SMCs of chromosome 15 origin. Using PCR amplification of microsatellite repeat sequences located distal to the regions included in the SMCs we have determined the parental origin of the two normal homologues in each case. We have identified paternal isodisomy of chromosome 6 in a female child with a supernumerary marker ring chromosome 6 in approximately 70% of peripheral blood lymphocytes. The marker was found to be of maternal origin. This is the second case of paternal isodisomy of chromosome 6 to be reported, and the first in association with a SMC resulting in a partial trisomy for a portion of the short arm of chromosome 6. In spite of this, the patient appears to be functioning appropriately for her age.

  16. Paternity and inheritance of wealth

    NASA Astrophysics Data System (ADS)

    Hartung, John

    1981-06-01

    One of the oldest conjectures in anthropology is that men transfer wealth to their sister's son when the biological paternity of their `own' children is in doubt1-12. Because maternity is certain, a man is necessarily related to his sister's son and his brother (see Fig. 1). It is argued here that relatedness to male heirs can be assured by passing wealth to sister's sons or down a line of brothers, whether the prevailing kinship system reckons those brothers matrilineally or patrilineally. It is also argued that when several transfers of wealth are considered, a man's likelihood of being cuckolded need not be unrealistically high13 for his successive matrilineal heirs to be more related to him than his successive patrilineal heirs (see Fig. 2). Cross-cultural data on sister's son/brother inheritance14 and frequency of extramarital sex for females15 support the hypothesis that men tend to transmit wealth to their sister's son and/or brother when the probability that their putative children are their genetic children is relatively low.

  17. A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

    PubMed Central

    Li, Hongjun; Liu, Xiao; Zhang, Guofan

    2012-01-01

    Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13?1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop. PMID:23077533

  18. Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

    PubMed Central

    Fernndez, Mara E.; Goszczynski, Daniel E.; Lirn, Juan P.; Villegas-Castagnasso, Egle E.; Carino, Mnica H.; Ripoli, Mara V.; Rogberg-Muoz, Andrs; Posik, Diego M.; Peral-Garca, Pilar; Giovambattista, Guillermo

    2013-01-01

    During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E?42, respectively. Generally 23 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ? 10?11). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording). PMID:23885200

  19. Acute effects of corticosterone injection on paternal behavior in California mouse (Peromyscus californicus) fathers.

    PubMed

    Harris, Breanna N; Perea-Rodriguez, Juan Pablo; Saltzman, Wendy

    2011-11-01

    Glucocorticoids are thought to mediate the disruption of parental behavior in response to acute and chronic stress. Previous research supports their role in chronic stress; however, no study has experimentally tested the effects of acute glucocorticoid elevation on paternal behavior. We tested the prediction that acute corticosterone (CORT) increases would decrease paternal behavior in California mouse fathers and would lead to longer-term effects on reproductive success, as even short-term increases in CORT have been shown to produce lasting effects on the hypothalamic-pituitary-adrenal axis. First-time fathers were injected with 30 mg/kg CORT, 60 mg/kg CORT or vehicle, or left unmanipulated. Interactions between the male and its pup(s) were recorded 1.5-2h after injection and scored for paternal and non-paternal behavior. Treatment groups were combined into control (unmanipulated + vehicle, n = 15) and CORT (30 mg/kg + 60 mg/kg, n = 16) for analysis based on resulting plasma CORT concentrations. CORT treatment did not alter paternal or non-paternal behaviors or any long-term measures (male body mass or temperature, pup growth rate, pup survival, interbirth interval, number or mass of pups born in the second litter). Fathers showed a significant rise in body mass at day 30 postpartum, followed by a decrease in body mass after the birth of the second litter; however, this pattern did not differ between the CORT and control groups. In summary, acute elevation of plasma CORT did not alter direct paternal behavior, body mass, or reproductive outcomes, suggesting that acute CORT elevation alone does not overtly disrupt paternal care in this biparental mammal. PMID:21939660

  20. Paternity testing using the poisonous sting in captive white-spotted eagle rays Aetobatus narinari: a non-invasive tool for captive sustainability programmes.

    PubMed

    Janse, M; Kappe, A L; Van Kuijk, B L M

    2013-03-01

    A group of captive white-spotted eagle rays Aetobatus narinari produced 20 offspring, with an unknown father. Part of the poisonous sting was removed from each fish and DNA was extracted from the epidermis for paternity research using eight microsatellite markers of which four were from another species Aetobatus flagellum. This non-invasive sampling technique can be applied on all members of Myliobatiformes. PMID:23464564

  1. Temporal changes of genetic population structure and diversity in the endangered Blakiston's fish owl (Bubo blakistoni) on Hokkaido Island, Japan, revealed by microsatellite analysis.

    PubMed

    Omote, Keita; Nishida, Chizuko; Takenaka, Takeshi; Masuda, Ryuichi

    2012-05-01

    The Blakiston's fish owl (Bubo blakistoni) population on Hokkaido Island, Japan, decreased to less than one hundred individuals over the last century due to habitat disruption by human activity. Although the ongoing conservation management has slightly restored the population, it remains endangered. In order to assess the genetic variation and population structure of the Blakiston's fish owl in Hokkaido, we genotyped eight microsatellite loci on 120 individuals sampled over the past three decades. The genotype data set showed low levels of genetic variation and gene flow among the geographically isolated five subpopulations. Comparative analysis of past and current populations indicated that some alleles shared by past individuals had been lost, and that genetic variation had declined over the last three decades. The result suggests that the genetic decline may have resulted from inbreeding and/or genetic drift due to bottlenecks in the Hokkaido population. The present study provides invaluable genetic information for the conservation and management of the endangered Blakiston's fish owl in Hokkaido. PMID:22559963

  2. Paternal Psychiatric Symptoms and Maladaptive Paternal Behavior in the Home during the Child Rearing Years

    ERIC Educational Resources Information Center

    Johnson, Jeffrey G.; Cohen, Patricia; Kasen, Stephanie; Brook, Judith S.

    2004-01-01

    Data from the Children in the Community Study, a community-based longitudinal study were used to investigate associations between paternal psychiatric disorders and child-rearing behaviors. Paternal psychiatric symptoms and behavior in the home were assessed among 782 families during the childhood and adolescence of the offspring. Paternal…

  3. Student's Microsatellite Project

    NASA Astrophysics Data System (ADS)

    Zelentsov, Victor; Kopik, Anatoliy; Karpenko, Stanislav; Mayorova, Victoria

    2002-01-01

    Nowadays BMSTU Youth space center carries on development of the microsatellite project. The project is based on principles of students direct involvement on all stages of development and maintenance of the satellite. The group of students was organized within the university with purpose of coordination of work at the program. Project current condition The work on creation of an experimental model of the micro satellite is performed. The aim is to define the structure and parameters of on-board devices (mass-overall dimensions characteristics, energy consumption and so on). developed. According to the simplified model an active stabilization system (three orthogonal electro-magnetic coils) and orientation characterization system (sunlight detector and magnitometer) are included in OCS structure. most suitable battery storage, power-supply controlling system. Student micro-satellite program goals 1.Scientific Information gaining in the field of Earth study- using perspective research methods. Studying of new devices behavior in space conditions. 2. Educative a. Students derive real experience of projecting, building of a spacecraft from the point of view of an experimenter, a constructor and a researcher. b. Organization of student's cooperation with key men of aerospace industry and other branches. c. Brainpower and material base preparation for micro-satellite systems' development. d. Attraction of youth interest to the topic, by: - Students' and pupils' groups attraction and involvement in experiments conduction and results processing. - Seminars and lections devoted to Earth study from the space organization - Specific scientific data distribution over World Wide Web. 3. International With purpose of program expansion, the developers' group looks to start of an international project. Within the project new experiments conduction and scientific information exchange are expected. 4. Status Bauman Moscow State Technical University's status improvement in the field of satellite system development.

  4. Combined Microsatellite Instability, MLH1 Methylation Analysis, and Immunohistochemistry for Lynch Syndrome Screening in Endometrial Cancers From GOG210: An NRG Oncology and Gynecologic Oncology Group Study

    PubMed Central

    Goodfellow, Paul J.; Billingsley, Caroline C.; Lankes, Heather A.; Ali, Shamshad; Cohn, David E.; Broaddus, Russell J.; Ramirez, Nilsa; Pritchard, Colin C.; Hampel, Heather; Chassen, Alexis S.; Simmons, Luke V.; Schmidt, Amy P.; Gao, Feng; Brinton, Louise A.; Backes, Floor; Landrum, Lisa M.; Geller, Melissa A.; DiSilvestro, Paul A.; Pearl, Michael L.; Lele, Shashikant B.; Powell, Matthew A.; Zaino, Richard J.; Mutch, David

    2015-01-01

    Purpose The best screening practice for Lynch syndrome (LS) in endometrial cancer (EC) remains unknown. We sought to determine whether tumor microsatellite instability (MSI) typing along with immunohistochemistry (IHC) and MLH1 methylation analysis can help identify women with LS. Patients and Methods ECs from GOG210 patients were assessed for MSI, MLH1 methylation, and mismatch repair (MMR) protein expression. Each tumor was classified as having normal MMR, defective MMR associated with MLH1 methylation, or probable MMR mutation (ie, defective MMR but no methylation). Cancer family history and demographic and clinical features were compared for the three groups. Lynch mutation testing was performed for a subset of women. Results Analysis of 1,002 ECs suggested possible MMR mutation in 11.8% of tumors. The number of patients with a family history suggestive of LS was highest among women whose tumors were classified as probable MMR mutation (P = .001). Lynch mutations were identified in 41% of patient cases classified as probable mutation (21 of 51 tested). One of the MSH6 Lynch mutations was identified in a patient whose tumor had intact MSH6 expression. Age at diagnosis was younger for mutation carriers than noncarriers (54.3 v 62.3 years; P < .01), with five carriers diagnosed at age > 60 years. Conclusion Combined MSI, methylation, and IHC analysis may prove useful in Lynch screening in EC. Twenty-four percent of mutation carriers presented with ECs at age > 60 years, and one carrier had an MSI-positive tumor with no IHC defect. Restricting Lynch testing to women diagnosed at age < 60 years or to women with IHC defects could result in missing a substantial fraction of genetic disease. PMID:26552419

  5. Low paternity skew and the influence of maternal kin in an egalitarian, patrilocal primate

    PubMed Central

    Strier, Karen B.; Chaves, Paulo B.; Mendes, Sérgio L.; Fagundes, Valéria; Di Fiore, Anthony

    2011-01-01

    Levels of reproductive skew vary in wild primates living in multimale groups depending on the degree to which high-ranking males monopolize access to females. Still, the factors affecting paternity in egalitarian societies remain unexplored. We combine unique behavioral, life history, and genetic data to evaluate the distribution of paternity in the northern muriqui (Brachyteles hypoxanthus), a species known for its affiliative, nonhierarchical relationships. We genotyped 67 individuals (22 infants born over a 3-y period, their 21 mothers, and all 24 possible sires) at 17 microsatellite marker loci and assigned paternity to all infants. None of the 13 fathers were close maternal relatives of females with which they sired infants, and the most successful male sired a much lower percentage of infants (18%) than reported for the most successful males in other species. Our findings of inbreeding avoidance and low male reproductive skew are consistent with the muriqui's observed social and sexual behavior, but the long delay (≥2.08 y) between the onset of male sexual behavior and the age at which males first sire young is unexpected. The allocation of paternity implicates individual male life histories and access to maternal kin as key factors influencing variation in paternal—and grandmaternal—fitness. The apparent importance of lifelong maternal investment in coresident sons resonates with other recent examinations of maternal influences on offspring reproduction. This importance also extends the implications of the “grandmother hypothesis” in human evolution to include the possible influence of mothers and other maternal kin on male reproductive success in patrilocal societies. PMID:22065786

  6. Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle.

    PubMed

    Phillips, Karl P; Jorgensen, Tove H; Jolliffe, Kevin G; Jolliffe, San-Marie; Henwood, Jock; Richardson, David S

    2013-04-01

    Postcopulatory sperm storage can serve a range of functions, including ensuring fertility, allowing delayed fertilization and facilitating sexual selection. Sperm storage is likely to be particularly important in wide-ranging animals with low population densities, but its prevalence and importance in such taxa, and its role in promoting sexual selection, are poorly known. Here, we use a powerful microsatellite array and paternal genotype reconstruction to assess the prevalence of sperm storage and test sexual selection hypotheses of genetic biases to paternity in one such species, the critically endangered hawksbill turtle, Eretmochelys imbricata. In the majority of females (90.7%, N = 43), all offspring were sired by a single male. In the few cases of multiple paternity (9.3%), two males fertilized each female. Importantly, the identity and proportional fertilization success of males were consistent across all sequential nests laid by individual females over the breeding season (up to five nests over 75 days). No males were identified as having fertilized more than one female, suggesting that a large number of males are available to females. No evidence for biases to paternity based on heterozygosity or relatedness was found. These results indicate that female hawksbill turtles are predominantly monogamous within a season, store sperm for the duration of the nesting season and do not re-mate between nests. Furthermore, females do not appear to be using sperm storage to facilitate sexual selection. Consequently, the primary value of storing sperm in marine turtles may be to uncouple mating and fertilization in time and avoid costly re-mating. PMID:23379838

  7. Paternity assignment and demographic closure in the New Zealand southern right whale.

    PubMed

    Carroll, Emma L; Childerhouse, Simon J; Christie, Mark; Lavery, Shane; Patenaude, Nathalie; Alexander, Alana; Constantine, Rochelle; Steel, Debbie; Boren, Laura; Scott Baker, C

    2012-08-01

    The identification and characterization of reproductively isolated subpopulations or 'stocks' are essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and 'gametic recapture' to examine the reproductive autonomy of southern right whales (Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother-calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark-recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (i) the proportion of paternities assigned will reflect the proportion of the male population sampled and (ii) the gametic mark-recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo-Pacific region. PMID:22726223

  8. Microsatellite analysis supports clonal propagation and reduced divergence of Trypanosoma vivax from asymptomatic to fatally infected livestock in South America compared to West Africa

    PubMed Central

    2014-01-01

    Background Mechanical transmission of the major livestock pathogen Trypanosoma vivax by other biting flies than tsetse allows its spread from Africa to the New World. Genetic studies are restricted to a small number of isolates and based on molecular markers that evolve too slowly to resolve the relationships between American and West African populations and, thus, unable us to uncover the recent history of T. vivax in the New World. Methods T. vivax genetic diversity, population structure and the source of outbreaks was investigated through the microsatellite multiloci (7 loci) genotype (MLGs) analysis in South America (47isolates from Brazil, Venezuela and French Guiana) and West Africa (12 isolates from The Gambia, Burkina Faso, Ghana, Benin and Nigeria). Relationships among MLGs were explored using phylogenetic, principal component and STRUCTURE analyses. Results Although closely phylogenetically related, for the first time, genetic differences were detected between T. vivax isolates from South America (11 genotypes/47 isolates) and West Africa (12 genotypes/12 isolates) with no MLGs in common. Diversity was far greater across West Africa than in South America, where genotypes from Brazil (MLG1-6), Venezuela (MLG7-10) and French Guiana (MLG11) shared similar but not identical allele composition. No MLG was exclusive to asymptomatic (endemic areas) or sick (outbreaks in non-endemic areas) animals, but only MLGs1, 2 and 3 were responsible for severe haematological and neurological disorders. Conclusions Our results revealed closely related genotypes of T. vivax in Brazil and Venezuela, regardless of endemicity and clinical conditions of the infected livestock. The MLGs analysis from T. vivax across SA and WA support clonal propagation, and is consistent with the hypothesis that the SA populations examined here derived from common ancestors recently introduced from West Africa. The molecular markers defined here are valuable to assess the genetic diversity, to track the source and dispersion of outbreaks, and to explore the epidemiological and pathological significance of T. vivax genotypes. PMID:24885708

  9. Anarchy in the UK: Detailed genetic analysis of worker reproduction in a naturally occurring British anarchistic honeybee, Apis mellifera, colony using DNA microsatellites.

    PubMed

    Chline, N; Ratnieks, F L W; Burke, T

    2002-09-01

    Anarchistic behaviour is a very rare phenotype of honeybee colonies. In an anarchistic colony, many workers' sons are reared in the presence of the queen. Anarchy has previously been described in only two Australian colonies. Here we report on a first detailed genetic analysis of a British anarchistic colony. Male pupae were present in great abundance above the queen excluder, which was clearly indicative of extensive worker reproduction and is the hallmark of anarchy. Seventeen microsatellite loci were used to analyse these male pupae, allowing us to address whether all the males were indeed workers' sons, and how many worker patrilines and individual workers produced them. In the sample, 95 of 96 of the males were definitely workers' sons. Given that approximately 1% of workers' sons were genetically indistinguishable from queen's sons, this suggests that workers do not move any queen-laid eggs between the part of the colony where the queen is present to the area above the queen excluder which the queen cannot enter. The colony had 16 patrilines, with an effective number of patrilines of 9.85. The 75 males that could be assigned with certainty to a patriline came from 7 patrilines, with an effective number of 4.21. They were the offspring of at least 19 workers. This is in contrast to the two previously studied Australian naturally occurring anarchist colonies, in which most of the workers' sons were offspring of one patriline. The high number of patrilines producing males leads to a low mean relatedness between laying workers and males of the colony. We discuss the importance of studying such colonies in the understanding of worker policing and its evolution. PMID:12207729

  10. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To better understand the genetic diversity of the cultivated Upland cotton (Gossypium hirsutum L.) and its structure at the molecular level, 193 Upland cotton cultivars collected from 26 countries were genotyped using 448 microsatellite markers. These markers were selected based on their mapping po...

  11. Development of microsatellite markers in peach [ Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry ( Prunus avium L.).

    PubMed

    Dirlewanger, E.; Cosson, P.; Tavaud, M.; Aranzana, J.; Poizat, C.; Zanetto, A.; Ars, P.; Laigret, F.

    2002-07-01

    We report the sequence of 41 primer pairs of microsatellites from a CT-enriched genomic library of the peach cultivar 'Merrill O'Henry'. Ten microsatellite-containing clones had sequences similar to plant coding sequences in databases and could be used as markers for known functions. For microsatellites segregating at least in one of the two Prunus F(2) progenies analyzed, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was evaluated in 27 peach and 21 sweet cherry cultivars. All primer pairs gave PCR-amplification products on peach and 33 on cherry (80.5%). Six PCR-amplifications revealed several loci (14.6%) in peach and eight (19.5%) in sweet cherry. Among the 33 single-locus microsatellites amplified in peach and sweet cherry, 13 revealed polymorphism both in peach and cherry, 19 were polymorphic only on peach and one was polymorphic only on cherry. The number of alleles per locus ranged from 1 to 9 for peach and from 1 to 6 on sweet cherry with an average of 4.2 and 2.8 in peach and sweet cherry, respectively. Cross-species amplification was tested within the Prunus species: Prunus avium L. (sweet cherry and mazzard), Prunus cerasus L. (sour cherry), Prunus domestica L. (European plum), Prunus amygdalus Batsch. (almond), Prunus armeniaca L. (apricot), Prunus cerasifera Ehrh. (Myrobalan plum). Plants from other genera of the Rosaceae were also tested: Malus (apple) and Fragaria (strawberry), as well as species not belonging to the Rosaceae: Castanea (chestnut tree), Juglans (walnut tree) and Vitis (grapevine). Six microsatellites gave amplification on all the tested species. Among them, one had an amplified region homologous to sequences encoding a MADS-box protein in Malus x domestica. Twelve microsatellites (29.3%) were amplified in all the Rosaceae species tested and 31 (75.6%) were amplified in all the six Prunus species tested. Thirty three (80.5%), 18 (43.9%) and 13 (31.7%) gave amplification on chestnut tree, grapevine and walnut tree, respectively. PMID:12582570

  12. Isolation of polymorphic microsatellite loci from the Chinese alligator (Alligator sinensis).

    PubMed

    Zhu, Haitao; Wu, Xiaobing; Xue, Hui; Wei, Lei; Hu, Yuling

    2009-05-01

    Ten microsatellite loci were isolated from the Chinese alligator (Alligator sinensis), using a partial genomic DNA library and an enrichment method. Fifty microsatellite repeats were screened from the library of 888 positive clones, 10 of which were polymorphic. These microsatellite loci developed here are another set of novel molecular markers for A. sinensis, and they will be suitable for population genetic studies as well as for kinship analysis. PMID:21564781

  13. Development of polymorphic microsatellite markers in Hessian fly, Mayetiola destructor (Say).

    PubMed

    Schemerhorn, Brandon J; Crane, Yan M; Morton, Philip K

    2008-11-01

    A microsatellite library was prepared from size-selected genomic DNA of Hessian fly (Mayetiola destructor). Approximately 81% of recovered clones hybridized with microsatellite motif-specific probes. Subsequently, 2350 clones were sequenced. Sixty-two individual flies from laboratory strains were used to test for reliability and polymorphism in 50 of the microsatellites by gel electrophoresis; 18 were further tested with capillary electrophoresis. Of these, 17 behaved as a polymorphic single locus appropriate for population analysis. PMID:21586046

  14. Microsatellite Instability Assay — EDRN Public Portal

    Cancer.gov

    Microsatellite analysis (MSA) is a promising new technique for the surveillance of bladder cancer. The technology, which permits the separation by electrophoresis of polymerase chain reaction (PCR)-amplified sequences from non-malignant and malignant sources, has been applied to the diagnosis of solid tumors arising in colon, lung, oropharynx, kidney and bladder. MSA can detect genetic changes indicative of carcinoma from urothelial cells obtained in voided urine specimens. The genetic profile of DNA purified from urine is compared to that of DNA purified from peripheral lymphocytes that are considered normal. Once the DNA from uroepithelial cells has been obtained, PCR is performed with specific oligonucleotide primers for each chromosomal locus. The PCR products are then examined for evidence of microsatellite instability (MSI) and loss of heterozygosity (LOH), which are genetic characteristics of epithelial tumors. Preliminary work shows that MSA detects 95% of cancers.

  15. W-SPECIFIC MICROSATELLITE LOCI DETECTED BY IN SILICO ANALYSIS, MAP TO CHROMOSOME Z OF THE CHICKEN GENOME

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unlike mammals, avian females are the heterogametic gender (ZW) and males are the homogametic (ZZ). The non-recombining, female-specific regions are maternally inherited. As such, they have a special value for matrilineal phylogenetic analysis of chicken populations and possibly for avian species in...

  16. 45 CFR 302.31 - Establishing paternity and securing support.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Establishing paternity and securing support. 302... HEALTH AND HUMAN SERVICES STATE PLAN REQUIREMENTS 302.31 Establishing paternity and securing support..., to establish the paternity of such child; and (2) In the case of any individual with respect to...

  17. 25 CFR 11.609 - Determination of paternity and support.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Determination of paternity and support. 11.609 Section 11... OFFENSES AND LAW AND ORDER CODE Domestic Relations 11.609 Determination of paternity and support. The Court of Indian Offenses shall have jurisdiction of all suits brought to determine the paternity of...

  18. 45 CFR 302.31 - Establishing paternity and securing support.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 2 2011-10-01 2011-10-01 false Establishing paternity and securing support. 302... HEALTH AND HUMAN SERVICES STATE PLAN REQUIREMENTS 302.31 Establishing paternity and securing support..., to establish the paternity of such child; and (2) In the case of any individual with respect to...

  19. 25 CFR 11.609 - Determination of paternity and support.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Determination of paternity and support. 11.609 Section 11... OFFENSES AND LAW AND ORDER CODE Domestic Relations 11.609 Determination of paternity and support. The Court of Indian Offenses shall have jurisdiction of all suits brought to determine the paternity of...

  20. Relationship of Paternity Status, Welfare Reform Period, and Racial/Ethnic Disparities in Infant Mortality.

    PubMed

    Ngui, Emmanuel M; Cortright, Alicia L; Michalski, Karen

    2015-09-01

    The objective of this study was to examine the relationship of paternity status, welfare reform period, and racial/ethnic disparities in infant mortality. The study used retrospective analysis of birth outcomes data from singleton birth/infant death data in Milwaukee, Wisconsin, from 1993 to 2009. Multivariate logistic regression was used to examine the relationship between paternity status, welfare reform period, and infant mortality, adjusting for maternal and infant characteristics. Data consisted of almost 185,000 singleton live births and 1,739 infant deaths. Although unmarried women with no father on record made up about 32% of the live births, they accounted for over two thirds of the infant deaths compared with married women with established paternity who made up 39% of live births but had about a quarter of infant deaths. After adjustments, any form of paternity establishment was protective against infant mortality across all racial/ethnic groups. Unmarried women with no father on record had twice to triple the odds of infant mortality among all racial/ethnic groups. The likelihood of infant mortality was only significantly greater for African American women in the postwelfare (1999-2004; odds ratio = 1.27; 95% confidence interval = 1.10-1.46) period compared with the 1993 to 1998 period. Study findings suggest that any form of paternity establishment may have protective effect against infant mortality. Welfare reform changes may have reduced some of the protection against infant mortality among unmarried African American women that was present before the welfare legislation. Policies and programs that promote or support increased paternal involvement and establishment of paternity may improve birth outcomes and help reduce infant mortality. PMID:25061086

  1. Relationships of maternal and paternal anthropometry with neonatal body size, proportions and adiposity in an Australian cohort.

    PubMed

    Pomeroy, Emma; Wells, Jonathan C K; Cole, Tim J; O'Callaghan, Michael; Stock, Jay T

    2015-04-01

    The patterns of association between maternal or paternal and neonatal phenotype may offer insight into how neonatal characteristics are shaped by evolutionary processes, such as conflicting parental interests in fetal investment and obstetric constraints. Paternal interests are theoretically served by maximizing fetal growth, and maternal interests by managing investment in current and future offspring, but whether paternal and maternal influences act on different components of overall size is unknown. We tested whether parents' prepregnancy height and body mass index (BMI) were related to neonatal anthropometry (birthweight, head circumference, absolute and proportional limb segment and trunk lengths, subcutaneous fat) among 1,041 Australian neonates using stepwise linear regression. Maternal and paternal height and maternal BMI were associated with birthweight. Paternal height related to offspring forearm and lower leg lengths, maternal height and BMI to neonatal head circumference, and maternal BMI to offspring adiposity. Principal components analysis identified three components of variability reflecting neonatal "head and trunk skeletal size," "adiposity," and "limb lengths." Regression analyses of the component scores supported the associations of head and trunk size or adiposity with maternal anthropometry, and limb lengths with paternal anthropometry. Our results suggest that while neonatal fatness reflects environmental conditions (maternal physiology), head circumference and limb and trunk lengths show differing associations with parental anthropometry. These patterns may reflect genetics, parental imprinting and environmental influences in a manner consistent with parental conflicts of interest. Paternal height may relate to neonatal limb length as a means of increasing fetal growth without exacerbating the risk of obstetric complications. PMID:25502164

  2. PCR and microsatellite analysis of diminazene aceturate resistance of bovine trypanosomes correlated to knowledge, attitude and practice of livestock keepers in South-Western Ethiopia.

    PubMed

    Moti, Y; De Deken, R; Thys, E; Van Den Abbeele, J; Duchateau, L; Delespaux, V

    2015-06-01

    African Animal Trypanosomosis is threatening the agricultural production and cattle breeding more severely than any other livestock disease in the continent, even more since the advent of drug resistance. A longitudinal study was conducted from November 2012 to May 2013 in the Ghibe valley to evaluate diminazene aceturate (DA) resistance and assess livestock owner's perception of trypanocidal drug use. Four Peasant Associations (PAs) were purposively selected and the cattle randomly sampled in each PAs. At the beginning of the study (t0), 106 bovines positive for trypanosomes by the haematocrit centrifugation technique (HCT) and 119 negative control animals were recruited for six months follow-up using HCT, 18S-PCR-RFLP, DpnII-PCR-RFLP and microsatellite analysis. Prevalence of trypanosomosis was 18.1% based on the HCT technique and the mean PCV value was 23.6±5.1% for the 587 sampled cattle. Out of the 106 HCT positive, 64 (60.4%) were positive for the presence of trypanosomes using the 18S-PCR-RFLP. Species detection showed 38 (59.4%) Trypanosoma congolense savannah, 18 (28.1%) Trypanosoma vivax, 5 (7.8%) Trypanosoma theileri and 3 (4.7%) T. congolense Kilifi. Among the T. congolense savannah samples, 31 (81.6%) showed a DA resistant RFLP profile, 2 (5.3%) a mixed profile and 5 did not amplify using the DpnII-PCR-RFLP. A positive HCT had a significant effect on PCV (p<0.001) with the mean PCV value equal to 24.4±0.2% in the absence of trypanosomes and to 20.9±0.3% in the presence of trypanosomes. PCV increased significantly (p<0.001) with 4.4±0.5% one month after treatment. All T. congolense savannah type were analyzed using microsatellite markers TCM1, TCM3 and TCM4. The main events were new infections (40.0%) and relapses (37.5%) with cures lagging at 22.5%. In 10 purposively selected PAs a semi-structured questionnaire was used. The average herd size was the highest in Abelti PA (6.7±1.8 TLU) and the mean herd size was statistically different (p=0.01) in the 10 PAs. Trypanosomosis was designated as the main disease affecting cattle by 97% of the respondents. DA was used by 95.5% of the farmers though more than half of them (51.9%) were not familiar with isometamidium (ISM). There was a trend to overdose young small animals and to underdose large ones. Oxen were treated very frequently (nearly 20 times/year) and calves almost never. To improve the situation in the Ghibe valley, extension messages should be delivered to promote a rational drug use, improved livestock management and the application of strategic vector control methods. PMID:25738729

  3. Microsatellite diversity and the demographic history of?modern?humans

    PubMed Central

    Jorde, Lynn B.; Rogers, Alan R.; Bamshad, Michael; Watkins, W. Scott; Krakowiak, Patrycja; Sung, Sandy; Kere, Juha; Harpending, Henry C.

    1997-01-01

    We have examined differences in diversity at 60 microsatellite loci among human population samples from three major continental groups to evaluate the hypothesis of greater African diversity in this rapidly evolving class of loci. Application of a statistical test that assumes equal mutation rates at all loci fails to demonstrate differences in microsatellite diversity, while a randomization test that does not make this assumption finds that Africans have significantly greater microsatellite diversity (P < 10?8) than do Asians and Europeans. Greater African diversity is most apparent at loci with smaller overall variance in allele size, suggesting that the record of population history has been erased at repeat loci with higher mutation rates. A power analysis shows that only 3540 microsatellites are needed to establish this difference statistically, demonstrating the considerable evolutionary information contained in these systems. On average, African populations have ?20% greater microsatellite diversity than do Asian and European populations. A comparison of continental diversity differences in microsatellites and mtDNA sequences suggests earlier demographic expansion of the ancestors of Africans. PMID:9096352

  4. Identification of the skeletal remains of Josef Mengele by DNA analysis.

    PubMed

    Jeffreys, A J; Allen, M J; Hagelberg, E; Sonnberg, A

    1992-09-01

    There has been considerable controversy over the identity of the skeletal remains exhumed in Brazil in 1985 and believed to be those of Dr Josef Mengele, the Auschwitz 'Angel of Death'. Bone DNA analysis was therefore conducted in an attempt to provide independent evidence of identity. Trace amounts of highly degraded human DNA were successfully extracted from the shaft of the femur. Despite the presence of a potent inhibitor of DNA amplification, microsatellite alleles could be reproducibly amplified from the femur DNA. Comparison of the femur DNA with DNA from Josef Mengele's son and wife revealed a bone genotype across 10 different loci fully compatible with paternity of Mengele's son. Less than 1 in 1800 Caucasian individuals unrelated to Mengele's son would by chance show full paternal inclusion. DNA analysis therefore provides very strong independent evidence that the remains exhumed from Brazil are indeed those of Josef Mengele. PMID:1398379

  5. Paternity Testing in a PBL Environment

    ERIC Educational Resources Information Center

    Casla, Alberto Vicario; Zubiaga, Isabel Smith

    2010-01-01

    Problem Based Learning (PBL) makes use of real-life scenarios to stimulate students' prior knowledge and to provide a meaningful context that is also related to the student's future professional work. In this article, Paternity testing is presented using a PBL approach that involves a combination of classroom, laboratory, and out-of-class

  6. Paternity Testing in a PBL Environment

    ERIC Educational Resources Information Center

    Casla, Alberto Vicario; Zubiaga, Isabel Smith

    2010-01-01

    Problem Based Learning (PBL) makes use of real-life scenarios to stimulate students' prior knowledge and to provide a meaningful context that is also related to the student's future professional work. In this article, Paternity testing is presented using a PBL approach that involves a combination of classroom, laboratory, and out-of-class…

  7. Adolescent Fathers: The Question of Paternity.

    ERIC Educational Resources Information Center

    Rozie-Battle, Judith L.

    1989-01-01

    Analyzes legislation and court decisions that affect unwed and/or adolescent African-American fathers. Addresses the following concerns: (1) paternity; (2) child support; and (3) legal rights and responsibilities. Recommends development of programs to help potential fathers understand their rights and responsibilities. (FMW)

  8. Paternal Attachment, Parenting Beliefs and Children's Attachment

    ERIC Educational Resources Information Center

    Howard, Kimberly S.

    2010-01-01

    Relationships between fathers' romantic attachment style, parenting beliefs and father-child attachment security and dependence were examined in a diverse sample of 72 fathers of young children. Paternal romantic attachment style was coded based on fathers' endorsement of a particular style represented in the Hazan and Shaver Three-Category

  9. Advancing Paternal Age and Simplex Autism

    ERIC Educational Resources Information Center

    Puleo, Connor Morrow; Schmeidler, James; Reichenberg, Abraham; Kolevzon, Alexander; Soorya, Latha V.; Buxbaum, Joseph D.; Silverman, Jeremy M.

    2012-01-01

    De novo events appear more common in female and simplex autism spectrum disorder (ASD) cases and may underlie greater ASD risk in older fathers' offspring. This study examined whether advancing paternal age predicts an increase in simplex (n = 90) versus multiplex ASD cases (n = 587) in 677 participants (340 families). Whether or not controlling…

  10. Paternal Attachment, Parenting Beliefs and Children's Attachment

    ERIC Educational Resources Information Center

    Howard, Kimberly S.

    2010-01-01

    Relationships between fathers' romantic attachment style, parenting beliefs and father-child attachment security and dependence were examined in a diverse sample of 72 fathers of young children. Paternal romantic attachment style was coded based on fathers' endorsement of a particular style represented in the Hazan and Shaver Three-Category…

  11. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes

    PubMed Central

    Lambrot, R.; Xu, C.; Saint-Phar, S.; Chountalos, G.; Cohen, T.; Paquet, M.; Suderman, M.; Hallett, M.; Kimmins, S.

    2013-01-01

    Epidemiological studies suggest that a fathers diet can influence offspring health. A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome. The epigenome includes heritable information such as DNA methylation. We hypothesize that the dietary supply of methyl donors will alter epigenetic reprogramming in sperm. Here we feed male mice either a folate-deficient or folate-sufficient diet throughout life. Paternal folate deficiency is associated with increased birth defects in the offspring, which include craniofacial and musculoskeletal malformations. Genome-wide DNA methylation analysis and the subsequent functional analysis identify differential methylation in sperm of genes implicated in development, chronic diseases such as cancer, diabetes, autism and schizophrenia. While >300 genes are differentially expressed in offspring placenta, only two correspond to genes with differential methylation in sperm. This model suggests epigenetic transmission may involve sperm histone H3 methylation or DNA methylation and that adequate paternal dietary folate is essential for offspring health. PMID:24326934

  12. First identification of polymorphic microsatellite markers in the Burgundy truffle, Tuber aestivum (Tuberaceae)1

    PubMed Central

    Molinier, Virginie; Murat, Claude; Morin, Emmanuelle; Gollotte, Armelle; Wipf, Daniel; Martin, Francis

    2013-01-01

    Premise of the study: Tuber aestivum, the most common truffle in Europe, plays an important role in the commercial truffle market. For the first time, microsatellite primers were developed to investigate polymorphism within this species. Methods and Results: Using direct shotgun pyrosequencing, 15 polymorphic microsatellites were identified out of the 7784 perfect microsatellites present in the 534620 reads obtained. Tested on 75 samples, these microsatellites were highly polymorphic. The number of alleles varied from four to 15, and the expected heterozygosity ranged from 0.266 to 0.620. A multilocus analysis allowed the identification of 63 genotypes over the 75 samples analyzed. Conclusions: Direct shotgun pyrosequencing is a fast and relatively low-cost technique allowing identification of microsatellites in nonmodel species. The microsatellites developed in this study will be useful in population genetic studies to infer the evolutionary history of this species. PMID:25202513

  13. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis

    PubMed Central

    Jia, Guanqing; Shi, Shenkui; Wang, Chunfang; Niu, Zhengang; Chai, Yang; Zhi, Hui; Diao, Xianmin

    2013-01-01

    Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C4 photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, NeighborJoining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China. PMID:23956411

  14. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis.

    PubMed

    Jia, Guanqing; Shi, Shenkui; Wang, Chunfang; Niu, Zhengang; Chai, Yang; Zhi, Hui; Diao, Xianmin

    2013-09-01

    Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C4 photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, Neighbor-Joining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China. PMID:23956411

  15. The effect of paternal age on offspring intelligence and personality when controlling for paternal trait level.

    PubMed

    Arslan, Ruben C; Penke, Lars; Johnson, Wendy; Iacono, William G; McGue, Matt

    2014-01-01

    Paternal age at conception has been found to predict the number of new genetic mutations. We examined the effect of father's age at birth on offspring intelligence, head circumference and personality traits. Using the Minnesota Twin Family Study sample we tested paternal age effects while controlling for parents' trait levels measured with the same precision as offspring's. From evolutionary genetic considerations we predicted a negative effect of paternal age on offspring intelligence, but not on other traits. Controlling for parental intelligence (IQ) had the effect of turning an initially positive association non-significantly negative. We found paternal age effects on offspring IQ and Multidimensional Personality Questionnaire Absorption, but they were not robustly significant, nor replicable with additional covariates. No other noteworthy effects were found. Parents' intelligence and personality correlated with their ages at twin birth, which may have obscured a small negative effect of advanced paternal age (<1% of variance explained) on intelligence. We discuss future avenues for studies of paternal age effects and suggest that stronger research designs are needed to rule out confounding factors involving birth order and the Flynn effect. PMID:24587224

  16. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao

    PubMed Central

    Ferraz dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches’ broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. PMID:26949967

  17. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    PubMed

    Ferraz Dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses; Micheli, Fabienne; Marcellino, Lucilia Helena

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. PMID:26949967

  18. Transcriptome Analysis of the Trachinotus ovatus: Identification of Reproduction, Growth and Immune-Related Genes and Microsatellite Markers

    PubMed Central

    Chao, Fang; Qiongyu, Liu; Zihao, Li; Xiaochun, Liu; Yong, Zhang; Shuisheng, Li; Haoran, Lin

    2014-01-01

    Background The Trachinotus ovatus (Teleostei, Carangidae) is an economically important marine fish species in the world. However, the lack of genomic information regarding this species limits our understanding of the genetics and biological mechanisms in Trachinotus ovatus. In this study, high throughput transcriptome sequencing was used to obtain comprehensive genomic information in Trachinotus ovatus. Principal Findings Transcriptome sequencing was performed by using Illumina paired-end sequencing technology. The 98,534,862 high quality reads were yielded, and were de novo assembled into 156,094 unigenes with an average sequence length of 1179 bp. Transcriptome annotation revealed that 75,586 and 67,923 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 67,923 unigenes were grouped into 25 Cluster of Orthologous Groups (COG) functional categories, 37,976 unigenes were clustered into 61 Gene Ontology (GO) terms, and 38,172 unigenes were assigned to 275 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on the transcriptome dataset, a large number of unigenes associated with reproduction, growth and immunity were identified. Furthermore, a total number of 38,794 simple sequence repeats (SSRs) were discovered and 16 polymorphic loci were characterized in Trachinotus ovatus. Conclusion/Significance The present study is the first transcriptome analysis of a fish species belonging to the genus Trachinotus and provides a valuable genomic resource for novel gene discovery, gene expression and regulation studies, and the identification of genetic markers in Trachinotus ovatus and the other fish of the genus Trachinotus. PMID:25303650

  19. Genomic characterization of EmsB microsatellite loci in Echinococcus multilocularis.

    PubMed

    Valot, Benoît; Knapp, Jenny; Umhang, Gérald; Grenouillet, Frédéric; Millon, Laurence

    2015-06-01

    EmsB is a molecular marker applied to Echinococcus multilocularis genotyping studies. This marker has largely been used to investigate the epidemiology of the parasite in different endemic foci. The present study has lifted the veil on the genetic structure of this microsatellite. By in silico analysis on the E. multilocularis genome the microsatellite was described in about 40 copies on the chromosome 5 of the parasite. Similar structure was found in the relative parasite Echinococcus granulosus, where the microsatellite was firstly described. The present study completes the first investigations made on the EmsB microsatellite origins and confirms the reliability of this highly discriminant molecular marker. PMID:25847697

  20. Discovering misattributed paternity in genetic counselling: different ethical perspectives in two countries.

    PubMed

    Tozzo, Pamela; Caenazzo, Luciana; Parker, Michael J

    2014-03-01

    Misattributed paternity or 'false' paternity is when a man is wrongly thought, by himself and possibly by others, to be the biological father of a child. Nowadays, because of the progression of genetics and genomics the possibility of finding misattributed paternity during familial genetic testing has increased. In contrast to other medical information, which pertains primarily to individuals, information obtained by genetic testing and/or pedigree analysis necessarily has implications for other biologically related members in the family. Disclosing or not a misattributed paternity has a number of different biological and social consequences for the people involved. Such an issue presents important ethical and deontological challenges. The debate centres on whether or not to inform the family and, particularly, whom in the family, about the possibility that misattributed paternity might be discovered incidentally, and whether or not it is the duty of the healthcare professional (HCP) to disclose the results and to whom. In this paper, we consider the different perspectives and reported problems, and analyse their cultural, ethical and legal dimensions. We compare the position of HCPs from an Italian and British point of view, particularly their role in genetic counselling. We discuss whether the Oviedo Convention of the Council of Europe (1997) can be seen as a basis for enriching the debate. PMID:23443210

  1. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

    PubMed Central

    2012-01-01

    Background Microsatellites or simple sequence repeats (SSRs) in expressed sequence tags (ESTs) are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica). Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54%) contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%). The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3%) di-SSRs, followed by the AAG motif, found in 342 (25.9%) tri-SSRs. Most (72.8%) tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO) annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size and number of SSR repeats, respectively. EST-SSR markers exhibited less polymorphism than genomic SSRs. Conclusions We have created a new open pipeline for developing EST-SSR markers and applied it in a comprehensive analysis of EST-SSRs and EST-SSR markers in C. japonica. The results will be useful in genomic analyses of conifers and other non-model species. PMID:22507374

  2. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.).

    PubMed

    Bhawna; Abdin, M Z; Arya, L; Verma, M

    2015-02-01

    Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd. PMID:25471016

  3. Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of Endangered Polyporus umbellatus

    PubMed Central

    Zhang, Yuejin; Chen, Yuanyuan; Wang, Ruihong; Zeng, Ailin; Deyholos, Michael K.; Shu, Jia; Guo, Hongbo

    2015-01-01

    A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences in Ganoderma lucidum obtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 natural Polyporus umbellatus accessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13 P. umbellatus accessions showed relatively high genetic diversity. The expected heterozygosity, Nei's gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups. PMID:26146636

  4. Influences of maternal and paternal PTSD on epigenetic regulation of the glucocorticoid receptor gene in Holocaust survivor offspring

    PubMed Central

    Desarnaud, Frank; Bader, Heather N.; Makotkine, Iouri; Flory, Janine D.; Bierer, Linda M.; Meaney, Michael J.

    2014-01-01

    Objective Differential effects of maternal and paternal PTSD have been observed in adult offspring of Holocaust survivors in both glucocorticoid receptor sensitivity and vulnerability to psychiatric disorder. The current study examined the relative influences of maternal and paternal PTSD on DNA methylation of the exon 1F promoter of the glucocorticoid receptor gene (NR3C1) in peripheral blood mononuclear cells (PBMCs), and its relationship to glucocorticoid receptor sensitivity, in Holocaust offspring. Method Adult offspring with at least one Holocaust survivor parent (n=80), and demographically similar participants without parental Holocaust exposure or PTSD (n=15) completed clinical interviews, self-report measures, and biological procedures. Blood samples were collected for analysis of glucocorticoid receptor gene exon 1F (GR-1F) promoter methylation and cortisol levels in response to low-dose dexamethasone, and two-way analysis of covariance was performed using maternal and paternal PTSD as main effects. Hierarchical-clustering analysis was used to permit visualization of maternal vs. paternal PTSD effects on clinical variables. Results A significant interaction demonstrated that in the absence of maternal PTSD, offspring with paternal PTSD showed higher GR-1F promoter methylation, whereas offspring with both maternal and paternal PTSD showed lower methylation. Lower GR-1F promoter methylation was significantly associated with greater post-dexamethasone cortisol suppression. The clustering analysis confirmed that maternal and paternal PTSD effects were differentially associated with clinical indicators. Conclusions This is the first study to demonstrate alterations of GR-1F promoter methylation in relation to parental PTSD and neuroendocrine outcomes. The moderation of paternal PTSD effects by maternal PTSD suggests different mechanisms for the intergenerational transmission of trauma-related vulnerabilities. PMID:24832930

  5. Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.)

    PubMed Central

    Liu, Huabo; Tang, Yan; Wu, Liping; Wang, Zhe; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

    2014-01-01

    Chinese jujube (Ziziphus jujuba Mill, 2n?=?2?=?24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba Dongzao using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for Dongzao. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars. PMID:24932973

  6. Microsatellites for Carpotroche brasiliensis (Flacourtiaceae), a useful species for agroforestry and ecosystem conservation1

    PubMed Central

    Bittencourt, Flora; Alves, Jackeline S.; Gaiotto, Fernanda A.

    2015-01-01

    Premise of the study: We developed microsatellite markers for Carpotroche brasiliensis (Flacourtiaceae), a dioecious tree that is used as a food resource by midsize animals of the Brazilian fauna. Methods and Results: We designed 30 primer pairs using next-generation sequencing and classified 25 pairs as polymorphic. Observed heterozygosity ranged from 0.5 to 1.0, and expected heterozygosity ranged from 0.418 to 0.907. The combined probability of exclusion was greater than 0.999 and the combined probability of identity was less than 0.001, indicating that these microsatellites are appropriate for investigations of genetic structure, individual identification, and paternity testing. Conclusions: The developed molecular tools may contribute to future studies of population genetics, answering ecological and evolutionary questions regarding efficient conservation strategies for C. brasiliensis. PMID:26697275

  7. In-silico mining, type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS-LRR regions of finger millet with rice.

    PubMed

    Kalyana Babu, B; Pandey, Dinesh; Agrawal, P K; Sood, Salej; Kumar, Anil

    2014-05-01

    In recent years, the increased availability of the DNA sequences has given the possibility to develop and explore the expressed sequence tags (ESTs) derived SSR markers. In the present study, a total of 1956 ESTs of finger millet were used to find the microsatellite type, distribution, frequency and developed a total of 545 primer pairs from the ESTs of finger millet. Thirty-two EST sequences had more than two microsatellites and 1357 sequences did not have any SSR repeats. The most frequent type of repeats was trimeric motif, however the second place was occupied by dimeric motif followed by tetra-, hexa- and penta repeat motifs. The most common dimer repeat motif was GA and in case of trimeric SSRs, it was CGG. The EST sequences of NBS-LRR region of finger millet and rice showed higher synteny and were found on nearly same positions on the rice chromosome map. A total of eight, out of 15 EST based SSR primers were polymorphic among the selected resistant and susceptible finger millet genotypes. The primer FMBLEST5 could able to differentiate them into resistant and susceptible genotypes. The alleles specific to the resistant and susceptible genotypes were sequenced using the ABI 3130XL genetic analyzer and found similarity to NBS-LRR regions of rice and finger millet and contained the characteristic kinase-2 and kinase 3a motifs of plant R-genes belonged to NBS-LRR region. The In-silico and comparative analysis showed that the genes responsible for blast resistance can be identified, mapped and further introgressed through molecular breeding approaches for enhancing the blast resistance in finger millet. PMID:24477586

  8. DNA content analysis of colorectal cancer defines a distinct microsatellite and chromosome stable group but does not predict response to radiotherapy

    PubMed Central

    Fadhil, Wakkas; Kindle, Karin; Jackson, Darryl; Zaitoun, Abed; Lane, Nina; Robins, Adrian; Ilyas, Mohammad

    2014-01-01

    Colorectal cancers (CRC) are thought to have genetic instability in the form of either microsatellite instability (MSI) or chromosomal instability (CIN). Recently, tumours have been described without either MSI or CIN, that is, microsatellite and chromosome stable (MACS) CRCs. We investigated the (i) frequency of the MACS-CRCs and (ii) whether this genotype predicted responsiveness to neoadjuvant chemoradiotherapy. To examine the frequency of MACS-CRCs, DNA content (ploidy) was examined in 89 sporadic microsatellite-stable CRCs using flow cytometry. The tumours were also screened for mutations in KRAS/BRAF/TP53/PIK3CA by QMC-PCR. To examine the value of tumour ploidy in predicting response to chemoradiotherapy, DNA content was tested in a separate group of 62 rectal cancers treated with neoadjuvant chemoradiotherapy. Fifty-one of 89 CRCs (57%) were aneuploid and 38 (43%) were diploid. There was no significant association between mutations in TP53/KRAS/BRAF/PIK3CA and ploidy. Testing of association between mutations revealed only mutual exclusivity of KRAS/BRAF mutation (P?microsatellite-stable CRCs with a mutation profile overlapping that of CRCs with CIN. A diploid genotype does not, however, predict the responsiveness to radiotherapy. PMID:24456329

  9. Displays of paternal mouse pup retrieval following communicative interaction with maternal mates

    PubMed Central

    Liu, Hong-Xiang; Lopatina, Olga; Higashida, Chiharu; Fujimoto, Hiroko; Akther, Shirin; Inzhutova, Alena; Liang, Mingkun; Zhong, Jing; Tsuji, Takahiro; Yoshihara, Toru; Sumi, Kohei; Ishiyama, Mizuho; Ma, Wen-Jie; Ozaki, Mitsunori; Yagitani, Satoshi; Yokoyama, Shigeru; Mukaida, Naofumi; Sakurai, Takeshi; Hori, Osamu; Yoshioka, Katsuji; Hirao, Atsushi; Kato, Yukio; Ishihara, Katsuhiko; Kato, Ichiro; Okamoto, Hiroshi; Cherepanov, Stanislav M.; Salmina, Alla B.; Hirai, Hirokazu; Asano, Masahide; Brown, David A.; Nagano, Isamu; Higashida, Haruhiro

    2013-01-01

    Compared with the knowledge of maternal care, much less is known about the factors required for paternal parental care. Here we report that new sires of laboratory mice, though not spontaneously parental, can be induced to show maternal-like parental care (pup retrieval) using signals from dams separated from their pups. During this interaction, the maternal mates emit 38-kHz ultrasonic vocalizations to their male partners, which are equivalent to vocalizations that occur following pheromone stimulation. Without these signals or in the absence of maternal mates, the sires do not retrieve their pups within 5?min. These results show that, in mice, the maternal parent communicates to the paternal parent to encourage pup care. This new paradigm may be useful in the analysis of the parental brain during paternal care induced by interactive communication. PMID:23299896

  10. Genome-wide semiquantitative microsatellite analysis of human hepatocellular carcinoma: discrete mapping of smallest region of overlap of recurrent chromosomal gains and losses.

    PubMed

    Nishimura, Takafumi; Nishida, Naoshi; Komeda, Toshiki; Fukuda, Yoshihiro; Ikai, Iwao; Yamaoka, Yoshio; Nakao, Kazuwa

    2006-05-01

    Recurrent chromosomal gains at 1q, 6p, 8q, and 17q, or losses at 1p, 4q, 6q, 8p, 9p, 13q, 16q, and 17p are common features of human hepatocellular carcinoma (HCC). For precise determination of the shortest region of overlap (SRO), 49 HCC obtained at the time of surgery or autopsy were subjected to comprehensive microsatellite analysis by using 400 markers distributed at almost equal distances throughout the 22 autosomes and X chromosomes. Each allele showing imbalance was subjected to comparative duplex polymerase chain reaction using a retained allele as an internal control to determine whether the imbalance was the result of chromosomal gain or loss. The following SRO of recurrent chromosomal gains and losses were determined: -1p36.22 approximately p36.33, D1S450-D1S2893, 5.0 mega-base pairs (Mbp); +1q23.3 approximately q25.3, D1S2878-D1S2619, 16.9 Mbp; -4q21.2 approximately q24, D4S2964-D4S1572, 23.0 Mbp; -6q23.3 approximately qter, D6S292-qter, 34.7 Mb; -8p22 approximately p23.1, D8S549-D8S550, 4.8 Mbp; +8q12.2 approximately q24.13, D8S260-D8S514, 61.8 Mbp; -13q13.3 approximately q22.1, D13S218-D13S156, 35.6 Mbp; -16q22.1 approximately qter, D16S503-qter, 26.7 Mbp; and -17p12 approximately pter, D17S921-pter, 14.2 Mbp. Contrary to our initial expectations, many HCC showed major deletions or additions of chromosome arms, so that a number of genes were included in the SRO. Although some putative oncogenes or tumor suppressor genes mapped in these SRO may be important, relative copy number changes of numerous other genes may affect pathogenesis of HCC. PMID:16682288

  11. The ethical debate on present day paternity testing practices.

    PubMed

    Mertens, G

    2006-01-01

    The last years, the number of paternity tests on buccal swabs sold over the internet as "test kits", has steeply increased. The commercial providers of these services facilitate controversial practices, including clandestine sampling at home, anonymous sending off for analysis, motherless testing and using "stolen" personal objects containing biological material (combs, cigarette butts). This has led to concern on the consequences on the family unit--especially the child--which may suffer emotionally, physically and financially. In reaction, legal initiatives are appearing throughout Europe. The UK Human Genetics Commission has advised that the non-consensual obtaining and analysis of personal genetic information should be a new criminal offence. The German Federal Court of Justice has ruled that paternity tests performed without the mother's knowledge are inadmissible as evidence in lawsuits. French law strictly forbids the application of DNA testing without the involvement of the court system. In Belgium, a proposal for law has been laid down where the offering to PMID:16792338

  12. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations

    PubMed Central

    2010-01-01

    Background Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol's modified frequentist test and the Bayesian FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRθ' statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations. PMID:20691068

  13. Managing misaligned paternity findings in research including sickle cell disease screening in Kenya: 'consulting communities' to inform policy.

    PubMed

    Marsh, Vicki; Kombe, Francis; Fitzpatrick, Ray; Molyneux, Sassy; Parker, Michael

    2013-11-01

    The management of misaligned paternity findings raises important controversy worldwide. It has mainly, however, been discussed in the context of high-income countries. Genetic and genomics research, with the potential to show misaligned paternity, are becoming increasingly common in Africa. During a genomics study in Kenya, a dilemma arose over testing and sharing information on paternal sickle cell disease status. This dilemma may be paradigmatic of challenges in sharing misaligned paternity findings in many research and health care settings. Using a deliberative approach to community consultation to inform research practice, we explored residents' views on paternal testing and sharing misaligned paternity information. Between December 2009 and November 2010, 63 residents in Kilifi County were engaged in informed deliberative small group discussions, structured to support normative reflection within the groups, with purposive selection to explore diversity. Analysis was based on a modified framework analysis approach, drawing on relevant social science and bioethics literature. The methods generated in-depth individual and group reflection on morally important issues and uncovered wide diversity in views and values. Fundamental and conflicting values emerged around the importance of family interests and openness, underpinned by disagreement on the moral implications of marital infidelity and withholding truth. Wider consideration of ethical issues emerging in these debates supports locally-held reasoning that paternal sickle cell testing should not be undertaken in this context, in contrast to views that testing should be done with or without the disclosure of misaligned paternity information. The findings highlight the importance of facilitating wider testing of family members of affected children, contingent on the development and implementation of national policies for the management of this inherited disorder. Their richness also illustrates the potential for the approach adopted in this study to strengthen community consultation. PMID:24034967

  14. Managing misaligned paternity findings in research including sickle cell disease screening in Kenya: Consulting communities to inform policy?

    PubMed Central

    Marsh, Vicki; Kombe, Francis; Fitzpatrick, Ray; Molyneux, Sassy; Parker, Michael

    2013-01-01

    The management of misaligned paternity findings raises important controversy worldwide. It has mainly, however, been discussed in the context of high-income countries. Genetic and genomics research, with the potential to show misaligned paternity, are becoming increasingly common in Africa. During a genomics study in Kenya, a dilemma arose over testing and sharing information on paternal sickle cell disease status. This dilemma may be paradigmatic of challenges in sharing misaligned paternity findings in many research and health care settings. Using a deliberative approach to community consultation to inform research practice, we explored residents' views on paternal testing and sharing misaligned paternity information. Between December 2009 and November 2010, 63 residents in Kilifi County were engaged in informed deliberative small group discussions, structured to support normative reflection within the groups, with purposive selection to explore diversity. Analysis was based on a modified framework analysis approach, drawing on relevant social science and bioethics literature. The methods generated in-depth individual and group reflection on morally important issues and uncovered wide diversity in views and values. Fundamental and conflicting values emerged around the importance of family interests and openness, underpinned by disagreement on the moral implications of marital infidelity and withholding truth. Wider consideration of ethical issues emerging in these debates supports locally-held reasoning that paternal sickle cell testing should not be undertaken in this context, in contrast to views that testing should be done with or without the disclosure of misaligned paternity information. The findings highlight the importance of facilitating wider testing of family members of affected children, contingent on the development and implementation of national policies for the management of this inherited disorder. Their richness also illustrates the potential for the approach adopted in this study to strengthen community consultation. PMID:24034967

  15. A rapid qPCR method for genetic sex identification of Salmo salar and Salmo trutta including simultaneous elucidation of interspecies hybrid paternity by high-resolution melt analysis.

    PubMed

    Angls d'Auriac, M B; Urke, H A; Kristensen, T

    2014-06-01

    This study presents an improved duplex quantitative polymerase chain reaction (qPCR) method using the master sex-determining gene sdY as a marker for simultaneous genetic sex identification of salmonids of the Salmo genus and paternity elucidation for Salmo salar Salmo trutta hybrids. This method will provide a new, simple and economical molecular tool for ecological studies of these species as well as for aquaculture purposes. PMID:24814478

  16. Tests of spatial and temporal factors influencing extra-pair paternity in red-winged blackbirds.

    PubMed

    Westneat, David F; Mays, Herman L

    2005-06-01

    Extra-pair paternity (EPP) is a widespread and highly variable reproductive phenomenon in birds. We tested the effects of habitat, spatial factors, and timing of breeding on the occurrence of EPP in red-winged blackbirds (Agelaius phoeniceus). We used PCR-amplified microsatellites to assess the paternity of 1479 nestlings from 537 broods on 235 territories over four breeding seasons. Over 4 years, 40% of nestlings were extra-pair. At least 27% of actual sires were non-neighbours, suggesting that males or females interacted over longer distances than in other populations of red-winged blackbirds. The level of EPP was significantly clumped within broods and males but not within females across broods. EPP was negatively related to the area of a male's territory. The spatial proximity of a female's nest to the territory boundary had no effect on total EPP, but tended to increase the probability of an EPP by a nearby male. We found no influence on EPP of the type of habitat on the territory or the level of nesting activity nearby. The time in the season when a nest was started and the synchrony of breeding also had no significant effect on the level of EPP. The age of the male, the age of his neighbours, and the interaction between the two had no effect on total EPP. However, older males were less likely to have an offspring sired by a neighbour on their territory. Males with older neighbours were also less likely to have offspring sired by a neighbour, particularly if they were new territory owners. The high variability in who gained and lost paternity, and the limited impact of spatial and temporal factors influencing it, have some interesting implications for theories seeking to explain mating patterns. PMID:15910334

  17. Multiple Paternity in the Norway Rat, Rattus norvegicus, from Urban Slums in Salvador, Brazil.

    PubMed

    Costa, Federico; Richardson, Jonathan L; Dion, Kirstin; Mariani, Carol; Pertile, Arsinoe C; Burak, Mary K; Childs, James E; Ko, Albert I; Caccone, Adalgisa

    2016-03-01

    The Norway rat, Rattus norvegicus, is one of the most important pest species globally and the main reservoir of leptospires causing human leptospirosis in the urban slums of tropical regions. Rodent control is a frequent strategy in those settings to prevent the disease but rapid growth from residual populations and immigration limit the long-term effectiveness of interventions. To characterize the breeding ecology of R. norvegicus and provide needed information for the level of genetic mixing, which can help identify inter-connected eradication units, we estimated the occurrence of multiple paternity, distances between mothers and sires, and inbreeding in rats from urban slum habitat in Salvador, Brazil. We genotyped 9 pregnant females, their 66 offspring, and 371 males at 16 microsatellite loci. Multiple paternity was observed in 22% (2/9) of the study litters. Of the 12 sires that contributed to the 9 litters, we identified 5 (42%) of those sires among our genotyped males. Related males were captured in close proximity to pregnant females (the mean inter-parent trapping distance per litter was 70 m, ±58 m SD). Levels of relatedness between mother-sire pairs were higher than expected and significantly higher than relatedness between all females and non-sire males. Our findings indicate multiple paternity is common, inbreeding is apparent, and that mother-sire dyads occur in close proximity within the study area. This information is relevant to improve the spatial definition of the eradication units that may enhance the effectiveness of rodent management programs aimed at preventing human leptospirosis. High levels of inbreeding may also be a sign that eradication efforts are successful. PMID:26733693

  18. Paternal Age, Paternal Presence and Children’s Health: An Observational Study

    PubMed Central

    Gardiner, Julian; Sutcliffe, Alastair G.; Melhuish, Edward; Barnes, Jacqueline

    2015-01-01

    In an observational study of 31,257 children we investigated the effects of paternal age at the time of the child’s birth, paternal absence and non-biological fathers on children’s health. Results are per 5 year change in paternal age. Older fathers were associated with lower rates of unintentional injuries, odds ratio (OR)=0.966, P=0.0027. There was a quadratic association between paternal age and risk of hospital admission, β=0.0121, P=0.0109, with minimum risk at paternal age 37.7. Absent fathers were associated with increased risk of hospital admission, OR=1.19, P<10−3, lower rates of complete immunizations to 9 months, OR=0.562, P<10−3, higher Strength and Difficulties Questionnaire (SDQ) difficulties scores: β=0.304, P=0.0024 (3 year olds), β=0.697, P<10−3 (5 year olds). Non-biological fathers were associated with increased risk of unintentional injury, OR=1.16, P=0.0319 and hospital admission, OR=1.26, P=0.0166; lower rates of complete immunizations to 9 months, OR=0.343, P=0.0309 and higher SDQ difficulties scores: β=0.908, P<10−3. PMID:25918623

  19. A microsatellite genetic linkage map of human chromosome 18

    SciTech Connect

    Straub, R.E.; Speer, M.C.; Luo, Ying; Ott, J.; Gilliam, T.C. ); Rojas, K.; Overhauser, J. )

    1993-01-01

    We isolated nine new microsatellite markers from chromosome 18 and further characterized and mapped eight microsatellites developed in other laboratories. We have constructed a framework linkage map of chromosome 18 that includes 14 microsatellite markers (12 dinucleotide and 2 tetranucleotide) and 2 RFLP markers. Cytogenetic localization for the microsatellites was performed by PCR amplification of IS somatic cell hybrids containing different deletions of chromosome 18. Twelve of the microsatellites and one of the RFLPs have heterozygosities greater than 70%. The average heterozygosity of the markers included in the map is 72%. In addition, we have made provisional placements of 3 more microsatellite markers and 2 more RFLP markers. The map lengths (in Kosambi centimorgans) are as follows: sex-averaged, 109.3 cM; male, 72.4 cM; female, 161.2 cM. The average distance between markers in the sex-averaged map is 7.3 cM, and the largest gap between markers is 16.7 cM. Analysis of the data for differences in the female:male map distance ratio revealed significant evidence for a constant difference in the ratio (X[sup 2]=32.25; df = 1; P < 0.001; ratio = 2.5:1). Furthermore, there was significant evidence in favor of a variable female:male map distance ratio across the chromosome compared to a constant distance ratio (X[sup 2] = 27.78; df = 14; P = 0.015). To facilitate their use in genomic screening for disease genes, all of the microsatellite markers used here can be amplified under standard PCR conditions, and most can be used in duplex PCR reactions. 36 refs., 3 figs., 4 tabs.

  20. Human mutagens: evidence from paternal exposure

    SciTech Connect

    Narod, S.A.; Douglas, G.R.; Nestmann, E.R.; Blakey, D.H.

    1988-01-01

    The importance of inherited mutations as a cause of human disease has been established clearly through examples of well-defined genetic anomalies, such as Down syndrome and retinoblastoma. Furthermore, it is suspected that environmental contaminants induce mutations resulting in increased risk for such defects in subsequent generations of persons exposed. The present lack of direct evidence for induced inherited genetic disorders in human beings hampers the development of risk estimation techniques for extrapolation from animal models. The most extensive prospective epidemiologic studies of inherited genetic effects have involved survivors of atomic bomb detonations and patients treated with cancer chemotherapy. In neither case has a significant elevation in inherited genetic effects or cancer been detected in the offspring of exposed individuals. Epidemiologic studies of subjects receiving chronic exposure may be confounded by the effect of maternal exposure during pregnancy. Consideration of only paternal exposure can minimize the confounding influence of teratogenicity, enhancing the resolving power of studies for inherited effects. Using this approach, retrospective (case-control) studies of childhood cancer patients have provided limited but suggestive evidence for inheritance of induced effects. Endpoints, such as congenital malformations and spontaneous abortion following paternal exposure, can also be considered as indicators of heritable mutagenic effects. For example, there is limited evidence suggesting that paternal exposure to anaesthetic gases may cause miscarriage and congenital abnormalities as a result of induced male germ cell mutations. 104 references.

  1. Religion as a means to assure paternity.

    PubMed

    Strassmann, Beverly I; Kurapati, Nikhil T; Hug, Brendan F; Burke, Erin E; Gillespie, Brenda W; Karafet, Tatiana M; Hammer, Michael F

    2012-06-19

    The sacred texts of five world religions (Buddhism, Christianity, Hinduism, Islam, and Judaism) use similar belief systems to set limits on sexual behavior. We propose that this similarity is a shared cultural solution to a biological problem: namely male uncertainty over the paternity of offspring. Furthermore, we propose the hypothesis that religious practices that more strongly regulate female sexuality should be more successful at promoting paternity certainty. Using genetic data on 1,706 father-son pairs, we tested this hypothesis in a traditional African population in which multiple religions (Islam, Christianity, and indigenous) coexist in the same families and villages. We show that the indigenous religion enables males to achieve a significantly (P = 0.019) lower probability of cuckoldry (1.3% versus 2.9%) by enforcing the honest signaling of menstruation, but that all three religions share tenets aimed at the avoidance of extrapair copulation. Our findings provide evidence for high paternity certainty in a traditional African population, and they shed light on the reproductive agendas that underlie religious patriarchy. PMID:22665788

  2. Religion as a means to assure paternity

    PubMed Central

    Strassmann, Beverly I.; Kurapati, Nikhil T.; Hug, Brendan F.; Burke, Erin E.; Gillespie, Brenda W.; Karafet, Tatiana M.; Hammer, Michael F.

    2012-01-01

    The sacred texts of five world religions (Buddhism, Christianity, Hinduism, Islam, and Judaism) use similar belief systems to set limits on sexual behavior. We propose that this similarity is a shared cultural solution to a biological problem: namely male uncertainty over the paternity of offspring. Furthermore, we propose the hypothesis that religious practices that more strongly regulate female sexuality should be more successful at promoting paternity certainty. Using genetic data on 1,706 fatherson pairs, we tested this hypothesis in a traditional African population in which multiple religions (Islam, Christianity, and indigenous) coexist in the same families and villages. We show that the indigenous religion enables males to achieve a significantly (P = 0.019) lower probability of cuckoldry (1.3% versus 2.9%) by enforcing the honest signaling of menstruation, but that all three religions share tenets aimed at the avoidance of extrapair copulation. Our findings provide evidence for high paternity certainty in a traditional African population, and they shed light on the reproductive agendas that underlie religious patriarchy. PMID:22665788

  3. Paternal Work Stress and Latent Profiles of Father-Infant Parenting Quality

    ERIC Educational Resources Information Center

    Goodman, W. Benjamin; Crouter, Ann C.; Lanza, Stephanie T.; Cox, Martha J.; Vernon-Feagans, Lynne

    2011-01-01

    The current study used latent profile analysis (LPA) to examine the implications of fathers' experiences of work stress for paternal behaviors with infants across multiple dimensions of parenting in a sample of fathers living in nonmetropolitan communities (N = 492). LPA revealed five classes of fathers based on levels of social-affective

  4. "I've Fixed Things Up": Paternal Identity of Substance-Dependent Fathers

    ERIC Educational Resources Information Center

    Peled, Einat; Gavriel-Fried, Belle; Katz, Noam

    2012-01-01

    This study deals with how substance-dependent men perceive their paternal identity. Data were based on in-depth semi-structured interviews with 12 Israeli fathers who were enrolled in methadone maintenance treatment. Content analysis revealed that participants had undergone a process of parental identity formation composed of four distinct stages:

  5. "I've Fixed Things Up": Paternal Identity of Substance-Dependent Fathers

    ERIC Educational Resources Information Center

    Peled, Einat; Gavriel-Fried, Belle; Katz, Noam

    2012-01-01

    This study deals with how substance-dependent men perceive their paternal identity. Data were based on in-depth semi-structured interviews with 12 Israeli fathers who were enrolled in methadone maintenance treatment. Content analysis revealed that participants had undergone a process of parental identity formation composed of four distinct stages:…

  6. The Effects of Paternalism Upon an Industrial Community's Participation in Schooling.

    ERIC Educational Resources Information Center

    Desmond, Cheryl T.

    The influence of paternalism upon a community's school district participation is discussed in this historical case study. Interviews and historical research explore the impact of the "welfare capitalism" of the Endicott Shoe Corporation and International Business Machines on Harrison City, New York, from 1890 through the present. An analysis of

  7. An Examination of Paternal Influence on High-Achieving Gifted Males

    ERIC Educational Resources Information Center

    Hebert, Thomas P.; Pagnani, Alexander R.; Hammond, Daniel R.

    2009-01-01

    The challenges facing contemporary boys are complex, highlighting the importance of positive paternal influence for young men to achieve success. This study examines the father-son relationships of 10 prominent gifted men of achievement to identify factors influencing talent development. Through biographical analysis, 6 significant themes were

  8. Indentification of 700 new microsatellite loci from cotton (G. hirsutum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite markers, also known as SSRs, comprise a keystone technology for genetic linkage analysis, QTL mapping, marker-assisted breeding, and genome analysis. In order to contribute to a growing body of molecular marker resources for cotton research and improvement, we developed primers to am...

  9. Paternal Origin of FGFR2 Mutations in Sporadic Cases of Crouzon Syndrome and Pfeiffer Syndrome

    PubMed Central

    Glaser, Rivka L.; Jiang, Wen; Boyadjiev, Simeon A.; Tran, Alissa K.; Zachary, Andrea A.; VanMaldergem, Lionel; Johnson, David; Walsh, Sinead; Oldridge, Michael; Wall, Steven A.; Wilkie, Andrew O. M.; Jabs, Ethylin Wang

    2000-01-01

    Crouzon syndrome and Pfeiffer syndrome are both autosomal dominant craniosynostotic disorders that can be caused by mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. To determine the parental origin of these FGFR2 mutations, the amplification refractory mutation system (ARMS) was used. ARMS PCR primers were developed to recognize polymorphisms that could distinguish maternal and paternal alleles. A total of 4,374 bases between introns IIIa and 11 of the FGFR2 gene were sequenced and were assayed by heteroduplex analysis, to identify polymorphisms. Two polymorphisms (1333TA/TATA and 2710 C/T) were found and were used with two previously described polymorphisms, to screen a total of 41 families. Twenty-two of these families were shown to be informative (11 for Crouzon syndrome and 11 for Pfeiffer syndrome). Eleven different mutations in the 22 families were detected by either restriction digest or allele-specific oligonucleotide hybridization of ARMS PCR products. We molecularly proved the origin of these different mutations to be paternal for all informative cases analyzed (P=2.410-7; 95% confidence limits 87%100%). Advanced paternal age was noted for the fathers of patients with Crouzon syndrome or Pfeiffer syndrome, compared with the fathers of control individuals (34.507.65 years vs. 30.451.28 years, P<.01). Our data on advanced paternal age corroborates and extends previous clinical evidence based on statistical analyses as well as additional reports of advanced paternal age associated with paternal origin of three sporadic mutations causing Apert syndrome (FGFR2) and achondroplasia (FGFR3). Our results suggest that older men either have accumulated or are more susceptible to a variety of germline mutations. PMID:10712195

  10. Paternal genetic history of the Basque population of Spain.

    PubMed

    Young, Kristin L; Sun, Guangyun; Deka, Ranjan; Crawford, Michael H

    2011-08-01

    This study examines the genetic variation in Basque Y chromosome lineages using data on 12 Y-short tandem repeat (STR) loci in a sample of 158 males from four Basque provinces of Spain (Alava, Vizcaya, Guipuzcoa, and Navarre). As reported in previous studies, the Basques are characterized by high frequencies of haplogroup R1b (83%). AMOVA analysis demonstrates genetic homogeneity, with a small but significant amount of genetic structure between provinces (Y-short tandem repeat loci STRs: 1.71%, p = 0.0369). Gene and haplotype diversity levels in the Basque population are on the low end of the European distribution (gene diversity: 0.4268; haplotype diversity: 0.9421). Post-Neolithic contribution to the paternal Basque gene pool was estimated by measuring the proportion of those haplogroups with a Time to Most Recent Common Ancestor (TMRCA) previously dated either prior (R1b, I2a2) or subsequent to (E1b1b, G2a, J2a) the Neolithic. Based on these estimates, the Basque provinces show varying degrees of post-Neolithic contribution in the paternal lineages (10.9% in the combined sample). PMID:21846204

  11. A MOLECULAR EXAMINATION OF RELATEDNESS, MULTIPLE PATERNITY, AND COHABITATION OF THE SOUTHERN PLAINS WOODRAT (NEOTOMA MICROPUS)

    PubMed Central

    Baxter, B. Dnate’; Mendez-Harclerode, Francisca M.; Fulhorst, Charles F.; Bradley, Robert D.

    2009-01-01

    Two hundred twenty-two individuals of the southern plains woodrat (Neotoma micropus) were captured from 198 excavated middens at 10 discrete collecting sites from a single population in south-central Texas. Field data, mitochondrial D-loop haplotypes, and polymorphic microsatellite loci (5–7) were used to determine genetic patterns in parentage, relatedness, and mating strategy. Microsatellite loci were highly polymorphic (average observed heterozygosity = 0.859) and were used to construct genotypes that were unique for each individual (probability of identical genotypes: 1 in 2,104,567). Results indicated a high frequency of multiple paternity (6 of 9 litters), evidence of repeat mating between the same 2 individuals, and no indication of male dominance at any collection site. Examination of these data suggested a promiscuous mating system. Within a site, average relatedness between adult females was similar to that between adult males. A higher level of cohabitation from that previously documented was recorded and finer-scale analyses revealed high levels of relatedness between most cohabiting individuals. Taken with results from other studies of mating behaviors of N. micropus, our results suggest that mating and social behavior of this species are likely influenced by population density. PMID:20011670

  12. Advanced paternal age increases the risk of schizophrenia and obsessivecompulsive disorder in a Chinese Han population

    PubMed Central

    Wu, Yuejing; Liu, Xiang; Luo, Hongrong; Deng, Wei; Zhao, Gaofeng; Wang, Qiang; Zhang, Lan; Ma, Xiaohong; Liu, Xiehe; Murray, Robin A.; Collier, David A.; Li, Tao

    2012-01-01

    Using the Structured Clinical Interview for DSM-IV, patient and non-patient version (SCID-P/NP), this study investigated 351 patients with schizophrenia, 122 with obsessivecompulsive disorder (OCD), and 238 unrelated healthy volunteers in a Chinese Han population. The relative risks posed by advanced paternal age for schizophrenia and OCD in offspring were computed under logistic regression analyses and adjusted for the participant's sex, age and co-parent age at birth. Compared to the offspring with paternal age of 2529years old, the relative risks rose from 2.660 to 10.183 in the paternal age range of 3034 and ?35. The relative risks for OCD increased from 2.225 to 5.413 in 3034 and ?35. For offspring with paternal age of <25, the odds ratios of developing schizophrenia and OCD were 0.628 and 0.289 respectively, whereas an association between increased maternal age and risk for schizophrenia/OCD was not seen. Interaction analysis showed an interaction effect between paternal age and maternal age at birth. Such a tendency of risk affected by parental age for schizophrenia and OCD existed after splitting out the data of early onset patients. Sex-specific analyses found that the relative risks for schizophrenia with paternal age of 3034 and ?35 in male offspring were 2.407 and 10.893, and in female offspring were 3.080 and 9.659. The relative risks for OCD with paternal age of 3034 and ?35 in male offspring were 3.493 and 7.373, and in female offspring 2.005 and 4.404. The mean paternal age of schizophrenia/OCD patients born before the early 1980s was much greater than that of patients who were born after then. The findings illustrated that advanced paternal age is associated with increased risk for both schizophrenia and OCD in a Chinese Han population, prominently when paternal age is over 35. Biological and non-biological mechanisms may both be involved in the effects of advanced paternal age on schizophrenia and OCD. PMID:22424906

  13. Development and characterization of microsatellite markers from tropical forage Stylosanthes species and analysis of genetic variability and cross-species transferability.

    PubMed

    Chandra, Amaresh; Tiwari, K K; Nagaich, D; Dubey, N; Kumar, S; Roy, A K

    2011-12-01

    A limited number of functional molecular markers has slowed the desired genetic improvement of Stylosanthes species. Hence, in an attempt to develop simple sequence repeat (SSR) markers, genomic libraries from Stylosanthes seabrana B.L. Maass & 't Mannetje (2n=2x=20) using 5' anchored degenerate microsatellite primers were constructed. Of the 76 new microsatellites, 21 functional primer pairs were designed. Because of the small number of primer pairs designed, 428 expressed sequence tag (EST) sequences from seven Stylosanthes species were also examined for SSR detection. Approximately 10% of sequences delivered functional primer pairs, and after redundancy elimination, 57 microsatellite repeats were selected. Tetranucleotides followed by trinucleotides were the major repeated sequences in Stylosanthes ESTs. In total, a robust set of 21 genomic-SSR (gSSR) and 20 EST-SSR (eSSR) markers were developed. These markers were analyzed for intraspecific diversity within 20 S. seabrana accessions and for their cross-species transferability. Mean expected (He) and observed (Ho) heterozygosity values with gSSR markers were 0.64 and 0.372, respectively, whereas with eSSR markers these were 0.297 and 0.214, respectively. Dendrograms having moderate bootstrap value (23%-94%) were able to distinguish all accessions of S. seabrana with gSSR markers, whereas eSSR markers showed 100% similarities between few accessions. The set of 21 gSSRs, from S. seabrana, and 20 eSSRs, from selected Stylosanthes species, with their high cross-species transferability (45% with gSSRs, 86% with eSSRs) will facilitate genetic improvement of Stylosanthes species globally. PMID:22088085

  14. Addressing policy barriers to paternal involvement during pregnancy.

    PubMed

    Alio, Amina P; Bond, M Jermane; Padilla, Yolanda C; Heidelbaugh, Joel J; Lu, Michael; Parker, Willie J

    2011-05-01

    Efforts to reduce infant mortality in the United States have failed to incorporate paternal involvement. Research suggests that paternal involvement, which has been recognized as contributing to child development and health for many decades, is likely to affect infant mortality through the mother's well-being, primarily her access to resources and support. In spite of that, systemic barriers facing the father and the influence on his involvement in the pregnancy have received little attention. The Commission on Paternal Involvement in Pregnancy Outcomes (CPIPO) has identified the most important social barriers to paternal involvement during pregnancy and outlined a set of key policy priorities aimed at fostering paternal involvement. This article summarizes the key recommendations, including equitable paternity leave, elimination of marriage as a tax and public assistance penalty, integration of fatherhood initiatives in MCH programs, support of low-income fathers through employment training, father inclusion in family planning services, and expansion of birth data collection to include father information. PMID:21472512

  15. Detecting Sex-Biased Gene Flow in African-Americans through the Analysis of Intra- and Inter-Population Variation at Mitochondrial DNA and Y- Chromosome Microsatellites

    PubMed Central

    Battaggia, C; Anagnostou, P; Bosch, I; Brisighelli, F; Destro-Bisol, G; Capocasa, M

    2012-01-01

    This study reports on variations at the mitochondrial DNA (mtDNA) hypervariable region 1 (HVR-1) and at seven Y-chromosome microsatellites in an African-American population sample from Chicago, IL, USA. Our results support the hypothesis that the population studied had undergone a European male-biased gene flow. We show that comparisons of intra-and inter-population diversity parameters between African-Americans, Europeans and Africans may help detect sex-biased gene flow, providing a complement to quantitative methods to estimate genetic admixture. PMID:24052726

  16. Effect of Paternal Age on Reproductive Outcomes of Intracytoplasmic Sperm Injection

    PubMed Central

    Zheng, Haiyan; Liu, Haiying; Huang, Qing; Liu, Jianqiao

    2016-01-01

    The impact of paternal age on reproduction, especially using assisted reproductive technologies, has not been well studied to date. To investigate the effect of paternal age on reproductive outcomes, here we performed a retrospective analysis of 2,627 intracytoplasmic sperm injection (ICSI) cycles performed at the Reproductive Medicine Center of the Third Affiliated Hospital of Guangzhou Medical University (China) between January 2007 and May 2015. Effect of paternal age on embryo quality [number of fertilized oocytes, 2 pronucleus zygotes (2PNs), viable embryos, and high-quality embryos] was analyzed by multiple linear regression. Relationships between paternal age and pregnancy outcomes were analyzed by binary logistic regression. After adjusting for female age, no association between paternal age and the following parameters of embryo quality was observed: number of fertilized oocytes (B = -0.032; 95% CI -0.069–0.005; P = 0.088), number of 2PNs (B = -0.005; 95% CI -0.044–0.034; P = 0.806), and number of viable embryos (B = -0.025; 95% CI -0.052–0.001; P = 0.062). However, paternal age negatively influenced the number of high-quality embryos (B = -0.020; 95% CI -0.040–0.000; P = 0.045). Moreover, paternal age had no effect on pregnancy outcomes (OR for a 5-year interval), including the rates of clinical pregnancy (OR 0.919; 95% CI 0.839–1.006; P = 0.067), ongoing pregnancy (OR 0.914; 95% CI 0.833–1.003; P = 0.058), early pregnancy loss (OR 1.019; 95% CI 0.823–1.263; P = 0.861), live births (OR 0.916; 95% CI 0.833–1.007; P = 0.070), and preterm births (OR 1.061; 95% CI 0.898–1.254; P = 0.485). Therefore, increased paternal age negatively influences the number of high-quality embryos, but has no effect on pregnancy outcomes in couples undergoing ICSI cycles. However, more studies including men aged over 60 years with a longer-term follow-up are needed. PMID:26901529

  17. Reporting for duty: the paternal function and clinical formulations.

    PubMed

    Davies, Nick

    2015-02-01

    The author highlights some developments in the theory of the preoedipal paternal function and paternal functionary and incorporates these ideas in developing clinical formulations for four clinical cases that privilege the preoedipal paternal function. In particular, four aspects of the preoedipal paternal function are identified, and for each a clinical case is discussed. Emphasis is placed on the necessity of widening clinical formulations to ensure clinicians have the widest possible set of clinical ideas and hence interventions and techniques at their fingertips. PMID:25688683

  18. Mosaicism for genome-wide paternal uniparental disomy with features of multiple imprinting disorders: diagnostic and management issues.

    PubMed

    Inbar-Feigenberg, Michal; Choufani, Sanaa; Cytrynbaum, Cheryl; Chen, Yi-An; Steele, Leslie; Shuman, Cheryl; Ray, Peter N; Weksberg, Rosanna

    2013-01-01

    Mosaicism for genome-wide paternal uniparental disomy (UPD) has been reported in only seven live born individuals to date. Clinical presentation includes manifestations of multiple paternal UPD syndromes with high variability, likely due to the variable levels of mosaicism in different somatic tissues. We report an eighth case in a female patient with mosaicism for genome-wide paternal UPD which highlights the complex clinical presentation. Our patient had features of Beckwith-Wiedemann syndrome (BWS), Angelman syndrome, and congenital hyperinsulinism. The clinical findings included prematurity, organomegaly, hemihyperplasia, developmental delay, benign tumors, and cystic lesions. The diagnosis in our patient was established utilizing microarray-based genome-wide DNA methylation analysis performed on leukocyte DNA. Targeted multiplex ligation-dependent probe amplification (MLPA) analysis of chromosome regions 11p15 and 15q13 confirmed mosaicism for paternal UPD at these genomic regions. This case represents the first report of microarray-based genome-wide DNA methylation analysis in the diagnosis of genome-wide paternal UPD. The application of microarray-based genome-wide DNA methylation analysis on selected individuals with complex clinical presentations could be a valuable diagnostic tool to improve the detection rate of mosaic genome-wide paternal UPD. This approach, which screens many loci simultaneously, is more cost-effective and less labor-intensive than performing multiple targeted DNA methylation-based assays. Identification of individuals with mosaicism for genome-wide paternal UPD is an important goal as it confers a low recurrence risk for the family and identifies individuals who require surveillance due to increased tumor risk. PMID:23239666

  19. Paternal dietary folate, B6 and B12 intake, and the risk of childhood brain tumors.

    PubMed

    Greenop, Kathryn R; Miller, Margaret; Bailey, Helen D; Scott, Rodney J; Attia, John; Bower, Carol; van Bockxmeer, Frank M; Ashton, Lesley J; Armstrong, Bruce K; Milne, Elizabeth

    2015-01-01

    It is biologically plausible that a paternal preconception diet low in nutrients related to DNA integrity could affect sperm DNA and subsequently risk of cancer in the offspring. The aim of this analysis was to investigate whether paternal preconception dietary folate, B6, or B12 intake was associated with the risk of childhood brain tumors (CBT) in an Australian case-control study. Cases <15 years of age were recruited from 10 Australian pediatric oncology centers between 2005 and 2010, and controls from random-digit dialing, frequency-matched to cases on age, sex, and state of residence. Paternal dietary information was obtained by food-frequency questionnaires. Nutrient values were energy adjusted and divided into tertiles for analysis by unconditional logistic regression. In fathers with relevant data (237 cases and 629 controls), no association with dietary folate and B6 and risk of CBT was seen; high B12 intake was associated with an increased risk of CBT (odds ratio highest vs. lowest tertile: 1.74, 95% confidence interval: 1.14, 2.66) without an increasing trend. These results do not support the hypothesis that paternal dietary folate intake influences the risk of CBT. The increased OR observed between dietary B12 intake and risk of CBT is without any certain explanation. PMID:25625505

  20. Heterozygosity increases microsatellite mutation rate.

    PubMed

    Amos, William

    2016-01-01

    Whole genome sequencing of families of Arabidopsis has recently lent strong support to the heterozygote instability (HI) hypothesis that heterozygosity locally increases mutation rate. However, there is an important theoretical difference between the impact on base substitutions, where mutation rate increases in regions surrounding a heterozygous site, and the impact of HI on sequences such as microsatellites, where mutations are likely to occur at the heterozygous site itself. At microsatellite loci, HI should create a positive feedback loop, with heterozygosity and mutation rate mutually increasing each other. Direct support for HI acting on microsatellites is limited and contradictory. I therefore analysed AC microsatellites in 1163 genome sequences from the 1000 genomes project. I used the presence of rare alleles, which are likely to be very recent in origin, as a surrogate measure of mutation rate. I show that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles. PMID:26740567

  1. Blueberry Microsatellite Markers Identify Cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six blueberry simple sequence repeat (SSR) markers or microsatellites were tested for the ability to amplify a polymorphic marker in eight American cranberry accessions. Sixteen SSRs resulted in informative and polymorphic SSR primer pairs and were used to fingerprint 16 economically important...

  2. Microsatellite instability in colorectal cancer

    PubMed Central

    Horvat, Matej; Stabuc, Borut

    2011-01-01

    Background Colorectal cancer (CRC) is the third most common cancer in the world. In 75% CRC develops sporadically, in 25% hereditary or as a consequence of inflammatory bowel disease. CRC carcinogenesis develops over many years. The cause of CRC in 85% is chromosomal instability (CIN) and in 15% microsatellite instability (MSI-H), where hereditary nonpolyposis colorectal cancer (HNPCC) represents 1020%. Microsatellite sequences (MS) are repeated sequences of short stretches of DNA all over the genome. Microsatellite stability (MSS) means MS are the same in each cell of an individual, whereas microsatellite instability (MSI-H) means MS differ in normal and cancer cells of an individual. The cause of MSI-H is a damaged mismatch repair mechanism (MMR), with the most important MMR proteins being MSH2, MLH1 and MSH6. Conclusions MSI-H seems to be an important prognostic factor in CRC and an important predictive factor of CRC chemotherapeutic treatment efficacy. Clinical trials conducted until now have shown contradictory findings in different chemotherapeutic settings, adjuvant and palliative; therefore MSI-H is going to be the object of the future research. The future of cancer treatment is in the individualized therapy based on molecular characteristics of the tumour, such as MSI-H in CRC. PMID:22933939

  3. Microsatellites from Conyza canadensis (horseweed)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite loci were identified from Conyza canadensis (horseweed). Primer pairs for 64 loci were developed and of these eight were optimized and screened using genomic DNA from 22 accessions of horseweed from North America. Most loci were polymorphic and the number of alleles per locus ranged ...

  4. Microsatellite instability in adenocarcinoma of the prostrate

    SciTech Connect

    Terrell, R.B.; Willie, A.H.; Cheville, J.C.

    1994-09-01

    Instability of tandem repeat sequences (microsatellites) has been reported to play a major etiologic role in familial colon cancer, as well as a potential role in the carcinogenesis of other sporadic neoplasms. These replication errors are the result of faulty DNA excision/repair function controlled at the gene level. In order to examine this phenomenon in prostate cancer, we screened 40 tumors with di-, tri- and tetranucleotide markers spanning eleven chromosomal loci. Microsatellite instability was observed overall in 3 of the 40 cases (7.5%). All changes were identified solely in tetranucleotide sequences (3 of 11 total markers analyzed). One tumor demonstrated repeat length expansions at two loci, while the other tumors did so at a single locus. Both Type 1 (>4 base pairs) and Type II (4 base pairs) mutations were identified. One of these cases also included metastatic nodal disease. Analysis of the metastatic tumor tissue revealed allelic patterns identical to the normal tissue control. A secondary screening of the mutated tumors demonstrated no repeat length alterations in 16 additional markers. A CAG repeat in the androgen receptor (AR) gene was also studied and demonstrated that 3 of 40 (7.5%) tumors contained mutations within this repeat. We concluded that microsatellite instability is uncommon in prostate adenocarcinoma appearing to occur more often in tetranucleotide repeat sequences and in an AR gene repeat. Additionally, these findings suggest that dysfunctional DNA excision/repair mechanisms, as evidenced by the low frequency of replication errors, are unlikely to play a major role in the natural history of prostate cancer.

  5. Genetic structure of brown trout (Salmo trutta) populations from Turkey based on microsatellite data.

    PubMed

    Arslan, Serdal; Bardakci, Fevzi

    2010-12-01

    This present study investigated micro- and macro-geographic microsatellite DNA variations using five polymorphic microsatellite loci from 27 brown trout populations in Turkey. Average number of alleles and average observed heterozygosity were 7.4 and 0.254, respectively. Even populations from the same sea basin and river system (the so called micro-geographic regions) had unique alleles. Genetic variation among the populations from macro-geographic regions (different sea basins and river systems) was 45.78%. The mtDNA lineages of brown trout that have previously been identified by mtDNA analyses were supported by the analysis of the microsatellite DNA data in general. The atak population, which belongs to the Tigris lineage, was clustered together with the Euphrates populations within the Adriatic mtDNA lineage, based on microsatellite data. Both mitochondrial and microsatellite DNA analyses have made it possible to determine a secondary contact between Adriatic and Tigris lineages. PMID:20963631

  6. Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo

    PubMed Central

    Wu, Chieh-Hsi; Drummond, Alexei J.

    2011-01-01

    We provide a framework for Bayesian coalescent inference from microsatellite data that enables inference of population history parameters averaged over microsatellite mutation models. To achieve this we first implemented a rich family of microsatellite mutation models and related components in the software package BEAST. BEAST is a powerful tool that performs Bayesian MCMC analysis on molecular data to make coalescent and evolutionary inferences. Our implementation permits the application of existing nonparametric methods to microsatellite data. The implemented microsatellite models are based on the replication slippage mechanism and focus on three properties of microsatellite mutation: length dependency of mutation rate, mutational bias toward expansion or contraction, and number of repeat units changed in a single mutation event. We develop a new model that facilitates microsatellite model averaging and Bayesian model selection by transdimensional MCMC. With Bayesian model averaging, the posterior distributions of population history parameters are integrated across a set of microsatellite models and thus account for model uncertainty. Simulated data are used to evaluate our method in terms of accuracy and precision of ? estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example. PMID:21385725

  7. Transferability of Rubus Microsatellite Markers for use in Black Raspberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites or simple sequence repeats (SSRs) are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. To date, SSR marker development in Rubus has focused on red raspberry (Rubus idaeus L., subgenu...

  8. Moral Status and the Wrongness of Paternalism

    PubMed Central

    Birks, David

    2014-01-01

    In this paper, I consider the view that paternalism is wrong when it demeans or diminishes the paternalizees moral status (the Moral Status Argument). I argue that we should reject the Moral Status Argument because it is both too narrow and too broad. It is too narrow because it cannot account for the wrongness of some of the most objectionable paternalistic interventions, namely strong paternalistic interventions. It is too broad because it is unable to distinguish between wrongful paternalistic acts that are plausibly considered more wrong than other wrongful paternalistic acts. PMID:25075133

  9. Targeted development of informative microsatellite (SSR) markers

    PubMed Central

    Hayden, M. J.; Sharp, P. J.

    2001-01-01

    We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat. PMID:11292858

  10. An Epigenetic Role for Disrupted Paternal Gene Expression in Postzygotic Seed Abortion in Arabidopsis Interspecific Hybrids.

    PubMed

    Kirkbride, Ryan C; Yu, Helen Hong; Nah, Gyoungju; Zhang, Changqing; Shi, Xiaoli; Chen, Z Jeffrey

    2015-12-01

    Interspecific hybrids often increase the levels of heterozygosity and hybrid vigor, but some interspecific hybrid seeds are aborted shortly after fertilization. The mechanism behind this postzygotic seed abortion is poorly understood. Here, we report genome-wide analysis of allelic expression changes in developing siliques and seeds in three F1 interspecific crosses between Arabidopsis thaliana (Col, Ler, or C24) and Arabidopsis arenosa. The majority of maternally expressed genes (MEGs) were shared among all three F1 interspecific crosses, whereas ?90% of 272 paternally expressed genes (PEGs) were found only in one or two F1 crosses, suggesting a role for disrupted paternal gene expression in seed abortion that varies in different crosses. Consistent with this notion, 12 PEGs in the infertile interspecific hybrids matched MEGs in fertile intraspecific hybrids. This disruption of PEGs in the interspecific hybrids was consistent with the upregulation of the genes in the paternal-excess interploidy cross (2X6) between a diploid mother and a hexaploid father, leading to the seed abortion. Moreover, a subset of PEGs in the interspecific crosses were also upregulated in the intraspecific hybrid met1XWT or meaXWT, in which the mutant of MET1 (DNA METHYLTRANSFERASE1) or MEDEA, a Polycomb Repressive Complex2gene, was used as the maternal parent. These data suggest that maternal epigenetic factors and paternal gene expression play important roles in the postzygotic seed abortion in interspecific hybrids or neo-allopolyploids. PMID:26409189

  11. Paternal phylogeography and genetic diversity of East Asian goats.

    PubMed

    Waki, A; Sasazaki, S; Kobayashi, E; Mannen, H

    2015-06-01

    This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3'-untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South-East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats. PMID:25917305

  12. Fathers and Families: Paternal Factors in Child Development.

    ERIC Educational Resources Information Center

    Biller, Henry B.

    Examining the implications of research findings concerning the impact of paternal involvement in child development, this book elaborates on how variations in paternal involvement affect many different dimensions of child and parent development. The 12 chapters discuss the role of fathers in regard to: (1) the advantages of two-parent families; (2)

  13. Postdivorce Paternal Disengagement: Failed Mourning and Role Fusion

    ERIC Educational Resources Information Center

    Baum, Nehami

    2006-01-01

    In this article, I suggest that postdivorce paternal disengagement may be rooted in the father's tendency to link his children and ex-wife as a single entity in consequence of his failure to adequately mourn the loss of his ex-wife and to redefine his paternal role and identity in distinction from his spousal role and identity. I also suggest that

  14. First Things First: Paternity and Child Support for Nonmarital Children.

    ERIC Educational Resources Information Center

    Slayton, Ann

    1993-01-01

    Establishing a child's legal paternity is the first step to gaining specific rights and benefits which can be critical to a child's well-being, such as emotional and financial security. Discusses specific procedures that Washington, Virginia, and other states have enacted to more easily establish paternity. (MDM)

  15. Parental Psychopathology and Paternal Child Neglect in Late Childhood

    ERIC Educational Resources Information Center

    Stewart, Chris; Mezzich, Ada C.; Day, Bang-Shiuh

    2006-01-01

    We aimed at determining the association of both severity of paternal and maternal substance use disorder (SUD) and psychiatric disorders with paternal child neglect severity during late childhood. The sample comprised 146 intact SUD (n=71) and non SUD (n=75) families with a 10-12 year old female or male biological offspring. The average age of

  16. Female reproductive synchrony predicts skewed paternity across primates

    PubMed Central

    Nunn, Charles L.; Schlke, Oliver

    2008-01-01

    Recent studies have uncovered remarkable variation in paternity within primate groups. To date, however, we lack a general understanding of the factors that drive variation in paternity skew among primate groups and across species. Our study focused on hypotheses from reproductive skew theory involving limited control and the use of paternity concessions by investigating how paternity covaries with the number of males, female estrous synchrony, and rates of extragroup paternity. In multivariate and phylogenetically controlled analyses of data from 27 studies on 19 species, we found strong support for a limited control skew model, with reproductive skew within groups declining as female reproductive synchrony and the number of males per group increase. Of these 2 variables, female reproductive synchrony explained more of the variation in paternity distributions. To test whether dominant males provide incentives to subordinates to resist matings by extragroup males, that is, whether dominants make concessions of paternity, we derived a novel prediction that skew is lower within groups when threat from outside the group exists. This prediction was not supported as a primary factor underlying patterns of reproductive skew among primate species. However, our approach revealed that if concessions occur in primates, they are most likely when female synchrony is low, as these conditions provide alpha male control of paternity that is assumed by concessions models. Collectively, our analyses demonstrate that aspects of male reproductive competition are the primary drivers of reproductive skew in primates. PMID:19018288

  17. Low frequency paternal transmission of plastid genes in Brassicaceae.

    PubMed

    Schneider, Anja; Stelljes, Christian; Adams, Caroline; Kirchner, Stefan; Burkhard, Gabi; Jarzombski, Sabine; Broer, Inge; Horn, Patricia; Elsayed, Ashraf; Hagl, Peter; Leister, Dario; Koop, Hans-Ulrich

    2015-04-01

    Plastid-encoded genes are maternally inherited in most plant species. Transgenes located on the plastid genome are thus within a natural confinement system, preventing their distribution via pollen. However, a low-frequency leakage of plastids via pollen seems to be universal in plants. Here we report that a very low-level paternal inheritance in Arabidopsis thaliana occurs under field conditions. As pollen donor an Arabidopsis accession (Ler-Ely) was used, which carried a plastid-localized atrazine resistance due to a point mutation in the psbA gene. The frequency of pollen transmission into F1 plants, based on their ability to express the atrazine resistance was 1.9 10(-5). We extended our analysis to another cruciferous species, the world-wide cultivated crop Brassica napus. First, we isolated a fertile and stable plastid transformant (T36) in a commercial cultivar of B. napus (cv Drakkar). In T36 the aadA and the bar genes were integrated in the inverted repeat region of the B. napus plastid DNA following particle bombardment of hypocotyl segments. Southern blot analysis confirmed transgene integration and homoplasmy of plastid DNA. Line T36 expressed Basta resistance from the inserted bar gene and this trait was used to estimate the frequency of pollen transmission into F1 plants. A frequency of <2.6 10(-5) was determined in the greenhouse. Taken together, our data show a very low rate of paternal plastid transmission in Brassicacea. Moreover, the establishment of plastid transformation in B. napus facilitates a safe use of this important crop plant for plant biotechnology. PMID:25343875

  18. Relationships of maternal and paternal anthropometry with neonatal body size, proportions and adiposity in an Australian cohort

    PubMed Central

    Pomeroy, Emma; Wells, Jonathan CK; Cole, Tim J; O'Callaghan, Michael; Stock, Jay T

    2015-01-01

    The patterns of association between maternal or paternal and neonatal phenotype may offer insight into how neonatal characteristics are shaped by evolutionary processes, such as conflicting parental interests in fetal investment and obstetric constraints. Paternal interests are theoretically served by maximizing fetal growth, and maternal interests by managing investment in current and future offspring, but whether paternal and maternal influences act on different components of overall size is unknown. We tested whether parents' prepregnancy height and body mass index (BMI) were related to neonatal anthropometry (birthweight, head circumference, absolute and proportional limb segment and trunk lengths, subcutaneous fat) among 1,041 Australian neonates using stepwise linear regression. Maternal and paternal height and maternal BMI were associated with birthweight. Paternal height related to offspring forearm and lower leg lengths, maternal height and BMI to neonatal head circumference, and maternal BMI to offspring adiposity. Principal components analysis identified three components of variability reflecting neonatal “head and trunk skeletal size,” “adiposity,” and “limb lengths.” Regression analyses of the component scores supported the associations of head and trunk size or adiposity with maternal anthropometry, and limb lengths with paternal anthropometry. Our results suggest that while neonatal fatness reflects environmental conditions (maternal physiology), head circumference and limb and trunk lengths show differing associations with parental anthropometry. These patterns may reflect genetics, parental imprinting and environmental influences in a manner consistent with parental conflicts of interest. Paternal height may relate to neonatal limb length as a means of increasing fetal growth without exacerbating the risk of obstetric complications. Am J Phys Anthropol 156:625–636, 2015. PMID:25502164

  19. A novel microsatellite control system

    SciTech Connect

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1998-02-01

    The authors are researching extremely simple yet quite capable analog pulse-coded neural networks for ``smaller-faster-cheaper`` spacecraft attitude and control systems. The will demonstrate a prototype microsatellite that uses their novel control method to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source. Though still in design infancy, the ``Nervous Net`` controllers described could allow for space missions not currently possible given conventional satellite hardware. Result, prospects and details are presented.

  20. Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites.

    PubMed

    Sudheer, Pamidimarri D V N; Rahman, Hifzur; Mastan, Shaik G; Reddy, Muppala P

    2010-12-01

    Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J. curcas as potential crop with superior agronomical traits. PMID:20221701

  1. Human paternal lineages, languages, and environment in the Caucasus.

    PubMed

    Tarkhnishvili, David; Gavashelishvili, Alexander; Murtskhvaladze, Marine; Gabelaia, Mariam; Tevzadze, Gigi

    2014-01-01

    Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible. PMID:25397702

  2. The impact of paternity on male-infant association in a primate with low paternity certainty

    PubMed Central

    Langos, Doreen; Kulik, Lars; Mundry, Roger; Widdig, Anja

    2013-01-01

    In multi-male groups where females mate promiscuously, male-infant associations have rarely been studied. However, recent studies have shown that males selectively support their offspring during agonistic conflicts with other juveniles and that father’s presence accelerates offspring maturation. Furthermore, it was shown that males invest in unrelated infants to enhance future mating success with the infant’s mother. Hence, infant care might provide fitness gain for males. Here we investigate male-infant associations in rhesus macaques (Macaca mulatta), a primate with low paternity certainty as females mate with multiple partners and males ensure paternity less efficiently through mate-guarding. We combined behavioral data with genetic paternity analyses of one cohort of the semifree-ranging population of Cayo Santiago (Puerto Rico) and recorded affiliative and aggressive interactions between focal subjects and adult males from birth to sexual maturation (0–4 years) of focal subjects. Our results revealed, that 9.6% of all interactions of focal subjects involved an adult male and 94% of all male-infant interactions were affiliative, indicating the rareness of male-infant aggression. Second and most interestingly, sires were more likely to affiliate with their offspring than non-sires with unrelated infants. This preference was independent of mother’s proximity and emphasized during early infancy. Male-infant affiliation rose with infant age and was pronounced between adult males and male rather than female focal subjects. Overall our results suggest that male-infant affiliation are also an important component in structuring primate societies and affiliation directed towards own offspring presumably represent low cost paternal care. PMID:23682587

  3. Paternal smoking and birthweight in Shanghai.

    PubMed Central

    Zhang, J; Ratcliffe, J M

    1993-01-01

    OBJECTIVES. Although maternal active smoking has been established to be associated with fetal growth retardation, evidence of an effect of environmental tobacco smoke exposure on birthweight is still limited and inconclusive. This study addressed the relationship between prenatal environmental tobacco smoke exposure and birthweight and fetal growth retardation in Shanghai, China. METHODS. Data on 1785 full-term live-born normal infants of nonsmoking mothers were used from the Shanghai Birth Defects and Perinatal Death Monitoring conducted between October 1986 and September 1987. Environmental tobacco smoke exposure was defined as exposure to paternal smoking. RESULTS. Infants with environmental tobacco smoking exposure were, on average, 30 g lower in birthweight than nonexposed infants, after adjustment for gestational age, parity, maternal age, and occupation. CONCLUSION. Consistent with previous research, this study suggests that environmental tobacco smoking exposure may have a modestly adverse effect on birthweight. PMID:8427324

  4. Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review.

    PubMed

    Kurz, Carolin; Hakimi, Maani; Kloor, Matthias; Grond-Ginsbach, Caspar; Gross-Weissmann, Marie-Luise; Bckler, Dittmar; von Knebel Doeberitz, Magnus; Dihlmann, Susanne

    2015-01-01

    Somatic DNA alterations are known to occur in atherosclerotic carotid artery lesions; however, their significance is unknown. The accumulation of microsatellite mutations in coding DNA regions may reflect a deficiency of the DNA mismatch repair (MMR) system. Alternatively, accumulation of these coding microsatellite mutations may indicate that they contribute to the pathology. To discriminate between these two possibilities, we compared the mutation frequencies in coding microsatellites (likely functionally relevant) with those in noncoding microsatellites (likely neutral). Genomic DNA was isolated from carotid endarterectomy (CEA) specimens of 26 patients undergoing carotid surgery and from 15 nonatherosclerotic control arteries. Samples were analyzed by DNA fragment analysis for instability at three noncoding (BAT25, BAT26, CAT25) and five coding (AIM2, ACVR2, BAX, CASP5, TGFBR2) microsatellite loci, with proven validity for detection of microsatellite instability in neoplasms. We found an increased frequency of coding microsatellite mutations in CEA specimens compared with control specimens (34.6 versus 0%; p = 0.0013). Five CEA specimens exhibited more than one frameshift mutation, and ACVR2 and CASP5 were affected most frequently (5/26 and 6/26). Moreover, the rate of coding microsatellite alterations (15/130) differed significantly from that of noncoding alterations (0/78) in CEA specimens (p = 0.0013). In control arteries, no microsatellite alterations were observed, neither in coding nor in noncoding microsatellite loci. In conclusion, the specific accumulation of coding mutations suggests that these mutations play a role in the pathogenesis of atherosclerotic carotid lesions, since the absence of mutations in noncoding microsatellites argues against general microsatellite instability, reflecting MMR deficiency. PMID:26070012

  5. Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review

    PubMed Central

    Kurz, Carolin; Hakimi, Maani; Kloor, Matthias; Grond-Ginsbach, Caspar; Gross-Weissmann, Marie-Luise; Bckler, Dittmar; von Knebel Doeberitz, Magnus; Dihlmann, Susanne

    2015-01-01

    Somatic DNA alterations are known to occur in atherosclerotic carotid artery lesions; however, their significance is unknown. The accumulation of microsatellite mutations in coding DNA regions may reflect a deficiency of the DNA mismatch repair (MMR) system. Alternatively, accumulation of these coding microsatellite mutations may indicate that they contribute to the pathology. To discriminate between these two possibilities, we compared the mutation frequencies in coding microsatellites (likely functionally relevant) with those in noncoding microsatellites (likely neutral). Genomic DNA was isolated from carotid endarterectomy (CEA) specimens of 26 patients undergoing carotid surgery and from 15 nonatherosclerotic control arteries. Samples were analyzed by DNA fragment analysis for instability at three noncoding (BAT25, BAT26, CAT25) and five coding (AIM2, ACVR2, BAX, CASP5, TGFBR2) microsatellite loci, with proven validity for detection of microsatellite instability in neoplasms. We found an increased frequency of coding microsatellite mutations in CEA specimens compared with control specimens (34.6 versus 0%; p = 0.0013). Five CEA specimens exhibited more than one frameshift mutation, and ACVR2 and CASP5 were affected most frequently (5/26 and 6/26). Moreover, the rate of coding microsatellite alterations (15/130) differed significantly from that of noncoding alterations (0/78) in CEA specimens (p = 0.0013). In control arteries, no microsatellite alterations were observed, neither in coding nor in noncoding microsatellite loci. In conclusion, the specific accumulation of coding mutations suggests that these mutations play a role in the pathogenesis of atherosclerotic carotid lesions, since the absence of mutations in noncoding microsatellites argues against general microsatellite instability, reflecting MMR deficiency. PMID:26070012

  6. Male age mediates reproductive investment and response to paternity assurance

    PubMed Central

    Benowitz, Kyle M.; Head, Megan L.; Williams, Camellia A.; Moore, Allen J.; Royle, Nick J.

    2013-01-01

    Theory predicts that male response to reduced paternity will depend on male state and interactions between the sexes. If there is little chance of reproducing again, then males should invest heavily in current offspring, regardless of their share in paternity. We tested this by manipulating male age and paternity assurance in the burying beetle Nicrophorus vespilloides. We found older males invested more in both mating effort and parental effort than younger males. Furthermore, male age, a component of male state, mediated male response to perceived paternity. Older males provided more prenatal care, whereas younger males provided less prenatal care, when perceived paternity was low. Adjustments in male care, however, did not influence selection acting indirectly on parents, through offspring performance. This is because females adjusted their care in response to the age of their partner, providing less care when paired with older males than younger males. As a result offspring, performance did not differ between treatments. Our study shows, for the first time, that a male state variable is an important modifier of paternityparental care trade-offs and highlights the importance of social interactions between males and females during care in determining male response to perceived paternity. PMID:23782889

  7. Paternal uniparental disomy 14 and related disorders

    PubMed Central

    Kagami, Masayo; Matsuoka, Kentaro; Nagai, Toshiro; Yamanaka, Michiko; Kurosawa, Kenji; Suzumori, Nobuhiro; Sekita, Yoichi; Miyado, Mami; Matsubara, Keiko; Fuke, Tomoko; Kato, Fumiko; Fukami, Maki; Ogata, Tsutomu

    2012-01-01

    Although recent studies in patients with paternal uniparental disomy 14 [upd(14)pat] and other conditions affecting the chromosome 14q32.2 imprinted region have successfully identified underlying epigenetic factors involved in the development of upd(14)pat phenotype, several matters, including regulatory mechanism(s) for RTL1 expression, imprinting status of DIO3 and placental histological characteristics, remain to be elucidated. We therefore performed molecular studies using fresh placental samples from two patients with upd(14)pat. We observed that RTL1 expression level was about five times higher in the placental samples of the two patients than in control placental samples, whereas DIO3 expression level was similar between the placental samples of the two patients and the control placental samples. We next performed histological studies using the above fresh placental samples and formalin-fixed and paraffin-embedded placental samples obtained from a patient with a maternally derived microdeletion involving DLK1, the-IG-DMR, the MEG3-DMR and MEG3. Terminal villi were associated with swollen vascular endothelial cells and hypertrophic pericytes, together with narrowed capillary lumens. DLK1, RTL1 and DIO3 proteins were specifically identified in vascular endothelial cells and pericytes, and the degree of protein staining was well correlated with the expression dosage of corresponding genes. These results suggest that RTL1as-encoded microRNA functions as a repressor of RTL1 expression, and argue against DIO3 being a paternally expressed gene. Furthermore, it is inferred that DLK1, DIO3 and, specially, RTL1 proteins, play a pivotal role in the development of vascular endothelial cells and pericytes. PMID:22917972

  8. Linkage analysis of juvenile myoclonic epilepsy and microsatellite loci spanning 61 cM of human chromosome 6p in 19 nuclear pedigrees provides no evidence for a susceptibility locus in this region

    SciTech Connect

    Elmslie, F.V.; Williamson, M.P.; Rees, M.

    1996-09-01

    Linkage analysis in separately ascertained families of probands with juvenile myoclonic epilepsy (JME) has previously provided evidence both for and against the existence of a locus (designated {open_quotes}EJM1{close_quotes}), on chromosome 6p, predisposing to a trait defined as either clinical JME, its associated electroencephalographic abnormality, or idiopathic generalized epilepsy. Linkage analysis was performed in 19 families in which a proband and at least one first- or two second-degree relatives have clinical JME. Family members were typed for seven highly polymorphic microsatellite markers on chromosome 6p: D6S260, D6S276, D6S291, D6S271, D6S465, D6S257, and D6S254. Pairwise and multipoint linkage analysis was carried out under the assumptions of autosomal dominant inheritance at 70% and 50% penetrance and autosomal recessive inheritance at 70% and 50% penetrance. No significant evidence in favor of linkage to the clinical trait of JME was obtained for any locus. The region formally excluded (LOD score <-2) by using multipoint analysis varies depending on the assumptions made concerning inheritance parameters and the proportion of linked families, {alpha} - that is, the degree of locus heterogeneity. Further analysis either classifying all unaffected individuals as unknown or excluding a subset of four families in which pyknoleptic absence seizures were present in one or more individuals did not alter these conclusions. 24 refs., 4 figs., 1 tab.

  9. Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers.

    PubMed

    Bigi, D; Marelli, S P; Randi, E; Polli, M

    2015-12-01

    Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability. PMID:26245492

  10. Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

    PubMed Central

    Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

    2013-01-01

    Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global FST ? = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global FST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

  11. Relatedness threshold for the production of female sexuals in colonies of a polygynous ant, Myrmica tahoensis, as revealed by microsatellite DNA analysis.

    PubMed Central

    Evans, J D

    1995-01-01

    The genetic relationships of colony members in the ant Myrmica tahoensis were determined on the basis of highly polymorphic microsatellite DNA loci. These analyses show that colonies fall into one of two classes. In roughly half of the sampled colonies, workers and female offspring appear to be full sisters. The remaining colonies contain offspring produced by two or more queens. Colonies that produce female sexuals are always composed of highly related females, while colonies that produce males often show low levels of nestmate relatedness. These results support theoretical predictions that workers should skew sex allocation in response to relatedness asymmetries found within colonies. The existence of a relatedness threshold below which female sexuals are not produced suggests a possible mechanism for worker perception of relatedness. Two results indicate that workers use genetic cues, not queen number, in making sex-allocation decisions. (i) The number of queens in a colony was not significantly correlated with either the level of relatedness asymmetry or the sex ratio. (ii) Sex-ratio shifts consistent with a genetically based mechanism of relatedness assessment were seen in an experiment involving transfers of larvae among unrelated nests. Thus workers appear to make sex-allocation decisions on the basis of larval cues and appear to be able to adjust sex ratios long after egg laying. Images Fig. 2 PMID:7604024

  12. Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction.

    PubMed

    Friar, E A; Ladoux, T; Roalson, E H; Robichaux, R H

    2000-12-01

    The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction. PMID:11123615

  13. Genetic evidence of extra-pair paternity and intraspecific brood parasitism in the monk parakeet

    PubMed Central

    2013-01-01

    Introduction The monk parakeet (Myiopsitta monachus) is a widespread invasive species native to southern South America that has become established in many regions of the world. Monk parakeets breed in a large, fully enclosed structure built from twigs, which consist of one to many individual brooding chambers. The species has been considered to be socially and genetically monogamous. However, genetic relatedness of adults to juveniles in the native area was found to be lower than expected for monogamy. To assess the significance of this discrepancy, we examined individual and population genetic patterns of microsatellite loci at two sites in Crdoba province, Argentina. Results We sampled 154 nestlings and 42 adults in Crdoba, Argentina. Mean value of pairwise relatedness of nestlings within chambers was about 0.40. Contrarily, relatedness of nestlings between chambers was close to zero. We found a considerable degree of variation in nestling pairwise relatedness and parentage within chambers, including chambers with combinations of unrelated, half-sib, and full-sib nestlings. The proportion of sibling relatedness indicated monogamy in 47% and extra pair-paternity in 40% of the chambers. We also found intra-brood parasitism in 3% of the chambers. Conclusions Our results indicate that the monk parakeet is sexually polygamous in its native range in Argentina, which is consistent with the observed mean value of relatedness of adults to juveniles of about 0.4. We also confirm the existence of intra-brood parasitism. High density of monk parakeets may favor occurrence of extra-pair paternity and intra-brood parasitism in the native sites. PMID:24209709

  14. Twelve polymorphic microsatellite loci from the Asian Citrus Psyllid, Diaphorina citri Kuwayama, the vector for citrus greening disease Huanglongbing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twelve polymorphic microsatellite markers were developed from microsatellite-enriched DNA libraries and mined from an EST library of Diaphorina citri, the vector of the devastating citrus greening disease (Huanglongbing). Analysis of 288 individuals from Florida, Texas, and Brazil showed allelic di...

  15. Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.

    PubMed

    Kabra, Ritika; Kapil, Aditi; Attarwala, Kherunnisa; Rai, Piyush Kant; Shanker, Asheesh

    2016-04-01

    Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1-6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx . In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria. PMID:27030027

  16. Molecular genetic analysis of Prader-Willi and Angelman syndromes

    SciTech Connect

    Kokkonen, H.M.; Kahkonen, T.M.; Leisti, J.

    1994-09-01

    Angelman (AS) and Prader-Willi (PWS) syndromes are caused by the loss of either maternal (AS) or paternal (PWS) contributions to chromosome 15q11-q13 region, which is subject to genomic imprinting. DNA methylation has been postulated to play a crucial role in genomic imprinting and the diagnostic test used is based on the differential parental methylation of 15q11-q13. We report here the DNA studies of 39 classical PWS and 12 AS patients. For DNA polymorphism and dosage studies we used nine genomic probes and five microsatellite markers specific for chromosome 15. To study the methylation patterns the probes DN34 (D15S9) and PW71 (D15S63), which show a parental-specific DNA methylation imprint, were used. Among the PWS patients, 29 (77%) cases with a deletion belonging to four different size classes and 9 (23%) with maternal uniparental disomy were found, respectively. Of the AS patients, 8 (67%) had a deletion, 1 (8%) paternal uniparental disomy and 3 (25%) biparental inheritance, respectively. Two sibs with biparental disomy showed a typical methylation pattern for AS, indicating that the maternal chromosome 15 carried a paternal methylation imprint. In the DNA methylation analysis the probe PW71 was useful: in our study it detected all deletions and uniparental disomy patients as well as potential imprinting mutations. The probe DN34 couldn`t identify patients which have a deletion outside the D15S9 locus. In the diagnosis of AS and PWS, the differential methylation of the parental 15q11-q13 offers a rapid diagnostic test but does not distinguish between a deletion and uniparental disomy. In our material the probe 4a.1, which detects DNA sequences from both the locus SNRPN (15q12) and SNRPNP1 (6pter-p21), proved to be reliable detecting all deletions. For detection of parental origin of deletion or uniparental disomy, microsatellite markers proved useful.

  17. Microsatellite primers for red drum (Sciaenops ocellatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this note, we document polymerase-chain-reaction (PCR) primer pairs for 101, nuclear-encoded microsatellites designed and developed from a red drum (Sciaenops ocellatus) genomic library. The 101 microsatellites (Genbank Accession Numbers EU015882-EU015982) were amplified successfully and used to...

  18. Sequence determinants of human microsatellite variability

    PubMed Central

    2009-01-01

    Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability. PMID:20015383

  19. AN ENHANCED MICROSATELLITE MAP OF DIPLOID FRAGARIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 novel codominant genomic microsatellites (SSRs) from Fragaria nubicola and a further 14 derived from an expressed sequence tagged library (EST-SSRs) of F. x ananassa. These, and an additional, 64 previous...

  20. The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus.

    PubMed

    Miller, Adam D; Van Rooyen, Anthony; Sweeney, Oisn F; Whiterod, Nick S; Weeks, Andrew R

    2013-07-01

    The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus. PMID:23644985

  1. Analysis of nrDNA sequences and microsatellite allele frequencies reveals a cryptic chanterelle species Cantharellus cascadensis sp. nov. from the American Pacific Northwest.

    PubMed

    Dunham, Susie M; O'Dell, Thomas E; Molina, Randy

    2003-10-01

    In the Pacific Northwest, yellow chanterelles have long been referred to as Cantharellus cibarius, synonymous with the European yellow chanterelle. Broad scale genetic surveys of North American chanterelles with C. cibarius-like morphology have demonstrated that the nrDNA internal transcribed spacer exhibits length variability, suggesting that this common morphology masks a species complex. Recently researchers have used morphological and genetic data to identify the yellow chanterelle most frequently harvested from American Pacific Northwest forests as C. formosus, a species once thought to be rare in the region. We present three genetic data sets and one morphological data set that characterize a previously undescribed, species of yellow chanterelle from the central Cascade Mountains of Oregon. Phylogenetic analyses of the nrDNA large subunit and ITS regions show that C. cascadensis sp. nov., along with two other yellow chanterelle taxa (C. cibarius var. roseocanus and European C. cibarius), are more closely related to white chanterelles (C. subalbidus) than they are to C. formosus. Data from five microsatellite loci provide evidence that C. formosus, C. subalbidus, and C. cascadensis sp. nov. do not interbreed when they co-occur spatially and temporally in Douglas fir-western hemlock forests. This demonstrates that these three sympatric chanterelles are biological species with boundaries congruent with those delineated by nrDNA phylogenetic clades. Morphological data indicate that the colour of the pileus and shape of the stipe can be used to separate fresh collections of the two yellow species now known to co-occur in Douglas fir-western hemlock forests in Oregon. PMID:14635765

  2. Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.).

    PubMed

    Huang, Jian; Yang, Xiaoting; Zhang, Chunmei; Yin, Xiao; Liu, Shipeng; Li, Xingang

    2015-01-01

    Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. 'Junzao' were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube. PMID:26406601

  3. Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems.

    PubMed

    Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

    2012-01-01

    Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

  4. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae), the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

    PubMed

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST?=?0.069 in C. sieboldii and GST?=?0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the existence of eastern refugia. PMID:24498103

  5. Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.)

    PubMed Central

    Huang, Jian; Yang, Xiaoting; Zhang, Chunmei; Yin, Xiao; Liu, Shipeng; Li, Xingang

    2015-01-01

    Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. ‘Junzao’ were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube. PMID:26406601

  6. Genetic Differentiation and Genetic Diversity of Castanopsis (Fagaceae), the Dominant Tree Species in Japanese Broadleaved Evergreen Forests, Revealed by Analysis of EST-Associated Microsatellites

    PubMed Central

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST?=?0.069 in C. sieboldii and GST?=?0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the existence of eastern refugia. PMID:24498103

  7. Canine Paternity Testing--Using Personal Experiences To Teach Science.

    ERIC Educational Resources Information Center

    Rascati, Ralph J.

    2002-01-01

    Outlines how an example from the field of animal husbandry is used in a DNA Technology course to motivate students to take a deeper interest in the material. Focuses on paternity testing in dogs. (DDR)

  8. Paternal RNA contributions in the Caenorhabditis elegans zygote

    PubMed Central

    Stoeckius, Marlon; Grün, Dominic; Rajewsky, Nikolaus

    2014-01-01

    Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the oocyte upon fertilization. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent Caenorhabditis elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about one hundred sixty paternal mRNAs are reproducibly expressed in the embryo and that about half of all assayed endogenous siRNAs and piRNAs are also of paternal origin. Together, our results suggest an unexplored paternal contribution to early development. PMID:24894551

  9. 45 CFR 303.5 - Establishment of paternity.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... paternity in any case involving incest or forcible rape, or in any case in which legal proceedings for... through video or audio equipment, and in writing, of the alternatives to, the legal consequences of,...

  10. 45 CFR 303.5 - Establishment of paternity.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... paternity in any case involving incest or forcible rape, or in any case in which legal proceedings for... through video or audio equipment, and in writing, of the alternatives to, the legal consequences of,...

  11. 45 CFR 303.5 - Establishment of paternity.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... paternity in any case involving incest or forcible rape, or in any case in which legal proceedings for... through video or audio equipment, and in writing, of the alternatives to, the legal consequences of,...

  12. Genetic variation, multiple paternity, and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata).

    PubMed

    González-Garza, Blanca Idalia; Stow, Adam; Sánchez-Teyer, Lorenzo Felipe; Zapata-Pérez, Omar

    2015-12-01

    The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within-rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs. PMID:26811751

  13. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

    USGS Publications Warehouse

    Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

  14. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations.

    PubMed

    Lemons, P R; Marshall, T C; McCloskey, S E; Sethi, S A; Schmutz, J A; Sedinger, J S

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies. PMID:24989354

  15. Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

    PubMed

    Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

    2015-01-01

    Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. PMID:25755666

  16. Identification and DUS Testing of Rice Varieties through Microsatellite Markers

    PubMed Central

    Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

    2015-01-01

    Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. PMID:25755666

  17. DETERMINATION OF GENETIC DIVERSITY AND PATERNITY IN THE GRAY-TAILED VOLE (MICROTUS CANICAUDUS) BY RAPD-PCR

    EPA Science Inventory

    Genetic relatedness of gray-tailed voles (Microtus canicaudus) was determined by random amplified polymorphic DNA (RAPD). This work is the first reported use of the RAPD method for pedigree analysis of M. canicaudus and demonstrates the feasibility of RAPD for assessing paternity...

  18. Same school, different conduct: rates of multiple paternity vary within a mixed-species breeding school of semi-pelagic cichlid fish (Cyprichromis spp.).

    PubMed

    Anderson, Caleb; Werdenig, Alexandra; Koblmller, Stephan; Sefc, Kristina M

    2016-01-01

    Mating system variability is known to exist between and within species, often due to environmental influences. An open question is whether, vice versa, similar environmental conditions entail congruent mating behavior, for example in terms of multiple paternity, in species or populations sharing largely comparable breeding modes. This study employed microsatellite markers to investigate the incidence of multiple paternity in Cyprichromis coloratus and Cyprichromis leptosoma, two sympatric, closely related, mouthbrooding Lake Tanganyika cichlids with similar ecological and behavioral characteristics including the formation of open-water schools. Mouthbrooding females of both species were collected from the same mixed-species breeding school at the same time, minimizing environmental variation during courtship and mating. In C.coloratus, four of 12 broods had more than one sire, with a mean of 1.33 reconstructed sires per brood. C.leptosoma exhibited multiple paternity in 18 of 22 broods, with a mean of 2.59 or 2.86 reconstructed sires per brood according to the programs gerud and colony, respectively. In addition, two broods were found to contain offspring transplanted from another brood. There was no significant difference in brood size between species, but mean sire number did differ significantly. Hence, substantial similarity in reproductive behavior along with shared environmental conditions during courtship and spawning did not lead to equal rates of polyandry or sneaking in the two species. PMID:26811772

  19. Effective Population Sizes with Multiple Paternity

    PubMed Central

    Sugg, D. W.; Chesser, R. K.

    1994-01-01

    While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics. PMID:7982568

  20. Paternal Transmission of Stressed-Induced Pathologies

    PubMed Central

    Dietz, David M.; LaPlant, Quincey; Watts, Emily L.; Hodes, Georgia E.; Russo, Scott J.; Feng, Jian; Oosting, Ronald S.; Vialou, Vincent; Nestler, Eric J.

    2011-01-01

    Background There has been recent interest in the possibility that epigenetic mechanisms might contribute to the trans-generational transmission of stress-induced vulnerability. Here, we focused on possible paternal transmission using the social defeat stress paradigm. Methods Adult male mice exposed to chronic social defeat stress, or control non-defeated mice, were bred with normal female mice and their offspring were assessed behaviorally for depressive- and anxiety-like measures. Plasma levels of corticosterone and vascular endothelial growth factor (VEGF) were also assayed. To directly assess the role of epigenetic mechanisms, we used in vitro fertilization (IVF); behavioral assessments were conducted on offspring of mice from IVF-control and IVF-defeated fathers. Results We show that both male and female offspring from defeated fathers exhibit increased measures of several depression- and anxiety-like behaviors. The male offspring of defeated fathers also display increased baseline plasma levels of corticosterone and decreased levels of VEGF. However, most of these behavioral changes were not observed when offspring were generated through IVF. Conclusion These results suggest that, while behavioral adaptations that occur after chronic social defeat stress can be transmitted from the father to his male and female F1 progeny, only very subtle changes might be transmitted epigenetically under the conditions tested. PMID:21679926

  1. A genome-wide microsatellite polymorphism database for the indica and japonica rice.

    PubMed

    Zhang, Zhonghua; Deng, Yajun; Tan, Jun; Hu, Songnian; Yu, Jun; Xue, Qingzhong

    2007-02-28

    Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR. PMID:17452422

  2. Cues of Paternal Uncertainty and Father to Child Physical Abuse as Reported by Mothers in Rio de Janeiro, Brazil

    ERIC Educational Resources Information Center

    Alexandre, Gisele Caldas; Nadanovsky, Paulo; Wilson, Margo; Daly, Martin; Moraes, Claudia Leite; Reichenheim, Michael

    2011-01-01

    Objective: Paternity is uncertain, so if paternal feelings evolved to promote fitness, we might expect them to vary in response to variables indicative of paternity probability. We therefore hypothesized that the risk of lapses of paternal affection, including abusive assaults on children, will be exacerbated by cues of non-paternity. Methods:…

  3. Cues of Paternal Uncertainty and Father to Child Physical Abuse as Reported by Mothers in Rio de Janeiro, Brazil

    ERIC Educational Resources Information Center

    Alexandre, Gisele Caldas; Nadanovsky, Paulo; Wilson, Margo; Daly, Martin; Moraes, Claudia Leite; Reichenheim, Michael

    2011-01-01

    Objective: Paternity is uncertain, so if paternal feelings evolved to promote fitness, we might expect them to vary in response to variables indicative of paternity probability. We therefore hypothesized that the risk of lapses of paternal affection, including abusive assaults on children, will be exacerbated by cues of non-paternity. Methods:

  4. Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure

    PubMed Central

    Liu, Nianjun; Chen, Liang; Wang, Shuang; Oh, Cheongeun; Zhao, Hongyu

    2005-01-01

    Single-nucleotide polymorphisms (SNPs) are a class of attractive genetic markers for population genetic studies and for identifying genetic variations underlying complex traits. However, the usefulness and efficiency of SNPs in comparison to microsatellites in different scientific contexts, e.g., population structure inference or association analysis, still must be systematically evaluated through large empirical studies. In this article, we use the Collaborative Studies on Genetics of Alcoholism (COGA) data from Genetic Analysis Workshop 14 (GAW14) to compare the performance of microsatellites and SNPs in the whole human genome in the context of population structure inference. A total of 328 microsatellites and 15,840 SNPs are used to infer population structure in 236 unrelated individuals. We find that, on average, the informativeness of random microsatellites is four to twelve times that of random SNPs for various population comparisons, which is consistent with previous studies. Our results also indicate that for the combined set of microsatellites and SNPs, SNPs constitute the majority among the most informative markers and the use of these SNPs leads to better inference of population structure than the use of microsatellites. We also find that the inclusion of less informative markers may add noise and worsen the results. PMID:16451635

  5. Uniparental isodisomy for paternal 7p and maternal 7q in a child with growth retardation.

    PubMed Central

    Eggerding, F. A.; Schonberg, S. A.; Chehab, F. F.; Norton, M. E.; Cox, V. A.; Epstein, C. J.

    1994-01-01

    Uniparental isodisomy resulting from the simultaneous presence of isochromosomes of the p and q arms of a chromosome and absence of a normal homologue is an exceptionally rare event. We have observed a growth-retarded female infant in whom the normal chromosome 7 homologues were replaced by what appeared cytogenetically to be isochromosomes of 7p and 7q. Polymorphic microsatellite loci spanning the length of 7p and 7q were analyzed in the proband and her parents to ascertain the parental origin and extent of heterozygosity of the proband's rearranged chromosomes. These studies demonstrated that the 7p alleles of the proband were derived only from the father, the 7q alleles were derived only from the mother, and there was homozygosity for all chromosome 7 loci analyzed. The mechanisms leading to the formation of the proband's isochromosomes could reflect abnormalities of cell division occurring at meiosis, postfertilization mitosis, or both. We believe that the present case may result from incomplete mitotic interchange in the pericentromeric regions of chromosome 7 homologues, with resolution by sister-chromatid reunion in an early, if not first, zygotic division. Phenotypically, our proband resembled three previously reported cases of maternal isodisomy for chromosome 7, suggesting that lack of paternal genes from 7q may result in a phenotype of short stature and growth retardation. Images Figure 1 PMID:7913578

  6. Uniparental isodisomy for paternal 7p and maternal 7q in a child with growth retardation

    SciTech Connect

    Eggerding, F.A.; Schonberg, S.A.; Cox, V.A.; Epstein, C.J. Univ. of California, San Francisco, CA ); Chehab, F.F.; Norton, M.E. )

    1994-08-01

    Uniparental isodisomy resulting from the simultaneous presence of isochromosomes of the p and q arms of a chromosome and absence of a normal homologue is an exceptionally rare event. The authors have observed a growth-retarded female infant in whom the normal chromosome 7 homologues were replaced by what appeared cytogenetically to be isochromosomes of 7p and 7q. Polymorphic microsatellite loci spanning the length of 7p and 7q were analyzed in the proband and her parents to ascertain the parental origin and extent of heterozygosity of the proband's rearranged chromosomes. These studies demonstrated that the 7p alleles of the proband were derived only from the father, the 7q alleles were derived only from the mother, and there was homozygosity for all chromosome 7 loci analyzed. The mechanisms leading to the formation of the proband's isochromosomes could reflect abnormalities of cell division occurring at meiosis, postfertilization mitosis, or both. The authors believe that the present case may result from incomplete mitotic interchange in the pericentromeric regions of chromosome 7 homologues, with resolution by sister-chromatid reunion in an early, if not first, zygotic division. Phenotypically, the proband resembled three previously reported cases of maternal isodisomy for chromosome 7, suggesting that lack of paternal genes from 7q may result in a phenotype of short stature and growth retardation. 76 refs., 5 figs., 2 tabs.

  7. Regulatory elements associated with paternally-expressed genes in the imprinted murine Angelman/Prader-Willi syndrome domain.

    PubMed

    Rodriguez-Jato, Sara; Shan, Jixiu; Khadake, Jyoti; Heggestad, Arnold D; Ma, Xiaojie; Johnstone, Karen A; Resnick, James L; Yang, Thomas P

    2013-01-01

    The Angelman/Prader-Willi syndrome (AS/PWS) domain contains at least 8 imprinted genes regulated by a bipartite imprinting center (IC) associated with the SNRPN gene. One component of the IC, the PWS-IC, governs the paternal epigenotype and expression of paternal genes. The mechanisms by which imprinting and expression of paternal genes within the AS/PWS domain - such as MKRN3 and NDN - are regulated by the PWS-IC are unclear. The syntenic region in the mouse is organized and imprinted similarly to the human domain with the murine PWS-IC defined by a 6 kb interval within the Snrpn locus that includes the promoter. To identify regulatory elements that may mediate PWS-IC function, we mapped the location and allele-specificity of DNase I hypersensitive (DH) sites within the PWS-IC in brain cells, then identified transcription factor binding sites within a subset of these DH sites. Six major paternal-specific DH sites were detected in the Snrpn gene, five of which map within the 6 kb PWS-IC. We postulate these five DH sites represent functional components of the murine PWS-IC. Analysis of transcription factor binding within multiple DH sites detected nuclear respiratory factors (NRF's) and YY1 specifically on the paternal allele. NRF's and YY1 were also detected in the paternal promoter region of the murine Mrkn3 and Ndn genes. These results suggest that NRF's and YY1 may facilitate PWS-IC function and coordinately regulate expression of paternal genes. The presence of NRF's also suggests a link between transcriptional regulation within the AS/PWS domain and regulation of respiration. 3C analyses indicated Mkrn3 lies in close proximity to the PWS-IC on the paternal chromosome, evidence that the PWS-IC functions by allele-specific interaction with its distal target genes. This could occur by allele-specific co-localization of the PWS-IC and its target genes to transcription factories containing NRF's and YY1. PMID:23390487

  8. Paternal obesity in a rodent model affects placental gene expression in a sex-specific manner.

    PubMed

    Binder, Natalie K; Beard, Sally A; Kaitu'u-Lino, Tu'uhevaha J; Tong, Stephen; Hannan, Natalie J; Gardner, David K

    2015-05-01

    Fetal growth restriction (FGR) is a major obstetric complication stemming from poor placental development. We have previously demonstrated that paternal obesity in mice is associated with impaired embryo development and significantly reduced fetal and placental weights. We hypothesised that the FGR observed in our rodent model of paternal diet-induced obesity is associated with alterations in metabolic, cell signalling and stress pathways. Male C57BL/6 mice were fed either a normal or high-fat diet for 10 weeks before sperm collection for IVF and subsequent embryo transfer. On embryonic day 14, placentas were collected and RNA extracted from both male and female placentas to assess mRNA expression of 24 target genes using custom RT-qPCR arrays. Peroxisome proliferator-activated receptor alpha (Ppara) and caspase-12 (Casp12) expression were significantly altered in male placentas from obese fathers compared with normal (P<0.05), but not female placentas. PPARA and CASP12 proteins were localised within the placenta to trophoblast giant cells by immunohistochemistry, and relative protein abundance was determined by western blot analysis. DNA was also extracted from the same placentas to determine methylation status. Global DNA methylation was significantly increased in female placentas from obese fathers compared with normal (P<0.05), but not male placentas. In this study, we demonstrate for the first time that paternal obesity is associated with changes in gene expression and methylation status of extraembryonic tissue in a sex-specific manner. These findings reinforce the negative consequences of paternal obesity before conception, and emphasise the need for more lifestyle advice for prospective fathers. PMID:25725082

  9. Associations between 2 paternal casein haplotypes and milk yield traits of Swiss Fleckvieh cattle.

    PubMed

    Braunschweig, Martin H

    2008-01-01

    Associations between casein haplotypes and milk yield traits of offspring from 5 Swiss Fleckvieh AI test bulls were investigated. The analysis was performed by using a daughter design, where each daughter inherited either paternal haplotype B-A1-A-A or B-A2-A-A for alleles of alpha s1-, beta-, alpha s2- and kappa-casein genes. The substitution effects of paternal CSN2 A1 versus A2 on protein yield deviations (YDs) were significant (P < 0.05), whereas their effects on milk and fat YDs were not. The paternal substitution effects of the CSN2 A1 versus the A2 allele on protein YDs within the 5 sires did not reach the significance level. This is due to the contrary allele substitution effect of a sire compared to the other 4 sires. The effects of maternal haplotypes on milk, protein and fat YDs were not significant. However, it is noteworthy that the effects of haplotypes with a low frequency in the population deviate largely from the most frequent haplotype B-A2-A-A. The effects of beta-lactoglobulin (BLG) genotypes were significant for protein YDs but not for milk and fat YDs. The association between the paternal CSN2 A1 and A2 alleles and milk protein YDs within sires but not milk and fat YDs indicate an interaction, which might be a consequence of CSN2 heterogeneity or a closely linked gene that is contributing to the estimated effects. PMID:18263971

  10. Paternal psychosocial work conditions and mental health outcomes: A case-control study

    PubMed Central

    Maggi, Stefania; Ostry, Aleck; Tansey, James; Dunn, James; Hershler, Ruth; Chen, Lisa; Hertzman, Clyde

    2008-01-01

    Background The role of social and family environments in the development of mental health problems among children and youth has been widely investigated. However, the degree to which parental working conditions may impact on developmental psychopathology has not been thoroughly studied. Methods We conducted a case-control study of several mental health outcomes of 19,833 children of sawmill workers and their association with parental work stress, parental socio-demographic characteristics, and paternal mental health. Results Multivariate analysis conducted with four distinct age groups (children, adolescents, young adults, and adults) revealed that anxiety based and depressive disorders were associated with paternal work stress in all age groups and that work stress was more strongly associated with alcohol and drug related disorders in adulthood than it was in adolescence and young adulthood. Conclusion This study provides support to the tenet that being exposed to paternal work stress during childhood can have long lasting effects on the mental health of individuals. PMID:18377651

  11. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity

    PubMed Central

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

  12. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity.

    PubMed

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

  13. A Novel Targeted Approach for Noninvasive Detection of Paternally Inherited Mutations in Maternal Plasma.

    PubMed

    van den Oever, Jessica M E; van Minderhout, Ivonne J H M; Harteveld, Cornelis L; den Hollander, Nicolette S; Bakker, Egbert; van der Stoep, Nienke; Boon, Elles M J

    2015-09-01

    The challenge in noninvasive prenatal diagnosis for monogenic disorders lies in the detection of low levels of fetal variants in the excess of maternal cell-free plasma DNA. Next-generation sequencing, which is the main method used for noninvasive prenatal testing and diagnosis, can overcome this challenge. However, this method may not be accessible to all genetic laboratories. Moreover, shotgun next-generation sequencing as, for instance, currently applied for noninvasive fetal trisomy screening may not be suitable for the detection of inherited mutations. We have developed a sensitive, mutation-specific, and fast alternative for next-generation sequencing-mediated noninvasive prenatal diagnosis using a PCR-based method. For this proof-of-principle study, noninvasive fetal paternally inherited mutation detection was performed using cell-free DNA from maternal plasma. Preferential amplification of the paternally inherited allele was accomplished through a personalized approach using a blocking probe against maternal sequences in a high-resolution melting curve analysis-based assay. Enhanced detection of the fetal paternally inherited mutation was obtained for both an autosomal dominant and a recessive monogenic disorder by blocking the amplification of maternal sequences in maternal plasma. PMID:26162331

  14. The Number of Alleles at a Microsatellite Defines the Allele Frequency Spectrum and Facilitates Fast Accurate Estimation of ?

    PubMed Central

    Haasl, Ryan J.; Payseur, Bret A.

    2010-01-01

    Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of ?, the population-scaled mutation rate, based on simulated data. Discovered relationships between ?, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite ?. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and ? values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics. PMID:20605970

  15. The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

    Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of ?, the population-scaled mutation rate, based on simulated data. Discovered relationships between ?, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite ?. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and ? values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics. PMID:20605970

  16. Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps.

    PubMed

    Mun, Jeong-Hwan; Kim, Dong-Jin; Choi, Hong-Kyu; Gish, John; Debell, Frdric; Mudge, Joanne; Denny, Roxanne; Endr, Gabriella; Saurat, Oliver; Dudez, Anne-Marie; Kiss, Gyorgy B; Roe, Bruce; Young, Nevin D; Cook, Douglas R

    2006-04-01

    Microsatellites are tandemly repeated short DNA sequences that are favored as molecular-genetic markers due to their high polymorphism index. Plant genomes characterized to date exhibit taxon-specific differences in frequency, genomic location, and motif structure of microsatellites, indicating that extant microsatellites originated recently and turn over quickly. With the goal of using microsatellite markers to integrate the physical and genetic maps of Medicago truncatula, we surveyed the frequency and distribution of perfect microsatellites in 77 Mbp of gene-rich BAC sequences, 27 Mbp of nonredundant transcript sequences, 20 Mbp of random whole genome shotgun sequences, and 49 Mbp of BAC-end sequences. Microsatellites are predominantly located in gene-rich regions of the genome, with a density of one long (i.e., > or = 20 nt) microsatellite every 12 kbp, while the frequency of individual motifs varied according to the genome fraction under analysis. A total of 1,236 microsatellites were analyzed for polymorphism between parents of our reference intraspecific mapping population, revealing that motifs (AT)n, (AG)n, (AC)n, and (AAT)n exhibit the highest allelic diversity. A total of 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and composing an estimated 70% of the euchromatic gene space. PMID:16489220

  17. Survey of compound microsatellites in multiple Lactobacillus genomes.

    PubMed

    Basharat, Zarrin; Yasmin, Azra

    2015-12-01

    Distinct simple sequence repeats with 2 or more individual microsatellites joined together or lying adjacent to each other are identified as compound microsatellites. Investigation of such composite microsatellites in the genomes of genus Lactobacillus was the aim of this study. In silico inspection of microsatellite clustering in genomes of 14 Lactobacillus species revealed a wealth of compound microsatellites. All of the mined compound microsatellites were imperfect, were composed of variant motifs, and increased in all genomes, with maximum distance (dMAX) increments of 10 to 50. The majority of these repeats were present in the coding regions. A correlation of microsatellite to compound microsatellite density was detected. The difference established in compound microsatellite division among eukaryotes, Escherichia coli, and lactobacilli is suggestive of diverse genomic features and elementary distinction between creation and fixation methods of compound microsatellites among these organisms. PMID:26445296

  18. The academic Chibis-M microsatellite

    NASA Astrophysics Data System (ADS)

    Zelenyi, L. M.; Gurevich, A. V.; Klimov, S. I.; Angarov, V. N.; Batanov, O. V.; Bogomolov, A. V.; Bogomolov, V. V.; Bodnar, L.; Vavilov, D. I.; Vladimirova, G. A.; Garipov, G. K.; Gotlib, V. M.; Dobriyan, M. B.; Dolgonosov, M. S.; Ivlev, N. A.; Kalyuzhnyi, A. V.; Karedin, V. N.; Karpenko, S. O.; Kozlov, V. M.; Kozlov, I. V.; Korepanov, V. E.; Lizunov, A. A.; Ledkov, A. A.; Nazarov, V. N.; Panasyuk, M. I.; Papkov, A. P.; Rodin, V. G.; Segedi, P.; Svertilov, S. I.; Sukhanov, A. A.; Ferenz, Ch.; Eysmont, N. A.; Yashin, I. V.

    2014-03-01

    This paper describes the scientific goals and design developments of the Chibis microsatellite platform and the Groza scientific equipment, which are aimed at studying new physical mechanisms of high-altitude electrical discharges in the atmosphere. A description of the Groza scientific equipment is presented, which is a united flying instrument that determines the basic requirements for the Chibis-M microsatellite. The problems of ground training of the space experiment, methods of launching the microsatellite in the ISS infrastructure into orbit, and command and telemetry control in flight, as well as the first scientific results, are presented.

  19. Microsatellite Instability in Colorectal Cancer

    PubMed Central

    Boland, C. Richard; Goel, Ajay

    2011-01-01

    Microsatellite instability (MSI) is a hypermutable phenotype caused by the loss of DNA mismatch repair activity. MSI is detected in about 15% of all colorectal cancers; 3% are of these are associated with Lynch syndrome and the other 12% are caused by sporadic, acquired hypermethylation of the promoter of the MLH1 gene, which occurs in tumors with the CpG island methylator phenotype. Colorectal tumors with MSI have distinctive features, including a tendency to arise in the proximal colon, lymphocytic infiltrate, and a poorly differentiated, mucinous or signet ring appearance. They have a slightly better prognosis than colorectal tumors without MSI and do not have the same response to chemotherapeutics. Discovery of MSI in colorectal tumors has increased awareness of the diversity of colorectal cancers and implications for specialized management of patients. PMID:20420947

  20. Characterization of 14 microsatellite markers for Silene acaulis (Caryophyllaceae)1

    PubMed Central

    Mller, Eike; Hlav?kov, Iva; Svoen, Mildrid Elvik; Alsos, Inger Greve; Eidesen, Pernille Bronken

    2015-01-01

    Premise of the study: Fifty candidate microsatellite markers, generated using 454 shotgun sequencing, were tested for the widespread arctic/alpine herb Silene acaulis (Caryophyllaceae). Methods and Results: Fourteen out of 50 markers resulted in polymorphic products with profiles that enabled interpretation. The numbers of alleles per locus ranged from two to six, and the expected heterozygosity per locus ranged from 0.06 to 0.68. Analysis of F0 and F1 samples proved that one allele was always inherited maternally. Four multiplex mixes have been developed. Conclusions: Microsatellite markers for this species will be a valuable tool to study detailed small-scale genetic patterns in an arctic/alpine herb and to relate them to demographic parameters. PMID:26421249

  1. Microsatellite instability in prostate cancer

    SciTech Connect

    Shan, A.L.; Wick, M.J.; Persons, D.L.

    1994-09-01

    Microsatellite instability (MIN) has been documented in hereditary nonpolyposis colorectal cancer (HNPCC) as well as in sporadic forms of human cancers. Two of the genes which appear to be responsible for this particular tumor phenotype, hMSH2 and hMLH1, have now been identified. To determine the potential role of these mutator genes in prostate cancer, we have examined 95 prostate adenocarcinomas (40 paraffin embedded and 55 fresh frozen) for the presence of genetic instability at four microsatellite markers. The markers are localized to chromosome arms 5q(APC-CA1), 8p(Mfd 210Z), 15q(635/636), and 17q(p53-CA). Patients from whom paraffin embedded material was obtained were divided into short term (<3 years, n=18), and long term (>3 years, n=22) survivors. Of the 95 tumors examined, only four tumors (4%) demonstrated MIN: two tumors demonstrated MIN at 3 loci (p53-CA, APC-CA1, 635/636), one tumor demonstrated MIN at 2 loci (APC-CA1 and 635/636), and one tumor demonstrated instability at 635/636 only. All tumors exhibiting MIN had Gleason scores of {ge} 4+4. A correlation between MIN and survival was not observed. Information on family history was limited. However, of the two patients demonstrating MIN at three loci, one patient was diagnosed with a second malignancy (TCC of the ureter), but otherwise had a negative family history, while the second patient had one first degree relative with esophageal cancer. The patient demonstrating MIN at two loci had a negative family history, while the remaining patient had two first degree relatives with cancer (prostate and stomach). These results suggest that hMSH2 and hMLH1 (as reflected by the small percentage of tumors displaying MIN) do not play a prominent role in the process of prostate tumorigenesis.

  2. Transgenerational inheritance of enhanced susceptibility to radiation-induced medulloblastoma in newborn Ptch1?/? mice after paternal irradiation.

    PubMed

    Paris, Lorena; Giardullo, Paola; Leonardi, Simona; Tanno, Barbara; Meschini, Roberta; Cordelli, Eugenia; Benassi, Barbara; Longobardi, Maria Grazia; Izzotti, Alberto; Pulliero, Alessandra; Mancuso, Mariateresa; Pacchierotti, Francesca

    2015-11-01

    The hypothesis of transgenerational induction of increased cancer susceptibility after paternal radiation exposure has long been controversial because of inconsistent results and the lack of a mechanistic interpretation. Here, exploiting Ptch1 heterozygous knockout mice, susceptible to spontaneous and radiation-induced medulloblastoma, we show that exposure of paternal germ cells to 1 Gy X-rays, at the spermatogonial stage, increased by a considerable 1.4-fold the offspring susceptibility to medulloblastoma induced by neonatal irradiation. This effect gained further biological significance thanks to a number of supporting data on the immunohistochemical characterization of the target tissue and preneoplastic lesions (PNLs). These results altogether pointed to increased proliferation of cerebellar granule cell precursors and PNLs cells, which favoured the development of frank tumours. The LOH analysis of tumor DNA showed Ptch1 biallelic loss in all tumor samples, suggesting that mechanisms other than interstitial deletions, typical of radiation-induced medulloblastoma, did not account for the observed increased cancer risk. This data was supported by comet analysis showing no differences in DNA damage induction and repair in cerebellar cells as a function of paternal irradiation. Finally, we provide biological plausibility to our results offering evidence of a possible epigenetic mechanism of inheritance based on radiation-induced changes of the microRNA profile of paternal sperm. PMID:26452034

  3. Maternal and paternal diversity in Xinjiang Kazakh population from China.

    PubMed

    Shan, W; Ren, Zh; Wu, W; Hao, H; Abulimiti, A; Chen, K; Zhang, F; Ma, Z; Zheng, X

    2014-11-01

    The ancient silk road of China passed through Xinjiang and facilitated gene exchanges from the East and the West which impacted on the genetic variation and structure of the nomadic Kazakh population residing there. In order to understand the nature of this genetic variation; 151 Xinjiang Kazakh samples were obtained from four main Kazakh groups and were analyzed using mtDNA and Y-chromosome markers. The Xinjiang Kazakh population is heterogeneous, showing the coexistence of matrilineal lineages with different origins. No genetic differentiation of mtDNA is observed among the four different regional Xinjiang Kazakh populations in Xinjiang by AMOVA and Networks. The genetic diversity of Y-STR loci is higher in Xinjiang Kazakhs (0.968 0.014) than the Kazakhs from Kazakhstan (0.629 0.071) and Russia (0.835 0.020). East Eurasians make a more than 50% contribution to the maternal and paternal lineages of Xinjiang Kazakhs. There is more gene flow from West Eurasian into the maternal lineages of Xinjiang Kazakh than to the Kazakhs from Russia and Kazakhstan. Moreover, mtDNA and Y-STR displayed high polymorphism in Xinjiang Kazakhs (the haplotype diversity and power of discrimination were 0.990 0.003, 0.9137 for mtDNA HVS and 0.968 0.014, 0.9489 for Y-STR system, respectively), suggesting they would be very useful and important markers for forensic analysis and population genetic studies. PMID:25739291

  4. The paternal function in Winnicott: the psychoanalytical frame.

    PubMed

    Faimberg, Haydée

    2014-08-01

    My first aim has been to identify the implicit assumptions underlying Winnicott's detailed notes on a fragment of an analysis dating from 1955 and published after his death. The importance given by Winnicott to the father figure as early as 1955 is one of my discoveries; another is the deep Freudian roots of his thinking. In this essay I propose a new way of linking together the concepts of 'paternal function' and the 'psychoanalytical frame'. Developing my hypothesis, I compare my reading of Winnicott and my way of reading José Bleger's study on the frame. Like Winnicott, I explore in detail a process of discovery, focusing on what the analyst and the patient are nor fully aware of …'as yet'. I am not proposing to unify Winnicott's and Bleger's thinking. My aim is to avoid the pitfall of eclecticism and, in so doing, to recognize both the related depths they sound in their thinking and their otherness. I want to share with the readers their 'meeting' in my mind. PMID:25229543

  5. FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent

    PubMed Central

    2013-01-01

    Background Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. Description FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. Conclusions FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance. PMID:24047532

  6. Paternally induced transgenerational inheritance of susceptibility to diabetes in mammals.

    PubMed

    Wei, Yanchang; Yang, Cai-Rong; Wei, Yan-Ping; Zhao, Zhen-Ao; Hou, Yi; Schatten, Heide; Sun, Qing-Yuan

    2014-02-01

    The global prevalence of prediabetes and type 2 diabetes (T2D) is increasing, and it is contributing to the susceptibility to diabetes and its related epidemic in offspring. Although the impacts of paternal impaired fasting blood glucose and glucose intolerance on the metabolism of offspring have been well established, the exact molecular and mechanistic basis that mediates these impacts remains largely unclear. Here we show that paternal prediabetes increases the susceptibility to diabetes in offspring through gametic epigenetic alterations. In our findings, paternal prediabetes led to glucose intolerance and insulin resistance in offspring. Relative to controls, offspring of prediabetic fathers exhibited altered gene expression patterns in the pancreatic islets, with down-regulation of several genes involved in glucose metabolism and insulin signaling pathways. Epigenomic profiling of offspring pancreatic islets revealed numerous changes in cytosine methylation depending on paternal prediabetes, including reproducible changes in methylation over several insulin signaling genes. Paternal prediabetes altered overall methylome patterns in sperm, with a large portion of differentially methylated genes overlapping with that of pancreatic islets in offspring. Our study uniquely revealed that prediabetes can be inherited transgenerationally through the mammalian germ line by an epigenetic mechanism. PMID:24449870

  7. Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes.

    PubMed

    McCauley, David E

    2013-12-01

    Plant mitochondrial genomes are usually transmitted to the progeny from the maternal parent. However, cases of paternal transmission are known and are perhaps more common than once thought. This review will consider recent evidence, both direct and indirect, of paternal transmission (leakage) of the mitochondrial genome of seed plants, especially in natural populations, and how this can result in offspring that carry a mixture of maternally and paternally derived copies of the genome; a type of heteroplasmy. It will further consider how this heteroplasmy facilitates recombination between genetically distinct partners; a process that can enhance mitochondrial genotypic diversity. This will then form the basis for a discussion of five evolutionary questions that arise from these observations. Questions include how plant mitochondrial genome evolution can be placed on a sexual to asexual continuum, whether cytoplasmic male sterility (CMS) facilitates the evolution of paternal leakage, whether paternal leakage is more likely in populations undergoing admixture, how leakage influences patterns of gene flow, and whether heteroplasmy occurs in natural populations at a frequency greater than predicted by crossing experiments. It is proposed that each of these questions offers fertile ground for future research on a diversity of plant species. PMID:23952142

  8. Microsatellite characterization of Cimarron Uruguayo dogs

    PubMed Central

    Gagliardi, Rosa; Llamb, Silvia; Garca, Cristina; Arruga, Mara Victoria

    2011-01-01

    Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity. PMID:21637561

  9. Update of mouse microsatellite database of Japan (MMDBJ).

    PubMed

    Sakai, Takahiro; Miura, Ikuo; Yamada-Ishibashi, Satomi; Wakita, Yayoi; Kohara, Yuki; Yamazaki, Yukiko; Inoue, Takeshi; Kominami, Ryo; Moriwaki, Kazuo; Shiroishi, Toshihiko; Yonekawa, Hiromichi; Kikkawa, Yoshiaki

    2004-04-01

    We updated a database of microsatellite marker polymorphisms found in inbred strains of the mouse, most of which were derived from the wild stocks of four Mus musculus subspecies, M. m. domesticus, M. m. musculus, M. m.castaneus and M. m. molossinus. The major aim of constructing this database was to establish the genetic status of these inbred strains as resources for linkage analysis and positional cloning. The inbred strains incorporated in our database are A/J, C57BL/6J, CBA/J, DBA/2J, SM/J, SWR/J, 129Sv/J, MSM/Ms, JF1/Ms, CAST/Ei, NC/Nga, BLG2/Ms, NJL/Ms, PGN2/Ms, SK/CamEi and SWN/Ms, which have not or have only been poorly incorporated in the Whitehead Institute/MIT (WI/MIT) microsatellite database. The number of polymorphic microsatellite loci incorporated in our database is over 1,000 in all strains, and the URL site for our database is located at http:// www.shigen.nig.ac.jp /mouse/mmdbj/mouse.html. PMID:15153678

  10. Inbreeding, microsatellite heterozygosity, and morphological traits in Lipizzan horses.

    PubMed

    Curik, I; Zechner, P; Slkner, J; Achmann, R; Bodo, I; Dovc, P; Kavar, T; Marti, E; Brem, G

    2003-01-01

    While the negative effects of inbreeding and reduced heterozygosity on fecundity and survival are well established, only a few investigations have been carried out concerning their influence on morphological traits. This topic is of particular interest for a small and closed population such as the Lipizzan horse. Thus, 27 morphological traits were measured in 360 Lipizzan mares and were regressed on the individual inbreeding coefficients, as well as on the individual heterozygosity and mean squared distances (mean d(2)) between microsatellite alleles within an individual. Both individual heterozygosity and mean d(2) were based on 17 microsatellite loci dispersed over 14 chromosomes. The results obtained by multivariate analysis reveal significant effects of stud (P <.0001), age at measurement (P <.0001), and mean d(2) (P =.0143). In univariate analyses, significant associations were obtained between length of pastern-hindlimbs and inbreeding coefficient (P <.01), length of cannons-hindlimb and mean d(2) (P <.01), and length of neck and mean d(2) (P <.001). After adjustment of single-test P values for multiple tests (Hochberg's step-up Bonferroni method), only the association of the length of neck and mean d(2) remained significant (P =.0213). Thus, no overall large effects of inbreeding, microsatellite heterozygosity, and mean d(2) on morphological traits were observed in the Lipizzan horse. PMID:12721224

  11. Experimental parasite infection reveals costs and benefits of paternal effects

    PubMed Central

    Kaufmann, Joshka; Lenz, Tobias L; Milinski, Manfred; Eizaguirre, Christophe

    2014-01-01

    Forces shaping an individual's phenotype are complex and include transgenerational effects. Despite low investment into reproduction, a father's environment and phenotype can shape its offspring's phenotype. Whether and when such paternal effects are adaptive, however, remains elusive. Using three-spined sticklebacks in controlled infection experiments, we show that sperm deficiencies in exposed males compared to their unexposed brothers functionally translated into reduced reproductive success in sperm competition trials. In non-competitive fertilisations, offspring of exposed males suffered significant costs of reduced hatching success and survival but they reached a higher body condition than their counterparts from unexposed fathers after experimental infection. Interestingly, those benefits of paternal infection did not result from increased resistance but from increased tolerance to the parasite. Altogether, these results demonstrate that parasite resistance and tolerance are shaped by processes involving both genetic and non-genetic inheritance and suggest a context-dependent adaptive value of paternal effects. PMID:25168056

  12. Mitochondrial microsatellite instability in patients with metastatic colorectal cancer.

    PubMed

    Venderbosch, S; van Vliet, S; Craenmehr, M H C; Simmer, F; de Haan, A F J; Punt, C J A; Koopman, M; Nagtegaal, I D

    2015-05-01

    Mitochondrial microsatellite instability (mtMSI), a change in length in mtDNA microsatellite sequences between normal and tumor tissue, has been described as a frequent occurrence in colorectal cancer (CRC). We evaluated the prevalence and prognostic value of mtMSI and its relation to nuclear microsatellite instability (MSI) in patients with metastatic CRC (mCRC). At six loci (D310, D514, D16184, ND1, ND5, and COX1), the mitochondrial DNA sequence was analyzed in normal and tumor tissue, and the mtMSI status was determined. We evaluated the prevalence and outcome in terms of overall survival (OS) in 83 CRC patients with a MSI tumor (including 39 patients with Lynch syndrome) and in 99 mCRC patients with a microsatellite stable (MSS) tumor. A meta-analysis was performed to compare our findings with existing data. mtMSI at the D-loop region was found in 54.4 % (99 out of 182) of all patients. Prevalence of mtMSI was most pronounced at the D310 locus (50.5 %). Prevalence of mtMSI at the D-loop region was not different among patients with MSI compared to MSS tumors. There was no effect of mtMSI on prognosis in patients with MSI or MSS tumors. Prevalence of mtMSI was high in mCRC patients with both MSI and MSS tumors, but there was no correlation with prognosis. mtMSI was particularly present at the D310 locus. PMID:25697538

  13. The effects of walls, paternity and ageing on sperm motility.

    PubMed

    Gee, C C; Zimmer-Faust, R K

    1997-12-01

    The measurement of sperm motility is critical when studying fertilization kinetics and chemotaxis. Analysis of motility has traditionally been carried out on cells in small fluid volumes on microscope slides. Several theoretical treatments suggest that drag forces significantly affect flagellar motion within 10 sperm body lengths of the slide surface. Understanding how sperm move in the absence of surface drag is crucial when considering natural locomotory patterns. To examine the effects of solid surfaces, motile sperm from sea urchins (Arbacia punctulata) were placed in a Plexiglas chamber (69 mmx45 mmx15.5 mm; length x width x height). A system was constructed to minimize convective flow by limiting temperature differences within the chamber to less than 0.1 degrees C. The movement of sperm was video-recorded at two levels: (3/4)100 micron (3 body lengths) and 5 mm (150 body lengths) below the chamber lid. When swimming speeds were measured using a computerized video motion-analysis system, a highly significant difference (P<0. 0001) between cells at the two depths was found. Cells nearest the lid swam at 174.6+/-5.9 micron s-1 (mean +/- s.e.m.), whereas those farther away slowed to only 111.1+/-9.9 micron s-1 (mean +/- s.e.m.). Swimming speed was also found to be significantly (P<0.01) affected by paternity, but not by sperm age. We conclude that viscous wall effects must be carefully considered in studies of sperm motility and chemotaxis. The analysis of sperm on a microscope slide may substantially exaggerate swimming speed. PMID:9364024

  14. Paternalism, autonomy and reciprocity: ethical perspectives in encounters with patients in psychiatric in-patient care

    PubMed Central

    2013-01-01

    Background Psychiatric staff members have the power to decide the options that frame encounters with patients. Intentional as well as unintentional framing can have a crucial impact on patients opportunities to be heard and participate in the process. We identified three dominant ethical perspectives in the normative medical ethics literature concerning how doctors and other staff members should frame interactions in relation to patients; paternalism, autonomy and reciprocity. The aim of this study was to describe and analyse statements describing real work situations and ethical reflections made by staff members in relation to three central perspectives in medical ethics; paternalism, autonomy and reciprocity. Methods All staff members involved with patients in seven adult psychiatric and six child and adolescent psychiatric clinics were given the opportunity to freely describe ethical considerations in their work by keeping an ethical diary over the course of one week and 173 persons handed in their diaries. Qualitative theory-guided content analysis was used to provide a description of staff encounters with patients and in what way these encounters were consistent with, or contrary to, the three perspectives. Results The majority of the statements could be attributed to the perspective of paternalism and several to autonomy. Only a few statements could be attributed to reciprocity, most of which concerned staff members acting contrary to the perspective. The result is presented as three perspectives containing eight values. Paternalism; 1) promoting and restoring the health of the patient, 2) providing good care and 3) assuming responsibility. Autonomy; 1) respecting the patients right to self-determination and information, 2) respecting the patients integrity and 3) protecting human rights. Reciprocity; 1) involving patients in the planning and implementation of their care and 2) building trust between staff and patients. Conclusions Paternalism clearly appeared to be the dominant perspective among the participants, but there was also awareness of patients right to autonomy. Despite a normative trend towards reciprocity in psychiatry throughout the Western world, identifying it proved difficult in this study. This should be borne in mind by clinics when considering the need for ethical education, training and supervision. PMID:24314345

  15. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys

    PubMed Central

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-01

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

  16. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.

    PubMed

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-01

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

  17. Paternal age at childbearing and offspring psychiatric and academic morbidity

    PubMed Central

    DOnofrio, Brian M.; Rickert, Martin E.; Frans, Emma; Kuja-Halkola, Ralf; Almqvist, Catarina; Sjlander, Arvid; Larsson, Henrik; Lichtenstein, Paul

    2013-01-01

    Summary Importance Advancing paternal age is associated with increased genetic mutations during spermatogenesis, which research suggests may cause psychiatric morbidity in the offspring. The effects of advancing paternal age at childbearing on offspring morbidity remains unclear, however, because of inconsistent epidemiological findings and the inability of previous studies to rigorously rule out confounding factors. Objective Examine the associations between advancing paternal age at childbearing and numerous indices of offspring morbidity. Setting Population-based cohort study in Sweden. Participants All individuals born in Sweden 19732001 (N=2,615,081), with subsets of the data used to predict childhood/adolescent morbidity. Design We estimated the risk for psychiatric and academic morbidity associated with advancing paternal age using several quasi-experimental designs, including the comparison of differentially exposed siblings, cousins, and first-born cousins. Exposure Paternal age at childbearing Main outcomes Psychiatric (autism, ADHD, psychosis, bipolar disorder, suicide attempt, and substance use problem) and academic (failing grades and low educational attainment) morbidity. Results In the population, advancing paternal age was associated with increased risk for some psychiatric disorders (e.g. autism, psychosis, and bipolar disorders) but decreased risk for the other indices of morbidity. In contrast, the sibling-comparison analyses indicated that advancing paternal age had a dose-response relationship with every index of morbidity, with the magnitude of the associations being as large or larger than the estimates in the entire population. Compared to offspring born to fathers 2025 years old, offspring of fathers 45 years+ were at heightened risk for autism (Hazard Ratio [HR]=3.45, 95% Confidence Intervals [CI]=1.627.33), ADHD (HR=13.13, CI=6.8525.16), psychosis (HR=2.07, CI=1.353.20), bipolar disorder (HR=24.70, CI=12.1250.31), suicide attempts (HR=2.72, CI=2.083.56), substance use problems (HR=2.44, CI=1.982.99), failing a grade (Odds Ratio [OR]=1.59, CI=1.371.85), and low educational attainment (OR=1.70, CI=1.501.93) in within-sibling comparisons. Additional analyses using several quasi-experimental designs obtained commensurate results, further strengthening the internal and external validity of the findings. Conclusions and Relevance Advancing paternal age is associated with increased risk for psychiatric and academic morbidity, with the magnitude of the risks being as large or larger than previous estimates. These findings are consistent with the hypothesis that new genetic mutations occurring during spermatogenesis are causally related to offspring morbidity. PMID:24577047

  18. Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs

    PubMed Central

    Pastorini, Jennifer; Zaramody, Alphonse; Curtis, Deborah J; Nievergelt, Caroline M; Mundy, Nicholas I

    2009-01-01

    Background Hybrid zones generally represent areas of secondary contact after speciation. The nature of the interaction between genes of individuals in a hybrid zone is of interest in the study of evolutionary processes. In this study, data from nuclear microsatellites and mitochondrial DNA sequences were used to genetically characterize hybridization between wild mongoose lemurs (Eulemur mongoz) and brown lemurs (E. fulvus) at Anjamena in west Madagascar. Results Two segments of mtDNA have been sequenced and 12 microsatellite loci screened in 162 brown lemurs and mongoose lemurs. Among the mongoose lemur population at Anjamena, we identified two F1 hybrids (one also having the mtDNA haplotype of E. fulvus) and six other individuals with putative introgressed alleles in their genotype. Principal component analysis groups both hybrids as intermediate between E. mongoz and E. fulvus and admixture analyses revealed an admixed genotype for both animals. Paternity testing proved one F1 hybrid to be fertile. Of the eight brown lemurs genotyped, all have either putative introgressed microsatellite alleles and/or the mtDNA haplotype of E. mongoz. Conclusion Introgression is bidirectional for the two species, with an indication that it is more frequent in brown lemurs than in mongoose lemurs. We conclude that this hybridization occurs because mongoose lemurs have expanded their range relatively recently. Introgressive hybridization may play an important role in the unique lemur radiation, as has already been shown in other rapidly evolving animals. PMID:19196458

  19. The Association of Paternal Mood and Infant Temperament: A Pilot Study

    ERIC Educational Resources Information Center

    Dave, Shreya; Nazareth, Irwin; Sherr, Lorraine; Senior, Rob

    2005-01-01

    Maternal depression is associated with adverse child development, but little is known about the effects of paternal depression. This pilot study estimated the prevalence of paternal depression and mood state, and assessed the relationship between paternal mood and infant temperament. The participants in the study were 98 fathers of newborn babies.

  20. 26 CFR 1.410(a)-9 - Maternity and paternity absence.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 5 2011-04-01 2011-04-01 false Maternity and paternity absence. 1.410(a)-9...(a)-9 Maternity and paternity absence. (a) Elapsed time(1) Rule. For purposes of applying the rules... sections 410(a)(5)(E) and 411(a)(6)(E) (relating to maternity or paternity absence), the severance...

  1. For Your Child's Sake...Establish Paternity [and] Collect Child Support.

    ERIC Educational Resources Information Center

    Administration for Children, Youth, and Families (DHHS), Washington, DC.

    These brochures explain briefly the importance of establishing paternity for unwed mothers. By establishing paternity and enforcing child support orders, fathers can be required to help raise their child legally and financially. The brochures consist of two separate sheets. "For Your Child's Sake...Establish Paternity" presents several questions

  2. The Doctor's Dilemma: Paternalisms in the Medicolegal History of Assisted Reproduction and Abortion.

    PubMed

    Swanson, Kara W

    2015-01-01

    This article analyzes the comparative history of the law and practice of abortion and assisted reproduction in the United States to consider the interplay between medical paternalism and legal paternalism. It supplements existing critiques of paternalism as harmful to women's equality with the medical perspective, as revealed through the writings of Alan F. Guttmacher, to consider when legal regulation might be warranted. PMID:26242953

  3. Allelic imbalance regions on chromosomes 8p, 17p and 19p related to metastasis of hepatocellular carcinoma: comparison between matched primary and metastatic lesions in 22 patients by genome-wide microsatellite analysis.

    PubMed

    Zhang, Lian-Hai; Qin, Lun-Xiu; Ma, Zeng-Chen; Ye, Sheng-Long; Liu, Yin-Kun; Ye, Qing-Hai; Wu, Xin; Huang, Wei; Tang, Zhao-You

    2003-05-01

    To understand the molecular mechanisms of metastasis in hepatocellular carcinoma (HCC), it is necessary to identify the accumulating genetic alterations during its progression as well as those responsible for the acquisition of metastatic potential in cancer cells. In our previous study, using comparative genomic hybridization (CGH), we found that loss on chromosome 8p is more frequent in metastatic lesions than in matched primary tumors of HCC. Thus, 8p deletion might contribute to HCC metastasis. To narrow the location of metastasis-related alteration regions, we analyzed 22 primary and matched metastatic lesions of HCC by genome-wide microsatellite analysis. Common regions with high levels of allelic imbalance (AI) were identified on 17p, 8p11-cen, 8p21-23, 4q32-qter, 4q13-23, 16q, and 1p33. Regions with increased AI in metastatic lesions were 8p23.3, 8p11.2, 17p11.2-13.3, 4q21-22, 4q32-qter, 8q24.1, 9p11, 9q31, 11q23.1, 13q14.1-31, 13q32-qter, 16p13.3, 16q13, 16q22, and 19p13.1, and these were considered to be related to the metastasis phenotype. Among them, loss on 8p was again proved to be related to progression and metastasis of HCC, and 8p23.3 and 8p11.2 were two likely regions harboring metastasis-related genes. It was also shown for the first time in HCC that AI of 19p13.1 might also be related to metastatic potential. These results provide some candidate regions for further study to identify putative genes suppressing metastasis of HCC. PMID:12734753

  4. Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: Facilitating the FAO Global Plan of Action for conserving animal genetic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites have been used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsa...

  5. Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability.

    PubMed

    Mlecnik, Bernhard; Bindea, Gabriela; Angell, Helen K; Maby, Pauline; Angelova, Mihaela; Tougeron, David; Church, Sarah E; Lafontaine, Lucie; Fischer, Maria; Fredriksen, Tessa; Sasso, Maristella; Bilocq, Amélie M; Kirilovsky, Amos; Obenauf, Anna C; Hamieh, Mohamad; Berger, Anne; Bruneval, Patrick; Tuech, Jean-Jacques; Sabourin, Jean-Christophe; Le Pessot, Florence; Mauillon, Jacques; Rafii, Arash; Laurent-Puig, Pierre; Speicher, Michael R; Trajanoski, Zlatko; Michel, Pierre; Sesboüe, Richard; Frebourg, Thierry; Pagès, Franck; Valge-Archer, Viia; Latouche, Jean-Baptiste; Galon, Jérôme

    2016-03-15

    Microsatellite instability in colorectal cancer predicts favorable outcomes. However, the mechanistic relationship between microsatellite instability, tumor-infiltrating immune cells, Immunoscore, and their impact on patient survival remains to be elucidated. We found significant differences in mutational patterns, chromosomal instability, and gene expression that correlated with patient microsatellite instability status. A prominent immune gene expression was observed in microsatellite-instable (MSI) tumors, as well as in a subgroup of microsatellite-stable (MSS) tumors. MSI tumors had increased frameshift mutations, showed genetic evidence of immunoediting, had higher densities of Th1, effector-memory T cells, in situ proliferating T cells, and inhibitory PD1-PDL1 cells, had high Immunoscores, and were infiltrated with mutation-specific cytotoxic T cells. Multivariate analysis revealed that Immunoscore was superior to microsatellite instability in predicting patients' disease-specific recurrence and survival. These findings indicate that assessment of the immune status via Immunoscore provides a potent indicator of tumor recurrence beyond microsatellite-instability staging that could be an important guide for immunotherapy strategies. PMID:26982367

  6. Paternal Involvement with Children: The Influence of Gender Ideologies

    ERIC Educational Resources Information Center

    Bulanda, Ronald E.

    2004-01-01

    Although prior social science research has established the ability of gender ideologies to influence the domestic division of labor, it has neglected to disentangle their potentially unique influence on paternal involvement with children. Past research examining the influence of gender ideology on parenting behaviors does not acknowledge potential

  7. Maternal Depression, Paternal Psychopathology, and Toddlers' Behavior Problems

    ERIC Educational Resources Information Center

    Dietz, Laura J.; Jennings, Kay Donahue; Kelley, Sue A.; Marshal, Michael

    2009-01-01

    This article examined the effects of maternal depression during the postpartum period (Time 1) on the later behavior problems of toddlers (Time 3) and tested if this relationship was moderated by paternal psychopathology during toddlers' lives and/or mediated by maternal parenting behavior observed during mother-child interaction (Time 2). Of the…

  8. Paternal exposure and counselling: experience of a Teratology Information Service.

    PubMed

    De Santis, Marco; Cesari, Elena; Cavaliere, Annafranca; Ligato, Maria Serena; Nobili, Elena; Visconti, Daniela; Caruso, Alessandro

    2008-09-01

    We describe paternal exposure and counselling in a selected population calling to an Italian Teratology Information Service (TIS). The majority of callers asked for paternal drug exposure (76%, drugs except chemotherapy) and treatment for cancer (17%, chemotherapy and/or radiotherapy). Others asked for exposure to diagnostic radiations (4%), recreational drugs (2%) and occupational chemicals (1%). Among paternal drugs neurological compounds, immunosuppressive drugs and antiviral agents were the main reasons for calling. In humans, there are no evidences of birth defects after paternal exposures, but to minimize any possible risk, counselling in men exposed to radio and chemotherapy should recommend delaying conception for at least 3 months after the end of the therapy. Male patients treated with drugs, whose teratogenic potential has been well assessed or suspected for maternal exposure, should be advised to practice effective birth control during therapy and up to one or two cycles of spermatogenesis and to avoid semen contact with vaginal walls during first trimester of pregnancy. PMID:18598753

  9. Paternalism & Deaf People: An Open Letter to Mme. Umuvyeyi.

    ERIC Educational Resources Information Center

    Lane, Harlan

    1988-01-01

    By describing the paternalism inherent in the parallels between the history of Burundi and that of deaf people, a letter to a woman in Burundi with five deaf children attempts to persuade her to allow her youngest to further her education in the United States. (LMO)

  10. Paternal Psychopathology: Relationship to Adolescent Substance Abuse and Deviant Behavior.

    ERIC Educational Resources Information Center

    Brown, Sandra A.; And Others

    Research has documented the genetic contribution of paternal alcoholism and Antisocial Personality Disorder as risk factors for adolescent deviant behavior, including substance abuse. Teens (n=147) between the ages of 12 and 19 years and their parents participated in the study. The sample consisted of 74 substance abusing teens/families drawn from

  11. Mechanisms and consequences of paternally transmitted chromosomal abnormalities

    SciTech Connect

    Marchetti, F; Wyrobek, A J

    2005-04-05

    Paternally transmitted chromosomal damage has been associated with pregnancy loss, developmental and morphological defects, infant mortality, infertility, and genetic diseases in the offspring including cancer. There is epidemiological evidence linking paternal exposure to occupational or environmental agents with an increased risk of abnormal reproductive outcomes. There is also a large body of literature on germ cell mutagenesis in rodents showing that treatment of male germ cells with mutagens has dramatic consequences on reproduction producing effects such as those observed in human epidemiological studies. However, we know very little about the etiology, transmission and early embryonic consequences of paternally-derived chromosomal abnormalities. The available evidence suggests that: (1) there are distinct patterns of germ cell-stage differences in the sensitivity of induction of transmissible genetic damage with male postmeiotic cells being the most sensitive; (2) cytogenetic abnormalities at first metaphase after fertilization are critical intermediates between paternal exposure and abnormal reproductive outcomes; and, (3) there are maternally susceptibility factors that may have profound effects on the amount of sperm DNA damage that is converted into chromosomal aberrations in the zygote and directly affect the risk for abnormal reproductive outcomes.

  12. Fine mapping of paternal sorting of mitochondria (Psm) in cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber is unique among plants because its mitochondrial DNA shows paternal transmission, is one of the largest known among all plants, due largely to short repetitive DNA motifs, and recombination among these repeats produces rearranged mitochondrial DNAs associated with strongly mosaic (MSC) phen...

  13. Paternal Factors and Schizophrenia Risk: De Novo Mutations and Imprinting

    PubMed Central

    Malaspina, Dolores

    2010-01-01

    There is a strong genetic component for schizophrenia risk, but it is unclear how the illness is maintained in the population given the significantly reduced fertility of those with the disorder. One possibility is that new mutations occur in schizophrenia vulnerability genes. If so, then those with schizophrenia may have older fathers, because advancing paternal age is the major source of new mutations in humans. This review describes several neurodevelopmental disorders that have been associated with de novo mutations in the paternal germ line and reviews data linking increased schizophrenia risk with older fathers. Several genetic mechanisms that could explain this association are proposed, including paternal germ line mutations, trinucleotide repeat expansions, and alterations in genetic imprinting in one or several genes involved in neurodevelopment. Animal models may be useful in exploring these and other explanations for the paternal age effect and they may provide a novel approach for gene identification. Finally, it is proposed that environmental exposures of the father, as well as those of the mother and developing fetus, may be relevant to the etiology of schizophrenia. PMID:11596842

  14. Maternal Depression, Paternal Psychopathology, and Toddlers' Behavior Problems

    ERIC Educational Resources Information Center

    Dietz, Laura J.; Jennings, Kay Donahue; Kelley, Sue A.; Marshal, Michael

    2009-01-01

    This article examined the effects of maternal depression during the postpartum period (Time 1) on the later behavior problems of toddlers (Time 3) and tested if this relationship was moderated by paternal psychopathology during toddlers' lives and/or mediated by maternal parenting behavior observed during mother-child interaction (Time 2). Of the

  15. Role-Playing for Inhibited Students in Paternal Communities.

    ERIC Educational Resources Information Center

    Al-Saadat, Abdullah I.; Afifi, Elhami A.

    1997-01-01

    Highlights classroom role playing in Saudi Arabian classrooms as a psychological aid that fosters self-confidence in inhibited, timid, hesitant, and passive students and relieves them of their paternal communicative limitations. Proposes an overall strategy for role-playing as an effective communicative activity that teachers can exploit to help

  16. Father Involvement: The Importance of Paternal Solo Care

    ERIC Educational Resources Information Center

    Wilson, Katherine R.; Prior, Margot R.

    2010-01-01

    Paternal time spent caring for children alone is qualitatively different from time together mediated by the presence of the mother and may be particularly relevant to father-child relations. Many fathers spend minimal time alone with their children. Indeed, it is still commonly referred to as "babysitting". We explored the concept of Solo Care as

  17. Fine mapping of paternal sorting of mitochondria (psm) in cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber is unique among plants because its mitochondrial DNA shows paternal transmission, is one of the largest known among all plants, due largely to short repetitive DNA motifs, and undergoes recombination among repeats to produce rearranged mitochondrial DNAs associated with strongly mosaic (MSC...

  18. Paternal Banking and Maternal Gatekeeping in Postdivorce Families

    ERIC Educational Resources Information Center

    Moore, Elena

    2012-01-01

    The research explores the way in which postseparated parents continue to exert a bidirectional force on each other following divorce and separation. The study draws on qualitative interviews with 39 separated mothers and fathers in Ireland, including five marital sets of former couples. The study found many fathers adopted a range of "paternal

  19. 45 CFR 303.5 - Establishment of paternity.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 2 2012-10-01 2012-10-01 false Establishment of paternity. 303.5 Section 303.5 Public Welfare Regulations Relating to Public Welfare OFFICE OF CHILD SUPPORT ENFORCEMENT (CHILD SUPPORT ENFORCEMENT PROGRAM), ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES STANDARDS FOR PROGRAM OPERATIONS §...

  20. Genetic Analyses of Sorting of Paternally Transmitted Mitochondrial DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The organelles are maternally transmitted in the vast majority of eukaryotes. However paternal transmission of plastids and mitochondria occurs rarely in plants. Cucumber is a unique model plant for organellar genetics because its three genomes show differential transmission: maternal for chlorop...

  1. Microsatellite instability in gallbladder carcinoma.

    PubMed

    Moy, Andrea P; Shahid, Mohammad; Ferrone, Cristina R; Borger, Darrell R; Zhu, Andrew X; Ting, David; Deshpande, Vikram

    2015-04-01

    The genetic abnormalities involved in the pathogenesis of gallbladder carcinoma (GBC) remain unclear. Microsatellite instability (MSI) has been described in many carcinomas, but little is known about the significance of mismatch repair in gallbladder carcinogenesis. Additionally, methylation status of long interspersed element-1 (LINE-1), a surrogate marker of global DNA methylation, has defined distinct subsets of other cancer types but has not been explored in GBC. Immunohistochemical expression of MSH2, MSH6, MLH1, and PMS2 and LINE-1 mRNA in situ hybridization was evaluated in 67 primary and 15 metastatic GBCs from 77 patients. Amplification of human epidermal growth factor receptor 2 (HER2) was evaluated by fluorescence in situ hybridization. Genotyping for 24 genes involved in carcinogenesis was performed using a multiplex PCR-based platform. MSI was present in 6 of 77 GBCs (7.8 %). Loss of MSH2/MSH6 was detected in five cases and loss of MLH1/PMS2 in one case. MSI status was not associated with Lynch syndrome, tumor grade, extracellular mucin, or tumor-infiltrating lymphocytes. There was no significant difference in mean overall survival of patients with and without MSI. Strong LINE-1 staining was identified in none of the GBC with MSI and in 36 of 69 (52 %) of those without MSI (p = 0.005), suggesting that LINE-1 in the former cohort was hypermethylated. All MSI tumors were negative for HER2 amplification, and TP53 and NRAS mutations were only found in GBC without MSI. MSI was identified in a minority of GBC cases. The strong correlation between global DNA methylation as measured by LINE-1 and loss of mismatch repair proteins suggests that methylation may account for the loss of these proteins. These hypermethylated tumors appear to represent a genetically unique cohort of gallbladder neoplasms, and the data suggests that demethylating agents may have a therapeutic value in this class of tumors. PMID:25680569

  2. TWO SEX-CHROMOSOME-LINKED MICROSATELLITE LOCI SHOW GEOGRAPHIC VARIANCE AMONG NORTH AMERICAN OSTRINIA NUBILALIS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A (GAAAAT)n repeat microsatellite was isolated from a partial Ostrinia nubilalis genomic library. Pedigree analysis indicated the marker was female specific, and referred to as Ostrinia nubilalis W-chromosome marker 1 (ONW1). Polymerase chain reaction (PCR) and DNA sequence analysis indicated that ...

  3. [Genetic diversity of microsatellite loci in captive Amur tigers].

    PubMed

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species. PMID:15640074

  4. Fragile X gene instability: anchoring AGGs and linked microsatellites.

    PubMed Central

    Zhong, N; Yang, W; Dobkin, C; Brown, W T

    1995-01-01

    Interspersed AGGs within the FMR1 gene CGG repeat region may anchor the sequence and prevent slippage during replication. In order to detect the AGG position variations, we developed a method employing partial MnlI restriction analysis and analyzed X chromosomes from 187 males, including 133 normal controls (117 with 20-34 and 16 with 35-52 repeats), plus 54 fragile X premutations with 56-180 repeats. Among controls, the interspersed AGG positions were highly polymorphic, with a heterozygosity of 91%. Among the control samples, 1.5% had no AGG positions, 25% had one, 71% had two, and 3% had three. Among the fragile X premutation samples, 63% had no AGG, while 37% had only one AGG. Analysis of premutation samples within fragile X families showed that variation occurred only within the 3' end of the region. Thus, the instability was polar. Controls with > or = 15 pure CGG repeats were associated with the longest alleles of two nearby microsatellites, FRAXAC1 with 20-21 repeats and DXS548 with 202-206 bp and with increased microsatellite heterozygosity. The association of long pure CGG regions, as with fragile X chromosomes, with the longer and more heterozygous microsatellite alleles suggests they may be related mechanistically. Further, our results do not support a recent suggestion that the frequency of fragile X alleles may be increasing. Finally, analysis of a set of nonhuman primate samples showed that long pure CGG tracks are variable in size and are located within the 3' region, which suggests that polar instability within FMR1 is evolutionarily quite old. Images Figure 1 PMID:7668261

  5. Chloroplast Microsatellite Diversity in Phaseolus vulgaris

    PubMed Central

    Desiderio, F.; Bitocchi, E.; Bellucci, E.; Rau, D.; Rodriguez, M.; Attene, G.; Papa, R.; Nanni, L.

    2012-01-01

    Evolutionary studies that are aimed at defining the processes behind the present level and organization of crop genetic diversity represent the fundamental bases for biodiversity conservation and use. A Mesoamerican origin of the common bean Phaseolus vulgaris was recently suggested through analysis of nucleotide polymorphism at the nuclear level. Here, we have used chloroplast microsatellites to investigate the origin of the common bean, on the basis of the specific characteristics of these markers (no recombination, haploid genome, uniparental inheritance), to validate these recent findings. Indeed, comparisons of the results obtained through analysis of nuclear and cytoplasmic DNA should allow the resolution of some of the contrasting information available on the evolutionary processes. The main outcomes of the present study are: (i) confirmation at the chloroplast level of the results obtained through nuclear data, further supporting the Mesoamerican origin of P. vulgaris, with central Mexico representing the cradle of its diversity; (ii) identification of a putative ancestral plastidial genome, which is characteristic of a group of accessions distributed from central Mexico to Peru, but which have not been highlighted beforehand through analyses at the nuclear level. Finally, the present study suggests that when a single species is analyzed, there is the need to take into account the complexity of the relationships between P. vulgaris and its closely related and partially intercrossable species P. coccineus and P. dumosus. Thus, the present study stresses the importance for the investigation of the speciation processes of these taxa through comparisons of both plastidial and nuclear variability. This knowledge will be fundamental not only from an evolutionary point of view, but also to put P. coccineus and P. dumosus germplasm to better use as a source of useful diversity for P. vulgaris breeding. PMID:23346091

  6. Association studies using random and "candidate" microsatellite loci in two infectious goat diseases

    PubMed Central

    2003-01-01

    We established a set of 30 microsatellites of Bovidae origin for use in a biodiversity study in Swiss and Creole goats. Additional microsatellites located within or next to "candidate" genes of interest, such as cytokine genes (IL4, INF-gamma) and MHC class II genes (DRB, DYA) were tested in the caprine species in order to detect possible associations with two infectious caprine diseases. Microsatellite analysis was undertaken using automated sequencers (ABI373 & 3100). In the first study, a total of 82 unrelated Creole goats, 37 resistant and 45 susceptible to Heartwater disease (Cowdriosis) were analysed. In this study, the two microsatellite loci DRBP1 (MHCII) and BOBT24 (IL4) were positively associated with disease susceptibility, demonstrating a corrected P-value of 0.002 and 0.005, respectively. In a second investigation, we tested 36 goats, naturally infected with the nematode parasite Trichostrongylus colubriformis. These animals were divided into a "low" and "high" excreting group on the basis of two independently recorded fecal egg counts. For this nematode resistance study, we detected a significant association of one of the alleles of the microsatellite locus SPS113 with "low" excretion (resistance). The MHC class II locus DYA (P19), was weakly associated with susceptibility in both diseases (Pc = 0.05). In future experiments, we will extend the sample size in order to verify the described associations. PMID:12927084

  7. Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus.

    PubMed Central

    Estoup, A; Wilson, I J; Sullivan, C; Cornuet, J M; Moritz, C

    2001-01-01

    Much progress has been made on inferring population history from molecular data. However, complex demographic scenarios have been considered rarely or have proved intractable. The serial introduction of the South-Central American cane toad Bufo marinus in various Caribbean and Pacific islands involves four major phases: a possible genetic admixture during the first introduction, a bottleneck associated with founding, a transitory population boom, and finally, a demographic stabilization. A large amount of historical and demographic information is available for those introductions and can be combined profitably with molecular data. We used a Bayesian approach to combine this information with microsatellite (10 loci) and enzyme (22 loci) data and used a rejection algorithm to simultaneously estimate the demographic parameters describing the four major phases of the introduction history. The general historical trends supported by microsatellites and enzymes were similar. However, there was a stronger support for a larger bottleneck at introductions for microsatellites than enzymes and for a more balanced genetic admixture for enzymes than for microsatellites. Very little information was obtained from either marker about the transitory population boom observed after each introduction. Possible explanations for differences in resolution of demographic events and discrepancies between results obtained with microsatellites and enzymes were explored. Limits of our model and method for the analysis of nonequilibrium populations were discussed. PMID:11779806

  8. Assessment of microsatellites in estimating inter- and intraspecific variation among Neotropical Crocodylus species.

    PubMed

    Bashyal, A; Gross, B A; Venegas-Anaya, M; Lowrance, F; Densmore Iii, L D

    2014-01-01

    We tested microsatellites that were developed for the saltwater crocodile (Crocodylus porosus) for cross-species amplification and to provide an estimate of inter- and intraspecific variation among four species of Neotropical crocodiles (C. rhombifer, C. intermedius, C. acutus, and C. moreletii). Our results indicated that with the exception of 2 loci in C. intermedius, all 10 microsatellite loci were successfully amplified in the 4 species, producing a set of variably sized alleles that ranged in number between 2 and 14 alleles per locus. Similarly, private alleles (i.e., unique alleles) also were reported in all 4 species for at least 3 loci. The mean observed and expected heterozygosities (averaged across species for all 10 loci combined) ranged from 0.39 to 0.77 and from 0.44 to 0.78, respectively. In addition to this, we evaluated these microsatellites in 2 populations of C. acutus and C. moreletii to assess their utility in estimating intraspecific levels of polymorphisms. These microsatellites also showed considerable allelic variation in population level analysis. The set of 10 microsatellite loci in our study had the potential to be used as a tool in population and conservation genetic studies of Neotropical crocodiles. PMID:25117304

  9. Multicolor FISH studies of male non-disjunction: Evidence for a paternal age effect

    SciTech Connect

    Griffin, D.K.; Millie, E.A.; Sheean, L.A.

    1994-09-01

    Approximately 5-10% of autosomal trisomies and the majority of sex chromosome aneuploidies are paternally derived, thus paternal non-disjunction is an important contributor to human chromosomal syndromes. We have been using multicolor FISH to screen for aneuploidy in sperm of normal males and to determine whether there is, among individuals or among chromosomes, variation in the likelihood of non-disjunction. Our initial studies based on analysis of 5000 sperm scored per chromosome in nine males identified significant differences in disomy rates for chromosomes 16, 18 and the sex chromosomes. We have now extended those analyses to a new series of 10 donors aged 22 to 45 to confirm or refute our observations of chromosome-specific differences in rates of disomy; to determine if the size of the centromeric (alpha satellite) sequences is related to non-disjunction frequency; and to determine if there is a paternal as well as a maternal age effect on non-disjunction. For these studies, we have used 3 color FISH for chromosomes 18 and the X and Y chromosomes to now score {approximately}20,000 sperm for each of 10 new donors. Our results provide little evidence for an effect of the size of the Y chromosome centromere on the frequency of sex chromosome disomy. However, we have found considerable variation in rates of disomy among individuals and have confirmed significant differences among chromosomes in the likelihood of non-disjunction; i.e., the rate of non-disjunction of the sex chromosomes is 3.5 -4 times greater than that of chromosome 18 and meiosis II errors are significantly more likely for the Y chromosome than for the X chromosome. Specifically, we have identified increases in the frequency of disomy 18 and both meiosis I (XY) and meiosis II (XX and YY) sex chromosome disomy although the effect is only significant for total sex chromosome disomy.

  10. Autism and increased paternal age related changes in global levels of gene expression regulation.

    PubMed

    Alter, Mark D; Kharkar, Rutwik; Ramsey, Keri E; Craig, David W; Melmed, Raun D; Grebe, Theresa A; Bay, R Curtis; Ober-Reynolds, Sharman; Kirwan, Janet; Jones, Josh J; Turner, J Blake; Hen, Rene; Stephan, Dietrich A

    2011-01-01

    A causal role of mutations in multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations in global levels of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for changes in the overall distribution of gene expression levels. For instance, in mice, variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in variance might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on RNA from peripheral blood lymphocytes (PBL) of children with autism (n?=?82) and controls (n?=?64). Variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance. A decrease in the variance in the distribution of gene expression levels in PBL was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Global regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other neurodevelopmental disorders. PMID:21379579

  11. Paternal age and congenital malformations in offspring in California, 1989-2002.

    PubMed

    Grewal, Jagteshwar; Carmichael, Suzan L; Yang, Wei; Shaw, Gary M

    2012-02-01

    This study examined the association between paternal age and a wide range of structural birth defects. Data were drawn from The California Birth Defects Monitoring Program, a population-based active surveillance system for collecting information on infants and fetuses with defects born between 1989 and 2002. The analysis included 46,114 cases with defects, plus a random sample of 36,838 non-malformed births. After adjustment for maternal age, risks of anomalies of the nervous system for 38 and 42 year-old fathers, as compared to 29 year-old fathers, were 1.05-fold [1.00, 1.11] and 1.10-fold [1.02, 1.18] higher, respectively. Similar results were observed for anomalies of the limbs, where 38 and 42 year-old fathers had a 1.06-fold [1.02, 1.11] and 1.11-fold [1.05, 1.18] higher risk, respectively. Risks of anomalies of the integument were 1.05-fold [1.00, 1.09] and 1.10-fold [1.03, 1.16] higher for 38 and 42 year olds, respectively. Young paternal age, i.e., less than 29 years, was associated with an increased risk of amniotic bands (OR: 0.87 [0.78, 0.97]), pyloric stenosis (OR: 0.93 [0.90, 0.96]) and anomalies of the great veins (OR: 0.93 [0.87, 1.00]). In sum, both advanced and young paternal age was associated with select birth defects in California between 1989 and 2002. PMID:21344170

  12. Estimating pollen flow using SSR markers and paternity exclusion: accounting for mistyping.

    PubMed

    Slavov, G T; Howe, G T; Gyaourova, A V; Birkes, D S; Adams, W T

    2005-09-01

    Highly informative genetic markers, such as simple sequence repeats (SSRs), can be used to directly measure pollen flow by parentage analysis. However, mistyping (i.e. false inference of genotypes caused by the occurrence of null alleles, mutations, and detection errors) can lead to substantial biases in the estimates obtained. Using computer simulations, we evaluated a direct method for estimating pollen immigration using SSR markers and a paternity exclusion approach. This method accounts for mistyping and does not rely on assumptions about the distribution of male reproductive success. If ignored, even minor rates of mistyping (1.5%) resulted in overestimating pollen immigration by up to 150%. When we required at least two mismatching loci before excluding candidate fathers from paternity, the resulting pollen immigration estimates had small biases for rates of mistyping up to 4.5%. Requiring at least three mismatches for exclusion was needed to minimize the upward biases of pollen immigration caused by rates of mistyping up to 10.5%. The minimum number of highly variable SSR loci needed to minimize cryptic gene flow and obtain reliable estimates of pollen immigration varied from five to seven for a sampling scheme applicable to most conifers (i.e. when paternal haplotypes can be unambiguously determined). Between five and nine highly variable SSR loci were needed for a more general sampling scheme that is applicable to all diploid seed plants. With moderately variable SSR markers, consistently accurate estimates of pollen immigration could be obtained only for rates of mistyping up to 4.5%. We developed the POLLEN FLOW (PFL) computer program which can be used to obtain unbiased and precise estimates of pollen immigration under a wide range of conditions, including population sizes as large as 600 parents and mistyping rates as high as 10.5%. PMID:16101777

  13. Hypomethylation of the paternally inherited LRRTM1 promoter linked to schizophrenia.

    PubMed

    Brucato, Nicolas; DeLisi, Lynn E; Fisher, Simon E; Francks, Clyde

    2014-10-01

    Epigenetic effects on psychiatric traits remain relatively under-studied, and it remains unclear what the sizes of individual epigenetic effects may be, or how they vary between different clinical populations. The gene LRRTM1 (chromosome 2p12) has previously been linked and associated with schizophrenia in a parent-of-origin manner in a set of affected siblings (LOD?=?4.72), indirectly suggesting a disruption of paternal imprinting at this locus in these families. From the same set of siblings that originally showed strong linkage at this locus, we analyzed 99 individuals using 454-bisulfite sequencing, from whole blood DNA, to measure the level of DNA methylation in the promoter region of LRRTM1. We also assessed seven additional loci that would be informative to compare. Paternal identity-by-descent sharing at LRRTM1, within sibling pairs, was linked to their similarity of methylation at the gene's promoter. Reduced methylation at the promoter showed a significant association with schizophrenia. Sibling pairs concordant for schizophrenia showed more similar methylation levels at the LRRTM1 promoter than diagnostically discordant pairs. The alleles of common SNPs spanning the locus did not explain this epigenetic linkage, which can therefore be considered as largely independent of DNA sequence variation and would not be detected in standard genetic association analysis. Our data suggest that hypomethylation at the LRRTM1 promoter, particularly of the paternally inherited allele, was a risk factor for the development of schizophrenia in this set of siblings affected with familial schizophrenia, and that had previously showed linkage at this locus in an affected-sib-pair context. PMID:25111784

  14. Paternal early experiences influence infant development through non-social mechanisms in Rhesus Macaques

    PubMed Central

    2015-01-01

    Background Early experiences influence the developing organism, with lifelong and potentially adaptive consequences. It has recently become clear that the effects of early experiences are not limited to the exposed generation, but can influence physiological and behavioral traits in the next generation. Mechanisms of transgenerational effects of parental early experiences on offspring development are often attributed to prenatal or postnatal parental influence, but recent data suggest that germ-line plasticity may also play a role in the transgenerational effects of early experiences. These non-genetic transgenerational effects are a potentially important developmental and evolutionary force, but the effects of parental experiences on behavior and physiology are not well understood in socially complex primates. In the non-human primate, the rhesus macaque, nursery rearing (NR) is an early life manipulation used for colony management purposes, and involves separating infants from parents early in life. We examined the effects of maternal and paternal early NR on infant rhesus macaque immunity, physiology, and behavior. Results We theorized that differences in behavior or physiology in the absence of parent-offspring social contact would point to biological and perhaps germ-line, rather than social, mechanisms of effect. Thus, all subjects were themselves NR. Male and female infant rhesus macaques (N= 206) were separated from parents and social groups in the first four days of life to undergo NR. These infants differed only in their degree of NR ancestry – whether their dams or sires were themselves NR. At 3-4 months of age, infants underwent a standardized biobehavioral assessment. Factors describing immunity, plasma cortisol, and emotion regulation were generated from these data using factor analysis. Paternal, but not maternal, NR was associated with greater emotionality and higher plasma cortisol, compared with infants born to CONTROL reared fathers. Conclusions These data suggest that macaque biobehavioral makeup is strongly influenced by paternal experiences, and via non-social mechanisms. PMID:26816514

  15. Rapid microsatellite development for tree peony and its implications

    PubMed Central

    2013-01-01

    Background Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences. Results In this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)n, with (G/C)n less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21–30 and 101–110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers. Conclusions The results of our large-scale SSR marker development using tree peony are valuable for investigating plant genomic structural evolution and elucidating phenotypic variation in this species during its evolution and artificial selection. The newly identified SSRs should be useful for genetic linkage map construction, QTL mapping, gene location and cloning, and molecular marker-assisted breeding. In addition, the genome-wide marker resources generated in this study should aid genomic studies of tree peony and related species. PMID:24341681

  16. [Paternal GNAS mutations: Which phenotypes? What genetic counseling?].

    PubMed

    Kottler, Marie-Laure

    2015-05-01

    Parental imprinting and the type of the genetic alteration play a determinant role in the phenotype expression of GNAS locus associated to pseudohypoparathyroidism (PHP). GNAS locus gives rise to several different messenger RNA transcripts that are derived from the paternal allele, the maternal allele, or both and can be either coding or non-coding. As a consequence, GNAS mutations lead to a wide spectrum of phenotypes. An alteration in the coding sequence of the gene leads to a haplo-insufficiency and a dysmorphic phenotype (Albright's syndrome or AHO). AHO is a clinical syndrome defined by specific physical features including short stature, obesity, round-shaped face, subcutaneous ossifications, brachymetarcapy (mainly of the 4th and 5th ray). If the alteration is on the maternal allele, there is a hormonal resistance to the PTH at the kidney level and to the TSH at the thyroid level. The phenotype is known as pseudohypoparathyroidism type 1a (PHP1a). If the alteration is on the paternal allele, ther