Stocking impacts the expression of candidate genes and physiological condition in introgressed brook charr (Salvelinus fontinalis) populations

PubMed Central

Lamaze, Fabien C; Garant, Dany; Bernatchez, Louis

2013-01-01

Translocation of plants and animal populations between environments is one of the major forms of anthropogenic perturbation experienced by pristine populations, and consequently, human-mediated hybridization by stocking practices between wild and exogenous conspecifics is of increasing concern. In this study, we compared the expression of seven candidate genes involved in multifactorial traits and regulatory pathways for growth as a function of level of introgressive hybridization between wild and domestic brook charr to test the null hypothesis of no effect of introgression on wild fish. Our analyses revealed that the expression of two of the genes tested, cytochrome c oxidase VIIa and the growth hormone receptor isoform I, was positively correlated with the level of introgression. We also observed a positive relationship between the extent of introgression and physiological status quantified by the Fulton's condition index. The expression of other genes was influenced by other variables, including year of sampling (reflecting different thermal conditions), sampling method and lake of origin. This is the first demonstration in nature that introgression from stocked populations has an impact on the expression of genes playing a role in important biological functions that may be related with fitness in wild introgressed populations. PMID:23467764

Life history traits and phenotypic selection among sunflower crop–wild hybrids and their wild counterpart: implications for crop allele introgression

PubMed Central

Kost, Matthew A; Alexander, Helen M; Jason Emry, D; Mercer, Kristin L

2015-01-01

Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop–wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop–wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early season traits to ascertain the likelihood, and routes, of crop allele introgression into wild sunflower populations. All cross types overwintered, emerged in the spring, and survived until flowering, indicating no early life history barriers to crop allele introgression. While selection indirectly favored earlier seedling emergence and taller early season seedlings, direct selection only favored greater early season leaf length. Further, there was cross type variation in the intensity of selection operating on leaf length. Thus, introgression of multiple early season crop-like traits, due to direct selection for greater early season leaf length, should not be impeded by any cross type and may proceed at different rates among generations. In sum, alleles underlying early season sunflower crop-like traits are likely to introgress into wild sunflower populations. PMID:26029263

Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression.

PubMed

Kost, Matthew A; Alexander, Helen M; Jason Emry, D; Mercer, Kristin L

2015-06-01

Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early season traits to ascertain the likelihood, and routes, of crop allele introgression into wild sunflower populations. All cross types overwintered, emerged in the spring, and survived until flowering, indicating no early life history barriers to crop allele introgression. While selection indirectly favored earlier seedling emergence and taller early season seedlings, direct selection only favored greater early season leaf length. Further, there was cross type variation in the intensity of selection operating on leaf length. Thus, introgression of multiple early season crop-like traits, due to direct selection for greater early season leaf length, should not be impeded by any cross type and may proceed at different rates among generations. In sum, alleles underlying early season sunflower crop-like traits are likely to introgress into wild sunflower populations.

An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes.

PubMed

Hohmann, Nora; Koch, Marcus A

2017-10-23

Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion.

The Genomic Signature of Crop-Wild Introgression in Maize

PubMed Central

Hufford, Matthew B.; Lubinksy, Pesach; Pyhäjärvi, Tanja; Devengenzo, Michael T.; Ellstrand, Norman C.; Ross-Ibarra, Jeffrey

2013-01-01

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes appeared resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these genomic regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly inform our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies. PMID:23671421

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes

PubMed Central

Sharbrough, Joel; Havird, Justin C.; Noe, Gregory R.; Warren, Jessica M.

2017-01-01

Abstract Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background. Therefore, mitonuclear interactions are also potentially relevant to hominin evolution. We performed a detailed accounting of mtDNA divergence among hominin lineages and used population-genomic data to test the hypothesis that mitonuclear incompatibilities have preferentially restricted the introgression of nuclear genes with mitochondrial functions. We found a small but significant underrepresentation of introgressed Neanderthal alleles at such nuclear loci. Structural analyses of mitochondrial enzyme complexes revealed that these effects are unlikely to be mediated by physically interacting sites in mitochondrial and nuclear gene products. We did not detect any underrepresentation of introgressed Denisovan alleles at mitochondrial-targeted loci, but this may reflect reduced power because locus-specific estimates of Denisovan introgression are more conservative. Overall, we conclude that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes. PMID:28854627

Widespread introgression of mountain hare genes into Fennoscandian brown hare populations.

PubMed

Levänen, Riikka; Thulin, Carl-Gustaf; Spong, Göran; Pohjoismäki, Jaakko L O

2018-01-01

In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.

Introgression of Aegilops speltoides segments in Triticum aestivum and the effect of the gametocidal genes.

PubMed

King, Julie; Grewal, Surbhi; Yang, Cai-Yun; Hubbart Edwards, Stella; Scholefield, Duncan; Ashling, Stephen; Harper, John A; Allen, Alexandra M; Edwards, Keith J; Burridge, Amanda J; King, Ian P

2018-02-12

Bread wheat (Triticum aestivum) has been through a severe genetic bottleneck as a result of its evolution and domestication. It is therefore essential that new sources of genetic variation are generated and utilized. This study aimed to generate genome-wide introgressed segments from Aegilops speltoides. Introgressions generated from this research will be made available for phenotypic analysis. Aegilops speltoides was crossed as the male parent to T. aestivum 'Paragon'. The interspecific hybrids were then backcrossed to Paragon. Introgressions were detected and characterized using the Affymetrix Axiom Array and genomic in situ hybridization (GISH). Recombination in the gametes of the F1 hybrids was at a level where it was possible to generate a genetic linkage map of Ae. speltoides. This was used to identify 294 wheat/Ae. speltoides introgressions. Introgressions from all seven linkage groups of Ae. speltoides were found, including both large and small segments. Comparative analysis showed that overall macro-synteny is conserved between Ae. speltoides and T. aestivum, but that Ae. speltoides does not contain the 4A/5A/7B translocations present in wheat. Aegilops speltoides has been reported to carry gametocidal genes, i.e. genes that ensure their transmission through the gametes to the next generation. Transmission rates of the seven Ae. speltoides linkage groups introgressed into wheat varied. A 100 % transmission rate of linkage group 2 demonstrates the presence of the gametocidal genes on this chromosome. A high level of recombination occurs between the chromosomes of wheat and Ae. speltoides, leading to the generation of large numbers of introgressions with the potential for exploitation in breeding programmes. Due to the gametocidal genes, all germplasm developed will always contain a segment from Ae. speltoides linkage group 2S, in addition to an introgression from any other linkage group. © The Authors 2017. Published by Oxford University Press on behalf of the Annals of Botany Company.

Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

PubMed Central

2012-01-01

Background If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. Results We first delimit a ca. 54,000 km2 area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. Conclusion The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the introgressed mitochondrial DNA and the signal derived from ecological niche modeling, we do not favor the hypothesis that foreign mitochondrial DNA was pulled into the T. macedonicus range by natural selection. PMID:22935041

Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models.

PubMed

Wielstra, Ben; Arntzen, Jan W

2012-08-30

If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. We first delimit a ca. 54,000 km(2) area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the introgressed mitochondrial DNA and the signal derived from ecological niche modeling, we do not favor the hypothesis that foreign mitochondrial DNA was pulled into the T. macedonicus range by natural selection.

Genetics of reproductive isolation in the Drosophila simulans clade: DNA marker-assisted mapping and characterization of a hybrid-male sterility gene, Odysseus (Ods).

PubMed

Perez, D E; Wu, C I; Johnson, N A; Wu, M L

1993-05-01

In this study, we address the question of whether there exist major genes that cause complete male sterility in the interspecific hybrids of Drosophila and, if they do, how these genes may be characterized at the molecular level. Our approach is to introgress small segments of the X chromosome from Drosophila mauritiana (or Drosophila sechellia) into Drosophila simulans by repeated backcrosses for more than 20 generations. The introgressions are monitored by both visible mutations and a series of DNA markers. We compare the extent of introgressions that cause male sterility with those that do not. If a major sterility factor exists, there should be a sharp boundary between these two classes of introgressions and their breakpoints should demarcate such a gene. Furthermore, if male sterility is the only major fitness effect associated with the introgression, recombination analysis should yield a pattern predicted by the classical three-point cross. Both the genetic and molecular analyses suggest the presence of a major sterility factor from D. mauritiana, which we named Odysseus (Ods), in the cytological interval of 16D. We thus formalize three criteria for inferring the existence of a major gene within an introgression: (1) complete penetrance of sterility, (2) complementarity in recombination analysis, and (3) physical demarcation. Introgressions of Ods from D. sechellia do not cause sterility. Twenty-two introgressions in our collection have breakpoints in this interval of about 500 kb, making it possible to delineate Ods more precisely for molecular identification. The recombination analysis also reveals the complexity of the introgressed segments--even relatively short ones may contain a second male sterility factor and partial viability genes and may also interfere with crossovers. The spermatogenic defects associated with Ods and/or a second factor were characterized by phase-contrast microscopy.

Adaptive introgression across species boundaries in Heliconius butterflies.

PubMed

Pardo-Diaz, Carolina; Salazar, Camilo; Baxter, Simon W; Merot, Claire; Figueiredo-Ready, Wilsea; Joron, Mathieu; McMillan, W Owen; Jiggins, Chris D

2012-01-01

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies.

Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference.

PubMed

Halas, Dominik; Simons, Andrew M

2014-01-01

Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We found evidence of multiple divergent populations within each species; much of the divergence within species has taken place during the Pleistocene. We also found evidence of a previously unknown cryptic species in the Upper Tennessee River which diverged from the remainder of the group during the Pliocene, and has undergone mitochondrial and nuclear introgression with E. zonale, in an apparent process of speciation reversal. We examined the effects that using varying types of recombination tests to eliminate the signal of recombination from nuclear loci would have on the phylogenetic placement of this introgressed lineage in our species tree analyses. Copyright © 2013 Elsevier Inc. All rights reserved.

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia.

PubMed

Wang, Ningning; Wang, Hongyan; Wang, Hui; Zhang, Di; Wu, Ying; Ou, Xiufang; Liu, Shuang; Dong, Zhenying; Liu, Bao

2010-08-26

It is widely recognized that interspecific hybridization may induce "genome shock", and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. A prominent component involved in the genome shock is reactivation of cryptic transposable elements (TEs) in the hybrid genome, which is often associated with alteration in the elements' epigenetic modifications like cytosine DNA methylation. We have previously reported that introgressants derived from hybridization between Oryza sativa (rice) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs, a copia retrotransposon Tos17 and a MITE mPing. It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants, their relevance to alteration in cytosine methylation, and their impact on expression of adjacent cellular genes. We document in this study that the Dart TE family was transpositionally reactivated followed by stabilization in all three studied introgressants (RZ1, RZ2 and RZ35) derived from introgressive hybridization between rice (cv. Matsumae) and Z. latifolia, while the TEs remained quiescent in the recipient rice genome. Transposon-display (TD) and sequencing verified the element's mobility and mapped the excisions and re-insertions to the rice chromosomes. Methylation-sensitive Southern blotting showed that the Dart TEs were heavily methylated along their entire length, and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line. Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted Dart-related TE copies indicated that whereas marked difference in the expression of all four genes in both tissues (leaf and root) were detected between the introgressants and their rice parental line under both normal and various stress conditions, the difference showed little association with the presence or absence of the newly mobilized Dart-related TEs. Introgressive hybridization has induced transpositional reactivation of the otherwise immobile Dart-related TEs in the parental rice line (cv. Matsumae), which was accompanied with a moderate alteration in the element's cytosine methylation. Significant difference in expression of the Dart-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions, but the alteration in gene expression was not coupled with the TEs.

Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther.

PubMed

Hostetler, Jeffrey A; Onorato, David P; Bolker, Benjamin M; Johnson, Warren E; O'Brien, Stephen J; Jansen, Deborah; Oli, Madan K

2012-01-01

Genetic introgression has been suggested as a management tool for mitigating detrimental effects of inbreeding depression, but the role of introgression in species conservation has been controversial, partly because population-level impacts of genetic introgressions are not well understood. Concerns about potential inbreeding depression in the endangered Florida panther (Puma concolor coryi) led to the release of eight female Texas pumas (P. c. stanleyana) into the Florida panther population in 1995. We used long-term reproductive data (1995-2008) collected from 61 female Florida panthers to estimate and model reproduction probability (probability of producing a litter) and litter size, and to investigate the influence of intentional genetic introgression on these parameters. Overall, 6-month probability of reproduction (±1SE) was 0.232 ± 0.021 and average litter size was 2.60 ± 0.09. Although F(1) admixed females had a lower reproduction probability than females with other ancestries, this was most likely because kittens born to F(1) females survive better; consequently, these females are unavailable for breeding until kittens are independent. There was no evidence for the effect of ancestry on litter size or of heterozygosity on probability of reproduction or litter size. In contrast, earlier studies have shown that genetic introgression positively affected Florida panther survival. Our results, along with those of earlier studies, clearly suggest that genetic introgression can have differential effects on components of fitness and highlight the importance of examining multiple demographic parameters when evaluating the effects of management actions.

[Effect of an introgression from Aegilops cylindrica host on manifestation of productivity traits in winter common wheat F2 plants].

PubMed

Kozub, N A; Sozinov, I A; sozinov, A A

2004-12-01

The effect of introgression of a chromosome 1D segment from Aegilops cylindrica to winter common wheat on productivity traits in F2 plants was studied using storage protein loci as genetic markers. An allele of the gliadin-coding Gli-D1 locus served as a marker of the introgression. Using of two- and three-locus interaction models, it was shown that the introgression tagged with Gli-D1 affected the manifestation of productivity traits (productive tillering, grain weight per plant and grain number per plant) through interaction with other marker storage protein loci: Glu-B1, Glu-D1, and Gli-B2.

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

PubMed Central

Pardo-Diaz, Carolina; Salazar, Camilo; Baxter, Simon W.; Merot, Claire; Figueiredo-Ready, Wilsea; Joron, Mathieu; McMillan, W. Owen; Jiggins, Chris D.

2012-01-01

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies. PMID:22737081

Introgression of wheat DNA markers from A, B and D genomes in early generation progeny of Aegilops cylindrica Host x Triticum aestivum L. hybrids.

PubMed

Schoenenberger, N; Felber, F; Savova-Bianchi, D; Guadagnuolo, R

2005-11-01

Introgression from allohexaploid wheat (Triticum aestivum L., AABBDD) to allotetraploid jointed goatgrass (Aegilops cylindrica Host, CCDD) can take place in areas where the two species grow in sympatry and hybridize. Wheat and Ae. cylindrica share the D genome, issued from the common diploid ancestor Aegilops tauschii Coss. It has been proposed that the A and B genome of bread wheat are secure places to insert transgenes to avoid their introgression into Ae. cylindrica because during meiosis in pentaploid hybrids, A and B genome chromosomes form univalents and tend to be eliminated whereas recombination takes place only in D genome chromosomes. Wheat random amplified polymorphic DNA (RAPD) fragments, detected in intergeneric hybrids and introgressed to the first backcross generation with Ae. cylindrica as the recurrent parent and having a euploid Ae. cylindrica chromosome number or one supernumerary chromosome, were assigned to wheat chromosomes using Chinese Spring nulli-tetrasomic wheat lines. Introgressed fragments were not limited to the D genome of wheat, but specific fragments of A and B genomes were also present in the BC1. Their presence indicates that DNA from any of the wheat genomes can introgress into Ae. cylindrica. Successfully located RAPD fragments were then converted into highly specific and easy-to-use sequence characterised amplified regions (SCARs) through sequencing and primer design. Subsequently these markers were used to characterise introgression of wheat DNA into a BC1S1 family. Implications for risk assessment of genetically modified wheat are discussed.

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

PubMed Central

Staubach, Fabian; Lorenc, Anna; Messer, Philipp W.; Tang, Kun; Petrov, Dmitri A.; Tautz, Diethard

2012-01-01

General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin. PMID:22956910

[Molecular-genetic analysis of wheat (T. aestivum L.) genome with introgression of Ae. cylindrica Host genetic elements].

PubMed

Galaev, A V; Sivolap, Iu M

2005-01-01

Wheat-aegilops hybrid plants Triticum aestivum L. (2n = 42) x Aegilops cylindrica Host (2n = 28) were investigated with using microsatellite markers. In two BC1F9 lines some genome modifications connected with losing DNA fragments of initial variety or appearing of Aegilops genome elements were detected. In some investigated hybrids new amplicons lacking in parental plants were found. Substitution of wheat chromosomes for aegilops chromosomes was not revealed. Analysis of microsatellite loci in BC2F5 plants showed stable introgression of aegilops genetic elements into wheat; elimination of some transferred aegilops DNA fragments in the course of backcrossing; decreasing size of introgressive elements after backcrossing. Introgressive lines were classified according to genome changes.

Conspecific Crop-Weed Introgression Influences Evolution of Weedy Rice (Oryza sativa f. spontanea) across a Geographical Range

PubMed Central

Xia, Han-Bing; Wang, Wei; Xia, Hui; Zhao, Wei; Lu, Bao-Rong

2011-01-01

Background Introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. Outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop. Methodology/Principal Findings Eleven weedy rice (Oryza sativa f. spontanea) populations from China were analyzed using microsatellite (SSR) fingerprints to study outcrossing rate and its relationship with genetic variability and differentiation. To estimate outcrossing, six highly polymorphic SSR loci were used to analyze >5500 progeny from 216 weedy rice families, applying a mixed mating model; to estimate genetic diversity and differentiation, 22 SSR loci were analyzed based on 301 weedy individuals. Additionally, four weed-crop shared SSR loci were used to estimate the influence of introgression from rice cultivars on weedy rice differentiation. Outcrossing rates varied significantly (0.4∼11.7%) among weedy rice populations showing relatively high overall Nei's genetic diversity (0.635). The observed heterozygosity was significantly correlated with outcrossing rates among populations (r2 = 0.783; P<0.001) although no obvious correlation between outcrossing rates and genetic diversity parameters was observed. Allelic introgression from rice cultivars to their coexisting weedy rice was detected. Weedy rice populations demonstrated considerable genetic differentiation that was correlated with their spatial distribution (r2 = 0.734; P<0.001), and possibly also influenced by the introgression from rice cultivars. Conclusions/Significance Outcrossing rates can significantly affect heterozygosity of populations, which may shape the evolutionary potential of weedy rice. Introgression from the conspecific crop rice can influence the genetic differentiation and possibly evolution of its coexisting weedy rice populations. PMID:21249201

Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

PubMed Central

Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

2018-01-01

Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation.

PubMed

Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun; Lu, Bao-Rong

2018-02-01

Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice ( Oryza rufipogon ) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars ( O. sativa ), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression.

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus.

PubMed

Whitney, Kenneth D; Randell, Rebecca A; Rieseberg, Loren H

2010-07-01

*Adaptive trait introgression is increasingly recognized as common. However, it is unclear whether adaptive genetic exchanges typically affect only a single trait, or instead affect multiple aspects of the phenotype. Here, we examine introgression of abiotic tolerance traits between two hybridizing North American sunflower species, Helianthus annuus and Helianthus debilis. *In two common gardens in the hybrid range, we measured 10 ecophysiological, phenological, and architectural traits for parents and their natural and artificial hybrids, and examined how fitness covaried with trait values. *Eight of the 10 traits showed patterns consistent with introgression from H. debilis into H. annuus, and suggested that H. debilis-like traits allowing rapid growth and reproduction before summer heat and drought have been favored in the hybrid range. Natural selection currently favors BC(1) hybrids with H. debilis-like branching traits. *We demonstrate that introgression has altered multiple aspects of the H. annuus phenotype in an adaptive manner, has affected traits relevant to both biotic and abiotic environments, and may have aided expansion of the H. annuus range into central Texas, USA.

[Detection of the introgression of genome elements of the Aegilops cylindrica host. into the Triticum aestivum L. genome by ISSR and SSR analysis].

PubMed

Galaev, A V; Babaiants, L T; Sivolap, Iu M

2004-12-01

To reveal sites of the donor genome in wheat crossed with Aegilops cylindrica, which acquired conferred resistance to fungal diseases, a comparative analysis of introgressive and parental forms was conducted. Two systems of PCR analysis, ISSR and SSR-PCR, were employed. Upon use of 7 ISSR primers in genotypes of 30 individual plants BC1 F9 belonging to lines 5/55-91 and 5/20-91, 19 ISSR loci were revealed and assigned to introgressive fragments of Aegilops cylindrica genome in Triticum aestivum. The 40 pairs of SSR primers allowed the detection of seven introgressive alleles; three of these alleles were located on common wheat chromosomes in the B genome, while four alleles, in the D genome. Based on data of microsatellite analysis, it was assumed that the telomeric region of the long arm of common wheat chromosome 6A also changed. ISSR and SSR methods were shown to be effective for detecting variability caused by introgression of foreign genetic material into the genome of common wheat.

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

PubMed Central

Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

2016-01-01

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece

PubMed Central

Vukić, Jasna; Šanda, Radek; Doadrio, Ignacio

2016-01-01

Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese. PMID:27906993

Variation and Functional Impact of Neanderthal Ancestry in Western Asia

PubMed Central

Taskent, Recep Ozgur; Alioglu, Nursen Duha; Fer, Evrim

2017-01-01

Abstract Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out of Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey. Our results confirmed previous observations that contemporary Western Asian populations, on an average, have lower levels of Neanderthal-introgressed DNA relative to other Eurasian populations. Modern Western Asians also show comparatively high variability in Neanderthal ancestry, which may be attributed to the complex demographic history of the region. We further replicated the previously described depletion of putatively functional sequences among Neanderthal-introgressed haplotypes. Still, we find dozens of common Neanderthal-introgressed haplotypes in the Turkish sample associated with human phenotypes, including anthropometric and metabolic traits, as well as the immune response. One of these haplotypes is unusually long and harbors variants that affect the expression of members of the CCR gene family and are associated with celiac disease. Overall, our results paint a complex first picture of the genomic impact of Neanderthal introgression in the Western Asian populations. PMID:29040546

Historic hybridization and persistence of a novel mito-nuclear combination in red-backed voles (genus Myodes)

PubMed Central

Runck, Amy M; Matocq, Marjorie D; Cook, Joseph A

2009-01-01

Background The role of hybridization in generating diversity in animals is an active area of discovery and debate. We assess hybridization across a contact zone of northern (Myodes rutilus) and southern (M. gapperi) red-backed voles using variation in skeletal features and both mitochondrial and nuclear loci. This transect extends approximately 550 km along the North Pacific Coast of North America and encompasses 26 populations (n = 485). We establish the history, geographic extent and directionality of hybridization, determine whether hybridization is ongoing, and assess the evolutionary stability of novel genomic combinations. Results Identification of M. rutilus and M. gapperi based on the degree of closure of the post-palatal bridge was concordant with the distribution of diagnostic nuclear MYH6 alleles; however, an 80 km zone of introgressed populations was identified. The introgressant form is characterized by having mitochondrial haplotypes closely related to the northern M. rutilus on a nuclear background and morphological characteristics of southern M. gapperi. Conclusion Introgression appears to have been historic as pure populations of M. rutilus are now isolated to the north from introgressants or pure M. gapperi by the LeConte Glacier. As we do not find pure M. rutilus or M. gapperi individuals throughout the distribution of the introgressant form, it appears that the introgressants are a self-sustaining entity not requiring continued hybridization between pure parental forms to generate this novel combination of characters. PMID:19460158

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

PubMed

Abrouk, Michael; Balcárková, Barbora; Šimková, Hana; Komínkova, Eva; Martis, Mihaela M; Jakobson, Irena; Timofejeva, Ljudmilla; Rey, Elodie; Vrána, Jan; Kilian, Andrzej; Järve, Kadri; Doležel, Jaroslav; Valárik, Miroslav

2017-02-01

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Divergence with gene flow within the recent chipmunk radiation (Tamias)

PubMed Central

Sullivan, J; Demboski, J R; Bell, K C; Hird, S; Sarver, B; Reid, N; Good, J M

2014-01-01

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection. PMID:24781803

Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

PubMed

Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

The variable genomic architecture of isolation between hybridizing species of house mice.

PubMed

Teeter, Katherine C; Thibodeau, Lisa M; Gompert, Zachariah; Buerkle, C Alex; Nachman, Michael W; Tucker, Priscilla K

2010-02-01

Studies of the genetics of hybrid zones can provide insight into the genomic architecture of species boundaries. By examining patterns of introgression of multiple loci across a hybrid zone, it may be possible to identify regions of the genome that have experienced selection. Here, we present a comparison of introgression in two replicate transects through the house mouse hybrid zone through central Europe, using data from 41 single nucleotide markers. Using both genomic and geographic clines, we found many differences in patterns of introgression between the two transects, as well as some similarities. We found that many loci may have experienced the effects of selection at linked sites, including selection against hybrid genotypes, as well as positive selection in the form of genotypes introgressed into a foreign genetic background. We also found many positive associations of conspecific alleles among unlinked markers, which could be caused by epistatic interactions. Different patterns of introgression in the two transects highlight the challenge of using hybrid zones to identify genes underlying isolation and raise the possibility that the genetic basis of isolation between these species may be dependent on the local population genetic make-up or the local ecological setting.

Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach

PubMed Central

Chiang, Yu-Chung; Huang, Bing-Hong; Chang, Chun-Wen; Wan, Yu-Ting; Lai, Shih-Jie; Huang, Shong; Liao, Pei-Chun

2013-01-01

The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct. PMID:23591840

Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar.

PubMed

Goedbloed, Daniel J; van Hooft, Pim; Lutz, Walburga; Megens, Hendrik-Jan; van Wieren, Sip E; Ydenberg, Ron C; Prins, Herbert H T

2015-12-01

Wildlife immune genes are subject to natural selection exerted by pathogens. In contrast, domestic immune genes are largely protected from pathogen selection by veterinary care. Introgression of domestic alleles into the wild could lead to increased disease susceptibility, but observations are scarce due to low introgression rates, low disease prevalence and reduced survival of domestic hybrids. Here we report the first observation of a deleterious effect of domestic introgression on disease prevalence in a free-living large mammal. A fraction of 462 randomly sampled free-living European wild boar (Sus scrofa) was genetically identified as recent wild boar-domestic pig hybrids based on 351 SNP data. Analysis of antibody prevalence against the bacterial pathogen Mycoplasma hyopneumoniae (Mhyo) showed an increased Mhyo prevalence in wild-domestic hybrids. We argue that the most likely mechanism explaining the observed association between domestic hybrid status and Mhyo antibody prevalence would be introgression of deleterious domestic alleles. We hypothesise that large-scale use of antibiotics in the swine breeding sector may have played a role in shaping the relatively deleterious properties of domestic swine immune genes and that domestic introgression may also lead to increased wildlife disease susceptibility in the case of other species.

Genome characterization of a breeding line derived from a cross between Oryza sativa and Oryza rufipogon.

PubMed

Keong, B P; Harikrishna, J A

2012-02-01

A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

PubMed Central

2017-01-01

Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity. PMID:28796803

Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression

PubMed Central

Rong, Jun; Xu, Shuhua; Meirmans, Patrick G.; Vrieling, Klaas

2013-01-01

Background and Aims Transgene introgression from crops into wild relatives may increase the resistance of wild plants to herbicides, insects, etc. The chance of transgene introgression depends not only on the rate of hybridization and the establishment of hybrids in local wild populations, but also on the metapopulation dynamics of the wild relative. The aim of the study was to estimate gene flow in a metapopulation for assessing and managing the risks of transgene introgression. Methods Wild carrots (Daucus carota) were sampled from 12 patches in a metapopulation. Eleven microsatellites were used to genotype wild carrots. Genetic structure was estimated based on the FST statistic. Contemporary (over the last several generations) and historical (over many generations) gene flow was estimated with assignment and coalescent methods, respectively. Key Results The genetic structure in the wild carrot metapopulation was moderate (FST = 0·082) and most of the genetic variation resided within patches. A pattern of isolation by distance was detected, suggesting that most of the gene flow occurred between neighbouring patches (≤1 km). The mean contemporary gene flow was 5 times higher than the historical estimate, and the correlation between them was very low. Moreover, the contemporary gene flow in roadsides was twice that in a nature reserve, and the correlation between contemporary and historical estimates was much higher in the nature reserve. Mowing of roadsides may contribute to the increase in contemporary gene flow. Simulations demonstrated that the higher contemporary gene flow could accelerate the process of transgene introgression in the metapopulation. Conclusions Human disturbance such as mowing may alter gene flow patterns in wild populations, affecting the metapopulation dynamics of wild plants and the processes of transgene introgression in the metapopulation. The risk assessment and management of transgene introgression and the control of weeds need to take metapopulation dynamics into consideration. PMID:24052560

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

PubMed Central

Grossen, Christine; Keller, Lukas; Biebach, Iris; Croll, Daniel

2014-01-01

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. PMID:24945814

Massive introgression drives species radiation at the range limit of Anopheles gambiae.

PubMed

Vicente, José L; Clarkson, Christopher S; Caputo, Beniamino; Gomes, Bruno; Pombi, Marco; Sousa, Carla A; Antao, Tiago; Dinis, João; Bottà, Giordano; Mancini, Emiliano; Petrarca, Vincenzo; Mead, Daniel; Drury, Eleanor; Stalker, James; Miles, Alistair; Kwiatkowski, Dominic P; Donnelly, Martin J; Rodrigues, Amabélia; Torre, Alessandra Della; Weetman, David; Pinto, João

2017-04-18

Impacts of introgressive hybridisation may range from genomic erosion and species collapse to rapid adaptation and speciation but opportunities to study these dynamics are rare. We investigated the extent, causes and consequences of a hybrid zone between Anopheles coluzzii and Anopheles gambiae in Guinea-Bissau, where high hybridisation rates appear to be stable at least since the 1990s. Anopheles gambiae was genetically partitioned into inland and coastal subpopulations, separated by a central region dominated by A. coluzzii. Surprisingly, whole genome sequencing revealed that the coastal region harbours a hybrid form characterised by an A. gambiae-like sex chromosome and massive introgression of A. coluzzii autosomal alleles. Local selection on chromosomal inversions may play a role in this process, suggesting potential for spatiotemporal stability of the coastal hybrid form and providing resilience against introgression of medically-important loci and traits, found to be more prevalent in inland A. gambiae.

Massive introgression drives species radiation at the range limit of Anopheles gambiae

PubMed Central

Vicente, José L.; Clarkson, Christopher S.; Caputo, Beniamino; Gomes, Bruno; Pombi, Marco; Sousa, Carla A.; Antao, Tiago; Dinis, João; Bottà, Giordano; Mancini, Emiliano; Petrarca, Vincenzo; Mead, Daniel; Drury, Eleanor; Stalker, James; Miles, Alistair; Kwiatkowski, Dominic P.; Donnelly, Martin J.; Rodrigues, Amabélia; Torre, Alessandra della; Weetman, David; Pinto, João

2017-01-01

Impacts of introgressive hybridisation may range from genomic erosion and species collapse to rapid adaptation and speciation but opportunities to study these dynamics are rare. We investigated the extent, causes and consequences of a hybrid zone between Anopheles coluzzii and Anopheles gambiae in Guinea-Bissau, where high hybridisation rates appear to be stable at least since the 1990s. Anopheles gambiae was genetically partitioned into inland and coastal subpopulations, separated by a central region dominated by A. coluzzii. Surprisingly, whole genome sequencing revealed that the coastal region harbours a hybrid form characterised by an A. gambiae-like sex chromosome and massive introgression of A. coluzzii autosomal alleles. Local selection on chromosomal inversions may play a role in this process, suggesting potential for spatiotemporal stability of the coastal hybrid form and providing resilience against introgression of medically-important loci and traits, found to be more prevalent in inland A. gambiae. PMID:28417969

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

DOE PAGES

Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya; ...

2015-01-24

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicatedmore » a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. Ultimately, these results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.« less

Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation.

PubMed

Scascitelli, M; Whitney, K D; Randell, R A; King, Matthew; Buerkle, C A; Rieseberg, L H

2010-02-01

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south-central USA: the common sunflower, Helianthus annuus ssp. annuus; a near-endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long-term migration rates were high, genome-wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of FST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson-Dobzhansky-Muller incompatibility.

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression.

PubMed

Clark, Lindsay V; Stewart, J Ryan; Nishiwaki, Aya; Toma, Yo; Kjeldsen, Jens Bonderup; Jørgensen, Uffe; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko; Sacks, Erik J

2015-07-01

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors

PubMed Central

Dannemann, Michael; Andrés, Aida M.; Kelso, Janet

2016-01-01

Pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. Although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. Archaic humans, who lived in Europe and Western Asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. It is therefore conceivable that modern humans entering Europe and Western Asia who admixed with them obtained a substantial immune advantage from the introgression of archaic alleles. Here we document a cluster of three Toll-like receptors (TLR6-TLR1-TLR10) in modern humans that carries three distinct archaic haplotypes, indicating repeated introgression from archaic humans. Two of these haplotypes are most similar to the Neandertal genome, and the third haplotype is most similar to the Denisovan genome. The Toll-like receptors are key components of innate immunity and provide an important first line of immune defense against bacteria, fungi, and parasites. The unusually high allele frequencies and unexpected levels of population differentiation indicate that there has been local positive selection on multiple haplotypes at this locus. We show that the introgressed alleles have clear functional effects in modern humans; archaic-like alleles underlie differences in the expression of the TLR genes and are associated with reduced microbial resistance and increased allergic disease in large cohorts. This provides strong evidence for recurrent adaptive introgression at the TLR6-TLR1-TLR10 locus, resulting in differences in disease phenotypes in modern humans. PMID:26748514

Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers.

PubMed

Fasahat, P; Muhammad, K; Abdullah, A; Wickneswari, R

2012-09-26

A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.

When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

PubMed Central

Shen, Jinhui; Borek, Dominika; Robbins, Robert K.; Opler, Paul A.; Otwinowski, Zbyszek; Grishin, Nick V.

2017-01-01

Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon. Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon. About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery. PMID:28179510

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicatedmore » a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. Ultimately, these results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.« less

Crossability of Triticum urartu and Triticum monococcum Wheats, Homoeologous Recombination, and Description of a Panel of Interspecific Introgression Lines

PubMed Central

Fricano, Agostino; Brandolini, Andrea; Rossini, Laura; Sourdille, Pierre; Wunder, Joerg; Effgen, Sigi; Hidalgo, Alyssa; Erba, Daniela; Piffanelli, Pietro; Salamini, Francesco

2014-01-01

Triticum monococcum (genome Am) and T. urartu (genome Au) are diploid wheats, with the first having been domesticated in the Neolithic Era and the second being a wild species. In a germplasm collection, rare wild T. urartu lines with the presence of T. monococcum alleles were found. This stimulated our interest to develop interspecific introgression lines of T. urartu in T. monococcum, a breeding tool currently implemented in several crop species. Moreover, the experiments reported were designed to reveal the existence in nature of Am/Au intermediate forms and to clarify whether the two species are at least marginally sexually compatible. From hand-made interspecific crosses, almost-sterile F1 plants were obtained when the seed-bearing parent was T. monococcum. A high degree of fertility was, however, evident in some advanced generations, particularly when T. urartu donors were molecularly more related to T. monococcum. Analysis of the marker populations demonstrated chromosome pairing and recombination in F1 hybrid plants. Forty-six introgression lines were developed using a line of T. monococcum with several positive agronomic traits as a recurrent parent. Microsatellite markers were tested on Au and Am genomes, ordered in a T. monococcum molecular map, and used to characterize the exotic DNA fragments present in each introgression line. In a test based on 28 interspecific introgression lines, the existence of genetic variation associated with T. urartu chromosome fragments was proven for the seed content of carotenoids, lutein, β-cryptoxanthin, and zinc. The molecular state of available introgression lines is summarized. PMID:25147190

Variation and Functional Impact of Neanderthal Ancestry in Western Asia.

PubMed

Taskent, Recep Ozgur; Alioglu, Nursen Duha; Fer, Evrim; Melike Donertas, Handan; Somel, Mehmet; Gokcumen, Omer

2017-12-01

Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out of Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey. Our results confirmed previous observations that contemporary Western Asian populations, on an average, have lower levels of Neanderthal-introgressed DNA relative to other Eurasian populations. Modern Western Asians also show comparatively high variability in Neanderthal ancestry, which may be attributed to the complex demographic history of the region. We further replicated the previously described depletion of putatively functional sequences among Neanderthal-introgressed haplotypes. Still, we find dozens of common Neanderthal-introgressed haplotypes in the Turkish sample associated with human phenotypes, including anthropometric and metabolic traits, as well as the immune response. One of these haplotypes is unusually long and harbors variants that affect the expression of members of the CCR gene family and are associated with celiac disease. Overall, our results paint a complex first picture of the genomic impact of Neanderthal introgression in the Western Asian populations. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

PubMed Central

Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya; Toma, Yo; Kjeldsen, Jens Bonderup; Jørgensen, Uffe; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko

2015-01-01

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1–39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6–27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars. PMID:25618143

Genomic Analysis Reveals Hypoxia Adaptation in the Tibetan Mastiff by Introgression of the Gray Wolf from the Tibetan Plateau.

PubMed

Miao, Benpeng; Wang, Zhen; Li, Yixue

2017-03-01

The Tibetan Mastiff (TM), a native of the Tibetan Plateau, has quickly adapted to the extreme highland environment. Recently, the impact of positive selection on the TM genome was studied and potential hypoxia-adaptive genes were identified. However, the origin of the adaptive variants remains unknown. In this study, we investigated the signature of genetic introgression in the adaptation of TMs with dog and wolf genomic data from different altitudes in close geographic proximity. On a genome-wide scale, the TM was much more closely related to other dogs than wolves. However, using the 'ABBA/BABA' test, we identified genomic regions from the TM that possibly introgressed from Tibetan gray wolf. Several of the regions, including the EPAS1 and HBB loci, also showed the dominant signature of selective sweeps in the TM genome. We validated the introgression of the two loci by excluding the possibility of convergent evolution and ancestral polymorphisms and examined the haplotypes of all available canid genomes. The estimated time of introgression based on a non-coding region of the EPAS1 locus mostly overlapped with the Paleolithic era. Our results demonstrated that the introgression of hypoxia adaptive genes in wolves from the highland played an important role for dogs living in hypoxic environments, which indicated that domestic animals could acquire local adaptation quickly by secondary contact with their wild relatives. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

PubMed

Bosse, Mirte; Lopes, Marcos S; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Frantz, Laurent A F; Harlizius, Barbara; Bastiaansen, John W M; Groenen, Martien A M

2015-12-22

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs. © 2015 The Author(s).

Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

PubMed

Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

2013-01-01

Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

Factors influencing gene introgression into the allotetraploid Coffea arabica L. from its diploid relatives.

PubMed

Herrera, Juan C; Combes, Marie C; Cortina, Hernando; Lashermes, Philippe

2004-12-01

Factors controlling gene introgression into cultivated arabica coffee (Coffea arabica L.) were investigated. Interspecific triploid hybrid plants between the tetraploid species C. arabica (2n = 44) and a diploid species (2n = 22), either Coffea canephora or Coffea eugenioides, were backcrossed to C. arabica (male parent). Flow cytometric analysis of the nuclear DNA content revealed that most of the BC(1) individuals derived from triploid hybrids involving C. eugenioides were tetraploid or nearly tetraploid. Among the gametes produced by the interspecific triploid hybrids, those possessing approximately 22 chromosomes appeared strongly favored. The amount of introgression in BC(1) individuals (21 and 43 for the BC(1) progenies involving C. canephora and C. eugenioides, respectively) was estimated using species-specific microsatellite markers. A large number of introgressed markers was observed in all BC(1) individuals. Nevertheless, while the frequency of introgressed markers seemed as expected, assuming random chromosome segregation and diploid gamete formation, in the BC(1) derived from triploid hybrids involving C. canephora, this frequency appeared significantly lower in the BC(1) derived from triploid hybrids involving C. eugenioides. Furthermore, the comparison of reciprocal progenies between C. arabica and triploid interspecific hybrids (C. arabica x C. canephora) used as male or female parent revealed a very strong effect of the backcross direction.

Metabolic Profiling and Physiological Analysis of a Novel Rice Introgression Line with Broad Leaf Size

PubMed Central

Zhao, Xiuqin; Zhang, Guilian; Wang, Yun; Zhang, Fan; Wang, Wensheng; Zhang, Wenhao; Fu, Binying; Xu, Jianlong; Li, Zhikang

2015-01-01

A rice introgression line, NIL-SS1, and its recurrent parent, Teqing, were used to investigate the influence of the introgression segment on plant growth. The current research showed NIL-SS1 had an increased flag leaf width, total leaf area, spikelet number per panicle and grain yield, but a decreased photosynthetic rate. The metabolite differences in NIL-SS1 and Teqing at different developmental stages were assessed using gas chromatography—mass spectrometry technology. Significant metabolite differences were observed across the different stages. NIL-SS1 increased the plant leaf nitrogen content, and the greatest differences between NIL-SS1 and Teqing occurred at the booting stage. Compared to Teqing, the metabolic phenotype of NIL-SS1 at the booting stage has closer association with those at the flowering stage. The introgression segment induced more active competition for sugars and organic acids (OAs) from leaves to the growing young spikes, which resulted in more spikelet number per plant (SNP). The results indicated the introgression segment could improve rice grain yield by increasing the SNP and total leaf area per plant, which resulted from the higher plant nitrogen content across growth stages and stronger competition for sugars and OAs of young spikes at the booting stage. PMID:26713754

Pervasive antagonistic interactions among hybrid incompatibility loci

PubMed Central

Josway, Sarah

2017-01-01

Species barriers, expressed as hybrid inviability and sterility, are often due to epistatic interactions between divergent loci from two lineages. Theoretical models indicate that the strength, direction, and complexity of these genetic interactions can strongly affect the expression of interspecific reproductive isolation and the rates at which new species evolve. Nonetheless, empirical analyses have not quantified the frequency with which loci are involved in interactions affecting hybrid fitness, and whether these loci predominantly interact synergistically or antagonistically, or preferentially involve loci that have strong individual effects on hybrid fitness. We systematically examined the prevalence of interactions between pairs of short chromosomal regions from one species (Solanum habrochaites) co-introgressed into a heterospecific genetic background (Solanum lycopersicum), using lines containing pairwise combinations of 15 chromosomal segments from S. habrochaites in the background of S. lycopersicum (i.e., 95 double introgression lines). We compared the strength of hybrid incompatibility (either pollen sterility or seed sterility) expressed in each double introgression line to the expected additive effect of its two component single introgressions. We found that epistasis was common among co-introgressed regions. Interactions for hybrid dysfunction were substantially more prevalent in pollen fertility compared to seed fertility phenotypes, and were overwhelmingly antagonistic (i.e., double hybrids were less unfit than expected from additive single introgression effects). This pervasive antagonism is expected to attenuate the rate at which hybrid infertility accumulates among lineages over time (i.e., giving diminishing returns as more reproductive isolation loci accumulate), as well as decouple patterns of accumulation of sterility loci and hybrid incompatibility phenotypes. This decoupling effect might explain observed differences between pollen and seed fertility in their fit to theoretical predictions of the accumulation of isolation loci, including the ‘snowball’ effect. PMID:28604770

Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams.

PubMed

Young, Michael K; Isaak, Daniel J; McKelvey, Kevin S; Wilcox, Taylor M; Bingham, Daniel M; Pilgrim, Kristine L; Carim, Kellie J; Campbell, Matthew R; Corsi, Matthew P; Horan, Dona L; Nagel, David E; Schwartz, Michael K

2016-01-01

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.S. northern Rocky Mountains. A consensus model performed well (AUC, 0.78-0.86; classification success, 72-82%; 10-fold cross validation, 70-82%) and predicted that rainbow trout introgression was significantly associated with warmer water temperatures, larger streams, proximity to warmer habitats and to recent sources of rainbow trout propagules, presence within the historical range of rainbow trout, and locations further east. Assuming that water temperatures will continue to rise in response to climate change and that levels of introgression outside the historical range of rainbow trout will equilibrate with those inside that range, we applied six scenarios across a 55,234-km stream network that forecast 9.5-74.7% declines in the amount of habitat occupied by westslope cutthroat trout populations of conservation value, but not the wholesale loss of such populations. We conclude that introgression between these taxa is predictably related to environmental conditions, many of which can be manipulated to foster largely genetically intact populations of westslope cutthroat trout and help managers prioritize conservation activities.

Introgressive hybridization: brown bears as vectors for polar bear alleles.

PubMed

Hailer, Frank

2015-03-01

The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male-biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture-free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach. © 2015 John Wiley & Sons Ltd.

Molecular footprints of the Holocene retreat of dwarf birch in Britain

PubMed Central

Wang, Nian; Borrell, James S; Bodles, William J A; Kuttapitiya, Anasuya; Nichols, Richard A; Buggs, Richard J A

2014-01-01

Past reproductive interactions among incompletely isolated species may leave behind a trail of introgressed alleles, shedding light on historical range movements. Betula pubescens is a widespread native tetraploid tree species in Britain, occupying habitats intermediate to those of its native diploid relatives, B. pendula and B. nana. Genotyping 1134 trees from the three species at 12 microsatellite loci, we found evidence of introgression from both diploid species into B. pubescens, despite the ploidy difference. Surprisingly, introgression from B. nana, a dwarf species whose present range is highly restricted in northern, high-altitude peat bogs, was greater than introgression from B. pendula, which is morphologically similar to B. pubescens and has a substantially overlapping range. A cline of introgression from B. nana was found extending into B. pubescens populations far to the south of the current B. nana range. We suggest that this genetic pattern is a footprint of a historical decline and/or northwards shift in the range of B. nana populations due to climate warming in the Holocene. This is consistent with pollen records that show a broader, more southerly distribution of B. nana in the past. Ecological niche modelling predicts that B. nana is adapted to a larger range than it currently occupies, suggesting additional factors such as grazing and hybridization may have exacerbated its decline. We found very little introgression between B. nana and B. pendula, despite both being diploid, perhaps because their distributions in the past have rarely overlapped. Future conservation of B. nana may partly depend on minimization of hybridization with B. pubescens, and avoidance of planting B. pendula near B. nana populations. PMID:24762172

Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams

PubMed Central

Young, Michael K.; Isaak, Daniel J.; McKelvey, Kevin S.; Wilcox, Taylor M.; Pilgrim, Kristine L.; Carim, Kellie J.; Campbell, Matthew R.; Corsi, Matthew P.; Horan, Dona L.; Nagel, David E.; Schwartz, Michael K.

2016-01-01

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.S. northern Rocky Mountains. A consensus model performed well (AUC, 0.78–0.86; classification success, 72–82%; 10-fold cross validation, 70–82%) and predicted that rainbow trout introgression was significantly associated with warmer water temperatures, larger streams, proximity to warmer habitats and to recent sources of rainbow trout propagules, presence within the historical range of rainbow trout, and locations further east. Assuming that water temperatures will continue to rise in response to climate change and that levels of introgression outside the historical range of rainbow trout will equilibrate with those inside that range, we applied six scenarios across a 55,234-km stream network that forecast 9.5–74.7% declines in the amount of habitat occupied by westslope cutthroat trout populations of conservation value, but not the wholesale loss of such populations. We conclude that introgression between these taxa is predictably related to environmental conditions, many of which can be manipulated to foster largely genetically intact populations of westslope cutthroat trout and help managers prioritize conservation activities. PMID:27828980

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

USGS Publications Warehouse

Kazyak, David C.; Rash, Jacob; Lubinski, Barbara A.; King, Tim L.

2018-01-01

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′ST = 0.718), and among most wild collections and hatchery strains (mean F′ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.

Genetics of hybrid male sterility between drosophila sibling species: a complex web of epistasis is revealed in interspecific studies.

PubMed

Palopoli, M F; Wu, C I

1994-10-01

To study the genetic differences responsible for the sterility of their male hybrids, we introgressed small segments of an X chromosome from Drosophila simulans into a pure Drosophila mauritiana genetic background, then assessed the fertility of males carrying heterospecific introgressions of varying size. Although this analysis examined less than 20% of the X chromosome (roughly 5% of the euchromatic portion of the D. simulans genome), and the segments were introgressed in only one direction, a minimum of four factors that contribute to hybrid male sterility were revealed. At least two of the factors exhibited strong epistasis: males carrying either factor alone were consistently fertile, whereas males carrying both factors together were always sterile. Distinct spermatogenic phenotypes were observed for sterile introgressions of different lengths, and it appeared that an interaction between introgressed segments also influenced the stage of spermatogenic defect. Males with one category of introgression often produced large quantities of motile sperm and were observed copulating, but never inseminated females. Evidently these two species have diverged at a large number of loci which have varied effects on hybrid male fertility. By extrapolation, we estimate that there are at least 40 such loci on the X chromosome alone. Because these species exhibit little DNA-sequence divergence at arbitrarily chosen loci, it seems unlikely that the extensive functional divergence observed could be due mainly to random genetic drift. Significant epistasis between conspecific genes appears to be a common component of hybrid sterility between recently diverged species of Drosophila. The linkage relationships of interacting factors could shed light on the role played by epistatic selection in the dynamics of the allele substitutions responsible for reproductive barriers between species.

Genetics of Hybrid Male Sterility between Drosophila Sibling Species: A Complex Web of Epistasis Is Revealed in Interspecific Studies

PubMed Central

Palopoli, M. F.; Wu, C. I.

1994-01-01

To study the genetic differences responsible for the sterility of their male hybrids, we introgressed small segments of an X chromosome from Drosophila simulans into a pure Drosophila mauritiana genetic background, then assessed the fertility of males carrying heterospecific introgressions of varying size. Although this analysis examined less than 20% of the X chromosome (roughly 5% of the euchromatic portion of the D. simulans genome), and the segments were introgressed in only one direction, a minimum of four factors that contribute to hybrid male sterility were revealed. At least two of the factors exhibited strong epistasis: males carrying either factor alone were consistently fertile, whereas males carrying both factors together were always sterile. Distinct spermatogenic phenotypes were observed for sterile introgressions of different lengths, and it appeared that an interaction between introgressed segments also influenced the stage of spermatogenic defect. Males with one category of introgression often produced large quantities of motile sperm and were observed copulating, but never inseminated females. Evidently these two species have diverged at a large number of loci which have varied effects on hybrid male fertility. By extrapolation, we estimate that there are at least 40 such loci on the X chromosome alone. Because these species exhibit little DNA-sequence divergence at arbitrarily chosen loci, it seems unlikely that the extensive functional divergence observed could be due mainly to random genetic drift. Significant epistasis between conspecific genes appears to be a common component of hybrid sterility between recently diverged species of Drosophila. The linkage relationships of interacting factors could shed light on the role played by epistatic selection in the dynamics of the allele substitutions responsible for reproductive barriers between species. PMID:7828817

The Predicted Cross Value for Genetic Introgression of Multiple Alleles

PubMed Central

Han, Ye; Cameron, John N.; Wang, Lizhi; Beavis, William D.

2017-01-01

We consider the plant genetic improvement challenge of introgressing multiple alleles from a homozygous donor to a recipient. First, we frame the project as an algorithmic process that can be mathematically formulated. We then introduce a novel metric for selecting breeding parents that we refer to as the predicted cross value (PCV). Unlike estimated breeding values, which represent predictions of general combining ability, the PCV predicts specific combining ability. The PCV takes estimates of recombination frequencies as an input vector and calculates the probability that a pair of parents will produce a gamete with desirable alleles at all specified loci. We compared the PCV approach with existing estimated-breeding-value approaches in two simulation experiments, in which 7 and 20 desirable alleles were to be introgressed from a donor line into a recipient line. Results suggest that the PCV is more efficient and effective for multi-allelic trait introgression. We also discuss how operations research can be used for other crop genetic improvement projects and suggest several future research directions. PMID:28122824

Inversion Monophyly in African Anopheline Malaria Vectors

PubMed Central

Garcia, B. A.; Caccone, A.; Mathiopoulos, K. D.; Powell, J. R.

1996-01-01

The African Anopheles gambiae complex of six sibling species has many polymorphic and fixed paracentric inversions detectable in polytene chromosomes. These have been used to infer phylogenetic relationships as classically done with Drosophila. Two species, A. gambiae and A. merus, were thought to be sister taxa based on a shared X inversion designated X(ag). Recent DNA data have conflicted with this phylogenetic inference as they have supported a sister taxa relationship of A. gambiae and A. arabiensis. A possible explanation is that the X(ag) is not monophyletic. Here we present data from a gene (soluble guanylate cyclase) within the X(ag) that strongly supports the monophyly of the X(ag). We conjecture that introgression may be occurring between the widely sympatric species A. gambiae and A. arabiensis and that the previous DNA phylogenies have been detecting the introgression. Evidently, introgression is not uniform across the genome, and species-specific regions, like the X-chromosome inversions, do not introgress probably due to selective elimination in hybrids and backcrosses. PMID:8807303

Asymmetric hybridization and introgression between pink salmon and chinook salmon in the Laurentian Great Lakes

USGS Publications Warehouse

Rosenfield, Jonathan A.; Todd, Thomas; Greil, Roger

2000-01-01

Among Pacific salmon collected in the St. Marys River, five natural hybrids of pink salmon Oncorhynchus gorbuscha and chinook salmon Oncorhynchus tshawytscha and one suspected backcross have been detected using morphologic, meristic, and color evidence. One allozyme (LDH, l-lactate dehydrogenase from muscle) and one nuclear DNA locus (growth hormone) for which species-specific fixed differences exist were analyzed to detect additional hybrids and to determine if introgression had occurred. Restriction fragment length polymorphism of mitochondrial DNA (mtDNA) was used to identify the maternal parent of each hybrid. Evidence of introgression was found among the five previously identified hybrids. All hybrid specimens had chinook salmon mtDNA, indicating that hybridization between chinook salmon and pink salmon in the St. Marys River is asymmetric and perhaps unidirectional. Ecological, physiological, and sexual selection forces may contribute to this asymmetric hybridization. Introgression between these highly differentiated species has implications for management, systematics, and conservation of Pacific salmon.

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

PubMed

Leduc-Robert, Geneviève; Maddison, Wayne P

2018-02-22

Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups. Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.

Strategies for durable resistance to the grapevine powdery mildew fungus, Erysiphe necator

USDA-ARS?s Scientific Manuscript database

Nearly all cultivars of Vitis vinifera are highly susceptible to the grapevine powdery mildew fungus, Erysiphe necator. Grape breeders around the world are working to introgress resistance from wild Vitis. Of the widely-used introgressions, most involve dominant, race-specific resistance phenotype...

Exotic germplasm introgression effects on adapted cotton genotypes

USDA-ARS?s Scientific Manuscript database

Our research is mainly focused on the objective of determining the effect of exotic germplasm introgression on agronomic and fiber properties of adapted cotton varieties. For this we studied eight populations derived by crossing two exotic parents (TX 245 and TX 1419) with four locally adapted culti...

Chromosome engineering techniques for targeted introgression of rust resistance from wild wheat relatives

USDA-ARS?s Scientific Manuscript database

Hexaploid wheat has relatively narrow genetic diversity due to its evolution and domestication processes compared to its wild relatives that often carry agronomically important traits including resistance to biotic and abiotic stresses. Many genes have been introgressed into wheat from wild relative...

Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs.

PubMed

Pastorini, Jennifer; Zaramody, Alphonse; Curtis, Deborah J; Nievergelt, Caroline M; Mundy, Nicholas I

2009-02-05

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. 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. 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.

Genomic Change, Retrotransposon Mobilization and Extensive Cytosine Methylation Alteration in Brassica napus Introgressions from Two Intertribal Hybridizations

PubMed Central

Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

2013-01-01

Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4–39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed. PMID:23468861

Chromosome engineering for alien gene introgression in wheat: Progress and prospective

USDA-ARS?s Scientific Manuscript database

Chromosome engineering is a useful strategy for introgression of desirable genes from wild relatives into cultivated wheat. However, it has been a challenge to transfer a small amount of alien chromatin containing the gene of interest from one genome to another non-homologous genome through classic...

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

USDA-ARS?s Scientific Manuscript database

Decades of intensive tomato breeding using wild germplasm has resulted in genomes of domesticated accessions (Solanum lycopersicum) to be intertwined with introgressions from their wild relatives. Here we present the first whole genome sequences of two tomato inbreds Gh13 and BTI87, both carrying a ...

Interspecific chromosome substitution lines from Gossypium barbadense and G. tomentosum in Upland cotton improvement

USDA-ARS?s Scientific Manuscript database

The merit of interspecific germplasm introgression has been well appreciated in many crop species, but it has not been exploited well in Upland cotton improvement. Wide-cross introgression typically requires considerable time and effort to circumvent and overcome biological, genetic, and cytogenetic...

"Bringing Taxonomy to the Service of Genetics": Edgar Anderson and Introgressive Hybridization.

PubMed

Kleinman, Kim

2016-12-01

In introgressive hybridization (the repeated backcrossing of hybrids with parental populations), Edgar Anderson found a source for variation upon which natural selection could work. In his 1953 review article "Introgressive Hybridization," he asserted that he was "bringing taxonomy to the service of genetics" whereas distinguished colleagues such as Theodosius Dobzhansky and Ernst Mayr did the precise opposite. His work as a geneticist particularly focused on linkage and recombination and was enriched by collaborations with Missouri Botanical Garden colleagues interested in taxonomy as well as with cytologists C.D. Darlington and Karl Sax. As the culmination of a biosystemtatic research program, Anderson's views challenged the mainstream of the Evolutionary Synthesis.

De novo assembly of a draft genome for Cucumis hystrix, the closest relative of cucumber

USDA-ARS?s Scientific Manuscript database

Cucumis hystrix (2n = 2x = 24, HH) is the only known species that is cross-compatible with cucumber and has a great potential for cucumber improvement, To facilitate introgression of C. hystrix chromatins into cucumber genetic background through development of introgression library, we sequenced two...

Transgressive variation for yield components and dynamic traits in Jefferson (Oryza sativa) x O. rufipogon introgression lines

USDA-ARS?s Scientific Manuscript database

Alleles from wild progenitors of crops can be a source of transgressive variation in modern cultivars. Introgressions from the Oryza rufipogon donor (IRGC104591) in an O. sativa tropical japonica cultivar (Jefferson) were shown to confer a yield advantage in multi-location field trials. Yield loci...

Effectiveness of the Ty3 introgression for conferring resistance in F3 families of tomato to begomoviruses in Guatemala

USDA-ARS?s Scientific Manuscript database

Begomoviruses have been the main cause of losses in tomato production in many subtropical and tropical regions and breeding begomovirus-resistant tomato hybrids has become a principle focus for control. Resistance genes from Solanum chilense and Solanum habrochaites have been introgressed into S. l...

A new species and introgression in eastern Asian hemlocks (Pinaceae: Tusga)

Treesearch

Garth Holman; Peter Del Tredici; Nathan Havill; Nam Sook Lee; Richard Cronn; Sarah Mathews; Linda Raubeson; Christopher S. Campbell

2017-01-01

Species delimitation in Pinaceae is often challenged by limited morphological differentiation and introgression. In Tsuga (hemlocks), species delimitation has been most challenging among northeastern Asian taxa, where the species are weakly marked morphologically and range in number from three to five in previous studies. Two low-copy nuclear four-...

Phenotypic and ionome profiling of Triticum aestivum x Aegilops tauschii introgression lines

USDA-ARS?s Scientific Manuscript database

Eighty-four single homozygous introgressions of the Aegilops tauschii D-genome in the ‘Chinese Spring’ genetic background were used to study phenotypic and ionome profiles during two years of field experiments. An augmented design was used with a repeated check of a local bread wheat cultivar was im...

The myth of natural barriers. Is transgene introgression by genetically modified crops an environmental risk?

PubMed

Guarnieri, Vincenzo; Benessia, Alice; Camino, Elena; Barbiero, Giuseppe

2008-01-01

Genetically modified (GM) crops under open field conditions are a complex and controversial issue. Ecologists are discussing about the possibility that a transgene belonging to GM plants could spread to native populations through a process known as introgression the stable incorporation of a gene in the host genome able to generate a differentiated population. The ecological consequences of a transgene introgression in plants or bacteria are not yet well understood, but could be significant. In this critical review we consider vertical and horizontal introgression. We analyse the biochemical and genetic constraints, and environmental factors that limit the possibility of transgene spread; meanwhile we show cases in which the natural barriers are overcome. Then we discuss the overall management of GM crops, noting the shortcomings and approximations of risk assessment based on linear thinking typical of the biomolecular approach. Finally we suggest to explicitly weight facts together with values and we encourage the undertaking of an ecological perspective, encompassing the complexity of (non-linear) relations between organisms and the environment.

An introgressed wing pattern acts as a mating cue.

PubMed

Sánchez, Angela P; Pardo-Diaz, Carolina; Enciso-Romero, Juan; Muñoz, Astrid; Jiggins, Chris D; Salazar, Camilo; Linares, Mauricio

2015-06-01

Heliconius butterflies provide good examples of both homoploid hybrid speciation and ecological speciation. In particular, examples of adaptive introgression have been detected among the subspecies of Heliconius timareta, which acquired red color pattern elements from H. melpomene. We tested whether the introgression of red wing pattern elements into H. timareta florencia might also be associated with incipient reproductive isolation (RI) from its close relative, H. timareta subsp. nov., found in the eastern Andes. No choice experiments show a 50% reduction in mating between females of H. t. subsp. nov. and males of H .t. florencia, but not in the reciprocal direction. In choice experiments using wing models, males of H. timareta subsp. nov. approach and court red phenotypes less than their own, whereas males of H. t. florencia prefer models with a red phenotype. Intrinsic postzygotic isolation was not detected in crosses between these H. timareta races. These results suggest that a color pattern trait gained by introgression is triggering RI between H. timareta subsp. nov. and H. t. florencia. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite

PubMed Central

McMullan, Mark; Gardiner, Anastasia; Bailey, Kate; Kemen, Eric; Ward, Ben J; Cevik, Volkan; Robert-Seilaniantz, Alexandre; Schultz-Larsen, Torsten; Balmuth, Alexi; Holub, Eric; van Oosterhout, Cock; Jones, Jonathan DG

2015-01-01

How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ∼1%. Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment. DOI: http://dx.doi.org/10.7554/eLife.04550.001 PMID:25723966

Advantages of using molecular coancestry in the removal of introgressed genetic material

PubMed Central

2013-01-01

Background When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA. Results This management method, which detects the ‘purest’ individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period. Conclusions Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach. PMID:23634969

Gene introgression into Coffea arabica by way of triploid hybrids (C. arabica x C. canephora).

PubMed

Herrera, J C; Combes, M C; Cortina, H; Alvarado, G; Lashermes, P

2002-12-01

Interspecific triploid hybrid plants between the tetraploid species Coffea arabica L. and the diploid species C. canephora P. were backcrossed to C. arabica. Although characterised by a low production and an important fruit dropping, all attempted crosses (ie, 6) generated BC(1) progenies. Flow cytometric analysis of the nuclear DNA content revealed that most of the BC1 individuals were nearly tetraploid. Among the male gametes produced by the interspecific triploid hybrids, those presenting a high number of chromosomes appeared strongly favoured. Only pollen mother cells having nearly 22 chromosomes were effective, the others leading to deficient endosperm and fruit dropping. Molecular markers (ie, microsatellite and AFLP) combined with evaluations of morphological characteristics and resistance to leaf rust were applied to verify the occurrence of gene transfer from C. canephora into C. arabica, and to estimate the amount of introgression present in BC(1) individuals. The results reveal a strong deficiency in the C. canephroa alleles indicating a severe counter-selection against the introgression of genetic material from C. canephora into C. arabica by way of triploid hybrids. However, introgressants displaying desirable traits such as a high resistance to leaf rust were obtained. The low level of introgression could be an advantage by facilitating the recovery of the recurrent parent and possibly reducing the number of required backcrosses. On the other hand, this could be a limitation when attempting the transfer of a complex trait or several simply inherited traits.

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

PubMed

Zhao, Keyan; Wright, Mark; Kimball, Jennifer; Eizenga, Georgia; McClung, Anna; Kovach, Michael; Tyagi, Wricha; Ali, Md Liakat; Tung, Chih-Wei; Reynolds, Andy; Bustamante, Carlos D; McCouch, Susan R

2010-05-24

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.

PubMed

Labate, Joanne A; Robertson, Larry D

2012-08-07

Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.

Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed.

PubMed

Qian, W; Meng, J; Li, M; Frauen, M; Sass, O; Noack, J; Jung, C

2006-06-01

In spite of its short history of being an oil crop in China, the Chinese semi-winter rapeseed (Brassica napus L., 2n = 38, AACC) has been improved rapidly by intentional introgression of genomic components from Chinese B. rapa (2n = 20, AA). As a result, the Chinese semi-winter rapeseed has diversified genetically from the spring and winter rapeseed grown in the other regions such as Europe and North America. The objectives of this study were to investigate the roles of the introgression of the genomic components from the Chinese B. rapa in widening the genetic diversity of rapeseed and to verify the role of this introgression in the evolution of the Chinese rapeseed. Ten lines of the new type of rapeseed, which were produced by introgression of Chinese B. rapa to Chinese normal rapeseed, were compared for genetic diversity using amplified fragment length polymorphism (AFLP) with three groups of 35 lines of the normal rapeseed, including 9 semi-winter rapeseed lines from China, 9 winter rapeseed lines from Europe and 17 spring rapeseed lines from Northern Europe, Canada and Australia. Analysis of 799 polymorphic fragments revealed that within the groups, the new type rapeseed had the highest genetic diversity, followed by the semi-winter normal rapeseed from China. Spring and winter rapeseed had the lowest genetic diversity. Among the groups, the new type rapeseed group had the largest average genetic distance to the other three groups. Principal component analysis and cluster analysis, however, could not separate the new type rapeseed group from Chinese normal rapeseed group. Our data suggested that the introgression of Chinese B. rapa could significantly diversify the genetic basis of the rapeseed and play an important role in the evolution of Chinese rapeseed. The use of new genetic variation for the exploitation of heterosis in Brassica hybrid breeding is discussed.

Mapping of stripe rust resistance gene in an Aegilops caudate introgression line in wheat and its genetic association with leaf rust resistance.

PubMed

Toor, Puneet Inder; Kaur, Satinder; Bansal, Mitaly; Yadav, Bharat; Chhuneja, Parveen

2016-12-01

A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distance of 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife

PubMed Central

Manen, Jean-François

2004-01-01

Background Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands), I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer) and two nuclear markers, the ribosomal internal transcribed spacer (ITS) and the nuclear encoded plastid glutamine synthetase (nepGS) were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively. Results The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism. Conclusions Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus Ilex. PMID:15550175

Simulation of introgression of the polled allele into the Holstein breed via conventional breeding versus gene editing

USDA-ARS?s Scientific Manuscript database

The objective of this study was to simulate the introgression of the polled allele into a dairy cattle population and compare the impact of using the methods of conventional breeding versus gene editing to increase the frequency of the polled allele. The rate of minor allele frequency (MAF) change, ...

Population diversity and evidence of introgression among the black oaks of California

Treesearch

Richard S. Dodd; Nasser Kashani; Zara Afzal-Rafii

2002-01-01

The black oaks of California include 4 tree species (California black oak, coast live oak, Shreve oak, interior live oak) that are known to hybridize. Complex patterns of population variation within each species are likely to result from these hybrid combinations and from subsequent introgressions. We have been studying population variation using biochemical and...

Introgression of the Kinetoplast DNA: An Unusual Evolutionary Journey in Trypanosoma cruzi.

PubMed

Tomasini, Nicolás

2018-02-01

Phylogenetic relationships between different lineages of Trypanosoma cruzi, the agent of Chagas disease, have been controversial for several years. However, recent phylogenetic and phylogenomic analyses clarified the nuclear relationships among such lineages. However, incongruence between nuclear and kinetoplast DNA phylogenies has emerged as a new challenge. This incongruence implies several events of mitochondrial introgression at evolutionary level. However, the mechanism that gave origin to introgressed lineages is unknown. Here, I will review and discuss how maxicircles of the kinetoplast were horizontally and vertically transferred between different lineages of T. cruzi. Finally, I will discuss what we know - and what we don't - about the kDNA transference and inheritance in the context of sexual reproduction in this parasite.

Evolution of postmating reproductive isolation: measuring the fitness effects of chromosomal regions containing hybrid male sterility factors.

PubMed

Johnson, N A; Wu, C I

1993-08-01

At least six regions of the X chromosome can cause male sterility when introgressed from Drosophila mauritiana into Drosophila simulans. In this article, we present the results of the other fitness effects caused by two X-linked regions that contain hybrid male sterility factors. In both regions, females that are heterozygous for an introgression with such a sterility factor produce substantially-fewer offspring than females heterozygous for an introgression that lacks the sterility factor. Thus, the hybrid male sterility factors, or other genes nearby, have substantial effects on female productivity. In contrast, hybrid male sterility factors have little or no effect on the relative viabilities of either sex. The evolutionary implications of these findings are discussed.

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population

PubMed Central

Galaverni, Marco; Caniglia, Romolo; Pagani, Luca; Fabbri, Elena; Boattini, Alessio; Randi, Ettore

2017-01-01

Abstract Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype–phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype–phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management. PMID:28549194

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

PubMed

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America

PubMed Central

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A.; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa. PMID:25379725

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

PubMed

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning.

PubMed

Wolters, Anne-Marie A; Caro, Myluska; Dong, Shufang; Finkers, Richard; Gao, Jianchang; Visser, Richard G F; Wang, Xiaoxuan; Du, Yongchen; Bai, Yuling

2015-10-01

A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line. Among tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato ('Heinz'). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa

USDA-ARS?s Scientific Manuscript database

A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plant...

Use of introgression lines to determine the ecophysiological basis for changes in water use efficiency and yield in California processing tomatoes

Treesearch

Felipe H. Barrios-Masias; Roger T. Chetelat; Nancy E. Grulke; Louise E. Jackson

2014-01-01

Field and greenhouse studies examined the effects of growth habit and chloroplast presence in leaf veins for their role in increasing agronomic water use efficiency and yields of California modern processing tomato (Solanum lycopersicum L.) cultivars. Five introgression lines (ILs), made with Solanum pennellii Cor. in the...

Climate, demography, and zoogeography predict introgression thresholds in salmonid hybrid zones in Rocky Mountain streams

Treesearch

Michael K. Young; Daniel J. Isaak; Kevin S. McKelvey; Taylor M. Wilcox; Daniel M. Bingham; Kristine L. Pilgrim; Kellie J. Carim; Matthew R. Campbell; Matthew P. Corsi; Dona L. Horan; David E. Nagel; Michael K. Schwartz

2016-01-01

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted...

Are genes faster than crabs? Mitochondrial introgression exceeds larval dispersal during population expansion of the invasive crab Carcinus maenas.

PubMed

Darling, John A; Tsai, Yi-Hsin Erica; Blakeslee, April M H; Roman, Joe

2014-10-01

Biological invasions offer unique opportunities to investigate evolutionary dynamics at the peripheries of expanding populations. Here, we examine genetic patterns associated with admixture between two distinct invasive lineages of the European green crab, Carcinus maenas L., independently introduced to the northwest Atlantic. Previous investigations based on mitochondrial DNA sequences demonstrated that larval dispersal driven by advective currents could explain observed southward displacement of an admixture zone between the two invasions. Comparison of published mitochondrial results with new nuclear data from nine microsatellite loci, however, reveals striking discordance in their introgression patterns. Specifically, introgression of mitochondrial genomes relative to nuclear background suggests that demographic processes such as sex-biased reproductive dynamics and population size imbalances-and not solely larval dispersal-play an important role in driving the evolution of the genetic cline. In particular, the unpredicted introgression of mitochondrial alleles against the direction of mean larval dispersal in the region is consistent with recent models invoking similar demographic processes to explain movements of genes into invading populations. These observations have important implications for understanding historical shifts in C. maenas range limits, and more generally for inferences of larval dispersal based on genetic data.

Are genes faster than crabs? Mitochondrial introgression exceeds larval dispersal during population expansion of the invasive crab Carcinus maenas

PubMed Central

Darling, John A.; Tsai, Yi-Hsin Erica; Blakeslee, April M. H.; Roman, Joe

2014-01-01

Biological invasions offer unique opportunities to investigate evolutionary dynamics at the peripheries of expanding populations. Here, we examine genetic patterns associated with admixture between two distinct invasive lineages of the European green crab, Carcinus maenas L., independently introduced to the northwest Atlantic. Previous investigations based on mitochondrial DNA sequences demonstrated that larval dispersal driven by advective currents could explain observed southward displacement of an admixture zone between the two invasions. Comparison of published mitochondrial results with new nuclear data from nine microsatellite loci, however, reveals striking discordance in their introgression patterns. Specifically, introgression of mitochondrial genomes relative to nuclear background suggests that demographic processes such as sex-biased reproductive dynamics and population size imbalances—and not solely larval dispersal—play an important role in driving the evolution of the genetic cline. In particular, the unpredicted introgression of mitochondrial alleles against the direction of mean larval dispersal in the region is consistent with recent models invoking similar demographic processes to explain movements of genes into invading populations. These observations have important implications for understanding historical shifts in C. maenas range limits, and more generally for inferences of larval dispersal based on genetic data. PMID:26064543

The shaping of modern human immune systems by multiregional admixture with archaic humans.

PubMed

Abi-Rached, Laurent; Jobin, Matthew J; Kulkarni, Subhash; McWhinnie, Alasdair; Dalva, Klara; Gragert, Loren; Babrzadeh, Farbod; Gharizadeh, Baback; Luo, Ma; Plummer, Francis A; Kimani, Joshua; Carrington, Mary; Middleton, Derek; Rajalingam, Raja; Beksac, Meral; Marsh, Steven G E; Maiers, Martin; Guethlein, Lisbeth A; Tavoularis, Sofia; Little, Ann-Margaret; Green, Richard E; Norman, Paul J; Parham, Peter

2011-10-07

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

PubMed Central

Abi-Rached, Laurent; Jobin, Matthew J; Kulkarni, Subhash; McWhinnie, Alasdair; Dalva, Klara; Gragert, Loren; Babrzadeh, Farbod; Gharizadeh, Baback; Luo, Ma; Plummer, Francis A; Kimani, Joshua; Carrington, Mary; Middleton, Derek; Rajalingam, Raja; Beksac, Meral; Marsh, Steven GE; Maiers, Martin; Guethlein, Lisbeth A; Tavoularis, Sofia; Little, Ann-Margaret; Green, Richard E; Norman, Paul J; Parham, Peter

2013-01-01

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic HLA class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems. PMID:21868630

Introgression of resistance to reniform nematode (Rotylenchulus reniformis) into upland cotton (Gossypium hirsutum) from Gossypium arboreum and a Gossypium hirsutum/Gossypium aridum bridging line

USDA-ARS?s Scientific Manuscript database

Gossypium hirsutum is the predominant cotton of commerce and all cultivars of this species are susceptible to the reniform nematode, Rotylenchulus reniformis. To introgress resistance to R. reniformis into the tetraploid 2(AD1) G. hirsutum, a resistant diploid A2-genome G. arboreum accession (A2-19...

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

PubMed Central

2012-01-01

Background Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Results Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Conclusion Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles. PMID:22871151

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash.

PubMed

Holdsworth, William L; LaPlant, Kyle E; Bell, Duane C; Jahn, Molly M; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

Dissection of resistance to Microdochium nivale in Lolium multiflorum/Festuca arundinacea introgression forms.

PubMed

Płażek, Agnieszka; Pociecha, Ewa; Augustyniak, Adam; Masajada, Katarzyna; Dziurka, Michał; Majka, Joanna; Perlikowski, Dawid; Pawłowicz, Izabela; Kosmala, Arkadiusz

2018-02-01

The potential of resistance to Microdochium nivale is still not recognized for numerous plant species. The forage grasses of Lolium-Festuca complex are important for grass-biomass production in the temperate regions. Lolium multiflorum is a grass with a high forage quality and productivity but also a relatively low resistance to M. nivale. On the contrary, F. arundinacea has a higher potential of resistance but simultaneously a significantly lower forage quality. These two species cross with each other and the intergeneric hybrids possess complementary characters of both genera. Herein, for the first time, we perform the research on L. multiflorum/F. arundinacea introgression forms to decipher mechanisms of resistance to M. nivale in that group of plants. Two forms with distinct levels of resistance were used as models in cytogenetic and biochemical studies. The resistant plant was shown to be a tetraploid with 28 L. multiflorum chromosomes, including one with three F. arundinacea introgressions. The susceptible introgression form revealed the unbalanced genomic structure and only 25 chromosomes. Twenty four chromosomes were shown to be L. multiflorum chromosomes, including one chromosome with F. arundinacea segment. One Festuca chromosome with additional two interstitial F. arundinacea segments, was also revealed in the susceptible form. The selected introgression forms differed in the accumulation profiles of total soluble carbohydrates, phytohormones, and phenolics in the leaf and crown tissue under the control and infection conditions. The higher amount of carbohydrates and salicylic acid in the leaves and crowns as well as a lower amount of abscisic acid in both studied organs and jasmonic acid in the crowns, were shown to be crucial for the expression of resistance to M. nivale in the analyzed hybrids. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Segregation distortion and genome-wide digenic interactions affect transmission of introgressed chromatin from wild cotton species.

PubMed

Chandnani, Rahul; Wang, Baohua; Draye, Xavier; Rainville, Lisa K; Auckland, Susan; Zhuang, Zhimin; Lubbers, Edward L; May, O Lloyd; Chee, Peng W; Paterson, Andrew H

2017-10-01

This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species. From an interspecific cross, Gossypium hirsutum × Gossypium mustelinum, we studied G. mustelinum (the most distant tetraploid relative of Upland cotton) allele retention in 35 BC 3 F 1 plants and segregation patterns in BC 3 F 2 populations totaling 3202 individuals, using 216 DNA marker loci. The average retention of donor alleles across BC 3 F 1 plants was higher than expected and the average frequency of G. mustelinum alleles in BC 3 F 2 segregating families was less than expected. Despite surprisingly high retention of G. mustelinum alleles in BC 3 F 1 , 46 genomic regions showed no introgression. Regions on chromosomes 3 and 15 lacking introgression were closely associated with possible small inversions previously reported. Nonlinear two-locus interactions are abundant among loci with single-locus segregation distortion, and among loci originating from one of the two subgenomes. Comparison of the present results with those of prior studies indicates different permeability of Upland cotton for donor chromatin from different allotetraploid relatives. Different contributions of subgenomes to two-locus interactions suggest different fates of subgenomes in the evolution of allotetraploid cottons. Transmission genetics of G. hirsutum × G. mustelinum crosses reveals allelic interactions, constraints on fixation and selection of donor alleles, and challenges with retention of introgressed chromatin for crop improvement.

High-Throughput Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines

PubMed Central

Honsdorf, Nora; March, Timothy John; Berger, Bettina; Tester, Mark; Pillen, Klaus

2014-01-01

Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform “The Plant Accelerator”, Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. PMID:24823485

Molecular, Physicochemical and Rheological Characteristics of Introgressive Triticale/Triticum monococcum ssp. monococcum Lines with Wheat 1D/1A Chromosome Substitution

PubMed Central

Salmanowicz, Bolesław P.; Langner, Monika; Wiśniewska, Halina; Apolinarska, Barbara; Kwiatek, Michał; Błaszczyk, Lidia

2013-01-01

Three sets of hexaploid introgressive triticale lines, with Triticum monococcum ssp. monococcum (cultivated einkorn wheat) genes and a bread wheat chromosome 1D substituted for chromosome 1A, and one set of secondary triticale lines were evaluated for grain and flour physicochemical and dough rheological characteristics in two generations (F7 and F8). Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) confirmed the 1D/1A chromosome substitution. The presence or absence of einkorn high-molecular-weight (HMW) glutenin subunits and the wheat Glu-D1d locus encoding the 5 + 10 subunits was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), capillary zone electrophoresis, and allele-specific molecular markers. Significant differences were found among physicochemical properties (with the exception of the Hagberg falling number) of all introgressive Triticale/T. monococcum lines and the secondary triticale lines. The wheat 1D/1A chromosome substitution also affected these properties. The results showed that in all introgressive triticale lines, the protein and gluten content, Zeleny sedimentation value, and water absorption capacity, were increased. The rheological parameters estimated using micro-farinograph, reomixer, and Kieffer dough extensibility systems also showed an appreciable increase in dough-mixing properties, maximum resistance to extension (Rmax), and dough extensibility. Introgressive Triticale/T. monococcum lines with 5 + 10 subunits have particularly favorable rheological parameters. The results obtained in this study suggest that the cultivated einkorn genome Am, in the context of hexaploid secondary triticale lines and with a wheat 1D/1A substitution, has the potential to improve gluten polymer interactions and be a valuable genetic resource for triticale quality improvement. PMID:23896593

Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil

PubMed Central

Yuan, Xiaoli; Bromley, Robin E.; Stouthamer, Richard

2012-01-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee. PMID:22544234

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers.

PubMed

Edet, Offiong Ukpong; Kim, June-Sik; Okamoto, Masanori; Hanada, Kousuke; Takeda, Tomoyuki; Kishii, Masahiro; Gorafi, Yasir Serag Alnor; Tsujimoto, Hisashi

2018-03-27

The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.

A general method for identifying major hybrid male sterility genes in Drosophila.

PubMed

Zeng, L W; Singh, R S

1995-10-01

The genes responsible for hybrid male sterility in species crosses are usually identified by introgressing chromosome segments, monitored by visible markers, between closely related species by continuous backcrosses. This commonly used method, however, suffers from two problems. First, it relies on the availability of markers to monitor the introgressed regions and so the portion of the genome examined is limited to the marked regions. Secondly, the introgressed regions are usually large and it is impossible to tell if the effects of the introgressed regions are the result of single (or few) major genes or many minor genes (polygenes). Here we introduce a simple and general method for identifying putative major hybrid male sterility genes which is free of these problems. In this method, the actual hybrid male sterility genes (rather than markers), or tightly linked gene complexes with large effects, are selectively introgressed from one species into the background of another species by repeated backcrosses. This is performed by selectively backcrossing heterozygous (for hybrid male sterility gene or genes) females producing fertile and sterile sons in roughly equal proportions to males of either parental species. As no marker gene is required for this procedure, this method can be used with any species pairs that produce unisexual sterility. With the application of this method, a small X chromosome region of Drosophila mauritiana which produces complete hybrid male sterility (aspermic testes) in the background of D. simulans was identified. Recombination analysis reveals that this region contains a second major hybrid male sterility gene linked to the forked locus located at either 62.7 +/- 0.66 map units or at the centromere region of the X chromosome of D. mauritiana.

Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.

PubMed

Nunney, Leonard; Yuan, Xiaoli; Bromley, Robin E; Stouthamer, Richard

2012-07-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

PubMed Central

Holdsworth, William L.; LaPlant, Kyle E.; Bell, Duane C.; Jahn, Molly M.; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection. PMID:27936008

Large-scale asymmetric introgression of cytoplasmic DNA reveals Holocene range displacement in a North American boreal pine complex

PubMed Central

Godbout, Julie; Yeh, Francis C; Bousquet, Jean

2012-01-01

Jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta var. latifolia) are two North American boreal hard pines that hybridize in their zone of contact in western Canada. The main objective of this study was to characterize their patterns of introgression resulting from past and recent gene flow, using cytoplasmic markers having maternal or paternal inheritance. Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) diversity was assessed in allopatric populations of each species and in stands from the current zone of contact containing morphological hybrids. Cluster analyses were used to identify genetic discontinuities among groups of populations. A canonical analysis was also conducted to detect putative associations among cytoplasmic DNA variation, tree morphology, and site ecological features. MtDNA introgression was extensive and asymmetric: it was detected in P. banksiana populations from the hybrid zone and from allopatric areas, but not in P. contorta populations. Very weak cpDNA introgression was observed, and only in P. banksiana populations. The mtDNA introgression pattern indicated that central Canada was first colonized by migrants from a P. contorta glacial population located west of the Rocky Mountains, before being replaced by P. banksiana migrating westward during the Holocene. In contrast, extensive pollen gene flow would have erased the cpDNA traces of this ancient presence of P. contorta. Additional evidence for this process was provided by the results of canonical analysis, which indicated that the current cpDNA background of trees reflected recent pollen gene flow from the surrounding dominant species rather than historical events that took place during the postglacial colonization. PMID:22957188

High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool.

PubMed

Henriques, Dora; Browne, Keith A; Barnett, Mark W; Parejo, Melanie; Kryger, Per; Freeman, Tom C; Muñoz, Irene; Garnery, Lionel; Highet, Fiona; Jonhston, J Spencer; McCormack, Grace P; Pinto, M Alice

2018-06-04

The natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression levels to more effectively monitor and manage A. m. mellifera conservatories.

Natural hybridization and introgression between Ligularia cymbulifera and L. tongolensis (Asteraceae, Senecioneae) in four different locations.

PubMed

Yu, Jiaojun; Kuroda, Chiaki; Gong, Xun

2014-01-01

Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus Ligularia Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in Ligularia. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in Ligularia from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (trnK-rps16, trnL-rpl32 and trnQ-5'rps16) of 149 accessions of putative hybrids and their putative parents (L. cymbulifera and L. tongolensis) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric L. vellerea and supported the hypothesis that those morphological intermediates were products of natural hybridization between L. cymbulifera and L. tongolensis. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in Ligularia indeed plays an important role in the species diversity.

Male mating strategy and the introgression of a growth hormone transgene.

PubMed

Valosaari, Kata-Riina; Aikio, Sami; Kaitala, Veijo

2008-11-01

Escaped transgenic organisms (GMO's) may threaten the populations of their wild relatives if able to hybridize with each other. The introgression of a growth enhancement transgene into a wild Atlantic salmon population may be affected by the transgene's effects not only on fitness parameters, but also on mating behaviour. Large anadromous GMO males are most preferred in mating, but a transgene can also give the large sneakers a reproductive advantage over the smaller wild individuals. With a simulation model, we studied whether the increase in the proportion and mating success of sneakers in transgenic and hybrid genotypes could facilitate the introgression of a transgene into wild population after the release of GMOs. The model combines population dynamics and Mendelian inheritance of a transgenic trait. We found that the introgression of the transgene is strongly affected by the greater mating preference of large GMO males. Furthermore, the difference in reproductive success between the anadromous versus sneaker strategy defines how much GMO's have to be preferred to be able to invade. These results emphasize the importance of detailed knowledge of reproductive systems and the effect of a transgene on the phenotype and behaviour of GMOs when assessing the consequences of their release or escape to the wild.

An Autosomal Factor from Drosophila Arizonae Restores Normal Spermatogenesis in Drosophila Mojavensis Males Carrying the D. Arizonae Y Chromosome

PubMed Central

Pantazidis, A. C.; Galanopoulos, V. K.; Zouros, E.

1993-01-01

Males of Drosophila mojavensis whose Y chromosome is replaced by the Y chromosome of the sibling species Drosophila arizonae are sterile. It is shown that genetic material from the fourth chromosome of D. arizonae is necessary and sufficient, in single dose, to restore fertility in these males. In introgression and mapping experiments this material segregates as a single Mendelian factor (sperm motility factor, SMF). Light and electron microscopy studies of spermatogenesis in D. mojavensis males whose Y chromosome is replaced by introgression with the Y chromosome of D. arizonae (these males are symbolized as mojY(a)) revealed postmeiotic abnormalities all of which are restored when the SMF of D. arizonae is co-introgressed (these males are symbolized as mojY(a)SMF(a)). The number of mature sperm per bundle in mojY(a)SMF(a) is slightly less than in pure D. mojavensis and is even smaller in males whose fertility is rescued by introgression of the entire fourth chromosome of D. arizonae. These observations establish an interspecific incompatibility between the Y chromosome and an autosomal factor (or more than one tightly linked factors) that can be useful for the study of the evolution of male hybrid sterility in Drosophila and the genetic control of spermatogenesis. PMID:8514139

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

PubMed Central

Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Cai, Wanshi; Lu, Liang; Zhao, Fangqing; Sun, Zhongsheng; Zhang, Jianxu

2017-01-01

Abstract Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation. PMID:28482038

Widespread unidirectional transfer of mitochondrial DNA: a case in western Palaearctic water frogs.

PubMed

Plötner, J; Uzzell, T; Beerli, P; Spolsky, C; Ohst, T; Litvinchuk, S N; Guex, G-D; Reyer, H-U; Hotz, H

2008-05-01

Interspecies transfer of mitochondrial (mt) DNA is a common phenomenon in plants, invertebrates and vertebrates, normally linked with hybridization of closely related species in zones of sympatry or parapatry. In central Europe, in an area north of 48 degrees N latitude and between 8 degrees and 22 degrees E longitude, western Palaearctic water frogs show massive unidirectional introgression of mtDNA: 33.7% of 407 Rana ridibunda possessed mtDNA specific for Rana lessonae. By contrast, no R. lessonae with R. ridibunda mtDNA was observed. That R. ridibunda with introgressed mitochondrial genomes were found exclusively within the range of the hybrid Rana esculenta and that most hybrids had lessonae mtDNA (90.4% of 335 individuals investigated) is evidence that R. esculenta serves as a vehicle for transfer of lessonae mtDNA into R. ridibunda. Such introgression has occurred several times independently. The abundance and wide distribution of individuals with introgressed mitochondrial genomes show that R. lessonae mt genomes work successfully in a R. ridibunda chromosomal background despite their high sequence divergence from R. ridibunda mtDNAs (14.2-15.2% in the ND2/ND3 genes). Greater effectiveness of enzymes encoded by R. lessonae mtDNA may be advantageous to individuals of R. ridibunda and probably R. esculenta in the northern parts of their ranges.

High-resolution genome-wide dissection of the two rules of speciation in Drosophila.

PubMed

Masly, John P; Presgraves, Daven C

2007-09-01

Postzygotic reproductive isolation is characterized by two striking empirical patterns. The first is Haldane's rule--the preferential inviability or sterility of species hybrids of the heterogametic (XY) sex. The second is the so-called large X effect--substitution of one species's X chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. Although the first rule has been well-established, the second rule remains controversial. Here, we dissect the genetic causes of these two rules using a genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background. We find that recessive hybrid incompatibilities outnumber dominant ones and that hybrid male steriles outnumber all other types of incompatibility, consistent with the dominance and faster-male theories of Haldane's rule, respectively. We also find that, although X-linked and autosomal introgressions are of similar size, most X-linked introgressions cause hybrid male sterility (60%) whereas few autosomal introgressions do (18%). Our results thus confirm the large X effect and identify its proximate cause: incompatibilities causing hybrid male sterility have a higher density on the X chromosome than on the autosomes. We evaluate several hypotheses for the evolutionary cause of this excess of X-linked hybrid male sterility.

High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila

PubMed Central

2007-01-01

Postzygotic reproductive isolation is characterized by two striking empirical patterns. The first is Haldane's rule—the preferential inviability or sterility of species hybrids of the heterogametic (XY) sex. The second is the so-called large X effect—substitution of one species's X chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. Although the first rule has been well-established, the second rule remains controversial. Here, we dissect the genetic causes of these two rules using a genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background. We find that recessive hybrid incompatibilities outnumber dominant ones and that hybrid male steriles outnumber all other types of incompatibility, consistent with the dominance and faster-male theories of Haldane's rule, respectively. We also find that, although X-linked and autosomal introgressions are of similar size, most X-linked introgressions cause hybrid male sterility (60%) whereas few autosomal introgressions do (18%). Our results thus confirm the large X effect and identify its proximate cause: incompatibilities causing hybrid male sterility have a higher density on the X chromosome than on the autosomes. We evaluate several hypotheses for the evolutionary cause of this excess of X-linked hybrid male sterility. PMID:17850182

Male mating strategy and the introgression of a growth hormone transgene

PubMed Central

Valosaari, Kata-Riina; Aikio, Sami; Kaitala, Veijo

2008-01-01

Escaped transgenic organisms (GMO's) may threaten the populations of their wild relatives if able to hybridize with each other. The introgression of a growth enhancement transgene into a wild Atlantic salmon population may be affected by the transgene's effects not only on fitness parameters, but also on mating behaviour. Large anadromous GMO males are most preferred in mating, but a transgene can also give the large sneakers a reproductive advantage over the smaller wild individuals. With a simulation model, we studied whether the increase in the proportion and mating success of sneakers in transgenic and hybrid genotypes could facilitate the introgression of a transgene into wild population after the release of GMOs. The model combines population dynamics and Mendelian inheritance of a transgenic trait. We found that the introgression of the transgene is strongly affected by the greater mating preference of large GMO males. Furthermore, the difference in reproductive success between the anadromous versus sneaker strategy defines how much GMO's have to be preferred to be able to invade. These results emphasize the importance of detailed knowledge of reproductive systems and the effect of a transgene on the phenotype and behaviour of GMOs when assessing the consequences of their release or escape to the wild. PMID:25567801

Chemical communication, sexual selection, and introgression in wall lizards.

PubMed

MacGregor, Hannah E A; Lewandowsky, Rachel A M; d'Ettorre, Patrizia; Leroy, Chloé; Davies, Noel W; While, Geoffrey M; Uller, Tobias

2017-10-01

Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters, but the associations were variable and inconsistent between lineages. In experimental contact zones, chemical composition was weakly associated with male reproductive success, and did not predict the likelihood of hybridization. Consistent with these results, introgression of chemical profiles in a natural hybrid zone resembled that of neutral nuclear genetic markers overall, but one compound in particular (tocopherol methyl ether) matched closely the introgression of visual sexual characters. These results imply that associations among male chemical profiles, sexual characters, and reproductive success largely reflect transient and environmentally driven effects, and that genetic divergence in chemical composition is largely neutral. We therefore suggest that femoral secretions in wall lizards primarily provide information about residency and individual identity rather than function as sexual signals. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Reticulate evolution and incomplete lineage sorting among the ponderosa pines.

PubMed

Willyard, Ann; Cronn, Richard; Liston, Aaron

2009-08-01

Interspecific gene flow via hybridization may play a major role in evolution by creating reticulate rather than hierarchical lineages in plant species. Occasional diploid pine hybrids indicate the potential for introgression, but reticulation is hard to detect because ancestral polymorphism is still shared across many groups of pine species. Nucleotide sequences for 53 accessions from 17 species in subsection Ponderosae (Pinus) provide evidence for reticulate evolution. Two discordant patterns among independent low-copy nuclear gene trees and a chloroplast haplotype are better explained by introgression than incomplete lineage sorting or other causes of incongruence. Conflicting resolution of three monophyletic Pinus coulteri accessions is best explained by ancient introgression followed by a genetic bottleneck. More recent hybridization transferred a chloroplast from P. jeffreyi to a sympatric P. washoensis individual. We conclude that incomplete lineage sorting could account for other examples of non-monophyly, and caution against any analysis based on single-accession or single-locus sampling in Pinus.

Archaic Adaptive Introgression in TBX15/WARS2

PubMed Central

Gokhman, David; Fumagalli, Matteo; Ko, Amy; Hansen, Torben; Moltke, Ida; Albrechtsen, Anders; Carmel, Liran; Huerta-Sánchez, Emilia

2017-01-01

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15. PMID:28007980

Systematic design for trait introgression projects.

PubMed

Cameron, John N; Han, Ye; Wang, Lizhi; Beavis, William D

2017-10-01

Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy. The Pareto plots can be used to make rational decisions concerning the trade-offs between maximizing the probability of success while minimizing costs and time. The systematic rigor associated with a cost, time and probability of success (CTP) framework is well suited to designing TI projects that require dynamic decision making. The CTP framework also revealed that previously identified 'best' strategies can be improved to be at least twice as effective without increasing time or expenses.

Development of cost-effective Hordeum chilense DNA markers: molecular aids for marker-assisted cereal breeding.

PubMed

Hernández, P; Dorado, G; Ramírez, M C; Laurie, D A; Snape, J W; Martín, A

2003-01-01

Hordeum chilense is a potential source of useful genes for wheat breeding. The use of this wild species to increase genetic variation in wheat will be greatly facilitated by marker-assisted introgression. In recent years, the search for the most suitable DNA marker system for tagging H. chilense genomic regions in a wheat background has lead to the development of RAPD and SCAR markers for this species. RAPDs represent an easy way of quickly generating suitable introgression markers, but their use is limited in heterogeneous wheat genetic backgrounds. SCARs are more specific assays, suitable for automatation or multiplexing. Direct sequencing of RAPD products is a cost-effective approach that reduces labour and costs for SCAR development. The use of SSR and STS primers originally developed for wheat and barley are additional sources of genetic markers. Practical applications of the different marker approaches for obtaining derived introgression products are described.

Continuous Morphological Variation Correlated with Genome Size Indicates Frequent Introgressive Hybridization among Diphasiastrum Species (Lycopodiaceae) in Central Europe

PubMed Central

Hanušová, Kristýna; Ekrt, Libor; Vít, Petr; Kolář, Filip; Urfus, Tomáš

2014-01-01

Introgressive hybridization is an important evolutionary process frequently contributing to diversification and speciation of angiosperms. Its extent in other groups of land plants has only rarely been studied, however. We therefore examined the levels of introgression in the genus Diphasiastrum, a taxonomically challenging group of Lycopodiophytes, using flow cytometry and numerical and geometric morphometric analyses. Patterns of morphological and cytological variation were evaluated in an extensive dataset of 561 individuals from 57 populations of six taxa from Central Europe, the region with the largest known taxonomic complexity. In addition, genome size values of 63 individuals from Northern Europe were acquired for comparative purposes. Within Central European populations, we detected a continuous pattern in both morphological variation and genome size (strongly correlated together) suggesting extensive levels of interspecific gene flow within this region, including several large hybrid swarm populations. The secondary character of habitats of Central European hybrid swarm populations suggests that man-made landscape changes might have enhanced unnatural contact of species, resulting in extensive hybridization within this area. On the contrary, a distinct pattern of genome size variation among individuals from other parts of Europe indicates that pure populations prevail outside Central Europe. All in all, introgressive hybridization among Diphasiastrum species in Central Europe represents a unique case of extensive interspecific gene flow among spore producing vascular plants that cause serious complications of taxa delimitation. PMID:24932509

Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars

PubMed Central

Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A.; Krugman, Tamar; Saranga, Yehoshua

2016-01-01

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm) and water-limited (290–320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass—specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance. PMID:27148287

Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids.

PubMed

Choleva, Lukas; Musilova, Zuzana; Kohoutova-Sediva, Alena; Paces, Jan; Rab, Petr; Janko, Karel

2014-01-01

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species.

PubMed

Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Cai, Wanshi; Lu, Liang; Zhao, Fangqing; Sun, Zhongsheng; Zhang, Jianxu

2017-09-01

Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Introgressive hybridization and latitudinal admixture clines in North Atlantic eels

PubMed Central

2014-01-01

Background Hybridization, the interbreeding of diagnosably divergent species, is a major focus in evolutionary studies. Eels, both from North America and Europe migrate through the Atlantic to mate in a vast, overlapping area in the Sargasso Sea. Due to the lack of direct observation, it is unknown how these species remain reproductively isolated. The detection of inter-species hybrids in Iceland suggests on-going gene flow, but few studies to date have addressed the influence of introgression on genetic differentiation in North Atlantic eels. Results Here, we show that while mitochondrial lineages remain completely distinct on both sides of the Atlantic, limited hybridization is detectable with nuclear DNA markers. The nuclear hybridization signal peaks in the northern areas and decreases towards the southern range limits on both continents according to Bayesian assignment analyses. By simulating increasing proportions of both F1 hybrids and admixed individuals from the southern to the northern-most locations, we were able to generate highly significant isolation-by-distance patterns in both cases, reminiscent of previously published data for the European eel. Finally, fitting an isolation-with-migration model to our data supports the hypothesis of recent asymmetric introgression and refutes the alternative hypothesis of ancient polymorphism. Conclusions Fluctuating degrees of introgressive hybridization between Atlantic eel species are sufficient to explain temporally varying correlations of geographic and genetic distances reported for populations of the European eel. PMID:24674242

Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea.

PubMed

Llopart, Ana; Lachaise, Daniel; Coyne, Jerry A

2005-09-01

Drosophila yakuba is widely distributed in sub-Saharan Africa, while D. santomea is endemic to the volcanic island of São Tomé in the Atlantic Ocean, 280 km west of Gabon. On São Tomé, D. yakuba is found mainly in open lowland forests, and D. santomea is restricted to the wet misty forests at higher elevations. At intermediate elevations, the species form a hybrid zone where hybrids occur at a frequency of approximately 1%. To determine the extent of gene flow between these species we studied polymorphism and divergence patterns in 29 regions distributed throughout the genome, including mtDNA and three genes on the Y chromosome. This multilocus approach, together with the comparison to the two allopatric species D. mauritiana and D. sechellia, allowed us to distinguish between forces that should affect all genes and forces that should act on some genes (e.g., introgression). Our results show that D. yakuba mtDNA has replaced that of D. santomea and that there is also significant introgression for two nuclear genes, yellow and salr. The majority of genes, however, has remained distinct. These two species therefore do not form a "hybrid swarm" in which much of the genome shows substantial introgression while disruptive selection maintains distinctness for only a few traits (e.g., pigmentation and male genitalia).

Fitness of Crop-Wild Hybrid Sunflower under Competitive Conditions: Implications for Crop-to-Wild Introgression

PubMed Central

Mercer, Kristin L.; Emry, D. Jason; Snow, Allison A.; Kost, Matthew A.; Pace, Brian A.; Alexander, Helen M.

2014-01-01

Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F1, F2, and BCw hybrids) under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F2 plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F2 hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking a full life cycle perspective. Additionally, due to effects of exogenous selection, a given hybrid generation may be especially well-suited to hastening introgression under particular environmental conditions. PMID:25295859

Fitness of crop-wild hybrid sunflower under competitive conditions: implications for crop-to-wild introgression.

PubMed

Mercer, Kristin L; Emry, D Jason; Snow, Allison A; Kost, Matthew A; Pace, Brian A; Alexander, Helen M

2014-01-01

Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F1, F2, and BCw hybrids) under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F2 plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F2 hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking a full life cycle perspective. Additionally, due to effects of exogenous selection, a given hybrid generation may be especially well-suited to hastening introgression under particular environmental conditions.

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula.

PubMed

Melo-Ferreira, J; Boursot, P; Randi, E; Kryukov, A; Suchentrunk, F; Ferrand, N; Alves, P C

2007-02-01

The climatic fluctuations during glaciations have affected differently arctic and temperate species. In the northern hemisphere, cooling periods induced the expansion of many arctic species to the south, while temperate species were forced to retract in southern refugia. Consequently, in some areas the alternation of these species set the conditions for competition and eventually hybridization. Hares in the Iberian Peninsula appear to illustrate this phenomenon. Populations of Iberian hare (Lepus granatensis), brown hare (Lepus europaeus) and broom hare (Lepus castroviejoi) in Northern Iberia harbour mitochondrial haplotypes from the mountain hare (Lepus timidus), a mainly boreal and arctic species presently absent from the peninsula. To understand the history of this past introgression we analysed sequence variation and geographical distribution of mitochondrial control region and cytochrome b haplotypes of L. timidus origin found in 378 specimens of these four species. Among 124 L. timidus from the Northern Palaearctic and the Alps we found substantial nucleotide diversity (2.3%) but little differentiation between populations. Based on the mismatch distribution of the L. timidus sequences, this could result from an expansion at a time of temperature decrease favourable to this arctic species. The nucleotide diversity of L. timidus mtDNA found in Iberian L. granatensis, L. europaeus and L. castroviejoi (183, 70 and 1 specimens, respectively) was of the same order as that in L. timidus over its range (1.9%), suggesting repeated introgression of multiple lineages. The structure of the coalescent of L. granatensis sequences indicates that hybridization with L. timidus was followed by expansion of the introgressed haplotypes, as expected during a replacement with competition, and occurred when temperatures started to rise, favouring the temperate species. Whether a similar scenario explains the introgression into Iberian L. europaeus remains unclear but it is possible that it hybridized with already introgressed L. granatensis.

Introgression of Chromosome 3Ns from Psathyrostachys huashanica into Wheat Specifying Resistance to Stripe Rust

PubMed Central

Kang, Houyang; Wang, Yi; Fedak, George; Cao, Wenguang; Zhang, Haiqin; Fan, Xing; Sha, Lina; Xu, Lili; Zheng, Youliang; Zhou, Yonghong

2011-01-01

Wheat stripe rust is a destructive disease in the cool and humid wheat-growing areas of the world. Finding diverse sources of stripe rust resistance is critical for increasing genetic diversity of resistance for wheat breeding programs. Stripe rust resistance was identified in the alien species Psathyrostachys huashanica, and a wheat- P. huashanica amphiploid line (PHW-SA) with stripe rust resistance was reported previously. In this study, a P. huashanica 3Ns monosomic addition line (PW11) with superior resistance to stripe rust was developed, which was derived from the cross between PHW-SA and wheat J-11. We evaluated the alien introgressions PW11-2, PW11-5 and PW11-8 which were derived from line PW11 for reaction to new Pst race CYR32, and used molecular and cytogenetic tools to characterize these lines. The introgressions were remarkably resistant to CYR32, suggesting that the resistance to stripe rust of the introgressions thus was controlled by gene(s) located on P. huashanica chromosome 3Ns. All derived lines were cytologically stable in term of meiotic chromosome behavior. Two 3Ns chromosomes of P. huashanica were detected in the disomic addition line PW11-2. Chromosomes 1B of substitution line PW11-5 had been replaced by a pair of P. huashanica 3Ns chromosomes. In PW11-8, a small terminal segment from P. huashanica chromosome arm 3NsS was translocated to the terminal region of wheat chromosomes 3BL. Thus, this translocated chromosome is designated T3BL-3NsS. These conclusions were further confirmed by SSR analyses. Two 3Ns-specific markers Xgwm181 and Xgwm161 will be useful to rapidly identify and trace the translocated fragments. These introgressions, which had significant characteristics of resistance to stripe rust, could be utilized as novel germplasms for wheat breeding. PMID:21760909

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

PubMed

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species.

PubMed

Wielstra, Ben; Arntzen, Jan W

2014-01-01

If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.

Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia.

PubMed

Chen, Ningbo; Cai, Yudong; Chen, Qiuming; Li, Ran; Wang, Kun; Huang, Yongzhen; Hu, Songmei; Huang, Shisheng; Zhang, Hucai; Zheng, Zhuqing; Song, Weining; Ma, Zhijie; Ma, Yun; Dang, Ruihua; Zhang, Zijing; Xu, Lei; Jia, Yutang; Liu, Shanzhai; Yue, Xiangpeng; Deng, Weidong; Zhang, Xiaoming; Sun, Zhouyong; Lan, Xianyong; Han, Jianlin; Chen, Hong; Bradley, Daniel G; Jiang, Yu; Lei, Chuzhao

2018-06-14

Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.

SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

PubMed

Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

2017-07-01

The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content. © 2016 John Wiley & Sons Ltd.

Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.

PubMed

Almeida, Pedro; Barbosa, Raquel; Bensasson, Douda; Gonçalves, Paula; Sampaio, José Paulo

2017-04-01

In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives. © 2017 John Wiley & Sons Ltd.

Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff.).

PubMed

Lei, Dongyang; Tan, Lubin; Liu, Fengxia; Chen, Liyun; Sun, Chuanqing

2013-03-01

Understanding the responses of rice plants to heat-stress is a challenging, yet crucial, endeavor. A set of introgression lines was previously developed using an advanced backcrossing strategy that involved the elite indica cultivar Teqing as the recipient and an accession of common wild rice (Oryza rufipongon Griff.) as the donor. In this study, we evaluated the responses of 90 of these previously developed introgression lines to heat stress. Five quantitative trait loci (QTLs) related to heat response were detected. The phenotypic variances explained by these QTLs ranged from 6.83% to 14.63%, and O. rufipogon-derived alleles at one locus reduced sensitivity to heat. A heat-sensitive introgression line, YIL106, was identified and characterized. Genotypic analysis demonstrated that YIL106 contained four introgressed segments derived from O. rufipongon and two QTLs (qHTS1-1 and qHTS3) related to heat response. Physiological tests, including measurements of chlorophyll content, electrolyte leakage, malondialdehyde content, and soluble sugar content, were consistent with the heat sensitivity observed in YIL106. Ultrastructural analysis of YIL106 mesophyll cells showed that they were severely damaged following heat stress. This suggests that modification of the cell membrane system is a primary response to heat stress in plants. Identification and characterization of the heat-sensitive line YIL106 may facilitate the isolation of genes associated with the response of rice plants to heat stress. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Transfer of Dicamba Tolerance from Sinapis arvensis to Brassica napus via Embryo Rescue and Recurrent Backcross Breeding.

PubMed

Jugulam, M; Ziauddin, Asma; So, Kenny K Y; Chen, Shu; Hall, J Christopher

2015-01-01

Auxinic herbicides (e.g. dicamba) are extensively used in agriculture to selectively control broadleaf weeds. Although cultivated species of Brassicaceae (e.g. Canola) are susceptible to auxinic herbicides, some biotypes of Sinapis arvensis (wild mustard) were found dicamba resistant in Canada. In this research, dicamba tolerance from wild mustard was introgressed into canola through embryo rescue followed by conventional breeding. Intergeneric hybrids between S. arvensis (2n = 18) and B. napus (2n = 38) were produced through embryo rescue. Embryo formation and hybrid plant regeneration was achieved. Transfer of dicamba tolerance from S. arvensis into the hybrid plants was determined by molecular analysis and at the whole plant level. Dicamba tolerance was introgressed into B. napus by backcrossing for seven generations. Homozygous dicamba-tolerant B. napus lines were identified. The ploidy of the hybrid progeny was assessed by flow cytometry. Finally, introgression of the piece of DNA possibly containing the dicamba tolerance gene into B. napus was confirmed using florescence in situ hybridization (FISH). This research demonstrates for the first time stable introgression of dicamba tolerance from S. arvensis into B. napus via in vitro embryo rescue followed by repeated backcross breeding. Creation of dicamba-tolerant B. napus varieties by this approach may have potential to provide options to growers to choose a desirable herbicide-tolerant technology. Furthermore, adoption of such technology facilitates effective weed control, less tillage, and possibly minimize evolution of herbicide resistant weeds.

Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.

PubMed

Combosch, David J; Vollmer, Steven V

2015-07-01

Discrepancies between morphology-based taxonomy and phylogenetic systematics are common in Scleractinian corals. In Pocillopora corals, nine recently identified genetic lineages disagree fundamentally with the 17 recognized Pocillopora species, including 5 major Indo-Pacific reef-builders. Pocillopora corals hybridize in the Tropical Eastern Pacific, so it is possible that some of the disagreement between the genetics and taxonomy may be due to introgressive hybridization. Here we used 6769 genome-wide SNPs from Restriction-site Associated DNA Sequencing (RAD-Seq) to conduct phylogenomic comparisons among three common, Indo-Pacific Pocillopora species - P. damicornis, P. eydouxi and P. elegans - within and between populations in the Tropical Eastern Pacific (TEP) and the Central Pacific. Genome-wide RAD-Seq comparisons of Central and TEP Pocillopora confirm that the morphospecies P. damicornis, P. eydouxi and P. elegans are not monophyletic, but instead fall into three distinct genetic groups. However, hybrid samples shared fixed alleles with their respective parental species and, even without strict monophyly, P. damicornis share a common set of 33 species-specific alleles across the Pacific. RAD-Seq data confirm the pattern of one-way introgressive hybridization among TEP Pocillopora, suggesting that introgression may play a role in generating shared, polyphyletic lineages among currently recognized Pocillopora species. Levels of population differentiation within genetic lineages indicate significantly higher levels of population differentiation in the Tropical Eastern Pacific than in the Central West Pacific. Copyright © 2015 Elsevier Inc. All rights reserved.

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.).

PubMed

Herrera, Juan Carlos; D'Hont, Angelique; Lashermes, Philippe

2007-07-01

Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hybrids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (Ca) appears rather considerable. Poor discrimination between C and Ca chromosomes supports the idea of low structural modifications of both genomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of either specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica.

Introgression of Swertia mussotii gene into Bupleurum scorzonerifolium via somatic hybridization

PubMed Central

2011-01-01

Background The wild herb Swertia mussotii is a source of the anti-hepatitis compounds swertiamarin, mangiferin and gentiopicroside. Its over-exploitation has raised the priority of producing these compounds heterologously. Somatic hybridization represents a novel approach for introgressing Swertia mussotii genes into a less endangered species. Results Protoplasts derived from calli of Bupleurum scorzonerifolium and S. mussotii were fused to produce 194 putative hybrid cell lines, of which three (all derived from fusions where the S. mussotii protoplasts were pre-treated for 30 s with UV light) later differentiated into green plants. The hybridity of the calli was confirmed by a combination of isozyme, RAPD and chromosomal analysis. The hybrid calli genomes were predominantly B. scorzonerifolium. GISH analysis of mitotic chromosomes confirmed that the irradiation of donor protoplasts increased the frequency of chromosome elimination and fragmentation. RFLP analysis of organellar DNA revealed that mitochondrial and chloroplast DNA of both parents coexisted and recombined in some hybrid cell lines. Some of the hybrid calli contained SmG10H from donor, and produced swertiamarin, mangiferin and certain volatile compounds characteristic of S. mussotii. The expression of SmG10H (geraniol 10-hydroxylase) was associated with the heterologous accumulation of swertiamarin. Conclusions Somatic hybrids between B. scorzonerifolium and S. mussotii were obtained, hybrids selected all contained introgressed nuclear and cytoplasmic DNA from S. mussotii; and some produced more mangiferin than the donor itself. The introgression of SmG10H was necessary for the accumulation of swertiamarin. PMID:21513581

SNP Discovery for mapping alien introgressions in wheat

PubMed Central

2014-01-01

Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants. PMID:24716476

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PubMed Central

Jiménez, Rosa Alicia

2016-01-01

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers. PMID:26788433

Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis.

PubMed

Verardi, A; Lucchini, V; Randi, E

2006-09-01

Occasional crossbreeding between free-ranging domestic dogs and wild wolves (Canis lupus) has been detected in some European countries by mitochondrial DNA sequencing and genotyping unlinked microsatellite loci. Maternal and unlinked genomic markers, however, might underestimate the extent of introgressive hybridization, and their impacts on the preservation of wild wolf gene pools. In this study, we genotyped 220 presumed Italian wolves, 85 dogs and 7 known hybrids at 16 microsatellites belonging to four different linkage groups (plus four unlinked microsatellites). Population clustering and individual assignments were performed using a Bayesian procedure implemented in structure 2.1, which models the gametic disequilibrium arising between linked loci during admixtures, aiming to trace hybridization events further back in time and infer the population of origin of chromosomal blocks. Results indicate that (i) linkage disequilibrium was higher in wolves than in dogs; (ii) 11 out of 220 wolves (5.0%) were likely admixed, a proportion that is significantly higher than one admixed genotype in 107 wolves found previously in a study using unlinked markers; (iii) posterior maximum-likelihood estimates of the recombination parameter r revealed that introgression in Italian wolves is not recent, but could have continued for the last 70 (+/- 20) generations, corresponding to approximately 140-210 years. Bayesian clustering showed that, despite some admixture, wolf and dog gene pools remain sharply distinct (the average proportions of membership to wolf and dog clusters were Q(w) = 0.95 and Q(d) = 0.98, respectively), suggesting that hybridization was not frequent, and that introgression in nature is counteracted by behavioural or selective constraints.

The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes

PubMed Central

Lin, Yen-Lung; Pavlidis, Pavlos; Karakoc, Emre; Ajay, Jerry; Gokcumen, Omer

2015-01-01

Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn’s disease. Our analyses suggest that these “exonic” deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes. PMID:25556237

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

PubMed Central

Melo-Ferreira, José; Vilela, Joana; Fonseca, Miguel M.; da Fonseca, Rute R.; Boursot, Pierre; Alves, Paulo C.

2014-01-01

Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive. PMID:24696399

Non-introgressive genome chimerisation by malsegregation in autodiploidised allotetraploids during meiosis of Saccharomyces kudriavzevii x Saccharomyces uvarum hybrids.

PubMed

Karanyicz, Edina; Antunovics, Zsuzsa; Kallai, Z; Sipiczki, M

2017-06-01

Saccharomyces strains with chimerical genomes consisting of mosaics of the genomes of different species ("natural hybrids") occur quite frequently among industrial and wine strains. The most widely endorsed hypothesis is that the mosaics are introgressions acquired via hybridisation and repeated backcrosses of the hybrids with one of the parental species. However, the interspecies hybrids are sterile, unable to mate with their parents. Here, we show by analysing synthetic Saccharomyces kudriavzevii x Saccharomyces uvarum hybrids that mosaic (chimeric) genomes can arise without introgressive backcrosses. These species are biologically separated by a double sterility barrier (sterility of allodiploids and F1 sterility of allotetraploids). F1 sterility is due to the diploidisation of the tetraploid meiosis resulting in MAT a /MAT α heterozygosity which suppresses mating in the spores. This barrier can occasionally be broken down by malsegregation of autosyndetically paired chromosomes carrying the MAT loci (loss of MAT heterozygosity). Subsequent malsegregation of additional autosyndetically paired chromosomes and occasional allosyndetic interactions chimerise the hybrid genome. Chromosomes are preferentially lost from the S. kudriavzevii subgenome. The uniparental transmission of the mitochondrial DNA to the hybrids indicates that nucleo-mitochondrial interactions might affect the direction of the genomic changes. We propose the name GARMe (Genome AutoReduction in Meiosis) for this process of genome reduction and chimerisation which involves no introgressive backcrossings. It opens a way to transfer genetic information between species and thus to get one step ahead after hybridisation in the production of yeast strains with beneficial combinations of properties of different species.

Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin.

PubMed

Lamer, James T; Ruebush, Blake C; Arbieva, Zarema H; McClelland, Michael A; Epifanio, John M; Sass, Greg G

2015-08-01

Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed-species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species-diagnostic SNPs (57 nuclear and one mitochondrial). Forty-four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental-like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later-generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F1 hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species. © 2015 John Wiley & Sons Ltd.

Integration of BpMADS4 on various linkage groups improves the utilization of the rapid cycle breeding system in apple.

PubMed

Weigl, Kathleen; Wenzel, Stephanie; Flachowsky, Henryk; Peil, Andreas; Hanke, Magda-Viola

2015-02-01

Rapid cycle breeding in apple is a new approach for the rapid introgression of agronomically relevant traits (e.g. disease resistances) from wild apple species into domestic apple cultivars (Malus × domestica Borkh.). This technique drastically shortens the long-lasting juvenile phase of apple. The utilization of early-flowering apple lines overexpressing the BpMADS4 gene of the European silver birch (Betula pendula Roth.) in hybridization resulted in one breeding cycle per year. Aiming for the selection of non-transgenic null segregants at the end of the breeding process, the flower-inducing transgene and the gene of interest (e.g. resistance gene) that will be introgressed by hybridization need to be located on different chromosomes. To improve the flexibility of the existing approach in apple, this study was focused on the development and characterization of eleven additional BpMADS4 overexpressing lines of four different apple cultivars. In nine lines, the flowering gene was mapped to different linkage groups. The differences in introgressed T-DNA sequences and plant genome deletions post-transformation highlighted the unique molecular character of each line. However, transgenic lines demonstrated no significant differences in flower organ development and pollen functionality compared with non-transgenic plants. Hybridization studies using pollen from the fire blight-resistant wild species accession Malus fusca MAL0045 and the apple scab-resistant cultivar 'Regia' indicated that BpMADS4 introgression had no significant effect on the breeding value of each transgenic line. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

X-y interactions underlie sperm head abnormality in hybrid male house mice.

PubMed

Campbell, Polly; Nachman, Michael W

2014-04-01

The genetic basis of hybrid male sterility in house mice is complex, highly polygenic, and strongly X linked. Previous work suggested that there might be interactions between the Mus musculus musculus X and the M. m. domesticus Y with a large negative effect on sperm head morphology in hybrid males with an F1 autosomal background. To test this, we introgressed the M. m. domesticus Y onto a M. m. musculus background and measured the change in sperm morphology, testis weight, and sperm count across early backcross generations and in 11th generation backcross males in which the opportunity for X-autosome incompatibilities is effectively eliminated. We found that abnormality in sperm morphology persists in M. m. domesticus Y introgression males, and that this phenotype is rescued by M. m. domesticus introgressions on the X chromosome. In contrast, the severe reductions in testis weight and sperm count that characterize F1 males were eliminated after one generation of backcrossing. These results indicate that X-Y incompatibilities contribute specifically to sperm morphology. In contrast, X-autosome incompatibilities contribute to low testis weight, low sperm count, and sperm morphology. Restoration of normal testis weight and sperm count in first generation backcross males suggests that a small number of complex incompatibilities between loci on the M. m. musculus X and the M. m. domesticus autosomes underlie F1 male sterility. Together, these results provide insight into the genetic architecture of F1 male sterility and help to explain genome-wide patterns of introgression across the house mouse hybrid zone.

Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.

PubMed

Chintalapati, Manjusha; Dannemann, Michael; Prüfer, Kay

2017-08-04

Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times. We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans. Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity.

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production.

PubMed

Thurber, Carrie S; Ma, Justin M; Higgins, Race H; Brown, Patrick J

2013-06-26

Sorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation. We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time. Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.

Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits.

PubMed

Caruso, G; Gomez, L D; Ferriello, F; Andolfi, A; Borgonuovo, C; Evidente, A; Simister, R; McQueen-Mason, S J; Carputo, D; Frusciante, L; Ercolano, M R

2016-04-05

Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for both food consumption and fuel conversion requires the establishment of new selection methods. A tomato Solanum pennellii introgression population was assessed for fruit yield, biomass phenotypic diversity, and for saccharification potential. Introgression lines 2-5, 2-6, 6-3, 7-2, 10-2 and 12-4 showed the best combination of fruit and residual biomass production. Lignin, cellulose, hemicellulose content and saccharification rate showed a wide variation in the tested lines. Within hemicellulose, xylose value was high in IL 6-3, IL 7-2 and IL 6-2, whereas arabinose showed a low content in IL 10-2, IL 6-3 and IL 2-6. The latter line showed also the highest ethanol potential production. Alkali pre-treatment resulted in the highest values of saccharification in most of lines tested, suggesting that chemical pretreatment is an important factor for improving biomass processability. Interestingly, extreme genotypes for more than one single trait were found, allowing the identification of better genotypes. Cell wall related genes mapping in genomic regions involved into tomato biomass production and digestibility variation highlighted potential candidate genes. Molecular expression profile of few of them provided useful information about challenged pathways. The screening of S. pennellii introgression population resulted very useful for delving into complex traits such as biomass production and digestibility. The extreme genotypes identified could be fruitfully employed for both genetic studies and breeding.

Scarce events of mitochondrial introgression in Trypanosoma cruzi: new case with a Bolivian strain.

PubMed

Barnabé, Christian; Brenière, Simone Frédérique

2012-12-01

Trypanosoma cruzi, the agent of Chagas disease, presents a predominantly clonal structure that has been shaped by recombination events leading to six genetic groups (DTUs, discrete typing units, TcI-TcVI). Several conventional and unconventional genetic exchange events have been described, including hybridization and mitochondrial introgression, which is explored here among Bolivian and Peruvian strains belonging to TcI because recombination events have been previously suspected by means of the MLMT method (multilocus microsatellite typing). We analyzed the variation of one nuclear (Gpi) and one mitochondrial (Nd1) gene among 60 TcI strains and 15 reference strains belonging to the six DTUs. The results clearly showed that one strain isolated from Triatoma infestans in the Cochabamba department (Bolivia) presented a genotype TcI for Gpi and a mitochondrial Nd1 genotype common to the DTUs TcIII, IV, V, and VI; this can be interpreted as a mitochondrial introgression event between distant DTUs. These kinds of events, although probably scarce, may have played an important role in the adaptive evolution of the species. Copyright © 2012 Elsevier B.V. All rights reserved.

Evidence of sexually dimorphic introgression in Pinaleno Mountain Apache trout

USGS Publications Warehouse

Porath, M.T.; Nielsen, J.L.

2003-01-01

The high-elevation headwater streams of the Pinaleno Mountains support small populations of threatened Apache trout Oncorhynchus apache that were stocked following the chemical removal of nonnative salmonids in the 1960s. A fisheries survey to assess population composition, growth, and size structure confirmed angler reports of infrequent occurrences of Oncorhynchus spp. exhibiting the external morphological characteristics of both Apache trout and rainbow trout O. mykiss. Nonlethal tissue samples were collected from 50 individuals in the headwaters of each stream. Mitochondrial DNA (mtDNA) sequencing and amplification of nuclear microsatellite loci were used to determine the levels of genetic introgression by rainbow trout in Apache trout populations at these locations. Sexually dimorphic introgression from the spawning of male rainbow trout with female Apache trout was detected using mtDNA and microsatellites. Estimates of the degree of hybridization based on three microsatellite loci were 10-88%. The use of nonlethal DNA genetic analyses can supplement information obtained from standard survey methods and be useful in assessing the relative importance of small and sensitive populations with a history of nonnative introductions.

Something old, something borrowed: admixture and adaptation in human evolution.

PubMed

Dannemann, Michael; Racimo, Fernando

2018-06-09

The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time. Copyright © 2018 Elsevier Ltd. All rights reserved.

A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization, localization, and introgression to O. sativa.

PubMed

Yan, H. H.; Liu, G. Q.; Cheng, Z. K.; Li, X. B.; Liu, G. Z.; Min, S. K.; Zhu, L.H.

2002-02-01

In the course of transferring the brown planthopper resistance from a diploid, CC-genome wild rice species, Oryza eichingeri (IRGC acc. 105159 and 105163), to the cultivated rice variety 02428, we have isolated many alien addition and introgression lines. The O. eichingeri chromatin in some of these lines has previously been identified using genomic in situ hybridization and molecular-marker analysis. Here we cloned a tandemly repetitive DNA sequence from O. eichingeri IRGC acc105163, and detected it in 25 introgression lines. This repetitive DNA sequence showed high specificity to the rice CC genome, but was absent from all the four tetraploid species with BBCC or CCDD genomes. The monomer in this repetitive DNA sequence is 325-366-bp long, with a copy number of about 5,000 per 1 C of the O. eichingerigenome, showing 88% homology to a repetitive DNA sequence isolated from Oryza officinalis(2n=2 x=24, CC). Fluorescent in situ hybridization revealed 11 signals distributed over eight O. eichingeri chromosomes, mostly in terminal or subterminal regions.

Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming.

PubMed

Miralles, Laura; Oremus, Marc; Silva, Mónica A; Planes, Serge; Garcia-Vazquez, Eva

2016-01-01

Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.

Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming

PubMed Central

Miralles, Laura; Oremus, Marc; Silva, Mónica A.; Planes, Serge; Garcia-Vazquez, Eva

2016-01-01

Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas. PMID:27508496

Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis

PubMed Central

Feder, Jeffrey L.; Xie, Xianfa; Rull, Juan; Velez, Sebastian; Forbes, Andrew; Leung, Brian; Dambroski, Hattie; Filchak, Kenneth E.; Aluja, Martin

2005-01-01

The Rhagoletis pomonella sibling species complex is a model for sympatric speciation by means of host plant shifting. However, genetic variation aiding the sympatric radiation of the group in the United States may have geographic roots. Inversions on chromosomes 1-3 affecting diapause traits adapting flies to differences in host fruiting phenology appear to exist in the United States because of a series of secondary introgression events from Mexico. Here, we investigate whether these inverted regions of the genome may have subsequently evolved to become more recalcitrant to introgression relative to collinear regions, consistent with new models for chromosomal speciation. As predicted by the models, gene trees for six nuclear loci mapping to chromosomes other than 1-3 tended to have shallower node depths separating Mexican and U.S. haplotypes relative to an outgroup sequence than nine genes residing on chromosomes 1-3. We discuss the implications of secondary contact and differential introgression with respect to sympatric host race formation and speciation in Rhagoletis, reconciling some of the seemingly dichotomous views of Mayr, Dobzhansky, and Bush concerning modes of divergence. PMID:15851672

Marker-assisted pyramiding of brown planthopper (Nilaparvata lugens Stål) resistance genes Bph1 and Bph2 on rice chromosome 12.

PubMed

Sharma, Prem N; Torii, Akihide; Takumi, Shigeo; Mori, Naoki; Nakamura, Chiharu

2004-01-01

Brown planthopper (BPH) (Nilaparvata lugens Stål) is a significant insect pest of rice (Oryza sativa L.). We constructed a gene-pyramided japonica line, in which two BPH resistance genes Bph1 and Bph2 on the long arm of chromosome 12 independently derived from two indica resistance lines were combined through the recombinant selection. The gene-pyramiding was achieved based on the previously constructed high-resolution linkage maps of the two genes. Two co-dominant and four dominant PCR-based markers flanking the loci were used to select for a homozygous recombinant line in a segregating population that was derived from a cross between the parental homozygous single-gene introgression lines. BPH bioassay showed that the resistance level of the pyramided line was equivalent to that of the Bph1-single introgression line, which showed a higher level of resistance than the Bph2-single introgression line. The pyramid line should provide a useful experimental means for studying the fine structure of the chromosomal region covering these two major BPH resistance genes.

Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss)

USGS Publications Warehouse

Ostberg, Carl O.; Hauser, Lorenz; Pritchard, Victoria L.; Garza, John C.; Naish, Kerry A.

2013-01-01

Chromosome rearrangements suppressed recombination in the hybrids. This result supports several previous findings demonstrating that recombination suppression restricts gene flow between chromosomes that differ by arrangement. Conservation of synteny and map order between the hybrid and rainbow trout maps and minimal segregation distortion in the hybrids suggest rainbow and Yellowstone cutthroat trout genomes freely introgress across chromosomes with similar arrangement. Taken together, these results suggest that rearrangements impede introgression. Recombination suppression across rearrangements could enable large portions of non-recombined chromosomes to persist within admixed populations.

Maize x Teosinte Hybrid Cobs Do Not Prevent Crop Gene Introgression.

PubMed

Chavez, Nancy B; Flores, Jose J; Martin, Joseph; Ellstrand, Norman C; Guadagnuolo, Roberto; Heredia, Sylvia; Welles, Shana R

2012-06-01

Maize x Teosinte Hybrid Cobs Do Not Prevent Crop Gene Introgression. Whether introgression from crops to wild relatives can occur is an important component of transgene risk assessment. In the case of maize, which co-occurs with its wild relative teosinte in Mexico, the possibility of introgression has been controversial. Maize is cross-compatible with teosinte, and spontaneous hybridization is known to occur. Some scientists have hypothesized that the maize x teosinte cob infructescence will prevent progeny dispersal, thus preventing introgression. Motivated by a prior study where we found maize x teosinte hybrid fruits naturally dispersed under field conditions, we tested whether hybrid cobs hold their fruits as tightly as maize cobs. We found the force required to detach hybrid fruits was substantially and significantly less than that for maize. Consequently, we expect that introgression of transgenes from maize into teosinte in Mexico should occur largely unimpeded by the hybrid cob.La mazorca o elote híbrido de maíz x teocintle no impide la introgresión de genes transgénicos provenientes del cultivo. La introgresión entre el maíz cultivado y el maíz silvestre, o teocintle, es un componente importante en la evaluación ambiental relacionada con los riesgos de la introducción de genes transgénicos. La posibilidad de introgresión entre el maíz domesticado y el teocintle ha sido un tema controversial, en particular en México, donde maíz y teocintle coexisten. El maíz es compatible con el teocintle y la hibridización espontánea ocurre entre ellos. Algunos científicos han planteado como hipótesis que al cruzar el maíz con teocintle, la estructura interna de la infrutescencia que sujeta los frutos conocida como la mazorca de maíz o el elote, impide la dispersión de la progenie evitando que la introgresión ocurra. Los resultados de un estudio previo evidencian la dispersión de los frutos híbridos del maíz x teocintle en condiciones naturales. Motivados por estos resultados, hemos decidido investigar si la mazorca o el elote de las infrutescencias del híbrido sujetan los frutos con una fuerza comparable o mayor a la del maíz. Nuestras mediciones implican que la fuerza necesaria para liberar los frutos híbridos son substancial y significativamente menores que aquellas necesarias para desprender los frutos del maíz. Como conclusión sugerimos que en México, la mazorca o el elote no representan una barrera que impida la introgresión de los genes transgénicos del maíz al teocintle.

Genetic analysis of a novel broad-spectrum powdery mildew resistance gene from the wheat-Agropyron cristatum introgression line Pubing 74.

PubMed

Lu, Yuqing; Yao, Miaomiao; Zhang, Jinpeng; Song, Liqiang; Liu, Weihua; Yang, Xinming; Li, Xiuquan; Li, Lihui

2016-09-01

A novel broad-spectrum powdery mildew resistance gene PmPB74 was identified in wheat- Agropyron cristatum introgression line Pubing 74. Development of wheat cultivars with broad-spectrum, durable resistance to powdery mildew has been restricted by lack of superior genetic resources. In this study, a wheat-A. cristatum introgression line Pubing 74, originally selected from a wide cross between the common wheat cultivar Fukuhokomugi (Fukuho) and Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genome PPPP), displayed resistance to powdery mildew at both the seedling and adult stages. The putative alien chromosomal fragment in Pubing 74 was below the detection limit of genomic in situ hybridization (GISH), but evidence for other non-GISH-detectable introgressions was provided by the presence of three STS markers specific to A. cristatum. Genetic analysis indicated that Pubing 74 carried a single dominant gene for powdery mildew resistance, temporarily designated PmPB74. Molecular mapping showed that PmPB74 was located on wheat chromosome arm 5DS, and flanked by markers Xcfd81 and HRM02 at genetic distances of 2.5 and 1.7 cM, respectively. Compared with other lines with powdery mildew resistance gene(s) on wheat chromosome arm 5DS, Pubing 74 was resistant to all 28 Blumeria graminis f. sp tritici (Bgt) isolates from different wheat-producing regions of northern China. Allelism tests indicated that PmPB74 was not allelic to PmPB3558 or Pm2. Our work showed that PmPB74 is a novel gene with broad resistance to powdery mildew, and hence will be helpful in broadening the genetic basis of powdery mildew resistance in wheat.

Introgression among three rockfish species (Sebastes spp.) in the Salish Sea, northeast Pacific Ocean

PubMed Central

Park, Linda K.; Hauser, Lorenz

2018-01-01

Interspecific hybridization is often seen as a major conservation issue, potentially threatening endangered species and decreasing biodiversity. In natural populations, the conservation implications of hybridization depends on both on anthropogenic factors and the evolutionary processes maintaining the hybrid zone. However, the timeline and patterns of hybridization in the hybrid zone are often not known. Therefore, species conservation becomes a concern when recent anthropogenic changes influence hybridization and not if hybridization is part of a long-term process. Here, we use sequence data from one mitochondrial gene, three nuclear introns and one nuclear exon to estimate the direction, geographic extent, frequency and possible timeline of hybridization between three rockfish species (Sebastes auriculatus, S. caurinus, S. maliger) in the Salish Sea, Washington, USA. We show that (i) introgression occurred much more frequently in the Salish Sea than on the outer coast, (ii) introgression was highly asymmetrical from S. maliger into the other two species, (iii) almost 40% of individuals in the Salish Sea were hybrids, with frequency of hybrids increasing with isolation from the coast, and (iv) all hybrids were later generation backcrosses rather than F1 hybrids. Our results suggest long-standing low-level hybridization rather than recent onset of interbreeding because of human induced environmental change, possibly facilitated by specific environmental conditions in the sub-basins of the Salish Sea, and by differences in population sizes during recolonization of the area after the last glaciation. This rockfish hybrid system, with asymmetrical introgression and the maintenance of parental species, may prove useful to study both mechanisms that maintain species boundaries and that facilitate speciation in the presence of rapid environmental change. PMID:29566070

Characterization of new allele influencing flowering time in bread wheat introgressed from Triticum militinae.

PubMed

Ivaničová, Zuzana; Jakobson, Irena; Reis, Diana; Šafář, Jan; Milec, Zbyněk; Abrouk, Michael; Doležel, Jaroslav; Järve, Kadri; Valárik, Miroslav

2016-09-25

Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat. Copyright © 2016 Elsevier B.V. All rights reserved.

Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

PubMed Central

Muñoz, Irene; Henriques, Dora; Johnston, J. Spencer; Chávez-Galarza, Julio; Kryger, Per; Pinto, M. Alice

2015-01-01

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs. PMID:25875986

Introgression of physiological traits for a comprehensive improvement of drought adaptation in crop plants

NASA Astrophysics Data System (ADS)

Sreeman, Sheshshayee M.; Vijayaraghavareddy, Preethi; Sreevathsa, Rohini; Rajendrareddy, Sowmya; Arakesh, Smitharani; Bharti, Pooja; Dharmappa, Prathibha; Soolanayakanahally, Raju

2018-04-01

Burgeoning population growth, industrial demand and the predicted global climate change resulting in erratic monsoon rains are expected to severely limit fresh water availability for agriculture both in irrigated and rainfed ecosystems. In order to remain food and nutrient secure, agriculture research needs to focus on devising strategies to save water in irrigated conditions and to develop superior cultivars with improved water productivity to sustain yield under rainfed conditions. Recent opinions accruing in the scientific literature strongly favour the adoption of a “trait based” approach for increasing water productivity especially the traits associated with maintenance of positive tissue turgor and maintenance of increased carbon assimilation as the most relevant traits to improve crop growth rates under water limiting conditions and to enhance water productivity. The advent of several water saving agronomic practices notwithstanding, a genetic enhancement strategy of introgressing distinct physiological, morphological and cellular mechanisms on to a single elite genetic background is essential for achieving a comprehensive improvement in drought adaptation in crop plants. The significant progress made in genomics, though would provide the necessary impetus, a clear understanding of the “traits” to be introgressed is the most essential need of the hour. Water uptake by a better root architecture, water conservation by preventing unproductive transpiration is crucial for maintaining positive tissue water relations. Improved carbon assimilation associated with carboxylation capacity and mesophyll conductance is equally important in sustaining crop growth rates under water limited conditions. Besides these major traits, we summarized the available information in literature on classifying various drought adaptive traits. We provide evidences that water-use efficiency when introgressed with moderately higher transpiration, would significantly enhance growth rates and water productivity in rice through an improved photosynthetic capacity.

Consequences of gene flow between oilseed rape (Brassica napus) and its relatives.

PubMed

Liu, Yongbo; Wei, Wei; Ma, Keping; Li, Junsheng; Liang, Yuyong; Darmency, Henri

2013-10-01

Numerous studies have focused on the probability of occurrence of gene flow between transgenic crops and their wild relatives and the likelihood of transgene escape, which should be assessed before the commercial release of transgenic crops. This review paper focuses on this issue for oilseed rape, Brassica napus L., a species that produces huge numbers of pollen grains and seeds. We analyze separately the distinct steps of gene flow: (1) pollen and seeds as vectors of gene flow; (2) spontaneous hybridization; (3) hybrid behavior, fitness cost due to hybridization and mechanisms of introgression; (4) and fitness benefit due to transgenes (e.g. herbicide resistance and Bt toxin). Some physical, biological and molecular means of transgene containment are also described. Although hybrids and first generation progeny are difficult to identify in fields and non-crop habitats, the literature shows that transgenes could readily introgress into Brassica rapa, Brassica juncea and Brassica oleracea, while introgression is expected to be rare with Brassica nigra, Hirschfeldia incana and Raphanus raphanistrum. The hybrids grow well but produce less seed than their wild parent. The difference declines with increasing generations. However, there is large uncertainty about the evolution of chromosome numbers and recombination, and many parameters of life history traits of hybrids and progeny are not determined with satisfactory confidence to build generic models capable to really cover the wide diversity of situations. We show that more studies are needed to strengthen and organize biological knowledge, which is a necessary prerequisite for model simulations to assess the practical and evolutionary outputs of introgression, and to provide guidelines for gene flow management. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Asymmetric gene introgression in two closely related Orchis species: evidence from morphometric and genetic analyses

PubMed Central

2012-01-01

Background In food-deceptive orchids of the genera Anacamptis, Neotinea and Orchis floral isolation has been shown to be weak, whereas late-acting reproductive barriers are mostly strong, often restricting hybridization to the F1 generation. Only in a few species hybridization extends beyond the F1 generation, giving rise to hybrid swarms. However, little is known about the abundance of later-generation hybrids and what factors drive their occurrence in hybrid populations. In this study, molecular analyses were combined with detailed morphological measurements in a hybrid population of two closely related Orchis species (Orchis militaris and O. purpurea) to investigate the hypothesis that the abundance of later-generation hybrids is driven by changes in floral characters after hybridization that exert selective pressures that in turn affect hybridization. Results Both the molecular and morphological data point to extensive genetic and morphological homogenization and asymmetric introgression. Estimating genomic clines from the multi-locus genotype data and testing for deviation from neutrality revealed that 30 out of 113 (27%) AFLP markers significantly deviated from neutral expectations. Plants with large floral displays or plant with flowers that resembled more O. purpurea had higher female fitness than plants with small floral displays or plants with flowers resembling more O. militaris, suggesting that directional selection may have contributed to the observed patterns of introgression. Conclusions These results indicate that in closely related orchid species hybridization and gene introgression may be partly driven by selection for floral traits of one of the parental types. However, because some pure individuals were still present in the studied population, the parental species appeared to be sufficiently isolated to survive the challenge of sympatry. PMID:22967086

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

PubMed

Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

2018-05-01

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression.

PubMed

Li, Runsheng; Ren, Xiaoliang; Bi, Yu; Ho, Vincy Wing Sze; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Lin, Tingting; Zhao, Yanmei; Miao, Long; Sarkies, Peter; Zhao, Zhongying

2016-09-01

Hybrid incompatibility (HI) prevents gene flow between species, thus lying at the heart of speciation genetics. One of the most common HIs is male sterility. Two superficially contradictory observations exist for hybrid male sterility. First, an introgression on the X Chromosome is more likely to produce male sterility than on autosome (so-called large-X theory); second, spermatogenesis genes are enriched on the autosomes but depleted on the X Chromosome (demasculinization of X Chromosome). Analysis of gene expression in Drosophila hybrids suggests a genetic interaction between the X Chromosome and autosomes that is essential for male fertility. However, the prevalence of such an interaction and its underlying mechanism remain largely unknown. Here we examine the interaction in nematode species by contrasting the expression of both coding genes and transposable elements (TEs) between hybrid sterile males and its parental nematode males. We use two lines of hybrid sterile males, each carrying an independent introgression fragment from Caenorhabditis briggsae X Chromosome in an otherwise Caenorhabditis nigoni background, which demonstrate similar defects in spermatogenesis. We observe a similar pattern of down-regulated genes that are specific for spermatogenesis between the two hybrids. Importantly, the down-regulated genes caused by the X Chromosome introgressions show a significant enrichment on the autosomes, supporting an epistatic interaction between the X Chromosome and autosomes. We investigate the underlying mechanism of the interaction by measuring small RNAs and find that a subset of 22G RNAs specifically targeting the down-regulated spermatogenesis genes is significantly up-regulated in hybrids, suggesting that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction. © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press.

More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers.

PubMed

Du, Fang K; Petit, Rémy J; Liu, Jian Quan

2009-04-01

Recent work has suggested that rates of introgression should be inversely related to levels of gene flow because introgressed populations cannot be 'rescued' by intraspecific gene flow if it is too low. Mitochondrial and chloroplast DNA (mtDNA and cpDNA) experience very different levels of gene flow in conifers due to their contrasted maternal and paternal modes of transmission, hence the prediction that mtDNA should introgress more readily than cpDNA in this group. Here, we use sequence data from both mtDNA and cpDNA to test this hypothesis in a group of closely related spruces species, the Picea asperata complex from China. Nine mitochondrial and nine chloroplast haplotypes were recovered from 459 individuals in 46 natural populations belonging to five species of the Picea asperata complex. Low variation was found in the two mtDNA introns along with a high level of differentiation among populations (G(ST) = 0.90). In contrast, we detected higher variation and lower differentiation among populations at cpDNA markers (G(ST) = 0.56), a trend shared by most conifer species studied so far. We found that cpDNA variation, although far from being fully diagnostic, is more species-specific than mtDNA variation: four groups of populations were identified using cpDNA markers, all of them related to species or groups of species, whereas for mtDNA, geographical variation prevails over species differentiation. The literature suggests that mtDNA haplotypes are often shared among related conifer species, whereas cpDNA haplotypes are more species-specific. Hence, increased intraspecific gene flow appears to decrease differentiation within species but not among species.

PERMANENT GENETIC RESOURCES: Consensus primers of cyp73 genes discriminate willow species and hybrids (Salix, Salicaceae).

PubMed

Trung, Le Quang; VAN Puyvelde, Karolien; Triest, Ludwig

2008-03-01

Consensus primers, based on exon sequences of the cyp73 gene family coding for cinnamate 4-hydroxylase (C4H) of the lignin biosynthesis pathway, were designed for the tetraploid willow species Salix alba and Salix fragilis. Diagnostic alleles at species level were observed among introns of three cyp73 genes and allowed unambiguous detection of the first generation and introgressed hybrids in populations. Progeny analysis of a female S. alba with a male introgressed hybrid confirmed the codominant inheritance of each intron. Sequences of the diagnostic alleles of both species were similar to those found in the hybrids. © 2007 The Authors.

Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum.

PubMed

Woodcock, M Ryan; Vaughn-Wolfe, Jennifer; Elias, Alexandra; Kump, D Kevin; Kendall, Katharina Denise; Timoshevskaya, Nataliya; Timoshevskiy, Vladimir; Perry, Dustin W; Smith, Jeramiah J; Spiewak, Jessica E; Parichy, David M; Voss, S Randal

2017-01-31

The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to the point where it is now possible to identify genes for mutant phenotypes. We used a positional cloning-candidate gene approach to identify molecular bases for two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in pigment cell morphogenesis and differentiation, whereas albino (a/a) mutants lack melanin. We identified in white mutants a transcriptional defect in endothelin 3 (edn3), encoding a peptide factor that promotes pigment cell migration and differentiation in other vertebrates. Transgenic restoration of Edn3 expression rescued the homozygous white mutant phenotype. We mapped the albino locus to tyrosinase (tyr) and identified polymorphisms shared between the albino allele (tyr a ) and tyr alleles in a Minnesota population of tiger salamanders from which the albino trait was introgressed. tyr a has a 142 bp deletion and similar engineered alleles recapitulated the albino phenotype. Finally, we show that historical introgression of tyr a significantly altered genomic composition of the laboratory axolotl, yielding a distinct, hybrid strain of ambystomatid salamander. Our results demonstrate the feasibility of identifying genes for traits in the laboratory Mexican axolotl.

Molecular identification of vectors of Leishmania in Colombia: mitochondrial introgression in the Lutzomyia townsendi series.

PubMed

Testa, J M; Montoya-Lerma, J; Cadena, H; Oviedo, M; Ready, P D

2002-12-01

The identity of the sandfly vectors of Leishmania braziliensis in Valle del Cauca Department, Colombia, was originally given as Lutzomyia townsendi, but then changed to L. youngi, another member of the L. townsendi series (Verrucarum group) with isomorphic females. To identify members of this series in Valle del Cauca, we analyzed the nuclear gene elongation factor-alpha (EF-alpha) and the mitochondrial gene cytochrome b (Cyt b). DNA sequences from the L. verrucarum series (L. columbiana, L. evansi and L. ovallesi) were used as outgroups. Flies from two locations on the western cordillera of the Andes were identified as L. townsendi s.s., according to male morphology and distinctive gene lineages. In the third location, on the central cordillera of the Andes, most specimens were identified as belonging to a geographical population of L. youngi, according to male morphology, an EF-alpha lineage shared with L. youngi from the Venezuelan-type locality, and a distinctive Cyt b sub-lineage. All other specimens were identified as L. youngi with the introgressed Cyt b sequences of L. townsendi. Such interspecific introgression implies that vectorial traits and ecological associations may no longer be viewed as fixed properties of different morphospecies.

[Chromosomal localization of the speltoidy gene, introgressed into bread wheat from Aegilops speltoides Tausch., and its interaction with the Q gene of Triticum spelta L].

PubMed

Simonov, A V; Pshenichnikova, T A

2012-11-01

The differences between bread wheat (Triticum aestivum L.) and spelt (Triticum spelta L.) in the shape of the spike and threshing character are determined by the allelic status of one major Q gene, mapped to the long arm of chromosome 5A. This gene is a member of the APETALA2 family of transcription factors and plays an important role in domestication of wheat. In the present study, using monosomic analysis, we determined the chromosomal localization of the Q(S)gene, introgressed into bread wheat from Aegilops speltoides Tausch. and homoallelic to the Q gene. It was demonstrated that the Q(S) gene was located in chromosome 5A of the bread wheat line from the Arsenal collection. This gene conferred spike speltoidy in the line itself, as well as in its hybrids with bread wheat cultivars. The Q(S) gene dominated over the bread wheat Q gene and was equally effective in the homo-, hemi-, and heterozygous states. In hybrids between the introgression line and a number of spring spelt accessions, interaction between the Q and Q(S) genes was observed, manifested as the formation of superspeltoid spike.

The Genetic Cost of Neanderthal Introgression

PubMed Central

Harris, Kelley; Nielsen, Rasmus

2016-01-01

Approximately 2–4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression. PMID:27038113

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

PubMed

Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

2017-03-01

Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments. Copyright © 2017 Elsevier Inc. All rights reserved.

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

PubMed Central

Currat, Mathias; Excoffier, Laurent

2011-01-01

Recent studies have revealed that 2–3% of the genome of non-Africans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both. These results suggesting the presence of very effective barriers to gene flow between the two species are robust to uncertainties about the exact demography of the Paleolithic populations, and they are also found to be compatible with the observed lack of mtDNA introgression. Our model additionally suggests that similarly low levels of introgression in Europe and Asia may result from distinct admixture events having occurred beyond the Middle East, after the split of Europeans and Asians. This hypothesis could be tested because it predicts that different components of Neanderthal ancestry should be present in Europeans and in Asians. PMID:21911389

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression.

PubMed

Currat, Mathias; Excoffier, Laurent

2011-09-13

Recent studies have revealed that 2-3% of the genome of non-Africans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both. These results suggesting the presence of very effective barriers to gene flow between the two species are robust to uncertainties about the exact demography of the Paleolithic populations, and they are also found to be compatible with the observed lack of mtDNA introgression. Our model additionally suggests that similarly low levels of introgression in Europe and Asia may result from distinct admixture events having occurred beyond the Middle East, after the split of Europeans and Asians. This hypothesis could be tested because it predicts that different components of Neanderthal ancestry should be present in Europeans and in Asians.

Introgressive Hybridization between Anciently Diverged Lineages of Silene (Caryophyllaceae)

PubMed Central

Petri, Anna; Pfeil, Bernard E.; Oxelman, Bengt

2013-01-01

Hybridization has played a major role during the evolution of angiosperms, mediating both gene flow between already distinct species and the formation of new species. Newly formed hybrids between distantly related taxa are often sterile. For this reason, interspecific crosses resulting in fertile hybrids have rarely been described to take place after more than a few million years after divergence. We describe here the traces of a reproductively successful hybrid between two ancestral species of Silene, diverged for about six million years prior to hybridization. No extant hybrids between the two parental lineages are currently known, but introgression of the RNA polymerase gene NRPA2 provides clear evidence of a temporary and fertile hybrid. Parsimony reconciliation between gene trees and the species tree, as well as consideration of clade ages, help exclude gene paralogy and lineage sorting as alternative hypotheses. This may represent one of the most extreme cases of divergence between species prior to introgressive hybridization discovered yet, notably at a homoploid level. Although species boundaries are generally believed to be stable after millions of years of divergence, we believe that this finding may indicate that gene flow between distantly related species is merely largely undetected at present. PMID:23861793

Environmental biosafety and transgenic potato in a centre of diversity for this crop.

PubMed

Celis, Carolina; Scurrah, Maria; Cowgill, Sue; Chumbiauca, Susana; Green, Jayne; Franco, Javier; Main, Gladys; Kiezebrink, Daan; Visser, Richard G F; Atkinson, Howard J

2004-11-11

The Nuffield Council on Bioethics suggests that introgression of genetic material into related species in centres of crop biodiversity is an insufficient justification to bar the use of genetically modified crops in the developing world. They consider that a precautionary approach to forgo the possible benefits invokes the fallacy of thinking that doing nothing is itself without risk to the poor. Here we report findings relevant to this and other aspects of environmental biosafety for genetically modified potato in its main centre of biodiversity, the central Andes. We studied genetically modified potato clones that provide resistance to nematodes, principal pests of Andean potato crops. We show that there is no harm to many non-target organisms, but gene flow occurs to wild relatives growing near potato crops. If stable introgression were to result, the fitness of these wild species could be altered. We therefore transformed the male sterile cultivar Revolucion to provide a genetically modified nematode-resistant potato to evaluate the benefits that this provides until the possibility of stable introgression to wild relatives is determined. Thus, scientific progress is possible without compromise to the precautionary principle.

Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species.

PubMed

Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Forister, Matthew L; Buerkle, C Alex

2012-07-01

Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here, we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two butterfly species (Lycaeides idas and L. melissa) also affect fitness in an admixed population. Locus-specific measures of genetic differentiation between L. idas and L. melissa and genomic introgression in hybrids varied across the genome. The most differentiated genetic regions were characterized by elevated L. idas ancestry in the admixed population, which occurs in L. idas-like habitat, consistent with the hypothesis that local adaptation contributes to speciation. Moreover, locus-specific measures of genetic differentiation (a metric of divergent selection) were positively associated with extreme genomic introgression (a metric of hybrid fitness). Interestingly, concordance of differentiation and introgression was only partial. We discuss multiple, complementary explanations for this partial concordance. © 2012 The Author(s).

Discordant introgression in a rapidly expanding hybrid swarm

USGS Publications Warehouse

Ward, Jessica L.; Blum, Mike J.; Walters, David M.; Porter, Brady A.; Burkhead, Noel; Freeman, Byron

2012-01-01

The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion, and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution of a hybrid swarm between native Cyprinella venusta and invasive Cyprinella lutrensis minnows. Discordant introgression of phenotype, microsatellite multilocus genotype, and mtDNA haplotype indicates that the observable expansion of the C. venusta x C. lutrensis hybrid swarm is a false invasion front. Both parental and hybrid individuals closely resembling C. lutrensis are numerically dominant in the expansion wake, indicating that the non-native parental phenotype may be selectively favored. These findings show that cryptic introgression can extend beyond the phenotypic boundaries of hybrid swarms and that hybrid swarms likely expand more rapidly than can be documented from phenotypic variation alone. Similarly, dominance of a single parental phenotype following an introduction event may lead to instances of species erosion being mistaken for species displacement without hybridization.

Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

USGS Publications Warehouse

Williams, Wyatt I.; Friedman, Jonathan M.; Gaskin, John F.; Norton, Andrew P.

2014-01-01

Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk (Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

Chapter 2: Genetic Variability in Nuclear Ribosomal and Chloroplast DNA in Utah (Juniperus Osteosperma) and Western (J. Occidentalis) Juniper (Cupressaceae): Evidence for Interspecific Gene Flow1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terry, Randall G.; Tausch, Robin J.; Nowak, Robert S.

1998-02-14

Early studies of evolutionary change in chloroplast DNA indicated limited variability within species. This finding has been attributed to relatively low rates of sequence evolution and has been maintained as justification for the lack of intraspecific sampling in studies examining, relationships at the species level and above. However, documentation of intraspecific variation in cpDNA has become increasingly common and has been attributed in many cases to ''chloroplast capture'' following genetic exchange across species boundaries. Rleseberg and Wendel (1993) list 37 cases of proposed hybridization in plants that include intraspecific variation in cpDNA, 24 (65%) of which they considered to bemore » probable instances of introgression. Rieseberg (1995) suspected that a review of the literature at that time would reveal over 100 cases of intraspecific variation in CPDNA that could be attributed to hybridization and introgression. That intraspecific variation in cpDNA is potentially indicative of hybridization is founded on the expectation that slowly evolving loci or genomes will produce greater molecular variation between than within species. In cases where a species is polymorphic for CPDNA and at least one of the molecular variants is diagnostic for a second species, interspecific hybridization is a plausible explanation. Incongruence between relationships suggested by cpDNA variation and those supported by other types of data (e.g., morphology or molecular data from an additional locus) provides additional support for introgression. One aspect of hybridization in both animals and plants that has become increasingly evident is incongruence in the phylogenetic and geographic distribution of cytoplasmic and nuclear markers. In most cases cytoplasmic introgression appears to be more pervasive than nuclear exchange. This discordance appears attributable to several factors including differences in the mutation rate, number of effective alleles, and modes of inheritance of cytoplasmic and nuclear loci. In addition, unidirectional introgression following an initial hybridization event can result in populations that have the cytoplasmic genome of one parental species and the nuclear genome of the other. In such cases, discordance in the phylogenetic, taxonomic, and geographic distribution of cytoplasmic and nuclear markers can provide insight into the biogeographic and population genetic forces affecting parental and hybrid populations.« less

Restricted gene flow at the micro- and macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism.

PubMed

Pujolar, José M; Lucarda, Alvise N; Simonato, Mauro; Patarnello, Tomaso

2011-04-14

The genetic structure of the marble trout Salmo trutta marmoratus, an endemic salmonid of northern Italy and the Balkan peninsula, was explored at the macro- and micro-scale level using a combination of mitochondrial DNA (mtDNA) and microsatellite data. Sequence variation in the mitochondrial control region showed the presence of nonindigenous haplotypes indicative of introgression from brown trout into marble trout. This was confirmed using microsatellite markers, which showed a higher introgression at nuclear level. Microsatellite loci revealed a strong genetic differentiation across the geographical range of marble trout, which suggests restricted gene flow both at the micro-geographic (within rivers) and macro-geographic (among river systems) scale. A pattern of Isolation-by-Distance was found, in which genetic samples were correlated with hydrographic distances. A general West-to-East partition of the microsatellite polymorphism was observed, which was supported by the geographic distribution of mitochondrial haplotypes. While introgression at both mitochondrial and nuclear level is unlikely to result from natural migration and might be the consequence of current restocking practices, the pattern of genetic substructuring found at microsatellites has been likely shaped by historical colonization patterns determined by the geological evolution of the hydrographic networks.

The eastern migratory caribou: the role of genetic introgression in ecotype evolution.

PubMed

Klütsch, Cornelya F C; Manseau, Micheline; Trim, Vicki; Polfus, Jean; Wilson, Paul J

2016-02-01

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada's Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.

Genetic characterization of hybridization and introgression between anadromous rainbow trout (oncorhynchus mykiss irideus) and coastal cutthroat trout (o. clarki clarki)

USGS Publications Warehouse

Young, W.P.; Ostberg, C.O.; Keim, P.; Thorgaard, G.H.

2001-01-01

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness.

Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow

PubMed Central

De La Torre, Amanda R; Roberts, David R; Aitken, Sally N

2014-01-01

The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21 000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both Fst outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors. PMID:24597663

A resource of large-scale molecular markers for monitoring Agropyron cristatum chromatin introgression in wheat background based on transcriptome sequences.

PubMed

Zhang, Jinpeng; Liu, Weihua; Lu, Yuqing; Liu, Qunxing; Yang, Xinming; Li, Xiuquan; Li, Lihui

2017-09-20

Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening. As a result, 6063 polymorphic EST-STS markers were specific for the A. cristatum P genome in the single-receipt wheat background. A total of 4956 randomly selected polymorphic EST-STS markers were further tested in eight wheat variety backgrounds, and 3070 markers displaying stable and polymorphic amplification were validated. These markers covered more than 98% of the A. cristatum genome, and the marker distribution density was approximately 1.28 cM. An application case of all EST-STS markers was validated on the A. cristatum 6 P chromosome. These markers were successfully applied in the tracking of alien A. cristatum chromatin. Altogether, this study provided a universal method of large-scale molecular marker development to monitor wild relative chromatin in wheat.

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga.

PubMed

Arbelaez, Juan D; Moreno, Laura T; Singh, Namrata; Tung, Chih-Wei; Maron, Lyza G; Ospina, Yolima; Martinez, César P; Grenier, Cécile; Lorieux, Mathias; McCouch, Susan

Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/ O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/ O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.

Progressive genome-wide introgression in agricultural Campylobacter coli

PubMed Central

Sheppard, Samuel K; Didelot, Xavier; Jolley, Keith A; Darling, Aaron E; Pascoe, Ben; Meric, Guillaume; Kelly, David J; Cody, Alison; Colles, Frances M; Strachan, Norval J C; Ogden, Iain D; Forbes, Ken; French, Nigel P; Carter, Philip; Miller, William G; McCarthy, Noel D; Owen, Robert; Litrup, Eva; Egholm, Michael; Affourtit, Jason P; Bentley, Stephen D; Parkhill, Julian; Maiden, Martin C J; Falush, Daniel

2013-01-01

Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10–11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution. PMID:23279096

Cisgenesis strongly improves introgression breeding and induced translocation breeding of plants.

PubMed

Jacobsen, Evert; Schouten, Henk J

2007-05-01

There are two ways for genetic improvement in classical plant breeding: crossing and mutation. Plant varieties can also be improved through genetic modification; however, the present GMO regulations are based on risk assessments with the transgenes coming from non-crossable species. Nowadays, DNA sequence information of crop plants facilitates the isolation of cisgenes, which are genes from crop plants themselves or from crossable species. The increasing number of these isolated genes, and the development of transformation protocols that do not leave marker genes behind, provide an opportunity to improve plant breeding while remaining within the gene pool of the classical breeder. Compared with induced translocation and introgression breeding, cisgenesis is an improvement for gene transfer from crossable plants: it is a one-step gene transfer without linkage drag of other genes, whereas induced translocation and introgression breeding are multiple step gene transfer methods with linkage drag. The similarity of the genes used in cisgenesis compared with classical breeding is a compelling argument to treat cisgenic plants as classically bred plants. In the case of the classical breeding method induced translocation breeding, the insertion site of the genes is a priori unknown, as it is in cisgenesis. This provides another argument to treat cisgenic plants as classically bred plants, by exempting cisgenesis of plants from the GMO legislations.

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs

PubMed Central

Yang, Jie; Huang, Lusheng; Yang, Ming; Fan, Yin; Li, Lin; Fang, Shaoming; Deng, Wenjiang; Cui, Leilei; Zhang, Zhen; Ai, Huashui; Wu, Zhenfang; Gao, Jun; Ren, Jun

2016-01-01

Vertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds. PMID:26781738

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

USGS Publications Warehouse

Scribner, Kim T.; Avise, John C.

1993-01-01

Spatial genetic structure in populations of mosquitofish (Gambusia) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrookito the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

Wallbank, Richard W R; Baxter, Simon W; Pardo-Diaz, Carolina; Hanly, Joseph J; Martin, Simon H; Mallet, James; Dasmahapatra, Kanchon K; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W Owen; Jiggins, Chris D

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

Genetic regulation of glucoraphanin accumulation in Beneforté® broccoli

PubMed Central

Traka, Maria H; Saha, Shikha; Huseby, Stine; Kopriva, Stanislav; Walley, Peter G; Barker, Guy C; Moore, Jonathan; Mero, Gene; den Bosch, Frans; Constant, Howard; Kelly, Leo; Schepers, Hans; Boddupalli, Sekhar; Mithen, Richard F

2013-01-01

Diets rich in broccoli (Brassica oleracea var italica) have been associated with maintenance of cardiovascular health and reduction in risk of cancer. These health benefits have been attributed to glucoraphanin that specifically accumulates in broccoli. The development of broccoli with enhanced concentrations of glucoraphanin may deliver greater health benefits. Three high-glucoraphanin F1 broccoli hybrids were developed in independent programmes through genome introgression from the wild species Brassica villosa. Glucoraphanin and other metabolites were quantified in experimental field trials. Global SNP analyses quantified the differential extent of B. villosa introgression The high-glucoraphanin broccoli hybrids contained 2.5–3 times the glucoraphanin content of standard hybrids due to enhanced sulphate assimilation and modifications in sulphur partitioning between sulphur-containing metabolites. All of the high-glucoraphanin hybrids possessed an introgressed B. villosa segment which contained a B. villosa Myb28 allele. Myb28 expression was increased in all of the high-glucoraphanin hybrids. Two high-glucoraphanin hybrids have been commercialised as Beneforté® broccoli. The study illustrates the translation of research on glucosinolate genetics from Arabidopsis to broccoli, the use of wild Brassica species to develop cultivars with potential consumer benefits, and the development of cultivars with contrasting concentrations of glucoraphanin for use in blinded human intervention studies. PMID:23560984

The eastern migratory caribou: the role of genetic introgression in ecotype evolution

PubMed Central

Klütsch, Cornelya F. C.; Manseau, Micheline; Trim, Vicki; Polfus, Jean; Wilson, Paul J.

2016-01-01

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada’s Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation. PMID:26998320

Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus.

PubMed

Durand, J D; Unlü, E; Doadrio, I; Pipoyan, S; Templeton, A R

2000-08-22

The phylogenetic relationships of 492 chub (Leuciscus cephalus) belonging to 89 populations across the species' range were assessed using 600 base pairs of cytochrome b. Furthermore, nine species belonging to the L. cephalus complex were also analysed (over the whole cytochrome b) in order to test potential allopatric hybridization with L. cephalus sensu stricto (i.e. the chub). Our results show that the chub includes four highly divergent lineages descending from a quick radiation that took place three million years ago. The geographical distribution of these lineages and results of the nested clade analysis indicated that the chub may have originated from Mesopotamia. Chub radiation probably occurred during an important vicariant event such as the isolation of numerous Turkish river systems, a consequence of the uplift of the Anatolian Plateau (formerly covered by a broad inland lake). Dispersion of these lineages arose from the changes in the European hydrographic network and, thus, the chub and endemic species of the L. cephalus complex met by secondary contacts. Our results show several patterns of introgression, from Leuciscus lepidus fully introgressed by chub mitochondrial DNA to Leuciscus borysthenicus where no introgression at all was detected. We assume that these hybridization events might constitute an important evolutionary process for the settlement of the chub in new environments in the Mediterranean area.

Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus.

PubMed Central

Durand, J D; Unlü, E; Doadrio, I; Pipoyan, S; Templeton, A R

2000-01-01

The phylogenetic relationships of 492 chub (Leuciscus cephalus) belonging to 89 populations across the species' range were assessed using 600 base pairs of cytochrome b. Furthermore, nine species belonging to the L. cephalus complex were also analysed (over the whole cytochrome b) in order to test potential allopatric hybridization with L. cephalus sensu stricto (i.e. the chub). Our results show that the chub includes four highly divergent lineages descending from a quick radiation that took place three million years ago. The geographical distribution of these lineages and results of the nested clade analysis indicated that the chub may have originated from Mesopotamia. Chub radiation probably occurred during an important vicariant event such as the isolation of numerous Turkish river systems, a consequence of the uplift of the Anatolian Plateau (formerly covered by a broad inland lake). Dispersion of these lineages arose from the changes in the European hydrographic network and, thus, the chub and endemic species of the L. cephalus complex met by secondary contacts. Our results show several patterns of introgression, from Leuciscus lepidus fully introgressed by chub mitochondrial DNA to Leuciscus borysthenicus where no introgression at all was detected. We assume that these hybridization events might constitute an important evolutionary process for the settlement of the chub in new environments in the Mediterranean area. PMID:11467433

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers

PubMed Central

Buzanskas, Marcos Eli; Ventura, Ricardo Vieira; Seleguim Chud, Tatiane Cristina; Bernardes, Priscila Arrigucci; Santos, Daniel Jordan de Abreu; Regitano, Luciana Correia de Almeida; de Alencar, Maurício Mello; Mudadu, Maurício de Alvarenga; Zanella, Ricardo; da Silva, Marcos Vinícius Gualberto Barbosa; Li, Changxi; Schenkel, Flavio Schramm; Munari, Danísio Prado

2017-01-01

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais—37.5% Zebu) and MA genetic group (MA: 65.6% Charolais—34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle. PMID:28182737

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers.

PubMed

Buzanskas, Marcos Eli; Ventura, Ricardo Vieira; Seleguim Chud, Tatiane Cristina; Bernardes, Priscila Arrigucci; Santos, Daniel Jordan de Abreu; Regitano, Luciana Correia de Almeida; Alencar, Maurício Mello de; Mudadu, Maurício de Alvarenga; Zanella, Ricardo; da Silva, Marcos Vinícius Gualberto Barbosa; Li, Changxi; Schenkel, Flavio Schramm; Munari, Danísio Prado

2017-01-01

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.

QTL controlling grain filling under terminal drought stress in a set of wild barley introgression lines.

PubMed

Honsdorf, Nora; March, Timothy J; Pillen, Klaus

2017-01-01

Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.

Breeding Potential of Introgression Lines Developed from Interspecific Crossing between Upland Cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis, Combining Ability and Genetic Effects

PubMed Central

Li, Xingli; Pei, Wenfeng

2016-01-01

Upland cotton (Gossypium hirstum L.), which produces more than 95% of the world natural cotton fibers, has a narrow genetic base which hinders progress in cotton breeding. Introducing germplasm from exotic sources especially from another cultivated tetraploid G. barbadense L. can broaden the genetic base of Upland cotton. However, the breeding potential of introgression lines (ILs) in Upland cotton with G. barbadense germplasm integration has not been well addressed. This study involved six ILs developed from an interspecific crossing and backcrossing between Upland cotton and G. barbadense and represented one of the first studies to investigate breeding potentials of a set of ILs using a full diallel analysis. High mid-parent heterosis was detected in several hybrids between ILs and a commercial cultivar, which also out-yielded the high-yielding cultivar parent in F1, F2 and F3 generations. A further analysis indicated that general ability (GCA) variance was predominant for all the traits, while specific combining ability (SCA) variance was either non-existent or much lower than GCA. The estimated GCA effects and predicted additive effects for parents in each trait were positively correlated (at P<0.01). Furthermore, GCA and additive effects for each trait were also positively correlated among generations (at P<0.05), suggesting that F2 and F3 generations can be used as a proxy to F1 in analyzing combining abilities and estimating genetic parameters. In addition, differences between reciprocal crosses in F1 and F2 were not significant for yield, yield components and fiber quality traits. But maternal effects appeared to be present for seed oil and protein contents in F3. This study identified introgression lines as good general combiners for yield and fiber quality improvement and hybrids with high heterotic vigor in yield, and therefore provided useful information for further utilization of introgression lines in cotton breeding. PMID:26730964

Breeding Potential of Introgression Lines Developed from Interspecific Crossing between Upland Cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis, Combining Ability and Genetic Effects.

PubMed

Zhang, Jinfa; Wu, Man; Yu, Jiwen; Li, Xingli; Pei, Wenfeng

2016-01-01

Upland cotton (Gossypium hirstum L.), which produces more than 95% of the world natural cotton fibers, has a narrow genetic base which hinders progress in cotton breeding. Introducing germplasm from exotic sources especially from another cultivated tetraploid G. barbadense L. can broaden the genetic base of Upland cotton. However, the breeding potential of introgression lines (ILs) in Upland cotton with G. barbadense germplasm integration has not been well addressed. This study involved six ILs developed from an interspecific crossing and backcrossing between Upland cotton and G. barbadense and represented one of the first studies to investigate breeding potentials of a set of ILs using a full diallel analysis. High mid-parent heterosis was detected in several hybrids between ILs and a commercial cultivar, which also out-yielded the high-yielding cultivar parent in F1, F2 and F3 generations. A further analysis indicated that general ability (GCA) variance was predominant for all the traits, while specific combining ability (SCA) variance was either non-existent or much lower than GCA. The estimated GCA effects and predicted additive effects for parents in each trait were positively correlated (at P<0.01). Furthermore, GCA and additive effects for each trait were also positively correlated among generations (at P<0.05), suggesting that F2 and F3 generations can be used as a proxy to F1 in analyzing combining abilities and estimating genetic parameters. In addition, differences between reciprocal crosses in F1 and F2 were not significant for yield, yield components and fiber quality traits. But maternal effects appeared to be present for seed oil and protein contents in F3. This study identified introgression lines as good general combiners for yield and fiber quality improvement and hybrids with high heterotic vigor in yield, and therefore provided useful information for further utilization of introgression lines in cotton breeding.

Mitochondrial introgression and complex biogeographic history of the genus Picea.

PubMed

Ran, Jin-Hua; Shen, Ting-Ting; Liu, Wen-Juan; Wang, Pei-Pei; Wang, Xiao-Quan

2015-12-01

Biogeographic history of plants is much more complex in the Northern Hemisphere than in the Southern Hemisphere due to that both the Bering and the North Atlantic land bridges contributed to floristic exchanges in the Cenozoic, which led to hybridization between congeneric species from different continents. It would be interesting to know how intercontinental gene flow and introgression have affected plant phylogenetic reconstruction and biogeographic inference. In this study, we reinvestigated the phylogenetic and biogeographic history of Picea, a main component of the Northern Hemisphere forest with many species that originated from recent radiation, using two chloroplast (cp), one mitochondrial (mt) and three single-copy nuclear gene markers. The generated gene trees are topologically highly discordant and the geographically closely related species generally show a close affinity of mtDNA rather than cp- or nuclear DNA, suggesting that inter- and intra-continental gene flow and mtDNA introgression might have occurred commonly. However, all gene trees resolved Picea breweriana as the basal-most lineage, which, together with fossil evidence, supports the North American origin hypothesis for the genus. Both dispersal and vicariance have played important roles in the evolution of Picea, and the Bering Land Bridge could have mediated the "North America to Eurasia" dispersal at least two times during the Miocene and Pliocene. Our study again demonstrates the importance of applying data from three genomes for a clear understanding of evolutionary histories in the pine family. Any markers from a single genome alone will not reveal a clear picture of the phylogenetic relationships among closely related congeneric species. In particular, mtDNA markers should be cautiously used, considering that introgression of the maternally inherited mtDNA with a lower rate of gene flow (by seeds) could have occurred much more frequently than that of the paternally inherited cpDNA with a higher rate of gene flow (by pollen) in Pinaceae. Copyright © 2015 Elsevier Inc. All rights reserved.

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.).

PubMed

Elkot, Ahmed Fawzy Abdelnaby; Chhuneja, Parveen; Kaur, Satinder; Saluja, Manny; Keller, Beat; Singh, Kuldeep

2015-01-01

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants. Thus, in addition to PM resistance, these progeny might also carry resistance to stem rust race Ug99.

Semi-permeable species boundaries in the coral genus Madracis: introgression in a brooding coral system.

PubMed

Frade, P R; Reyes-Nivia, M C; Faria, J; Kaandorp, J A; Luttikhuizen, P C; Bak, R P M

2010-12-01

Introgressive hybridization is described in several phylogenetic studies of mass-spawning corals. However, the prevalence of this process among brooding coral species is unclear. We used a mitochondrial (mtDNA: nad5) and two nuclear (nDNA: ATPSα and SRP54) intron markers to explore species barriers in the coral genus Madracis and address the role of hybridization in brooding systems. Specimens of six Caribbean Madracis morphospecies were collected from 5 to 60 m depth at Buoy One, Curaçao, supplemented by samples from Aruba, Trinidad & Tobago and Bermuda. Polymerase chain reaction and denaturing gradient gel electrophoresis were coupled to detect distinct alleles within single colonies. The recurrent nDNA phylogenetic non-monophyly among taxa is only challenged by Madracis senaria, the single monophyletic species within the genus. nDNA AMOVAs indicated overall statistical divergence (0.1% significance level) among species but pairwise comparisons of genetic differentiation revealed some gene exchange between Madracis taxa. mtDNA sequences clustered in two main groups representing typical shallow and deep water Madracis species. Madracis pharensis shallow and deep colonies (with threshold at about 23-24 m) clustered in different mtDNA branches, together with their depth-sympatric congenerics. This divergence was repeated for the nDNA (ATPSα) suggestive of distinct M. pharensis depth populations. These matched the vertical distribution of the dinoflagellate symbionts hosted by M. pharensis, with Symbiodinium ITS2 type B7 in the shallows but type B15 in the deep habitats, suggesting symbiont-related disruptive selection. Recurrent non-monophyly of Madracis taxa and high levels of shared polymorphism reflected in ambiguous phylogenetic networks indicate that hybridization is likely to have played a role in the evolution of the genus. Using coalescent forward-in-time simulations, lineage sorting alone was rejected as an explanation to the SRP54 genetic variation contained in Madracis mirabilis and Madracis decactis (species with an old fossil record), showing that introgressive hybridization has taken place between these species, either directly or through the gene pool of other Madracis taxa. Madracis widespread non-monophyly and the absence of statistical divergence between some species suggest that introgressive hybridization plays an important role in the evolution of the genus. Different reproductive traits and symbiont signatures of taxa forming distinct genetic clusters also point to the same conclusion. We suggest that Madracis morphospecies remain recognizable because introgressive hybridization is non-pervasive and/or because disruptive selection is in action. Copyright © 2010 Elsevier Inc. All rights reserved.

Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing

PubMed Central

Ma, Xin; Fu, Yongcai; Zhao, Xinhui; Jiang, Liyun; Zhu, Zuofeng; Gu, Ping; Xu, Wenying; Su, Zhen; Sun, Chuanqing; Tan, Lubin

2016-01-01

Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349 kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs. PMID:27251022

Genetic Introgression and the Survival of Florida Panther Kittens

PubMed Central

Hostetler, Jeffrey A.; Onorato, David P.; Nichols, James D.; Johnson, Warren E.; Roelke, Melody E.; O’Brien, Stephen J.; Jansen, Deborah; Oli, Madan K.

2010-01-01

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982-2008 and a live recapture-dead recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0 – 1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data. PMID:21113436

HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

PubMed

Ward, Ben J; van Oosterhout, Cock

2016-03-01

HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/. © 2015 John Wiley & Sons Ltd.

Genetic introgression and the survival of Florida panther kittens

USGS Publications Warehouse

Hostetler, Jeffrey A.; Onorato, David P.; Nichols, James D.; Johnson, Warren E.; Roelke, Melody E.; O'Brien, Stephen J.; Jansen, Deborah; Oli, Madan K.

2010-01-01

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.

Ecological Impacts of Reverse Speciation in Threespine Stickleback.

PubMed

Rudman, Seth M; Schluter, Dolph

2016-02-22

Young species are highly prone to extinction via increased gene flow after human-caused environmental changes. This mechanism of biodiversity loss, often termed reverse speciation or introgressive extinction, is of exceptional interest because the parent species are typically highly differentiated ecologically. Reverse speciation events are potentially powerful case studies for the role of evolution in driving ecological changes, as the phenotypic shifts associated with introgressive extinction can be large and they occur over particularly short timescales. Furthermore, reverse speciation can lead to novel phenotypes, which may in turn produce novel ecological effects. Here we investigate the ecological shift associated with reverse speciation in threespine stickleback fish using a field study and a replicated experiment. We find that an instance of introgressive extinction had cascading ecological consequences that altered the abundance of both aquatic prey and the pupating aquatic insects that emerged into the terrestrial ecosystem. The community and ecosystem impacts of reverse speciation were novel, and yet they were also predictable based on ecological and morphological considerations. The study suggests that knowledge about the community ecology and changes in functional morphology of a dominant species may lead to some predictive power for the ecological effects of evolutionary change. Moreover, the rapid nature and resultant ecological impacts associated with reverse speciation demonstrates the interplay between biodiversity, evolutionary change, and ecosystem function. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genetic complexity underlying hybrid male sterility in Drosophila.

PubMed

Sawamura, Kyoichi; Roote, John; Wu, Chung-I; Yamamoto, Masa-Toshi

2004-02-01

Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility.

Genetic complexity underlying hybrid male sterility in Drosophila.

PubMed Central

Sawamura, Kyoichi; Roote, John; Wu, Chung-I; Yamamoto, Masa-Toshi

2004-01-01

Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility. PMID:15020468

Genetic regulation of glucoraphanin accumulation in Beneforté broccoli.

PubMed

Traka, Maria H; Saha, Shikha; Huseby, Stine; Kopriva, Stanislav; Walley, Peter G; Barker, Guy C; Moore, Jonathan; Mero, Gene; van den Bosch, Frans; Constant, Howard; Kelly, Leo; Schepers, Hans; Boddupalli, Sekhar; Mithen, Richard F

2013-06-01

· Diets rich in broccoli (Brassica oleracea var italica) have been associated with maintenance of cardiovascular health and reduction in risk of cancer. These health benefits have been attributed to glucoraphanin that specifically accumulates in broccoli. The development of broccoli with enhanced concentrations of glucoraphanin may deliver greater health benefits. · Three high-glucoraphanin F1 broccoli hybrids were developed in independent programmes through genome introgression from the wild species Brassica villosa. Glucoraphanin and other metabolites were quantified in experimental field trials. Global SNP analyses quantified the differential extent of B. villosa introgression · The high-glucoraphanin broccoli hybrids contained 2.5-3 times the glucoraphanin content of standard hybrids due to enhanced sulphate assimilation and modifications in sulphur partitioning between sulphur-containing metabolites. All of the high-glucoraphanin hybrids possessed an introgressed B. villosa segment which contained a B. villosa Myb28 allele. Myb28 expression was increased in all of the high-glucoraphanin hybrids. Two high-glucoraphanin hybrids have been commercialised as Beneforté broccoli. · The study illustrates the translation of research on glucosinolate genetics from Arabidopsis to broccoli, the use of wild Brassica species to develop cultivars with potential consumer benefits, and the development of cultivars with contrasting concentrations of glucoraphanin for use in blinded human intervention studies. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.)

PubMed Central

Elkot, Ahmed Fawzy Abdelnaby; Chhuneja, Parveen; Kaur, Satinder; Saluja, Manny; Keller, Beat; Singh, Kuldeep

2015-01-01

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4 - 62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants. Thus, in addition to PM resistance, these progeny might also carry resistance to stem rust race Ug99. PMID:26066332

Asymmetric introgression between sympatric molestus and pipiens forms of Culex pipiens (Diptera: Culicidae) in the Comporta region, Portugal.

PubMed

Gomes, Bruno; Sousa, Carla A; Novo, Maria T; Freitas, Ferdinando B; Alves, Ricardo; Côrte-Real, Ana R; Salgueiro, Patrícia; Donnelly, Martin J; Almeida, António P G; Pinto, João

2009-11-06

Culex pipiens L. is the most widespread mosquito vector in temperate regions. This species consists of two forms, denoted molestus and pipiens, that exhibit important behavioural and physiological differences. The evolutionary relationships and taxonomic status of these forms remain unclear. In northern European latitudes molestus and pipiens populations occupy different habitats (underground vs. aboveground), a separation that most likely promotes genetic isolation between forms. However, the same does not hold in southern Europe where both forms occur aboveground in sympatry. In these southern habitats, the extent of hybridisation and its impact on the extent of genetic divergence between forms under sympatric conditions has not been clarified. For this purpose, we have used phenotypic and genetic data to characterise Cx. pipiens collected aboveground in Portugal. Our aims were to determine levels of genetic differentiation and the degree of hybridisation between forms occurring in sympatry, and to relate these with both evolutionary and epidemiological tenets of this biological group. Autogeny and stenogamy was evaluated in the F1 progeny of 145 individual Cx. pipiens females. Bayesian clustering analysis based on the genotypes of 13 microsatellites revealed two distinct genetic clusters that were highly correlated with the alternative traits that define pipiens and molestus. Admixture analysis yielded hybrid rate estimates of 8-10%. Higher proportions of admixture were observed in pipiens individuals suggesting that more molestus genes are being introgressed into the pipiens form than the opposite. Both physiological/behavioural and genetic data provide evidence for the sympatric occurrence of molestus and pipiens forms of Cx. pipiens in the study area. In spite of the significant genetic differentiation between forms, hybridisation occurs at considerable levels. The observed pattern of asymmetric introgression probably relates to the different mating strategies adopted by each form. Furthermore, the differential introgression of molestus genes into the pipiens form may induce a more opportunistic biting behaviour in the latter thus potentiating its capacity to act as a bridge-vector for the transmission of arboviral infections.

Genetic Evidence of Hybridization between the Endangered Native Species Iguana delicatissima and the Invasive Iguana iguana (Reptilia, Iguanidae) in the Lesser Antilles: Management Implications.

PubMed

Vuillaume, Barbara; Valette, Victorien; Lepais, Olivier; Grandjean, Frédéric; Breuil, Michel

2015-01-01

The worldwide increase of hybridization in different groups is thought to have become more important with the loss of isolating barriers and the introduction of invasive species. This phenomenon could result in the extinction of endemic species. This study aims at investigating the hybridization dynamics between the endemic and threatened Lesser Antillean iguana (Iguana delicatissima) and the invasive common green iguana (Iguana iguana) in the Lesser Antilles, as well as assessing the impact of interspecific hybridization on the decline of I. delicatissima. 59 I. delicatissima (5 localities), 47 I. iguana (12 localities) and 27 hybrids (5 localities), who were all identified based on morphological characters, have been genotyped at 15 microsatellites markers. We also sequenced hybrids using ND4 mitochondrial loci to further investigate mitochondrial introgression. The genetic clustering of species and hybrid genetic assignment were performed using a comparative approach, through the implementation of a Discriminant Analysis of Principal Component (DAPC) based on statistics, as well as genetic clustering approaches based on the genetic models of several populations (Structure, NewHybrids and HIest), in order to get full characterization of hybridization patterns and introgression dynamics across the islands. The iguanas identified as hybrids in the wild, thanks to morphological analysis, were all genetically F1, F2, or backcrosses. A high proportion of individuals were also the result of a longer-term admixture. The absence of reproductive barriers between species leads to hybridization when species are in contact. Yet morphological and behavioral differences between species could explain why males I. iguana may dominate I. delicatissima, thus resulting in short-term species displacement and extinction by hybridization and recurrent introgression from I. iguana toward I. delicatissima. As a consequence, I. delicatissima gets eliminated through introgression, as observed in recent population history over several islands. These results have profound implications for species management of the endangered I. delicatissima and practical conservation recommendations are being discussed in the light of these findings.

Asymmetric introgression between sympatric molestus and pipiens forms of Culex pipiens (Diptera: Culicidae) in the Comporta region, Portugal

PubMed Central

2009-01-01

Background Culex pipiens L. is the most widespread mosquito vector in temperate regions. This species consists of two forms, denoted molestus and pipiens, that exhibit important behavioural and physiological differences. The evolutionary relationships and taxonomic status of these forms remain unclear. In northern European latitudes molestus and pipiens populations occupy different habitats (underground vs. aboveground), a separation that most likely promotes genetic isolation between forms. However, the same does not hold in southern Europe where both forms occur aboveground in sympatry. In these southern habitats, the extent of hybridisation and its impact on the extent of genetic divergence between forms under sympatric conditions has not been clarified. For this purpose, we have used phenotypic and genetic data to characterise Cx. pipiens collected aboveground in Portugal. Our aims were to determine levels of genetic differentiation and the degree of hybridisation between forms occurring in sympatry, and to relate these with both evolutionary and epidemiological tenets of this biological group. Results Autogeny and stenogamy was evaluated in the F1 progeny of 145 individual Cx. pipiens females. Bayesian clustering analysis based on the genotypes of 13 microsatellites revealed two distinct genetic clusters that were highly correlated with the alternative traits that define pipiens and molestus. Admixture analysis yielded hybrid rate estimates of 8-10%. Higher proportions of admixture were observed in pipiens individuals suggesting that more molestus genes are being introgressed into the pipiens form than the opposite. Conclusion Both physiological/behavioural and genetic data provide evidence for the sympatric occurrence of molestus and pipiens forms of Cx. pipiens in the study area. In spite of the significant genetic differentiation between forms, hybridisation occurs at considerable levels. The observed pattern of asymmetric introgression probably relates to the different mating strategies adopted by each form. Furthermore, the differential introgression of molestus genes into the pipiens form may induce a more opportunistic biting behaviour in the latter thus potentiating its capacity to act as a bridge-vector for the transmission of arboviral infections. PMID:19895687

Genetic Evidence of Hybridization between the Endangered Native Species Iguana delicatissima and the Invasive Iguana iguana (Reptilia, Iguanidae) in the Lesser Antilles: Management Implications

PubMed Central

Vuillaume, Barbara; Valette, Victorien; Lepais, Olivier; Grandjean, Frédéric; Breuil, Michel

2015-01-01

The worldwide increase of hybridization in different groups is thought to have become more important with the loss of isolating barriers and the introduction of invasive species. This phenomenon could result in the extinction of endemic species. This study aims at investigating the hybridization dynamics between the endemic and threatened Lesser Antillean iguana (Iguana delicatissima) and the invasive common green iguana (Iguana iguana) in the Lesser Antilles, as well as assessing the impact of interspecific hybridization on the decline of I. delicatissima. 59 I. delicatissima (5 localities), 47 I. iguana (12 localities) and 27 hybrids (5 localities), who were all identified based on morphological characters, have been genotyped at 15 microsatellites markers. We also sequenced hybrids using ND4 mitochondrial loci to further investigate mitochondrial introgression. The genetic clustering of species and hybrid genetic assignment were performed using a comparative approach, through the implementation of a Discriminant Analysis of Principal Component (DAPC) based on statistics, as well as genetic clustering approaches based on the genetic models of several populations (Structure, NewHybrids and HIest), in order to get full characterization of hybridization patterns and introgression dynamics across the islands. The iguanas identified as hybrids in the wild, thanks to morphological analysis, were all genetically F1, F2, or backcrosses. A high proportion of individuals were also the result of a longer-term admixture. The absence of reproductive barriers between species leads to hybridization when species are in contact. Yet morphological and behavioral differences between species could explain why males I. iguana may dominate I. delicatissima, thus resulting in short-term species displacement and extinction by hybridization and recurrent introgression from I. iguana toward I. delicatissima. As a consequence, I. delicatissima gets eliminated through introgression, as observed in recent population history over several islands. These results have profound implications for species management of the endangered I. delicatissima and practical conservation recommendations are being discussed in the light of these findings. PMID:26046351

Introgression of a 4D chromosomal fragment into durum wheat confers aluminium tolerance

PubMed Central

Han, Chang; Ryan, Peter R.; Yan, ZeHong; Delhaize, Emmanuel

2014-01-01

Background and Aim Aluminium (Al3+) inhibits root growth of sensitive plant species and is a key factor that limits durum wheat (Triticum turgidum) production on acid soils. The aim of this study was to enhance the Al3+ tolerance of an elite durum cultivar by introgression of a chromosomal fragment from hexaploid wheat (Triticum aestivum) that possesses an Al3+ tolerance gene. Methods A 4D(4B) substitution line of durum wheat ‘Langdon’ was backcrossed to ‘Jandaroi’, a current semi-dwarf Australian durum. In the second backcross, using ‘Jandaroi’ as the recurrent parent, a seedling was identified where TaALMT1 on chromosome 4D was recombined with the Rht-B1b locus on chromosome 4B to yield an Al3+-tolerant seedling with a semi-dwarf habit. This seedling was used in a third backcross to generate homozygous sister lines with contrasting Al3+ tolerances. The backcrossed lines were characterized and compared with selected cultivars of hexaploid wheat for their Al3+ and Na+ tolerances in hydroponic culture as well as in short-term experiments to assess their growth on acid soil. Key Results Analysis of sister lines derived from the third backcross showed that the 4D chromosomal fragment substantially enhanced Al3+ tolerance. The ability to exclude Na+ from leaves was also enhanced, indicating that the chromosomal fragment possessed the Kna1 salt tolerance locus. Although Al3+ tolerance of seminal roots was enhanced in acid soil, the development of fine roots was not as robust as found in Al3+-tolerant lines of hexaploid wheat. Analysis of plant characteristics in the absence of Al3+ toxicity showed that the introgressed fragment did not affect total grain yield but reduced the weight of individual grains. Conclusions The results show that it is possible to increase substantially the Al3+ tolerance of an elite durum wheat cultivar by introgression of a 4D chromosomal fragment. Further improvements are possible, such as introducing additional genes to enhance the Al3+ tolerance of fine roots and by eliminating the locus on the chromosomal fragment responsible for smaller grain weights. PMID:24737716

Crop-to-wild gene flow, introgression and possible fitness effects of transgenes.

PubMed

Jenczewski, Eric; Ronfort, Joëlle; Chèvre, Anne-Marie

2003-01-01

Crop-to-wild gene flow has received close attention over the past ten years in connection with the development and cultivation of transgenic crops. In this paper, we review key examples of crop/wild sympatry and overlapping flowering phenology, pollen and seed dispersal, the barriers to hybridisation and introgression, the evolution and fate of interspecific hybrids, their fitness, and the potential cost of transgenes. We pay particular attention to ways in which the evolution and divergence between crops and their wild relatives may interfere with these successive steps. Our review suggests that crop-to-weed gene flow is highly idiosyncratic and that crop gene dispersion will certainly be very difficult to preclude totally. Future directions for research should thus focus on the long-term establishment and effects of transgenes on natural communities.

Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks.

PubMed

Corrigan, Shannon; Maisano Delser, Pierpaolo; Eddy, Corey; Duffy, Clinton; Yang, Lei; Li, Chenhong; Bazinet, Adam L; Mona, Stefano; Naylor, Gavin J P

2017-05-01

We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

PubMed Central

Figueiró, Henrique V.; Li, Gang; Trindade, Fernanda J.; Assis, Juliana; Pais, Fabiano; Fernandes, Gabriel; Santos, Sarah H. D.; Hughes, Graham M.; Komissarov, Aleksey; Antunes, Agostinho; Trinca, Cristine S.; Rodrigues, Maíra R.; Linderoth, Tyler; Bi, Ke; Silveira, Leandro; Azevedo, Fernando C. C.; Kantek, Daniel; Ramalho, Emiliano; Brassaloti, Ricardo A.; Villela, Priscilla M. S.; Nunes, Adauto L. V.; Teixeira, Rodrigo H. F.; Morato, Ronaldo G.; Loska, Damian; Saragüeta, Patricia; Gabaldón, Toni; Teeling, Emma C.; O’Brien, Stephen J.; Nielsen, Rasmus; Coutinho, Luiz L.; Oliveira, Guilherme; Murphy, William J.; Eizirik, Eduardo

2017-01-01

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. PMID:28776029

Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement.

PubMed

Wang, Gui-Xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-Ying; Zhang, Yue-Yun; Wang, You-Ping; Liu, Fan

2016-01-01

Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower "Korso" (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard "G1/1" (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from "Korso." Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of "G1/1" DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers.

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

PubMed Central

Decker, Jared E.; McKay, Stephanie D.; Rolf, Megan M.; Kim, JaeWoo; Molina Alcalá, Antonio; Sonstegard, Tad S.; Hanotte, Olivier; Götherström, Anders; Seabury, Christopher M.; Praharani, Lisa; Babar, Masroor Ellahi; Correia de Almeida Regitano, Luciana; Yildiz, Mehmet Ali; Heaton, Michael P.; Liu, Wan-Sheng; Lei, Chu-Zhao; Reecy, James M.; Saif-Ur-Rehman, Muhammad; Schnabel, Robert D.; Taylor, Jeremy F.

2014-01-01

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation. PMID:24675901

Efficient QTL detection for nonhost resistance in wild lettuce: backcross inbred lines versus F2 population

PubMed Central

Pelgrom, K.; Stam, P.; Lindhout, P.

2008-01-01

In plants, several population types [F2, recombinant inbred lines, backcross inbred lines (BILs), etc.] are used for quantitative trait locus (QTL) analyses. However, dissection of the trait of interest and subsequent confirmation by introgression of QTLs for breeding purposes has not been as successful as that predicted from theoretical calculations. More practical knowledge of different QTL mapping approaches is needed. In this recent study, we describe the detection and mapping of quantitative resistances to downy mildew in a set of 29 BILs of cultivated lettuce (L. sativa) containing genome segments introgressed from wild lettuce (L. saligna). Introgression regions that are associated with quantitative resistance are considered to harbor a QTL. Furthermore, we compare this with results from an already existing F2 population derived from the same parents. We identified six QTLs in our BIL approach compared to only three in the F2 approach, while there were two QTLs in common. We performed a simulation study based on our actual data to help us interpret them. This revealed that two newly detected QTLs in the BILs had gone unnoticed in the F2, due to a combination of recessiveness of the trait and skewed segregation, causing a deficit of the wild species alleles. This study clearly illustrates the added value of extended genetic studies on two different population types (BILs and F2) to dissect complex genetic traits. PMID:18251002

Second chance for the plains bison

USGS Publications Warehouse

Freese, Curtis H.; Aune, K.; Boyd, D.; Derr, James N.; Forrest, Steven C.; Gates, C. Cormack; Gogan, Peter J.; Grassel, Shaun M.; Halbert, Natalie D.; Kunkel, Kyran; Redford, Kent

2007-01-01

Before European settlement the plains bison (Bison bison bison) numbered in the tens of millions across most of the temperate region of North America. Within the span of a few decades during the mid- to late-1800s its numbers were reduced by hunting and other factors to a few hundred. The plight of the plains bison led to one of the first major movements in North America to save an endangered species. A few individuals and the American Bison Society rescued the remaining animals. Attempts to hybridize cattle and bison when bison numbers were low resulted in extensive cattle gene introgression in bison. Today, though approximately 500,000 plains bison exist in North America, few are free of cattle gene introgression, 96% are subject to anthropogenic selection for commodity production, and only 4% are in herds managed primarily for conservation purposes. Small herd size, artificial selection, cattle-gene introgression, and other factors threaten the diversity and integrity of the bison genome. In addition, the bison is for all practical purposes ecologically extinct across its former range, with multiple consequences for grassland biodiversity. Urgent measures are needed to conserve the wild bison genome and to restore the ecological role of bison in grassland ecosystems. Socioeconomic trends in the Great Plains, combined with new information about bison conservation needs and new conservation initiatives by both the public and public sectors, have set the stage for significant progress in bison conservation over the next few years.

Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula.

PubMed

Cotrim, Helena; Monteiro, Filipa; Sousa, Eva; Pinto, Manuel J; Fay, Michael F

2016-04-01

Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation. Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis. Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes. Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators. © 2016 Botanical Society of America.

When and how did Bos indicus introgress into Mongolian cattle?

PubMed

Yue, Xiangpeng; Li, Ran; Liu, Li; Zhang, Yunsheng; Huang, Jieping; Chang, Zhenhua; Dang, Ruihua; Lan, Xianyong; Chen, Hong; Lei, Chuzhao

2014-03-10

The Mongolian cattle are one of the most widespread breeds with strictly Bos taurus morphological features in northern China. In our current study, we presented a diversity of mitochondrial DNA (mtDNA) D-loop region and Y chromosome SNP markers in 25 male and 8 female samples of Mongolian cattle from the Xinjiang Uygur autonomous region in Western China, and detected 21 B. taurus and four Bos indicus (zebu) mtDNA haplotypes. Among four B. indicus mtDNA haplotypes, two haplotypes belonged to I1 haplogroup and the remaining two haplotypes belonged to I2 haplogroup. In contrast, all 25 male Mongolian cattle samples revealed B. taurus Y chromosome haplotype and no B. indicus haplotypes were found. Historical and archeological records indicate that B. taurus was introduced to Xinjiang during the second millennium BC and B. indicus appeared in this region by the second century AD. The two types of cattle coexisted for many centuries in Xinjiang, as depicted in clay and wooden figurines unearthed in the Astana cemetery in Turfan (3rd-8th century AD). Multiple lines of evidence suggest that the earliest B. indicus introgression in the Mongolian cattle may have occurred during the 2nd-7th centuries AD through the Silk Road around the Xinjiang region. This conclusion differs from the previous hypothesis that zebu introgression to Mongolian cattle happened during the Mongol Empire era in the 13th century. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

PubMed Central

2018-01-01

Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors’ origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage. PMID:29385126

Introgression and susceptibility to disease in a wild population of rainbow trout

USGS Publications Warehouse

Currens, K.P.; Hemmingsen, A.R.; French, R.A.; Buchanan, D.V.; Schreck, C.B.; Li, H.W.

1997-01-01

We examined susceptibility of wild rainbow trout Oncorhynchus mykiss from the Metolius River, a tributary of the Deschutes River, Oregon, to genetic introgression and ceratomyxosis as a result of stocking nonnative hatchery rainbow trout. Ceratomyxa shasta, an enzootic myxosporean parasite that can be lethal to nonnative hatchery rainbow trout, might have been limiting the interbreeding of hatchery and wild rainbow trout in the river. However, rainbow trout from the Metolius River had allozyme frequencies intermediate between those of wild and hatchery fish at LDH-B2* and sSOD-1*, two diagnostic genetic loci that allow the inland subspecies of rainbow trout to be distinguished from hatchery strains of coastal origin. They also had notable frequencies of ADA-1*85, an allele documented in hatchery rainbow trout but rarely seen in wild populations. We also found that rainbow trout in the Metolius River averaged 138.9 scales in the lateral series, intermediate between the counts for 9 coastal or nonnative hatchery populations, which always had fewer than 140 scales, and 10 inland populations, which always had more than 140 scales. Disease challenges revealed that rainbow trout from the Metolius River had much greater susceptibility to C. shasta than rainbow trout from the Deschutes River, which have genetic resistance to the lethal disease. Based on these data, we concluded that introgression with nonnative hatchery rainbow trout has reduced the abilities of wild rainbow trout in the Metolius River to survive when conditions for ceratomyxosis infection occur.

Genotypic characterization and species identification of Fasciola spp. with implications regarding the isolates infecting goats in Vietnam.

PubMed

Nguyen, Thanh Giang Thi; Van De, Nguyen; Vercruysse, Jozef; Dorny, Pierre; Le, Thanh Hoa

2009-12-01

Ribosomal RNA sequences (361 or 362bp) of the second internal transcribed spacer 2 (ITS-2) and a portion of mitochondrial cox1 (423bp) for Fasciola spp. obtained from specimens collected in indigenous and hybrid goats and sheep in Vietnam were characterized for genotypic status and hybridization/introgression. Alignment of 48 ITS-2 sequences (also those from goats and sheep in this study) indicates that F. gigantica and F. hepatica differ typically from each other at seven sites whereas one of these is a distinguishing deletion (T) at the 327th position in F. gigantica relative to F. hepatica. The isolates from the mountainous goats in the North of Vietnam (Yen Bai province) showed the ITS-2 composition relatively identical to that of F. hepatica. The ITS-2 sequences from populations of Fasciola isolates in goats had probably experienced introgression/hybridization as reported previously in other ruminants and humans. All Vietnamese goat-of-origin specimens had high pairwise percentage of mitochondrial cox1 sequences to F. gigantica (97-100%), and very low identity to F. hepatica (91-93%), suggesting their maternal linkage to be traced to F. gigantica. The presence of hybrid and/or introgressed populations of liver flukes bearing genetic material from both F. hepatica and F. gigantica in the goats/sheep in Vietnam, regardless of indigenous or imported hosts, appears to be the first demonstration from a tropical country.

Influence of Introgression and Geological Processes on Phylogenetic Relationships of Western North American Mountain Suckers (Pantosteus, Catostomidae)

PubMed Central

Unmack, Peter J.; Dowling, Thomas E.; Laitinen, Nina J.; Secor, Carol L.; Mayden, Richard L.; Shiozawa, Dennis K.; Smith, Gerald R.

2014-01-01

Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression. PMID:24619087

Widespread introgression in deep-sea hydrothermal vent mussels.

PubMed

Breusing, Corinna; Vrijenhoek, Robert C; Reusch, Thorsten B H

2017-01-13

The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis, living along the Mid-Atlantic Ridge. Admixture was found to be asymmetric with respect to the parental species, while introgression was more widespread geographically than previously recognized. Admixed individuals with a majority of alleles from one of the parental species were most frequent in habitats corresponding to that species. Mussels found at a geographically intermediate vent field constituted a genetically mixed population that showed no evidence for hybrid incompatibilities, a finding that does not support a previously inferred tension zone model. Our analyses indicate that B. azoricus and B. puteoserpentis hybridize introgressively across a large geographic area without evidence for general hybrid incompatibilities. While these findings shed new light onto the genetic structure of this hybrid zone, many aspects about its nature still remain obscure. Our study sets a baseline for further research that should primarily focus on the acquisition of additional mussel samples and environmental data, a detailed exploration of vent areas and hidden populations as well as genomic analyses in both mussel hosts and their bacterial symbionts.

Differential pollinator effectiveness and importance in a milkweed (Asclepias, Apocynaceae) hybrid zone.

PubMed

Stoepler, Teresa M; Edge, Andrea; Steel, Anna; O'Quinn, Robin L; Fishbein, Mark

2012-03-01

Exceptions to the ideal of complete reproductive isolation between species are commonly encountered in diverse plant, animal, and fungal groups, but often the causative ecological processes are poorly understood. In flowering plants, the outcome of hybridization depends in part on the effectiveness of pollinators in interspecific pollen transport. In the Asclepias exaltata and A. syriaca (Apocynaceae) hybrid zone in Shenandoah National Park, Virginia, extensive introgression has been documented. The objectives of this study were to (1) determine the extent of pollinator overlap among A. exaltata, A. syriaca, and their hybrids and (2) identify the insect taxa responsible for hybridization and introgression. We observed focal plants of parental species and hybrids to measure visitation rate, visit duration, and per-visit pollinia removal and deposition, and we calculated pollinator effectiveness and importance. Visitation rates varied significantly between the 2 yr of the study. Overall, Apis mellifera, Bombus sp., and Epargyreus clarus were the most important pollinators. However, Bombus sp. was the only visitor that was observed to both remove and insert pollinia for both parent species as well as hybrids. We conclude that Bombus may be a key agent of hybridization and introgression in these sympatric milkweed populations, and hybrids are neither preferred nor selected against by pollinators. Thus, we have identified a potential mechanism for how hybrids act as bridges to gene flow between A. exaltata and A. syriaca. These results provide insights into the breakdown of prezygotic isolating mechanisms.

Weak Population Structure in European Roe Deer (Capreolus capreolus) and Evidence of Introgressive Hybridization with Siberian Roe Deer (C. pygargus) in Northeastern Poland

PubMed Central

Olano-Marin, Juanita; Plis, Kamila; Sönnichsen, Leif; Borowik, Tomasz; Niedziałkowska, Magdalena; Jędrzejewska, Bogumiła

2014-01-01

We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus). The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp) of mitochondrial DNA (mtDNA) control region. Genetic diversity was high, and a low degree of genetic differentiation among sampling areas was observed with both microsatellites and mtDNA. No evidence of genetic differentiation between roe deer inhabiting open fields and forested areas was found, indicating that the ability of the species to exploit these contrasting environments might be the result of its phenotypic plasticity. Half of the studied individuals carried an mtDNA haplotype that did not belong to C. capreolus, but to a related species that does not occur naturally in the area, the Siberian roe deer (C. pygargus). No differentiation between individuals with Siberian and European mtDNA haplotypes was detected at microsatellite loci. Introgression of mtDNA of Siberian roe deer into the genome of European roe deer has recently been detected in eastern Europe. Such introgression might be caused by human-mediated translocations of Siberian roe deer within the range of European roe deer or by natural hybridization between these species in the past. PMID:25271423

Existence of vigorous lineages of crop-wild hybrids in Lettuce under field conditions.

PubMed

Hooftman, Danny A P; Hartman, Yorike; Oostermeijer, J Gerard B; Den Nijs, Hans J C M

2009-01-01

Plant to plant gene flow is a route of environmental exposure for GM plants specifically since crosses with wild relatives could lead to the formation of more vigorous hybrids, which could increase the rate of introgression and the environmental impact. Here, we test the first step in the process of potential transgene introgression: whether hybrid vigor can be inherited to the next generation, which could lead to fixation of altered, i.e., elevated, quantitative traits. The potential for a permanent elevated fitness was tested using individual autogamous progeny lineages of hybrids between the crop Lactuca sativa (Lettuce) and the wild species Lactuca serriola (Prickly Lettuce). We compared progeny from motherplants grown under either greenhouse or field conditions. The survival of young plants depended strongly on maternal environment. Furthermore, we observed that offspring reproductive fitness components were correlated with maternal fitness. Our study demonstrates that post-zygotic genotypic sorting at the young plants stage reduces the number of genotypes non-randomly, leading to inheritance of high levels of reproductive traits in the surviving hybrid lineages, compared to the pure wild relatives. Consequently, directional selection could lead to displacement of the pure wild relative and fixation of more vigorous genome segments originating from crops, stabilizing plant traits at elevated levels. Such information can be used to indentify segments which are less likely to introgress into wild relative populations as a target for transgene insertion. © ISBR, EDP Sciences, 2010.

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

PubMed

Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

2011-10-01

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.

Risk and efficacy of human-enabled interspecific hybridization for climate-change adaptation: Response to Hamilton and Miller (2016)

USGS Publications Warehouse

Kovach, Ryan P.; Luikart, Gordon; Lowe, Winsor H.; Boyer, Matthew C.; Muhlfeld, Clint C.

2016-01-01

Hamilton and Miller (2016) provide an interesting and provocative discussion of how hybridization and introgression can promote evolutionary potential in the face of climate change. They argue that hybridization—mating between individuals from genetically distinct populations—can alleviate inbreeding depression and promote adaptive introgression and evolutionary rescue. We agree that deliberate intraspecific hybridization (mating between individuals of the same species) is an underused management tool for increasing fitness in inbred populations (i.e., genetic rescue; Frankham 2015; Whiteley et al. 2015). The potential risks and benefits of assisted gene flow have been discussed in the literature, and an emerging consensus suggests that mating between populations isolated for approximately 50–100 generations can benefit fitness, often with a minor risk of outbreeding depression (Frankham et al. 2011; Aitken & Whitlock 2013; Allendorf et al. 2013).

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

NASA Astrophysics Data System (ADS)

Almeida, Pedro; Gonçalves, Carla; Teixeira, Sara; Libkind, Diego; Bontrager, Martin; Masneuf-Pomarède, Isabelle; Albertin, Warren; Durrens, Pascal; Sherman, David James; Marullo, Philippe; Todd Hittinger, Chris; Gonçalves, Paula; Sampaio, José Paulo

2014-06-01

In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with human-driven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum.

U.S. EPA regulation of plant-incorporated protectants: assessment of impacts of gene flow from pest-resistant plants.

PubMed

Wozniak, Chris A; Martinez, Jeannette C

2011-06-08

The U.S. Environmental Protection Agency licenses pesticide-expressing plants under the authority of the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA). Transgenes and their pesticidal products represent pesticides under FIFRA and are referred to as plant-incorporated protectants (PIPs). When sexually compatible wild relatives (SCWR) are sympatric with PIP crops, there is a need to assess the potential for adverse effects to man and the environment resulting from transgene introgression in accord with FIFRA requirements. Genetic compatibility, introgression, weediness of SCWR × PIP hybrids, seed dispersal, and dormancy, among other parameters, as well as effects on other species (herbivores and beneficial insects), all need to be considered as part of the risk assessment for experimental use under Section 5 or registration under Section 3 of FIFRA. EPA is currently developing data requirements and guidance toward addressing potential gene flow impacts from PIPs.

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

PubMed Central

Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

2012-01-01

The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

Hybridization Reveals the Evolving Genomic Architecture of Speciation

PubMed Central

Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

2014-01-01

SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

Application of Genomic In Situ Hybridization in Horticultural Science

PubMed Central

Ramzan, Fahad; Lim, Ki-Byung

2017-01-01

Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants. PMID:28459054

Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement

PubMed Central

Wang, Gui-xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-ying; Zhang, Yue-yun; Wang, You-ping; Liu, Fan

2016-01-01

Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower “Korso” (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard “G1/1” (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from “Korso.” Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of “G1/1” DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers. PMID:27625659

Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

PubMed Central

Macaya-Sanz, D; Suter, L; Joseph, J; Barbará, T; Alba, N; González-Martínez, S C; Widmer, A; Lexer, C

2011-01-01

Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F1's. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC1) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC1 revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across ‘porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones. PMID:21587301

Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species.

PubMed

Macaya-Sanz, D; Suter, L; Joseph, J; Barbará, T; Alba, N; González-Martínez, S C; Widmer, A; Lexer, C

2011-10-01

Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F(1)'s. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC(1)) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC(1) revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across 'porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones.

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression.

PubMed

Lexer, C; Fay, M F; Joseph, J A; Nica, M-S; Heinze, B

2005-04-01

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long-lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the "model tree" genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome-wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (N(e)) in this species (P. alba N(e)c. 500-550; P. tremula N(e)c. 550-700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.

Developing Rice with High Yield under Phosphorus Deficiency: Pup1 Sequence to Application1[W][OA

PubMed Central

Chin, Joong Hyoun; Gamuyao, Rico; Dalid, Cheryl; Bustamam, Masdiar; Prasetiyono, Joko; Moeljopawiro, Sugiono; Wissuwa, Matthias; Heuer, Sigrid

2011-01-01

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) confers tolerance of phosphorus deficiency in soil and is currently one of the most promising QTLs for the development of tolerant rice (Oryza sativa) varieties. To facilitate targeted introgression of Pup1 into intolerant varieties, the gene models predicted in the Pup1 region in the donor variety Kasalath were used to develop gene-based molecular markers that are evenly distributed over the fine-mapped 278-kb QTL region. To validate the gene models and optimize the markers, gene expression analyses and partial allelic sequencing were conducted. The markers were tested in more than 80 diverse rice accessions revealing three main groups with different Pup1 allele constitution. Accessions with tolerant (group I) and intolerant (group III) Pup1 alleles were distinguished from genotypes with Kasalath alleles at some of the analyzed loci (partial Pup1; group II). A germplasm survey additionally confirmed earlier data showing that Pup1 is largely absent from irrigated rice varieties but conserved in varieties and breeding lines adapted to drought-prone environments. A core set of Pup1 markers has been defined, and sequence polymorphisms suitable for single-nucleotide polymorphism marker development for high-throughput genotyping were identified. Following a marker-assisted backcrossing approach, Pup1 was introgressed into two irrigated rice varieties and three Indonesian upland varieties. First phenotypic evaluations of the introgression lines suggest that Pup1 is effective in different genetic backgrounds and environments and that it has the potential to significantly enhance grain yield under field conditions. PMID:21602323

Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation.

PubMed

Chattopadhyay, Balaji; Garg, Kritika M; Kumar, A K Vinoth; Doss, D Paramanantha Swami; Rheindt, Frank E; Kandula, Sripathi; Ramakrishnan, Uma

2016-02-18

The Oriental fruit bat genus Cynopterus, with several geographically overlapping species, presents an interesting case study to evaluate the evolutionary significance of coexistence versus isolation. We examined the morphological and genetic variability of congeneric fruit bats Cynopterus sphinx and C. brachyotis using 405 samples from two natural contact zones and 17 allopatric locations in the Indian subcontinent; and investigated the population differentiation patterns, evolutionary history, and the possibility of cryptic diversity in this species pair. Analysis of microsatellites, cytochrome b gene sequences, and restriction digestion based genome-wide data revealed that C. sphinx and C. brachyotis do not hybridize in contact zones. However, cytochrome b gene sequences and genome-wide SNP data helped uncover a cryptic, hitherto unrecognized cynopterine lineage in northeastern India coexisting with C. sphinx. Further analyses of shared variation of SNPs using Patterson's D statistics suggest introgression between this lineage and C. sphinx. Multivariate analyses of morphology using genetically classified grouping confirmed substantial morphological overlap between C. sphinx and C. brachyotis, specifically in the high elevation contact zones in southern India. Our results uncover novel diversity and detect a pattern of genetic introgression in a cryptic radiation of bats, demonstrating the complicated nature of lineage diversification in this poorly understood taxonomic group. Our results highlight the importance of genome-wide data to study evolutionary processes of morphologically similar species pairs. Our approach represents a significant step forward in evolutionary research on young radiations of non-model species that may retain the ability of interspecific gene flow.

A new 2DS·2RL Robertsonian translocation transfers stem rust resistance gene Sr59 into wheat.

PubMed

Rahmatov, Mahbubjon; Rouse, Matthew N; Nirmala, Jayaveeramuthu; Danilova, Tatiana; Friebe, Bernd; Steffenson, Brian J; Johansson, Eva

2016-07-01

A new stem rust resistance gene Sr59 from Secale cereale was introgressed into wheat as a 2DS·2RL Robertsonian translocation. Emerging new races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici), from Africa threaten global wheat (Triticum aestivum L.) production. To broaden the resistance spectrum of wheat to these widely virulent African races, additional resistance genes must be identified from all possible gene pools. From the screening of a collection of wheat-rye (Secale cereale L.) chromosome substitution lines developed at the Swedish University of Agricultural Sciences, we described the line 'SLU238' 2R (2D) as possessing resistance to many races of P. graminis f. sp. tritici, including the widely virulent race TTKSK (isolate synonym Ug99) from Africa. The breakage-fusion mechanism of univalent chromosomes was used to produce a new Robertsonian translocation: T2DS·2RL. Molecular marker analysis and stem rust seedling assays at multiple generations confirmed that the stem rust resistance from 'SLU238' is present on the rye chromosome arm 2RL. Line TA5094 (#101) was derived from 'SLU238' and was found to be homozygous for the T2DS·2RL translocation. The stem rust resistance gene on chromosome 2RL arm was designated as Sr59. Although introgressions of rye chromosome arms into wheat have most often been facilitated by irradiation, this study highlights the utility of the breakage-fusion mechanism for rye chromatin introgression. Sr59 provides an additional asset for wheat improvement to mitigate yield losses caused by stem rust.

The genetic basis of Haldane's rule and the nature of asymmetric hybrid male sterility among Drosophila simulans, Drosophila mauritiana and Drosophila sechellia.

PubMed

Zeng, L W; Singh, R S

1993-05-01

Haldane's rule (i.e., the preferential hybrid sterility and inviability of heterogametic sex) has been known for 70 years, but its genetic basis, which is crucial to the understanding of the process of species formation, remains unclear. In the present study, we have investigated the genetic basis of hybrid male sterility using Drosophila simulans, Drosophila mauritiana and Drosophila sechellia. An introgression of D. sechellia Y chromosome into a fairly homogenous background of D. simulans did not show any effect of the introgressed Y on male sterility. The substitution of D. simulans Y chromosome into D. sechellia, and both reciprocal Y chromosome substitutions between D. simulans and D. mauritiana were unsuccessful. Introgressions of cytoplasm between D. simulans and D. mauritiana (or D. sechellia) also did not have any effect on hybrid male sterility. These results rule out the X-Y interaction hypothesis as a general explanation of Haldane's rule in this species group and indicate an involvement of an X-autosome interaction. Models of symmetrical and asymmetrical X-autosome interaction have been developed which explain the Y chromosome substitution results and suggest that evolution of interactions between different genetic elements in the early stages of speciation is more likely to be of an asymmetrical nature. The model of asymmetrical X-autosome interaction also predicts that different sets of interacting genes may be involved in different pairs of related species and can account for the observation that hybrid male sterility in many partially isolated species is often nonreciprocal or unidirectional.

Genetics of reproductive isolation in the Drosophila simulans clade: complex epistasis underlying hybrid male sterility.

PubMed

Cabot, E L; Davis, A W; Johnson, N A; Wu, C I

1994-05-01

We have analyzed the sterility associated with introgressions of the distal one-fourth of the X chromosome from either Drosophila mauritiana or Drosophila sechellia into the genome of Drosophila simulans using a series of visible and DNA markers. Because in Drosophila hybrids, male sterility is usually complete and is often tightly linked with each of several markers used in crosses, a simple genetic basis has generally been assumed. In our low resolution mapping experiment, we were not able to reject the null hypothesis that a single gene, introgressed from either D. mauritiana or D. sechellia, is the cause of male sterility. High resolution mapping, however, reveals a much more complex picture. At least three distinct factors from D. mauritiana, or two from D. sechellia, were identified that need to be jointly present to confer full sterility. Each individual factor by itself is relatively ineffective in causing sterility, or even a partial spermatogenic defect. Moreover, there appear to be more sterility factors on comparable introgressions from D. mauritiana than from D. sechellia. On the basis of these observations, we propose a model which suggests that multilocus weak allele interactions are a very common cause of reproductive incompatibility between closely related species. We also present theoretical argument and empirical evidence against extrapolating the results of within-species analysis to interpret the genetic basis of species differences. The implications of this model on the theories of evolution of species differences and the attempt to understand the mechanisms of hybrid sterility/inviability at the molecular level are discussed.

The Genetic Basis of Haldane's Rule and the Nature of Asymmetric Hybrid Male Sterility among Drosophila Simulans, Drosophila Mauritiana and Drosophila Sechellia

PubMed Central

Zeng, L. W.; Singh, R. S.

1993-01-01

Haldane's rule (i.e., the preferential hybrid sterility and inviability of heterogametic sex) has been known for 70 years, but its genetic basis, which is crucial to the understanding of the process of species formation, remains unclear. In the present study, we have investigated the genetic basis of hybrid male sterility using Drosophila simulans, Drosophila mauritiana and Drosophila sechellia. An introgression of D. sechellia Y chromosome into a fairly homogenous background of D. simulans did not show any effect of the introgressed Y on male sterility. The substitution of D. simulans Y chromosome into D. sechellia, and both reciprocal Y chromosome substitutions between D. simulans and D. mauritiana were unsuccessful. Introgressions of cytoplasm between D. simulans and D. mauritiana (or D. sechellia) also did not have any effect on hybrid male sterility. These results rule out the X-Y interaction hypothesis as a general explanation of Haldane's rule in this species group and indicate an involvement of an X-autosome interaction. Models of symmetrical and asymmetrical X-autosome interaction have been developed which explain the Y chromosome substitution results and suggest that evolution of interactions between different genetic elements in the early stages of speciation is more likely to be of an asymmetrical nature. The model of asymmetrical X-autosome interaction also predicts that different sets of interacting genes may be involved in different pairs of related species and can account for the observation that hybrid male sterility in many partially isolated species is often nonreciprocal or unidirectional. PMID:8514134

Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves.

PubMed

Schweizer, Rena M; Durvasula, Arun; Smith, Joel; Vohr, Samuel H; Stahler, Daniel R; Galaverni, Marco; Thalmann, Olaf; Smith, Douglas W; Randi, Ettore; Ostrander, Elaine A; Green, Richard E; Lohmueller, Kirk E; Novembre, John; Wayne, Robert K

2018-05-01

Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.

Different Evolutionary History for Basque Diaspora Populations in USA and Argentina Unveiled by Mitochondrial DNA Analysis.

PubMed

Baeta, Miriam; Núñez, Carolina; Cardoso, Sergio; Palencia-Madrid, Leire; Piñeiro-Hermida, Sergio; Arriba-Barredo, Miren; Villanueva-Millán, María Jesús; M de Pancorbo, Marian

2015-01-01

The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.

Sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane is one of the most important crops globally, providing most of the world’s sugar and bio-energy (ethanol and electricity). This contribution has been underpinned by the successful introgression of genes from wild germplasm, particularly from Saccharum spontaneum, by breeders in the early 1...

ESTABLISHMENT OF TRANSGENIC CREEPING BENTGRASS (AGROSTIS STOLONIFERA L.) IN NON-AGRONOMIC HABITATS

EPA Science Inventory

Concerns about genetically modified crops include transgene flow to compatible wild species and potential unintended ecological consequences associated with transgene introgression. To date, there has been little empirical documentation of the relative frequency of establishment...

Introgression and pyramiding into common bean market class fabada of genes conferring resistance to anthracnose and potyvirus.

PubMed

Ferreira, Juan José; Campa, Ana; Pérez-Vega, Elena; Rodríguez-Suárez, Cristina; Giraldez, Ramón

2012-03-01

Anthracnose and bean common mosaic (BCM) are considered major diseases in common bean crop causing severe yield losses worldwide. This work describes the introgression and pyramiding of genes conferring genetic resistance to BCM and anthracnose local races into line A25, a bean genotype classified as market class fabada. Resistant plants were selected using resistance tests or combining resistance tests and marker-assisted selection. Lines A252, A321, A493, Sanilac BC6-Are, and BRB130 were used as resistance sources. Resistance genes to anthracnose (Co-2 ( C ), Co-2 ( A252 ) and Co-3/9) and/or BCM (I and bc-3) were introgressed in line A25 through six parallel backcrossing programs, and six breeding lines showing a fabada seed phenotype were obtained after six backcross generations: line A1258 from A252; A1231 from A321; A1220 from A493; A1183 and A1878 from Sanilac BC6-Are; and line A2418 from BRB130. Pyramiding of different genes were developed using the pedigree method from a single cross between lines obtained in the introgression step: line A1699 (derived from cross A1258 × A1220), A2438 (A1220 × A1183), A2806 (A1878 × A2418), and A3308 (A1699 × A2806). A characterization based on eight morpho-agronomic traits revealed a limited differentiation among the obtained breeding lines and the recurrent line A25. However, using a set of seven molecular markers linked to the loci used in the breeding programs it was possible to differentiate the 11 fabada lines. Considering the genetic control of the resistance in resistant donor lines, the observed segregations in the last backcrossing generation, the reaction against the pathogens, and the expression of the molecular markers it was also possible to infer the genotype conferring resistance in the ten fabada breeding lines obtained. As a result of these breeding programs, genetic resistance to three anthracnose races controlled by genes included in clusters Co-2 and Co-3/9, and genetic resistance to BCM controlled by genotype I + bc-3 was combined in the fabada line A3308.

Development of a genetic sexing strain in Bactrocera carambolae (Diptera: Tephritidae) by introgression of sex sorting components from B. dorsalis, Salaya1 strain.

PubMed

Isasawin, Siriwan; Aketarawong, Nidchaya; Lertsiri, Sittiwat; Thanaphum, Sujinda

2014-01-01

The carambola fruit fly, Bactrocera carambolae Drew & Hancock is a high profile key pest that is widely distributed in the southwestern ASEAN region. In addition, it has trans-continentally invaded Suriname, where it has been expanding east and southward since 1975. This fruit fly belongs to Bactrocera dorsalis species complex. The development and application of a genetic sexing strain (Salaya1) of B. dorsalis sensu stricto (s.s.) (Hendel) for the sterile insect technique (SIT) has improved the fruit fly control. However, matings between B. dorsalis s.s. and B. carambolae are incompatible, which hinder the application of the Salaya1 strain to control the carambola fruit fly. To solve this problem, we introduced genetic sexing components from the Salaya1 strain into the B. carambolae genome by interspecific hybridization. Morphological characteristics, mating competitiveness, male pheromone profiles, and genetic relationships revealed consistencies that helped to distinguish Salaya1 and B. carambolae strains. A Y-autosome translocation linking the dominant wild-type allele of white pupae gene and a free autosome carrying a recessive white pupae homologue from the Salaya1 strain were introgressed into the gene pool of B. carambolae. A panel of Y-pseudo-linked microsatellite loci of the Salaya1 strain served as markers for the introgression experiments. This resulted in a newly derived genetic sexing strain called Salaya5, with morphological characteristics corresponding to B. carambolae. The rectal gland pheromone profile of Salaya5 males also contained a distinctive component of B. carambolae. Microsatellite DNA analyses confirmed the close genetic relationships between the Salaya5 strain and wild B. carambolae populations. Further experiments showed that the sterile males of Salaya5 can compete with wild males for mating with wild females in field cage conditions. Introgression of sex sorting components from the Salaya1 strain to a closely related B. carambolae strain generated a new genetic sexing strain, Salaya5. Morphology-based taxonomic characteristics, distinctive pheromone components, microsatellite DNA markers, genetic relationships, and mating competitiveness provided parental baseline data and validation tools for the new strain. The Salaya5 strain shows a close similarity with those features in the wild B. carambolae strain. In addition, mating competitiveness tests suggested that Salaya5 has a potential to be used in B. carambolae SIT programs based on male-only releases.

Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression

PubMed Central

2013-01-01

Background The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure. Results The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. Conclusions The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa. PMID:24021154

Hybridization, mitochondrial DNA phylogeography, and prediction of the early stages of reproductive isolation: lessons from New Zealand cicadas (genus Kikihia).

PubMed

Marshall, David C; Hill, Kathy B R; Cooley, John R; Simon, Chris

2011-07-01

One of the major tenets of the modern synthesis is that genetic differentiation among subpopulations is translated over time into genetic differentiation among species. Phylogeographic exploration is therefore essential to the study of speciation because it can reveal the presence of subpopulations that may go on to become species or that may already represent cryptic species. Acoustic species-specific mating signals provide a significant advantage for the recognition of cryptic or incipient species. Because the majority of species do not have such easily recognized premating signals, data from acoustically signaling species can serve as a valuable heuristic tool. Acoustic signals are also convenient tools for recognizing hybridization events. Here, we demonstrate that evidence of hybridization in the form of intermediate song phenotypes is present in many contact zones between species of the New Zealand grass cicadas of the Kikihia muta species complex and that recurring mitochondrial DNA (mtDNA) introgression has created misleading patterns that make it difficult to identify certain taxa using song or mtDNA alone. In one case, introgression appears to have occurred between allopatric taxa by dispersal of introgressed populations of an intermediary species ("hybridization by proxy"). We also present a comparison of mtDNA-tree- and song-based taxonomies obtained for the K. muta complex. We find that 12 mtDNA candidate species are identified using shifts in phylogenetic branching rate found by a single-threshold mixed Yule-coalescent lineage model, while only 7 candidate species are identified using songs. Results from the Yule-coalescent model are dependent on factors such as the number of modeled thresholds and the inclusion of duplicate haplotypes. Genetic distances within song species reach a maximum at about 0.028 substitutions/site when likely cases of hybridization and introgression are excluded. Large genetic breaks or "gaps" are not observed between some northern (warmer climate) song clades, possibly because climate-induced bottlenecks have been less severe. These results support ongoing calls for multimarker genetic studies as well as "integrative taxonomy" that combines information from multiple character sources, including behavior, ecology, geography, and morphology. © The Author(s) 2011. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

PubMed Central

2011-01-01

Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression. PMID:21939538

Parallel evolution or purifying selection, not introgression, explain similarity in the pyrethroid detoxification linked GSTE4 of Anopheles gambiae and An. arabiensis

PubMed Central

Wilding, C.S.; Weetman, D.; Rippon, E.J.; Steen, K.; Mawejje, H.D.; Barsukov, I.; Donnelly, M.J.

2014-01-01

Insecticide resistance is a major impediment to the control of vectors and pests of public health importance and is a strongly selected trait capable of rapid spread, sometimes even between closely-related species. Elucidating the mechanisms generating insecticide resistance in mosquito vectors of disease, and understanding the spread of resistance within and between populations and species are vital for the development of robust resistance management strategies. Here we studied the mechanisms of resistance in two sympatric members of the Anopheles gambiae species complex – the major vector of malaria in sub-Saharan Africa – in order to understand how resistance has developed and spread in eastern Uganda, a region with some of the highest levels of malaria. In eastern Uganda, where the mosquitoes Anopheles arabiensis and An. gambiae can be found sympatrically, low levels of hybrids (0.4%) occur, offering a route for introgression of adaptively important variants between species. In independent microarray studies of insecticide resistance, Gste4, an insect-specific glutathione S-transferase, was among the most significantly up-regulated genes in both species. To test the hypothesis of interspecific introgression, we sequenced 2.3kbp encompassing Gste4. Whilst this detailed sequencing ruled out introgression, we detected strong positive selection acting on Gste4. However, these sequences, followed by haplotype-specific qPCR, showed that the apparent up-regulation in An. arabiensis is a result of allelic variation across the microarray probe binding sites which artefactually elevates the gene expression signal. Thus, face-value acceptance of microarray data can be misleading and it is advisable to conduct a more detailed investigation of the causes and nature of such signal. The identification of positive selection acting on this locus led us to functionally express and characterise allelic variants of GSTE4. Although the in vitro data do not support a direct role for GSTE4 in metabolism, they do support a role for this enzyme in insecticide sequestration. Thus, the demonstration of a role for an up-regulated gene in metabolic resistance to insecticides should not be limited to simply whether it can metabolise insecticide; such a strict criterion would argue against the involvement of GSTE4 despite the weight of evidence to the contrary. PMID:25213601

The establishment of genetically engineered canola populations in the U.S.

EPA Science Inventory

Concerns regarding the commercial release of genetically engineered (GE) crops include naturalization, introgression to sexually compatible relatives and the transfer of beneficial traits to native and weedy species through hybridization. To date there have been few documented re...

ESTABLISHMENT OF TRANSGENETIC HERBICIDE-RESISTANT CREEPING BENTGRASS (AGROSTIS STOLONIFERA L.) IN NONAGRONOMIC HABITATS

EPA Science Inventory

Concerns about genetically modified (GM) crops include transgene flow to compatible wild species and unintended ecological consequences of potential transgene introgression. However, there has been little empirical documentation of establishment and distribution of transgenic pla...

Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression.

PubMed

Peng, Ting; Sun, Xiaochun; Mumm, Rita H

2014-01-01

From a breeding standpoint, multiple trait integration (MTI) is a four-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) using backcross breeding, ultimately regaining the performance attributes of the target hybrid along with reliable expression of the value-added traits. In the light of the overarching goal of recovering equivalent performance in the finished conversion, this study focuses on the first step of MTI, single event introgression, exploring the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events, incorporating eight events into the female hybrid parent and seven into the male parent. Single event introgression is conducted in parallel streams to convert the recurrent parent (RP) for individual events, with the primary objective of minimizing residual non-recurrent parent (NRP) germplasm, especially in the chromosomal proximity to the event (i.e. linkage drag). In keeping with a defined lower limit of 96.66 % overall RP germplasm recovery (i.e. ≤120 cM NRP germplasm given a genome size of 1,788 cM), a breeding goal for each of the 15 single event conversions was developed: <8 cM of residual NRP germplasm across the genome with ~1 cM in the 20 cM region flanking the event. Using computer simulation, we aimed to identify optimal breeding strategies for single event introgression to achieve this breeding goal, measuring efficiency in terms of number of backcross generations required, marker data points needed, and total population size across generations. Various selection schemes classified as three-stage, modified two-stage, and combined selection conducted from BC1 through BC3, BC4, or BC5 were compared. The breeding goal was achieved with a selection scheme involving five generations of marker-aided backcrossing, with BC1 through BC3 selected for the event of interest and minimal linkage drag at population size of 600, and BC4 and BC5 selected for the event of interest and recovery of the RP germplasm across the genome at population size of 400, with selection intensity of 0.01 for all generations. In addition, strategies for choice of donor parent to facilitate conversion efficiency and quality were evaluated. Two essential criteria for choosing an optimal donor parent for a given RP were established: introgression history showing reduction of linkage drag to ~1 cM in the 20 cM region flanking the event and genetic similarity between the RP and potential donor parents. Computer simulation demonstrated that single event conversions with <8 cM residual NRP germplasm can be accomplished by BC5 with no genetic similarity, by BC4 with 30 % genetic similarity, and by BC3 with 86 % genetic similarity using previously converted RPs as event donors. This study indicates that MTI to produce a 'quality' 15-event-stacked hybrid conversion is achievable. Furthermore, it lays the groundwork for a comprehensive approach to MTI by outlining a pathway to produce appropriate starting materials with which to proceed with event pyramiding and trait fixation before version testing.

RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress

PubMed Central

2011-01-01

Background In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. Results Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the accumulation of the RBCS1 protein under water stress. Altogether, the results presented here suggest that the content of RBCS was not responsible for the loss of photosynthetic capacity that is commonly observed in water-stressed coffee plants. Conclusion We showed that the CaCe homeolog was expressed in C. eugenioides and non-introgressed ("pure") genotypes of C. arabica but that it was undetectable in C. canephora. On the other hand, the CaCc homeolog was expressed in C. canephora but highly repressed in C. arabica. Expression of the CaCc homeolog was enhanced in C. arabica cultivars that experienced recent introgression with C. canephora. For both C. canephora and C. arabica species, total RBCS1 gene expression was highly reduced with WS. Unexpectedly, the accumulation of RBCS1 protein was observed in the leaves of C. canephora under WS, possibly coming from nocturnal RBCS1 expression. These results suggest that the increase in the amount of RBCS1 protein could contribute to the antioxidative function of photorespiration in water-stressed coffee plants. PMID:21575242

Wild tomato introgressions that confer resistance to begomoviruses in Guatemala

USDA-ARS?s Scientific Manuscript database

Begomoviruses, whitefly-transmitted geminiviruses, are one of the major diseases of tomatoes in subtropical and tropical regions. In Guatemala, several bipartite begomoviruses and the monopartite geminivirus, Tomato yellow leaf curl virus, are present. Three experiments were conducted to evaluate th...

IDENTIFICATION OF ESCAPED TRANSGENIC CREEPING BENTGRASS IN OREGON

EPA Science Inventory

When transgenic plants are cultivated near wild species that are sexually compatible with the crop, gene flow between the crop and wild plants is possible. A resultant concern is that transgene flow and transgene introgression within wild populations could have unintended ecologi...

Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.

PubMed

Thalapati, Sudhakar; Batchu, Anil K; Neelamraju, Sarla; Ramanan, Rajeshwari

2012-06-01

Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.

Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions

PubMed Central

Yin, Xinyou

2012-01-01

To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background. PMID:22888131

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

PubMed Central

Schuster, Tanja M.; Setaro, Sabrina D.; Tibbits, Josquin F. G.; Batty, Erin L.; Fowler, Rachael M.; McLay, Todd G. B.; Wilcox, Stephen; Ades, Peter K.

2018-01-01

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9–10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes. PMID:29668710

Occasional hybridization between a native and invasive Senecio species in Australia is unlikely to contribute to invasive success.

PubMed

Dormontt, Eleanor E; Prentis, Peter J; Gardner, Michael G; Lowe, Andrew J

2017-01-01

Hybridization between native and invasive species can facilitate introgression of native genes that increase invasive potential by providing exotic species with pre-adapted genes suitable for new environments. In this study we assessed the outcome of hybridization between native Senecio pinnatifolius var. pinnatifolius A.Rich. (dune ecotype) and invasive Senecio madagascariensis Poir. to investigate the potential for introgression of adaptive genes to have facilitated S. madagascariensis spread in Australia. We used amplified fragment length polymorphisms (141 loci) and nuclear microsatellites (2 loci) to genotype a total of 118 adults and 223 seeds from S. pinnatifolius var. pinnatifolius and S. madagascariensis at one allopatric and two shared sites. We used model based clustering and assignment methods to establish whether hybrid seed set and mature hybrids occur in the field. We detected no adult hybrids in any population. Low incidence of hybrid seed set was found at Lennox Head where the contact zone overlapped for 20 m (6% and 22% of total seeds sampled for S. pinnatifolius var. pinnatifolius and S. madagascariensis respectively). One hybrid seed was detected at Ballina where a gap of approximately 150 m was present between species (2% of total seeds sampled for S. madagascariensis ). We found no evidence of adult hybrid plants at two shared sites. Hybrid seed set from both species was identified at low levels. Based on these findings we conclude that introgression of adaptive genes from S. pinnatifolius var. pinnatifolius is unlikely to have facilitated S. madagascariensis invasions in Australia. Revisitation of one site after two years could find no remaining S. pinnatifolius var.  pinnatifolius , suggesting that contact zones between these species are dynamic and that S. pinnatifolius var.  pinnatifolius may be at risk of displacement by S. madagascariensis in coastal areas.

Genomics of a revived breed: Case study of the Belgian campine cattle

PubMed Central

Wijnrocx, Katrien; Colinet, Frédéric G.; Gengler, Nicolas; Hulsegge, Bettine; Windig, Jack J.; Buys, Nadine

2017-01-01

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed’s authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed. PMID:28426822

Convergent evolution of Darwin's finches caused by introgressive hybridization and selection.

PubMed

Grant, Peter R; Grant, B Rosemary; Markert, Jeffrey A; Keller, Lukas F; Petren, K

2004-07-01

Between 1973 and 2003 mean morphological features of the cactus finch, Geospiza scandens, and the medium ground finch, G. fortis, populations on the Galápagos island of Daphne Major were subject to fluctuating directional selection. An increase in bluntness or robustness in the beak of G. scandens after 1990 can only partly be explained by selection. We use 16 microsatellite loci to test predictions of the previously proposed hypothesis that introgressive hybridization contributed to the trend, resulting in genes flowing predominantly from G. fortis to G. scandens. To identify F1 hybrids and backcrosses we use pedigrees where known, supplemented by the results of assignment tests based on 14 autosomal loci when parents were not known. We analyze changes in morphology and allelic composition in the two populations over a period of 15-20 years. With samples that included F1 hybrids and backcrosses, the G. scandens population became more similar to the G. fortis population both genetically and morphologically. Gene flow between species was estimated to be three times greater from G. fortis to G. scandens than in the opposite direction, resulting in a 20% reduction in the genetic difference between the species. Nevertheless, removing identified F1 hybrids and backcrosses from the total sample and reanalyzing the traits did not eliminate the convergence. The two species also converged in beak shape by 22.2% and in body size by 45.5%. A combination of introgressive hybridization and selection jointly provide the best explanation of convergence in morphology and genetic constitution under the changed ecological conditions following a major El Niño event in 1983. The study illustrates how species without postmating barriers to gene exchange can alternate between convergence and divergence when environmental conditions oscillate.

Introgression between cultivars and wild populations of Momordica charantia L. (Cucurbitaceae) in Taiwan.

PubMed

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae) in Taiwan

PubMed Central

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes. PMID:22754378

Genomic divergence and lack of introgressive hybridization between two 13-year periodical cicadas support life cycle switching in the face of climate change.

PubMed

Koyama, Takuya; Ito, Hiromu; Fujisawa, Tomochika; Ikeda, Hiroshi; Kakishima, Satoshi; Cooley, John R; Simon, Chris; Yoshimura, Jin; Sota, Teiji

2016-11-01

Life history evolution spurred by post-Pleistocene climatic change is hypothesized to be responsible for the present diversity in periodical cicadas (Magicicada), but the mechanism of life cycle change has been controversial. To understand the divergence process of 13-year and 17-year cicada life cycles, we studied genetic relationships between two synchronously emerging, parapatric 13-year periodical cicada species in the Decim group, Magicicada tredecim and M. neotredecim. The latter was hypothesized to be of hybrid origin or to have switched from a 17-year cycle via developmental plasticity. Phylogenetic analysis using restriction-site-associated DNA sequences for all Decim species and broods revealed that the 13-year M. tredecim lineage is genomically distinct from 17-year Magicicada septendecim but that 13-year M. neotredecim is not. We detected no significant introgression between M. tredecim and M. neotredecim/M. septendecim thus refuting the hypothesis that M. neotredecim are products of hybridization between M. tredecim and M. septendecim. Further, we found that introgressive hybridization is very rare or absent in the contact zone between the two 13-year species evidenced by segregation patterns in single nucleotide polymorphisms, mitochondrial lineage identity and head width and abdominal sternite colour phenotypes. Our study demonstrates that the two 13-year Decim species are of independent origin and nearly completely reproductively isolated. Combining our data with increasing observations of occasional life cycle change in part of a cohort (e.g. 4-year acceleration of emergence in 17-year species), we suggest a pivotal role for developmental plasticity in Magicicada life cycle evolution. © 2016 John Wiley & Sons Ltd.

Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton.

PubMed

Xu, Peng; Gao, Jin; Cao, Zhibin; Chee, Peng W; Guo, Qi; Xu, Zhenzhen; Paterson, Andrew H; Zhang, Xianggui; Shen, Xinlian

2017-06-01

A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC 4 F 2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC 4 F 3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F 2 population, supporting these genes as candidates for qFL-chr1.

Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross between Gossypium hirsutum and G. mustelinum.

PubMed

Wang, Baohua; Zhuang, Zhimin; Zhang, Zhengsheng; Draye, Xavier; Shuang, Lan-Shuan; Shehzad, Tariq; Lubbers, Edward L; Jones, Don; May, O Lloyd; Paterson, Andrew H; Chee, Peng W

2017-01-01

The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum (Upland cotton) was dissected using 21 BC 3 F 2 and 12 corresponding BC 3 F 2:3 and BC 3 F 2:4 families. The BC 3 F 2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC 3 -derived families were phenotyped for fiber strength (STR) and fineness (Micronaire, MIC). A total of 42 quantitative trait loci (QTLs) were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses. Alleles from G. mustelinum increased STR for eight of 15 and reduced MIC for 15 of 27 QTLs. Significant among-family genotypic effects ( P < 0.001) were detected in 13 and 10 loci for STR and MIC respectively, and five loci showed significant ( P < 0.001) genotype × family interaction for MIC. These results support the hypothesis that fiber quality improvement for Upland cotton could be realized by introgressing G. mustelinum alleles although complexities due to the different effects of genetic background on introgressed chromatin might be faced. Building on prior work with G. barbadense, G. tomentosum , and G. darwinii , QTL mapping involving introgression of G. mustelinum alleles offers new allelic variation to Upland cotton germplasm.

Hybrid zone formation and contrasting outcomes of secondary contact over transects in common toads.

PubMed

Arntzen, Jan W; de Vries, Wouter; Canestrelli, Daniele; Martínez-Solano, Iñigo

2017-10-01

Much progress in speciation research stems from documenting patterns of morphological and genetic variation in hybrid zones. Contrasting patterns of marker introgression in different sections of the contact can provide valuable insights on the relative importance of various evolutionary mechanisms maintaining species differences in the face of hybridization and gene flow and on hybrid zone temporal and spatial dynamics. We studied species interactions in the common toads Bufo bufo and B. spinosus in France and northwestern Italy using morphological and molecular data from the mitochondrial and nuclear genomes in an extensive survey, including two independent transects west and east of the Alps. At both, we found sharp, coincident and concordant nuclear genetic transitions. However, morphological clines were wider or absent and mtDNA introgression was asymmetric. We discuss alternative, nonexclusive hypotheses about evolutionary processes generating these patterns, including drift, selection, long-distance dispersal and spatial shifts in hybrid zone location and structure. The distribution of intraspecific mtDNA lineages supports a scenario in which B. bufo held a local refugium during the last glacial maximum. Present-day genetic profiles are best explained by an advance of B. spinosus from a nearby Iberian refugium, largely superseding the local B. bufo population, followed by an advance of B. bufo from the Balkans, with prongs north and south of the Alps, driving B. spinosus southwards. A pendulum moving hybrid zone, first northwards and then southwards, explains the wide areas of introgression at either side of the current position of the contact zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.

PubMed

Ravago-Gotanco, Rachel; de la Cruz, Talna Lorena; Pante, Ma Josefa; Borsa, Philippe

2018-01-01

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

PubMed

Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

2016-05-01

A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources. Published by Oxford University Press on behalf of the American Genetic Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae).

PubMed

Leavitt, Dean H; Bezy, Robert L; Crandall, Keith A; Sites, Jack W

2007-11-01

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.

Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs.

PubMed

Palma-Silva, C; Wendt, T; Pinheiro, F; Barbará, T; Fay, Michael F; Cozzolino, S; Lexer, C

2011-08-01

The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot. © 2011 Blackwell Publishing Ltd.

Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

PubMed Central

Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; Schranz, M Eric; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; Michelmore, Richard W; van Tienderen, Peter H

2014-01-01

The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. PMID:25360276

The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

PubMed

Sun, Fengming; Fan, Guangyi; Hu, Qiong; Zhou, Yongming; Guan, Mei; Tong, Chaobo; Li, Jiana; Du, Dezhi; Qi, Cunkou; Jiang, Liangcai; Liu, Weiqing; Huang, Shunmou; Chen, Wenbin; Yu, Jingyin; Mei, Desheng; Meng, Jinling; Zeng, Peng; Shi, Jiaqin; Liu, Kede; Wang, Xi; Wang, Xinfa; Long, Yan; Liang, Xinming; Hu, Zhiyong; Huang, Guodong; Dong, Caihua; Zhang, He; Li, Jun; Zhang, Yaolei; Li, Liangwei; Shi, Chengcheng; Wang, Jiahao; Lee, Simon Ming-Yuen; Guan, Chunyun; Xu, Xun; Liu, Shengyi; Liu, Xin; Chalhoub, Boulos; Hua, Wei; Wang, Hanzhong

2017-11-01

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat.

PubMed

Rey, Elodie; Abrouk, Michael; Keeble-Gagnère, Gabriel; Karafiátová, Miroslava; Vrána, Jan; Balzergue, Sandrine; Soubigou-Taconnat, Ludivine; Brunaud, Véronique; Martin-Magniette, Marie-Laure; Endo, Takashi R; Bartoš, Jan; Appels, Rudi; Doležel, Jaroslav

2018-03-06

Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat-barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35 301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Metabolic engineering of tomato fruit organic acid content guided by biochemical analysis of an introgression line.

PubMed

Morgan, Megan J; Osorio, Sonia; Gehl, Bernadette; Baxter, Charles J; Kruger, Nicholas J; Ratcliffe, R George; Fernie, Alisdair R; Sweetlove, Lee J

2013-01-01

Organic acid content is regarded as one of the most important quality traits of fresh tomato (Solanum lycopersicum). However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here, we used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of tricarboxylic acid cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts, suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analyzed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A green fluorescent protein fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a, was exclusively mitochondrial when transiently expressed in tobacco (Nicotiana tabacum) leaves. Both aconitase transcripts were decreased in fruit from transgenic lines, and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants, and as a consequence, total carboxylic acid content was increased by 50% at maturity.

Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

PubMed Central

Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

2016-01-01

Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions. PMID:27807437

Metabolic Engineering of Tomato Fruit Organic Acid Content Guided by Biochemical Analysis of an Introgression Line1[W][OA

PubMed Central

Morgan, Megan J.; Osorio, Sonia; Gehl, Bernadette; Baxter, Charles J.; Kruger, Nicholas J.; Ratcliffe, R. George; Fernie, Alisdair R.; Sweetlove, Lee J.

2013-01-01

Organic acid content is regarded as one of the most important quality traits of fresh tomato (Solanum lycopersicum). However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here, we used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of tricarboxylic acid cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts, suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analyzed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A green fluorescent protein fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a, was exclusively mitochondrial when transiently expressed in tobacco (Nicotiana tabacum) leaves. Both aconitase transcripts were decreased in fruit from transgenic lines, and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants, and as a consequence, total carboxylic acid content was increased by 50% at maturity. PMID:23166354

Assessing the prevalence of hybridization between sympatric Canis species surrounding the red wolf (Canis rufus) recovery area in North Carolina.

PubMed

Bohling, Justin H; Waits, Lisette P

2011-05-01

Predicting spatial patterns of hybridization is important for evolutionary and conservation biology yet are hampered by poor understanding of how hybridizing species can interact. This is especially pertinent in contact zones where hybridizing populations are sympatric. In this study, we examined the extent of red wolf (Canis rufus) colonization and introgression where the species contacts a coyote (C. latrans) population in North Carolina, USA. We surveyed 22,000km(2) in the winter of 2008 for scat and identified individual canids through genetic analysis. Of 614 collected scats, 250 were assigned to canids by mitochondrial DNA (mtDNA) sequencing. Canid samples were genotyped at 6-17 microsatellite loci (nDNA) and assigned to species using three admixture criteria implemented in two Bayesian clustering programs. We genotyped 82 individuals but none were identified as red wolves. Two individuals had red wolf mtDNA but no significant red wolf nDNA ancestry. One individual possessed significant red wolf nDNA ancestry (approximately 30%) using all criteria, although seven other individuals showed evidence of red wolf ancestry (11-21%) using the relaxed criterion. Overall, seven individuals were classified as hybrids using the conservative criteria and 37 using the relaxed criterion. We found evidence of dog (C. familiaris) and gray wolf (C. lupus) introgression into the coyote population. We compared the performance of different methods and criteria by analyzing known red wolves and hybrids. These results suggest that red wolf colonization and introgression in North Carolina is minimal and provide insights into the utility of Bayesian clustering methods to detect hybridization. © 2011 Blackwell Publishing Ltd.

Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L.

PubMed Central

Raman, Rosy; Qiu, Yu; Coombes, Neil; Song, Jie; Kilian, Andrzej; Raman, Harsh

2017-01-01

Seed lost due to easy pod dehiscence at maturity (pod shatter) is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata) and identified quantitative trait loci (QTL) for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE). In comparison to B. napus (RE = 2.16 mJ), B. carinata accessions had higher RE values (2.53 to 20.82 mJ). A genetic linkage map of an F2 population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE) and BC73524 (shatter prone with low RE) comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F2 and F2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3) that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools. PMID:29250080

Development of somatic hybrids Solanum × michoacanum Bitter. (Rydb.) (+) S. tuberosum L. and autofused 4x S. × michoacanum plants as potential sources of late blight resistance for potato breeding.

PubMed

Smyda, P; Jakuczun, H; Dębski, K; Sliwka, J; Thieme, R; Nachtigall, M; Wasilewicz-Flis, I; Zimnoch-Guzowska, E

2013-08-01

Phytophthora infestans resistant somatic hybrids of S. × michoacanum (+) S. tuberosum and autofused 4 x S. × michoacanum were obtained. Our material is promising to introgress resistance from S. × michoacanum into cultivated potato background. Solanum × michoacanum (Bitter.) Rydb. (mch) is a wild diploid (2n = 2x = 24) potato species derived from spontaneous cross of S. bulbocastanum and S. pinnatisectum. This hybrid is a 1 EBN (endosperm balance number) species and can cross effectively only with other 1 EBN species. Plants of mch are resistant to Phytophthora infestans (Mont) de Bary. To introgress late blight resistance genes from mch into S. tuberosum (tbr), genepool somatic hybridization between mch and susceptible diploid potato clones (2n = 2x = 24) or potato cultivar Rywal (2n = 4x = 48) was performed. In total 18,775 calli were obtained from postfusion products from which 1,482 formed shoots. The Simple Sequence Repeat (SSR), Cleaved Amplified Polymorphic Sequences (CAPS) and Random Amplified Polymorphic DNA (RAPD) analyses confirmed hybrid nature of 228 plants and 116 autofused 4x mch. After evaluation of morphological features, flowering, pollen stainability, tuberization and ploidy level, 118 somatic hybrids and 116 autofused 4x mch were tested for late blight resistance using the detached leaf assay. After two seasons of testing three somatic hybrids and 109 4x mch were resistant. Resistant forms have adequate pollen stainability for use in crossing programme and are a promising material useful for introgression resistance from mch into the cultivated potato background.

The responses of crop - wild Brassica hybrids to simulated herbivory and interspecific competition: implications for transgene introgression.

PubMed

Sutherland, Jamie P; Justinova, Lenka; Poppy, Guy M

2006-01-01

Brassica rapa grows as a wild and weedy species throughout the world and is the most likely recipient of transgenes from GM oilseed rape. For transgene introgression to occur, the critical step which must be realized, is the formation of an F1 hybrid. Concerns exist that hybrid populations could be more vigorous and competitive compared to the parental species. This study examines the effect of simulated herbivory and interspecific competition on the vegetative and reproductive performance of non-transgenic F1 hybrids and their parental lines. Several vegetative and reproductive performance measures were used to determine the effect of simulated herbivory and competition on the Brassica lines, including leaf length and biomass for herbivory and seedling height and biomass for competition. For defoliation experiments, B. rapa showed little response in terms of leaf length but B. napus and the F1 hybrid responded negatively. Brassica rapa showed elevated biomass responses, but B. napus and the hybrid demonstrated negative responses to defoliation. Defoliation at the cotyledon stage had a slight effect upon final biomass with the F1 hybrid performing significantly worse than B. napus, although seed counts were not significantly different. For the series of competition experiments, hybrids seemed to be more similar to B. rapa in terms of early seedling growth and reproductive measures. The underperformance of hybrid plants when challenged by herbivory and competition, could potentially decrease survivorship and explain the rarity of hybrids in field surveys. However, should transgene introgression occur, the dynamics of hybrids could change radically thus increasing the risk of gene flow from a transgenic oilseed rape crop to the wild recipient.

Identification of Neosho Smallmouth Bass (Micropterus dolomieu velox) stocks for possible introduction into Grand Lake, Oklahoma

USGS Publications Warehouse

Taylor, Andrew T.; Long, James M.; Schwemm, Michael R.; Tringali, Michael D.; Brewer, Shannon K.

2016-01-01

Stocking black basses (Micropterus spp.) is a common practice used to increase angling opportunities in impoundments; however, when non-native black basses are introduced they often invade riverine habitats where they threaten the persistence of other fishes, including native black basses. Neosho Smallmouth Bass (M. dolomieu velox) is endemic to portions of the Ozark Highlands and Boston Mountains ecoregions and is threatened by introductions of non-native Smallmouth Bass (“SMB”) forms. Because of recent interest in stocking SMB into Grand Lake o’ the Cherokees, we assessed the suitability of local Neosho SMB populations as potential broodstock sources by assessing introgression with non-native SMB forms, as well as characterizing population structure and genetic diversity. The majority of Neosho SMB populations contained low, but non-negligible, genomic proportions of two genetically distinct non-native SMB forms. Introgression was highest in the Illinois River upstream of Lake Tenkiller, where Tennessee ‘lake strain’ SMB were stocked in the early 1990’s. We recovered three genetically distinct clusters of Neosho SMB at the uppermost hierarchical level of population structure: a distinct Illinois River cluster and two Grand River clusters that appear to naturally mix at some sites. Genetic diversity measures generally increased with stream size, and smaller populations with low diversity measures may benefit from immigration of novel genetic material. Overall, introgression with non-native SMB forms appears to pose a prominent threat to Neosho SMB; however, relatively intact populations of Neosho SMB exist in some Grand Lake o’ the Cherokees tributaries. Results could be used in developing a stocking program that promotes and sustains existing genetic diversity within and among Neosho SMB populations.

Introgression of A- and B-genome of tetraploid triticale chromatin into tetraploid rye.

PubMed

Wiśniewska, H; Kwiatek, M; Kulak-Książczyk, S; Apolinarska, B

2013-11-01

An improvement of rye is one of the mainstream goals of current breeding. Our study is concerned with the introduction of the tetraploid triticale (ABRR) into the 4x rye (RRRR) using classical methods of distant crossing. One hundred fifty BC1F9 hybrid plants [(4x rye × 4x triticales) × 4x rye] obtained from a backcrossing program were studied. The major aim of this work was to verify the presence of an introgressed A- and B- genome chromatin of triticale in a collection of the 4x rye-tiritcale hybrids and to determine their chromosome compositions. In the present study, karyotypes of the previously reported BC1F2s and BC1F3s were compared with that of the BC1F9 generation as obtained after several subsequent open pollinations. The genomic in situ hybridisation (GISH) allowed us to identify 133 introgression forms in which chromosome numbers ranged between 26 and 32. Using four DNA probes (5S rDNA, 25S rDNA, pSc119.2 and pAs1), the fluorescence in situ hybridisation (FISH) was carried out to facilitate an exact chromosome identification in the hybrid plants. The combination of the multi-colour GISH with the repetitive DNA FISH singled out five types of translocated chromosomes: 2A.2R, 4A.4R, 5A.5R, 5B.5R and 7A.7R among the examined BC1F9s. The reported translocation lines could serve as valuable sources of wheat chromatin suitable for further improvements of rye.

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees.

PubMed

Bourret, V; O'Reilly, P T; Carr, J W; Berg, P R; Bernatchez, L

2011-03-01

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

PubMed Central

Bourret, V; O'Reilly, P T; Carr, J W; Berg, P R; Bernatchez, L

2011-01-01

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions. PMID:21224876

Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod

PubMed Central

Unmack, Peter J.; Dyer, Fiona J.; Lintermans, Mark

2016-01-01

Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs. PMID:27812407

Effects of stacked quantitative resistances to downy mildew in lettuce do not simply add up.

PubMed

den Boer, Erik; Pelgrom, Koen T B; Zhang, Ningwen W; Visser, Richard G F; Niks, Rients E; Jeuken, Marieke J W

2014-08-01

In a stacking study of eight resistance QTLs in lettuce against downy mildew, only three out of ten double combinations showed an increased resistance effect under field conditions. Complete race nonspecific resistance to lettuce downy mildew, as observed for the nonhost wild lettuce species Lactuca saligna, is desired in lettuce cultivation. Genetic dissection of L. saligna's complete resistance has revealed several quantitative loci (QTL) for resistance with field infection reductions of 30-50 %. To test the effect of stacking these QTL, we analyzed interactions between homozygous L. saligna CGN05271 chromosome segments introgressed into the genetic background of L. sativa cv. Olof. Eight different backcross inbred lines (BILs) with single introgressions of 30-70 cM and selected predominately for quantitative resistance in field situations were intercrossed. Ten developed homozygous lines with stacked introgression segments (double combinations) were evaluated for resistance in the field. Seven double combinations showed a similar infection as the individual most resistant parental BIL, revealing epistatic interactions with 'less-than-additive' effects. Three double combinations showed an increased resistance level compared to their parental BILs and their interactions were additive, 'less-than-additive' epistatic and 'more-than-additive' epistatic, respectively. The additive interaction reduced field infection by 73 %. The double combination with a 'more-than-additive' epistatic effect, derived from a combination between a susceptible and a resistant BIL with 0 and 30 % infection reduction, respectively, showed an average field infection reduction of 52 %. For the latter line, an attempt to genetically dissect its underlying epistatic loci by substitution mapping did not result in smaller mapping intervals as none of the 22 substitution lines reached a similar high resistance level. Implications for breeding and the inheritance of L. saligna's complete resistance are discussed.

Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus-Raphanus raphanistrum Model.

PubMed

Adamczyk-Chauvat, Katarzyna; Delaunay, Sabrina; Vannier, Anne; François, Caroline; Thomas, Gwenaëlle; Eber, Frédérique; Lodé, Maryse; Gilet, Marie; Huteau, Virginie; Morice, Jérôme; Nègre, Sylvie; Falentin, Cyril; Coriton, Olivier; Darmency, Henri; Alrustom, Bachar; Jenczewski, Eric; Rousseau-Gueutin, Mathieu; Chèvre, Anne-Marie

2017-07-01

The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties ( Brassica napus , AACC, 2 n  = 38) by a local population of wild radish ( Raphanus raphanistrum , RrRr, 2 n  = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0-28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow. Copyright © 2017 by the Genetics Society of America.

Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species.

PubMed

Gaudeul, Myriam; Gardner, Martin F; Thomas, Philip; Ennos, Richard A; Hollingsworth, Pete M

2014-09-05

New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.

Intervarietal and intravarietal genetic structure in Douglas-fir: nuclear SSRs bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization

PubMed Central

van Loo, Marcela; Hintsteiner, Wolfgang; Pötzelsberger, Elisabeth; Schüler, Silvio; Hasenauer, Hubert

2015-01-01

Douglas-fir (Pseudotsuga menziesii) is one of numerous wide-range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty-eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice-covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management. PMID:26140197

Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize.

PubMed

Hossain, Firoz; Muthusamy, Vignesh; Pandey, Neha; Vishwakarma, Ashish K; Baveja, Aanchal; Zunjare, Rajkumar U; Thirunavukkarasu, Nepolean; Saha, Supradip; Manjaiah, Kanchikeri M Manjaiah; Prasanna, Boddupalli M; Gupta, Hari S

2018-03-01

Maize is a valuable source of food and feed worldwide. Maize endosperm protein is, however nutritionally poor due to the reduced levels of two essential amino acids, lysine and tryptophan. In this study, recessive opaque2 (o2) allele that confers enhanced endosperm lysine and tryptophan, was introgressed using marker-assisted backcross breeding into three normal inbred lines (HKI323, HKI1105 and HKI1128). These are the parental lines of three popular medium-maturing single cross hybrids (HM4, HM8 and HM9) in India. Gene-based simple sequence repeat (SSR) markers (umc1066 and phi057) were successfully deployed for introgression of o2 allele. Background selection using genome-based SSRs helped in recovering > 96% of recurrent parent genome. The newly developed quality protein maize (QPM) inbreds showed modified kernels (25-50% opaqueness) coupled with high degree of phenotypic resemblance to the respective recipient lines, including grain yield. In addition, endosperm protein quality showed increased lysine and tryptophan in the inbreds to the range of 52-95% and 47-118%, respectively. The reconstituted QPM hybrids recorded significant enhancement of endosperm lysine (48-74%) and tryptophan (55-100%) in the endosperm. The QPM hybrids exhibited high phenotypic similarity with the original hybrids for morphological and yield contributing traits along with responses to some major diseases like turcicum leaf blight and maydis leaf blight. The grain yield of QPM hybrids was at par with their original versions under multilocation testing. These elite, high-yielding QPM hybrids with improved protein quality have been released and notified for commercial cultivation, and hold significant promise for improving nutritional security.

Winter-injury following horticultural treatments to overcome juvenility in citrus seedlings

USDA-ARS?s Scientific Manuscript database

Citrus seedling juvenility delays new hybrid evaluation, slows cultivar release, and slows introgression of new traits. A horticultural program reported to overcome citrus juvenility was tested at the Whitmore Citrus Research Foundation farm (Lake County), using replicated Hirado Buntan x Clementine...

Genomic heterogeneity and structural variation in soybean near-isogenic lines

USDA-ARS?s Scientific Manuscript database

Near-isogenic lines (NILs) are a critical genetic resource for the soybean research community. The ability to identify and characterize the genes driving the phenotypic differences between NILs is limited by the degree to which differential genetic introgressions can be resolved. Furthermore, the ...

Successful introgression of abiotic stress tolerance from wild tepary bean to common bean

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris L.) production is severely limited due to abiotic stresses, including drought and sub-zero temperatures. Tepary bean (Phaseolus acutifolius Gray), a relative of common bean, has demonstrated tolerance to these stresses. Preliminary studies screening tepary accessions ...

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

PubMed Central

Posth, Cosimo; Wißing, Christoph; Kitagawa, Keiko; Pagani, Luca; van Holstein, Laura; Racimo, Fernando; Wehrberger, Kurt; Conard, Nicholas J.; Kind, Claus Joachim; Bocherens, Hervé; Krause, Johannes

2017-01-01

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods. PMID:28675384

Conservation of the introgressed European water frog complex using molecular tools.

PubMed

Holsbeek, G; Maes, G E; De Meester, L; Volckaert, F A M

2009-03-01

In Belgium, the Pelophylax esculentus complex has recently been subjected to multiple introductions of non-native water frogs, increasing the occurrence of hybridisation events. In the present study, we tested the reliability of morphometric and recently developed microsatellite tools to identify introgression and to determine the origin of exotic Belgian water frogs. By analysing 150 individuals of each taxon of the P. esculentus complex and an additional 60 specimens of the introduced P. cf. bedriagae, we show that neither of the currently available tools appears to have sufficient power to reliably distinguish all Belgian water frog species. We therefore aimed at increasing the discriminatory power of a microsatellite identification tool by developing a new marker panel with additional microsatellite loci. By adding only two new microsatellite loci (RlCA5 and RlCA1b20), all taxa of the P. esculentus complex could be distinguished from each other with high confidence. Three more loci (Res3, Res5 and Res17) provided a powerful discrimination of the exotic species.

Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping.

PubMed

Gaiero, Paola; van de Belt, José; Vilaró, Francisco; Schranz, M Eric; Speranza, Pablo; de Jong, Hans

2017-03-01

A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.

A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice.

PubMed

Hamaoka, Norimitsu; Yasui, Hideshi; Yamagata, Yoshiyuki; Inoue, Yoko; Furuya, Naruto; Araki, Takuya; Ueno, Osamu; Yoshimura, Atsushi

2017-12-01

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC 5 F 2 and F 3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24.

A Gondwanan Imprint on Global Diversity and Domestication of Wine and Cider Yeast Saccharomyces uvarum

PubMed Central

Almeida, Pedro; Gonçalves, Carla; Teixeira, Sara; Libkind, Diego; Bontrager, Martin; Masneuf-Pomarède, Isabelle; Albertin, Warren; Durrens, Pascal; Sherman, David; Marullo, Philippe; Hittinger, Chris Todd; Gonçalves, Paula; Sampaio, José Paulo

2016-01-01

In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with human-driven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum. PMID:24887054

Leaf-Encapsulated Vaccines: Agroinfiltration and Transient Expression of the Antigen Staphylococcal Endotoxin B in Radish Leaves

PubMed Central

Liu, Pei-Feng; Wang, Yanhan; Ulrich, Robert G.; Simmons, Christopher W.; VanderGheynst, Jean S.; Gallo, Richard L.

2018-01-01

Transgene introgression is a major concern associated with transgenic plant-based vaccines. Agroinfiltration can be used to selectively transform nonreproductive organs and avoid introgression. Here, we introduce a new vaccine modality in which Staphylococcal enterotoxin B (SEB) genes are agroinfiltrated into radishes (Raphanw sativus L.), resulting in transient expression and accumulation of SEB in planta. This approach can simultaneously express multiple antigens in a single leaf. Furthermore, the potential of high-throughput vaccine production was demonstrated by simultaneously agroinfiltrating multiple radish leaves using a multichannel pipette. The expression of SEB was detectable in two leaf cell types (epidermal and guard cells) in agroinfiltrated leaves. ICR mice intranasally immunized with homogenized leaves agroinfiltrated with SEB elicited detectable antibody to SEB and displayed protection against SEB-induced interferon-gamma (IFN-γ) production. The concept of encapsulating antigens in leaves rather than purifying them for immunization may facilitate rapid vaccine production during an epidemic disease. PMID:29577048

The origin of Chinese domestic horses revealed with novel mtDNA variants.

PubMed

Yang, Yunzhou; Zhu, Qiyun; Liu, Shuqin; Zhao, Chunjiang; Wu, Changxin

2017-01-01

The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe. © 2016 Japanese Society of Animal Science.

Genetic interactions underlying hybrid male sterility in the Drosophila bipectinata species complex.

PubMed

Mishra, Paras Kumar; Singh, Bashisth Narayan

2006-06-01

Understanding genetic mechanisms underlying hybrid male sterility is one of the most challenging problems in evolutionary biology especially speciation. By using the interspecific hybridization method roles of Y chromosome, Major Hybrid Sterility (MHS) genes and cytoplasm in sterility of hybrid males have been investigated in a promising group, the Drosophila bipectinata species complex that consists of four closely related species: D. pseudoananassae, D. bipectinata, D. parabipectinata and D. malerkotliana. The interspecific introgression analyses show that neither cytoplasm nor MHS genes are involved but X-Y interactions may be playing major role in hybrid male sterility between D. pseudoananassae and the other three species. The results of interspecific introgression analyses also show considerable decrease in the number of males in the backcross offspring and all males have atrophied testes. There is a significant positive correlation between sex - ratio distortion and severity of sterility in backcross males. These findings provide evidence that D. pseudoananassae is remotely related with other three species of the D. bipectinata species complex.

Six rice chromosome segment substitution lines libraries with O. rufipogon introgressions

USDA-ARS?s Scientific Manuscript database

Chromosome segment substitution lines (CSSLs) are a powerful tool for identifying naturally occurring, favorable alleles in unadapted germplasm. Six CSSL libraries in rice (Oryza sativa) were developed from crosses between three different accessions ('Khao Pa', W1944, IRGC105567) of the rice progeni...

Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat

USDA-ARS?s Scientific Manuscript database

Wheat (Triticum spp.) has a narrow genetic basis due to its allopolyploid origin. However, wheat has numerous wild relatives usable for expanding genetic variability of its genome through meiotic homoeologous recombination. Traditionally, laborious cytological analyses have been employed to detect h...

Exotic germplasm introgression effect on agronomic and fiber properties of upland cotton

USDA-ARS?s Scientific Manuscript database

Genetic diversity is an important breeder’s tool for selection and improvement in crop cultivar development. Any successful breeding program depends on selecting superior quality parents. Lack of genetic diversity limits the potential of the breeder in selecting elite parents. Genetic uniformity pre...

Genetic and epigenetic changes in somatic hybrid introgression lines between wheat and tall wheatgrass

USDA-ARS?s Scientific Manuscript database

Broad phenotypic variations were induced in derivatives of an asymmetric somatic hybridization of bread wheat (Triticum aestivum) and tall wheatgrass (Thinopyrum ponticum Podp); however, how did these variations happened was unknown. We explored the nature of these variations by cytogenetic assays ...

Genomic heterogeneity and structural variation in soybean near isogenic lines

USDA-ARS?s Scientific Manuscript database

Near-isogenic lines (NILs) are a critical genetic resource for the soybean research community. The ability to identify and characterize the genes driving the phenotypic differences between NILs is limited by the degree to which differential genetic introgressions can be resolved. Furthermore, the ge...

Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations

USDA-ARS?s Scientific Manuscript database

Teosinte (Zea mays ssp. parviglumis) has greater genetic diversity than maize inbreds and landraces (Z. mays ssp. mays). There are, however, limited genetic resources to efficiently evaluate and tap this diversity. To broaden resources for genetic diversity studies in maize, we developed and evaluat...

Can genomics boost productivity of orphan crops?

USDA-ARS?s Scientific Manuscript database

Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

Fine Mapping and Introgressing a Fissure Resistance Locus

USDA-ARS?s Scientific Manuscript database

Rice (Oryza sativa L.) kernel fissuring is a major concern of both rice producers and millers. Fissures are small cracks in rice kernels that increase breakage among kernels when transported or milled, which decrease the value of processed rice. This study employed molecular gene tagging methods to ...

Germplasm release: Tetraploid potato clones with resistance to common scab

USDA-ARS?s Scientific Manuscript database

Common scab caused by the soil-borne bacterium Streptomyces scabies is a serious disease for the potato industry. We have identified a strong source of resistance in the diploid wild relative Solanum chacoense. This resistance has been introgressed into tetraploid cultivated potato via unilateral se...

Development of a genetic sexing strain in Bactrocera carambolae (Diptera: Tephritidae) by introgression of sex sorting components from B. dorsalis, Salaya1 strain

PubMed Central

2014-01-01

Background The carambola fruit fly, Bactrocera carambolae Drew & Hancock is a high profile key pest that is widely distributed in the southwestern ASEAN region. In addition, it has trans-continentally invaded Suriname, where it has been expanding east and southward since 1975. This fruit fly belongs to Bactrocera dorsalis species complex. The development and application of a genetic sexing strain (Salaya1) of B. dorsalis sensu stricto (s.s.) (Hendel) for the sterile insect technique (SIT) has improved the fruit fly control. However, matings between B. dorsalis s.s. and B. carambolae are incompatible, which hinder the application of the Salaya1 strain to control the carambola fruit fly. To solve this problem, we introduced genetic sexing components from the Salaya1 strain into the B. carambolae genome by interspecific hybridization. Results Morphological characteristics, mating competitiveness, male pheromone profiles, and genetic relationships revealed consistencies that helped to distinguish Salaya1 and B. carambolae strains. A Y-autosome translocation linking the dominant wild-type allele of white pupae gene and a free autosome carrying a recessive white pupae homologue from the Salaya1 strain were introgressed into the gene pool of B. carambolae. A panel of Y-pseudo-linked microsatellite loci of the Salaya1 strain served as markers for the introgression experiments. This resulted in a newly derived genetic sexing strain called Salaya5, with morphological characteristics corresponding to B. carambolae. The rectal gland pheromone profile of Salaya5 males also contained a distinctive component of B. carambolae. Microsatellite DNA analyses confirmed the close genetic relationships between the Salaya5 strain and wild B. carambolae populations. Further experiments showed that the sterile males of Salaya5 can compete with wild males for mating with wild females in field cage conditions. Conclusions Introgression of sex sorting components from the Salaya1 strain to a closely related B. carambolae strain generated a new genetic sexing strain, Salaya5. Morphology-based taxonomic characteristics, distinctive pheromone components, microsatellite DNA markers, genetic relationships, and mating competitiveness provided parental baseline data and validation tools for the new strain. The Salaya5 strain shows a close similarity with those features in the wild B. carambolae strain. In addition, mating competitiveness tests suggested that Salaya5 has a potential to be used in B. carambolae SIT programs based on male-only releases. PMID:25471905

Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression

USDA-ARS?s Scientific Manuscript database

• Premise of Study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that can serve ...

Introgression and dispersal among spotted owl (Strix occidentatlis) subspecies.

Treesearch

W.Chris Funk; Eric D. Forsman; Thomas D. Mullins; Susan M. Haig

2008-01-01

Population genetics plays an increasingly important role in the conservation and management of declining species, particularly for defining taxonomic units. Subspecies are recognized by several conservation organizations and countries and receive legal protection under the US Endangered Species Act (ESA). Two subspecies of spotted owls, northern (Strix...

Yield stability in genotypes derived through basic breeding

USDA-ARS?s Scientific Manuscript database

The sugarcane variety ‘LCP 85-384’ was derived through basic (introgression) breeding, and after its release in 1995, the variety quickly gained acreage in the state of Louisiana. The primary reason for the popularity of the variety was the plant vigor and increase in the number of ratoon harvests ...

Oryza rufipogon introgressions improve yield in the U.S. cultivar Jefferson

USDA-ARS?s Scientific Manuscript database

An advanced backcross (BC2) population was developed to explore the breeding value of the wild ancestral species O. rufipogon (IRGC 105491) in a cross with the tropical japonica US variety, cv Jefferson. Early generation selection eliminated lines which possessed undesirable traits such as dormancy,...

Molecular confirmation of Gossypium hirsutum chromosome substitution lines

USDA-ARS?s Scientific Manuscript database

The primary gene pool for tetraploid cotton species includes G. hirsutum L., as well as the other four 2n=52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien chromosome subst...

Multiple disease resistance to fungal and oomycete pathogens using a recombinant inbred line population in pepper

USDA-ARS?s Scientific Manuscript database

Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hotspo...

Levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

USDA-ARS?s Scientific Manuscript database

A high density panel of more than 777000 genome-wide single nucleotide polymorphisms (SNPs) were used to investigate the population structure of Nelore and Gir, compared to seven other populations worldwide. Principal Component Analysis and model-based ancestry estimation clearly separate the indici...

Ecological segregation moderates a climactic conclusion to trout hybridization

Treesearch

Michael K. Young; Daniel J. Isaak; Kevin S. McKelvey; Taylor M. Wilcox; Matthew R. Campbell; Matthew P. Corsi; Dona Horan; Michael K. Schwartz

2017-01-01

Invasive hybridization, in which an introduced species may introgressively hybridize with a native taxon and threaten its persistence, is prominently featured in the conservation literature. One of the most frequently cited examples of this phenomenon involves interactions between native westslope cutthroat trout Oncorhynchus clarkii lewisi and introduced rainbow trout...

Studies of a new hybrid taxon in the Artemisia tridentata (Asteraceae: Anthemideae) complex

Treesearch

Heather D. Garrison; Leila M. Shultz; E. Durant McArthur

2013-01-01

Members of the Artemisia tridentata complex (ASTERACEAE: Anthemideae: Artemisia subgen. Tridentatae) have adapted to changing environmental conditions through geographic migration, introgression, and hybridization. These processes have resulted in morphologic and genetic variation. A presumed hybrid ("Bonneville" big sagebrush) of the complex occurs in the...

Introgression of resistance-conferring ALS mutations in herbicide-resistant weedy rice

USDA-ARS?s Scientific Manuscript database

Weedy red rice (Oryza sativa) competes aggressively with rice, reducing yields and grain quality. Clearfield™ rice, a nontransgenic, herbicide-resistant (HR) rice introduced in 2002 to control weedy rice, has resulted in some ALS-resistant weedy rice apparently due to gene flow. Studies were conduct...

Validation of molecular markers associated with perpetual flowering in octoploid Fragaria germplasm

USDA-ARS?s Scientific Manuscript database

Perpetual flowering (PF) is a highly desirable trait within cultivated strawberries (Fragaria ×ananassa) for the commercial and home garden markets. The most widely used source of the PF trait was originally introgressed from a wild Fragaria virginiana subsp. glauca accession collected in the Wasatc...

Tracking of wild allele introgressions in a peanut chromosome segment substitution line population

USDA-ARS?s Scientific Manuscript database

Cultivated peanut arose from the hybridization of the diploids Arachis duranensis (A genome progenitor) and Arachis ipaensis (B genome progenitor), followed by spontaneous chromosome doubling to yield the current allotetraploid state (AABB; 2n=4x=40). This genetic heritage, short period since polyp...

A discriminant analysis of introgression between Quercus prinus L. and Quercus alba L.

Treesearch

F. Thomas Ledig; Robert W. Wilson; John W. Duffield; Gerald Maxwell

1969-01-01

The natural hybrid between rock chestnut oak, Q. prinus, and white oak, Q. alba, was named Q. x saulii by Schneider (1904). The nomenclature used herein follows that of Little (1953). Q. x saulii is frequently identified throughout the area of sympatry of...

Introgression of Globodera resistance into the russet market class

USDA-ARS?s Scientific Manuscript database

Two species of potato cyst nematode (Globodera rostochiensis and G. pallida,) have been identified in the U.S. and are under quarantine regulations, with a third newly identified species (G. ellingtonae) not categorized as a quarantined pest. Management of G. rostochiensis in the state of New York ...

Potential of diazotrophic bacteria associated with sugarcane for energycane production

USDA-ARS?s Scientific Manuscript database

Crosses between sugarcane and wild species of Saccharum and other closely related genera are made to introgress new genes from the wild species into sugarcane. Characteristics of the progeny from these crosses may include increased biomass and the ability to be grown in a broader geographical range ...

From hybrid swarms to swarms of hybrids

USDA-ARS?s Scientific Manuscript database

The introgression of modern humans (Homo sapiens) with Neanderthals 40,000 YBP after a half-million years of separation, may have led to the best example of a hybrid swarm on earth. Modern trade and transportation in support of the human hybrids has continued to introduce additional species, genotyp...

Discernible but limited introgression has occurred where Trichinella nativa and the T6 genotype occur in sympatry

USDA-ARS?s Scientific Manuscript database

The genetic diversity within and among parasite populations provides clues to their evolutionary history. Here, we sought to determine whether mitochondrial and microsatellite variation could be used to evaluate the extent of differentiation, gene flow and historical reproductive isolation among the...

DEVELOPMENT OF MOLECULAR MONITORING TECHNOLOGIES TO MEASURE TRANSGENE FLOW AND INTROGRESSION IN CROP AND NON-CROP PLANT SPECIES

EPA Science Inventory

The Gene Flow Project at the US Environmental Protection Agency, Western Ecology Division is developing methodologies for ecological risk assessments of transgene flow using Agrostis and Brassica engineered with CP4 EPSPS genes that confer resistance to glyphosate herbicide. In ...

Identification of race-specific resistance in North American Vitis species limiting Erysiphe necator hyphal growth

USDA-ARS?s Scientific Manuscript database

While race-specific resistance against powdery mildews is well documented in small grains, race specificity against grapevine powdery mildew (Erysiphe necator) is undocumented. In the current study, two sources of powdery mildew resistance introgressed into Vitis vinifera were evaluated in the gree...

Introgression lines of Triticum aestivum x Aegilops tauschii: Agronomic and nutritional value

USDA-ARS?s Scientific Manuscript database

Eighty-five single homozygous substitution lines (SLs) of the Aegilops tauschii D genome in Chinese Spring (CS) hexaploid wheat (Triticum aestivum L.) genetic background were evaluated for agronomic, phenotypic and ionome profiles during three years of field experiments. An augmented design with a r...

Linkage Map Construction and QTL Analysis of Agronomic and Fiber Quality Traits in Cotton.

USDA-ARS?s Scientific Manuscript database

The superior fiber properties of Gossypium barbadense L. serve as a source of novel variation for improving fiber quality in Upland cotton (G. hirsutum L.), but introgression from G. barbadense has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an e...

MlAB10: a Triticum turgidum subsp. dicoccoides derived powdery mildew resistance gene identified in common wheat

USDA-ARS?s Scientific Manuscript database

Powdery mildew is an economically important disease in wheat growing areas with a cool maritime environment. Host genetic resistance is the most economical, consistent, and environmentally sound method of control. NC97BGTAB10 is a germplasm line containing powdery mildew resistance introgressed fr...

Israeli acute paralysis virus in Africanized honey bees in southeastern Brazilian Apiaries

USDA-ARS?s Scientific Manuscript database

Honey bee losses in Brazil have been observed over the past few years. These losses share somewhat similar symptoms with the syndrome known as Colony Collapse Disorder (CCD) in the USA. After more than a half century of introgression from Apis mellifera subsp. scutellata, Africanized honey bees have...

Patterns of genetic variation suggest introgression between zoysia species based on simple sequence markers (SSRs) and inflorescence traits

USDA-ARS?s Scientific Manuscript database

Zoysia spp. are warm-season turfgrasses widely used across the southern United States in residential lawns, commercial landscapes, and golf courses for their superior heat and drought tolerances. Information regarding the population structure and levels of admixture present within U.S. germplasm col...

A spontaneous segmental deletion from chromosome arm 3DL enhances Fusarium head blight resistance in wheat

USDA-ARS?s Scientific Manuscript database

Much effort has been directed at identifying sources of resistance to Fusarium head blight (FHB) in wheat. We sought to identify molecular markers for what we hypothesized was a new major FHB resistance locus originating from the wheat cultivar 'Freedom' and introgressed into the susceptible wheat c...

Introgression between divergent corn borer species in a region of sympatry: implications on the evolution and adaptation of pest arthropods

USDA-ARS?s Scientific Manuscript database

The Asian corn borer, Ostrinia furnacalis, and European corn borer, O. nubilalis (Lepidoptera: Crambidae) cause damage to cultivated maize in spatially distinct geographies, and have evolved divergent hydrocarbons as the basis of sexual communication. The Yili area of Xinjiang Province China repres...

Transmission of scab resistance to tetraploid potato via unilateral sexual polyploidization

USDA-ARS?s Scientific Manuscript database

Resistance to common scab continues to be a high priority trait for potato breeders. We have identified a source of resistance in the diploid wild potato relative Solanum chacoense and have introgressed it into cultivated potato by crossing it to a dihaploid. A clone generated by crossing two full-s...

Validation of yield enhancing QTLs from a low-yielding wild ancestor of rice

USDA-ARS?s Scientific Manuscript database

A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite U.S. variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTLs). Fifty B...

Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

USDA-ARS?s Scientific Manuscript database

Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a costeffective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chrom...

Identification of a solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL

USDA-ARS?s Scientific Manuscript database

A major resource for tomato quality improvement and gene discovery is the collection of introgression lines (ILs) of cultivated Solanum lycopersicum that contain different, defined chromosomal segments derived from the wild tomato relative, S. pennellii. Among these lines, IL4-4, in which the bottom...

Hybridization between ecotypes in a phenotypically and ecologically heterogeneous population of Iris savannarum (Iridaceae) in Florida.

USDA-ARS?s Scientific Manuscript database

Iris series Hexagonae is a small, monophyletic complex of 5 species and associated hybrid populations, popularly known as the “Louisiana irises.” The Hexagonae alliance of Iris have been recognized as a textbook case of introgressive hybridization based on numerous studies in Louisiana. We previou...

Registration of RMBUP-C4, a random mated population with Gossypium hirsutum L. alleles, introgresssed into Upland cotton germplasm

USDA-ARS?s Scientific Manuscript database

RMBUP-C4 (Random Mated Barbadense Upland Population Cycle 4) (Reg. No. GP_____: PI______) is a unique random mated germplasm population of Upland cotton (Gossypium hirsutum L.) which has introgression of G. barbadense L. alleles. This population involved five cycles of random mating beginning ...

Whole genome sequencing of a begomovirus-resistant tomato inbred reveals introgressions from wild Solanum species

USDA-ARS?s Scientific Manuscript database

The low cost of next generation sequencing (NGS) technology and the availability of a large number of well annotated plant genomes has made sequencing technology useful to breeding programs. With the published high quality tomato reference genome of the processing cultivar Heinz 1706, we can now uti...

Genetic analysis of kernel traits in maize-teosinte introgression populations

USDA-ARS?s Scientific Manuscript database

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is mos...

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome

USDA-ARS?s Scientific Manuscript database

The domestication of Asian rice (Oryza sativa) was a complex process and substantial ambiguity remains regarding the timing, number, and locations of domestication events. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests at least two independent domesticati...

Preserving rice quality: fine mapping and introgressing a fissure resistance locus

USDA-ARS?s Scientific Manuscript database

Rice (Oryza sativa L.) kernel fissuring is a major concern of both rice producers and millers. Fissures are small cracks in the rice kernels that increase the percentage of breakage among the kernels when they are transported and milled, which decreases the value of processed rice. This study employ...

Sources of stem rust resistance in wheat-alien introgression lines

USDA-ARS?s Scientific Manuscript database

Stem rust, caused by Puccinia graminis f. sp. tritici, is one of the most devastating diseases of wheat and the novel highly virulent race of TTKSK and its lineage are threatening wheat production worldwide. The objective of the study was to identify new sources of resistance in wheat-alien introgre...

Identification of rare recombinants leads to tightly linked markers for nematode resistance in peanut

USDA-ARS?s Scientific Manuscript database

Strong host resistance to root-knot nematode (RKN; Meloidogyne arenaria) introgressed from a wild diploid species to cultivated peanut was previously shown to be located on a large chromosomal region of linkage group A09. Little to no recombination in mapping populations has hindered fine mapping o...

Genetic effects of chromosomes 01, 04, and 18 from three tetraploid gossypium species in topcrosses with five elite cultivars

USDA-ARS?s Scientific Manuscript database

Chromosome substitution lines (CSL) have been developed for selected chromosomes from two tetraploid species of Gossypium and have been shown to be effective ways to target introgression of useful alleles from exotic tetraploid species into Upland cotton, G. hirsutum L. Genetic effects of chromosome...

Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands.

PubMed

Setoguchi, H; Watanabe, I

2000-06-01

Hybridization and introgression play important roles in plant evolution, and their occurrence on the oceanic islands provides good examples of plant speciation and diversification. Restriction fragment length polymorphisms (RFLPs) and trnL (UAA) 3'exon-trnF (GAA) intergenic spacer (IGS) sequences of chloroplast DNA (cpDNA), and the sequences of internal transcribed spacer (ITS) of nuclear ribosomal DNA were examined to investigate the occurrence of gene transfer in Ilex species on the Bonin Islands and the Ryukyu Islands in Japan. A gene phylogeny for the plastid genome is in agreement with the morphologically based taxonomy, whereas the nuclear genome phylogeny clusters putatively unrelated endemics both on the Bonin and the Ryukyu Islands. Intersectional hybridization and nuclear gene flow were independently observed in insular endemics of Ilex on both sets of islands without evidence of plastid introgression. Gene flow observed in these island systems can be explained by ecological features of insular endemics, i.e., limits of distribution range or sympatric distribution in a small land area.

Differential predation on tadpoles influences the potential effects of hybridization between Hyla cinerea and Hyla gratiosa

USGS Publications Warehouse

Gunzburger, M.S.

2005-01-01

Long-term effects of hybridization and introgression are influenced by performance of hybrids in habitats of parental species. The treefrogs Hyla cinerea and Hyla gratiosa, which typically breed in permanent and temporary habitats, respectively, have occasionally hybridized throughout the Southeastern United States. To predict in which of the parental habitats effects of hybridization might be strongest, I performed experiments to evaluate predation on tadpoles of H. cinerea, H. gratiosa, and F1 hybrids with predators typical of the breeding habitats of the parental species. Hybrid tadpoles had lower survival with sunfish than odonate naiad (dragonfly) predators and tended to increase hiding behavior in response to sunfish predation. Tadpoles of H. gratiosa also had higher survival with odonates than sunfish, but H. cinerea had similar survival with both predator types. These results suggest that hybrids are most likely to survive and return to breed in temporary habitats used by H. gratiosa. Thus, hybridization and introgression might be more likely to have adverse effects on populations of H. gratiosa than H. cinerea. Copyright 2005 Society for the Study of Amphibians and Reptiles.

Spread of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, Oncorhynchus mykiss

USGS Publications Warehouse

Hitt, Nathaniel P.; Frissell, Christopher A.; Muhlfeld, Clint C.; Fred W. Allendorf,

2003-01-01

We examined spatial and temporal patterns of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, O. mykiss, in streams of the Flathead River system in Montana, U.S.A. We detected hybridization in 24 of 42 sites sampled from 1998 to 2001. We found new Oncorhynchus mykiss introgression in seven of 11 sample populations that were determined to be nonhybridized in 1984. Patterns of spatial autocorrelation and linkage disequilibrium indicated that hybridization is spreading among sites and is advancing primarily via post-F1 hybrids. Although hybridized populations were distributed widely throughout the study area, the genetic contribution from O. mykiss decreased with increasing upstream distance from the Flathead River mainstem, suggesting that O. mykiss introgression is spreading in an upstream direction. The spread of hybridization may be constrained more by demographic than by environmental factors, given that (i) hybridized populations generally encompassed the range of environmental variability in nonhybridized populations, and (ii) hybridization status was more strongly associated with neighborhood statistics than measured environmental gradients.

Genome data from a sixteenth century pig illuminate modern breed relationships

PubMed Central

Ramírez, O; Burgos-Paz, W; Casas, E; Ballester, M; Bianco, E; Olalde, I; Santpere, G; Novella, V; Gut, M; Lalueza-Fox, C; Saña, M; Pérez-Enciso, M

2015-01-01

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds. PMID:25204303

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

PubMed Central

Hallsworth-Pepin, Kymberlie; Martin, John; Mitreva, Makedonka

2017-01-01

Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance. We identified variation linking candidate resistance genes to each drug class. Putative mechanisms included target site polymorphism, changes in likely regulatory regions and copy number variation in efflux transporters. This work elucidates the genetic architecture of multiple anthelmintic resistance in a parasitic nematode for the first time and establishes a framework for future studies of anthelmintic resistance in nematode parasites of humans. PMID:28644839

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

PubMed

Bray, T C; Hall, S J G; Bruford, M W

2014-02-01

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario. © 2013 Blackwell Verlag GmbH.

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

PubMed Central

Jinam, Timothy A.; Phipps, Maude E.; Aghakhanian, Farhang; Majumder, Partha P.; Datar, Francisco; Stoneking, Mark; Sawai, Hiromi; Nishida, Nao; Tokunaga, Katsushi; Kawamura, Shoji; Omoto, Keiichi

2017-01-01

Abstract Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the “First Sundaland People.” To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People. PMID:28854687

Spontaneous gene flow from rapeseed (Brassica napus) to wild Brassica oleracea

PubMed Central

Ford, Caroline S; Allainguillaume, Joël; Grilli-Chantler, Phil; Cuccato, Giulia; Allender, Charlotte J; Wilkinson, Mike J

2006-01-01

Research on the environmental risks of gene flow from genetically modified (GM) crops to wild relatives has traditionally emphasized recipients yielding most hybrids. For GM rapeseed (Brassica napus), interest has centred on the ‘frequently hybridizing’ Brassica rapa over relatives such as Brassica oleracea, where spontaneous hybrids are unreported in the wild. In two sites, where rapeseed and wild B. oleracea grow together, we used flow cytometry and crop-specific microsatellite markers to identify one triploid F1 hybrid, together with nine diploid and two near triploid introgressants. Given the newly discovered capacity for spontaneous introgression into B. oleracea, we then surveyed associated flora and fauna to evaluate the capacity of both recipients to harm cohabitant species with acknowledged conservational importance. Only B. oleracea occupies rich communities containing species afforded legislative protection; these include one rare micromoth species that feeds on B. oleracea and warrants further assessment. We conclude that increased attention should now focus on B. oleracea and similar species that yield few crop-hybrids, but possess scope to affect rare or endangered associates. PMID:17015343

Spontaneous gene flow from rapeseed (Brassica napus) to wild Brassica oleracea.

PubMed

Ford, Caroline S; Allainguillaume, Joël; Grilli-Chantler, Phil; Cuccato, Giulia; Allender, Charlotte J; Wilkinson, Mike J

2006-12-22

Research on the environmental risks of gene flow from genetically modified (GM) crops to wild relatives has traditionally emphasized recipients yielding most hybrids. For GM rapeseed (Brassica napus), interest has centred on the 'frequently hybridizing' Brassica rapa over relatives such as Brassica oleracea, where spontaneous hybrids are unreported in the wild. In two sites, where rapeseed and wild B. oleracea grow together, we used flow cytometry and crop-specific microsatellite markers to identify one triploid F1 hybrid, together with nine diploid and two near triploid introgressants. Given the newly discovered capacity for spontaneous introgression into B. oleracea, we then surveyed associated flora and fauna to evaluate the capacity of both recipients to harm cohabitant species with acknowledged conservational importance. Only B. oleracea occupies rich communities containing species afforded legislative protection; these include one rare micromoth species that feeds on B. oleracea and warrants further assessment. We conclude that increased attention should now focus on B. oleracea and similar species that yield few crop-hybrids, but possess scope to affect rare or endangered associates.

Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

PubMed Central

Pirault, Pauline; Danvy, Sophy; Verrier, Etienne; Leroy, Grégoire

2013-01-01

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges. PMID:23630596

Host subspecific viral strains in European house mice: Murine cytomegalovirus in the Eastern (Mus musculus musculus) and Western house mouse (Mus musculus domesticus).

PubMed

Čížková, Dagmar; Baird, Stuart J E; Těšíková, Jana; Voigt, Sebastian; Ľudovít, Ďureje; Piálek, Jaroslav; Goüy de Bellocq, Joëlle

2018-06-09

Murine cytomegalovirus (MCMV) has been reported from house mice (Mus musculus) worldwide, but only recently from Eastern house mice (M. m. musculus), of particular interest because they form a semi-permeable species barrier in Europe with Western house mice, M. m. domesticus. Here we report genome sequences of EastMCMV (from Eastern mice), and set these in the context of MCMV genomes from genus Mus hosts. We show EastMCMV and WestMCMV are genetically distinct. Phylogeny splitting analyses show a genome wide (94%) pattern consistent with no West-East introgression, the major exception (3.8%) being a genome-terminal region of duplicated genes involved in host immune system evasion. As expected from its function, this is a region of maintenance of ancestral polymorphism: The lack of clear splitting signal cannot be interpreted as evidence of introgression. The EastMCMV genome sequences reported here can therefore serve as a well-described resource for exploration of murid MCMV diversity. Copyright © 2018 Elsevier Inc. All rights reserved.

Paramutation-like features of multiple natural epialleles in tomato.

PubMed

Gouil, Quentin; Baulcombe, David C

2018-03-20

Freakish and rare or the tip of the iceberg? Both phrases have been used to refer to paramutation, an epigenetic drive that contravenes Mendel's first law of segregation. Although its underlying mechanisms are beginning to unravel, its understanding relies only on a few examples that may involve transgenes or artificially generated epialleles. By using DNA methylation of introgression lines as an indication of past paramutation, we reveal that the paramutation-like properties of the H06 locus in hybrids of Solanum lycopersicum and a range of tomato relatives and cultivars depend on the timing of sRNA production and conform to an RNA-directed mechanism. In addition, by scanning the methylomes of tomato introgression lines for shared regions of differential methylation that are absent in the S. lycopersicum parent, we identify thousands of candidate regions for paramutation-like behaviour. The methylation patterns for a subset of these regions segregate with non Mendelian ratios, consistent with secondary paramutation-like interactions to variable extents depending on the locus. Together these results demonstrate that paramutation-like epigenetic interactions are common for natural epialleles in tomato, but vary in timing and penetrance.

Conservation genetics of the endangered Shenandoah salamander (Plethodon shenandoah, Plethodontidae)

USGS Publications Warehouse

Carpenter, D.W.; Jung, R.E.; Sites, J.W.

2001-01-01

The Shenandoah salamander (Plethodon shenandoah) is restricted to three isolated talus outcrops in Shenandoah National Park, VA, USA and has one of the smallest ranges of any tetrapod vertebrate. This species was listed as endangered under the US Endangered Species Act in 1989 over concern that direct competition with the red-backed salamander (Plethodon cinereus), successional habitat changes, and human impacts may cause its decline and possible extinction. We address two issues herein: (1) whether extensive introgression (through long-term hybridization) is present between the two species and threatens the survival of P. shenandoah, and (2) the level of population structure within P. shenandoah. We provide evidence from mtDNA haplotypes that shows no genetic differentiation among the three isolates of P. shenandoah, suggesting that their fragmentation is a geologically recent event, and/or that the isolates are still connected by occasional gene flow. There is also no evidence for extensive introgression of alleles in either direction between P. cinereus and P. shenandoah, which suggests that P. shenandoah may not be in danger of being genetically swamped out through hybridization with P. cinereus.

Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes

PubMed Central

Sharma, Shivali; Upadhyaya, H. D.; Varshney, R. K.; Gowda, C. L. L.

2013-01-01

The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs. PMID:23970889

Molecular cytogenetic and morphological characterization of two wheat-barley translocation lines

PubMed Central

Ivanizs, László; Farkas, András; Linc, Gabriella; Molnár-Láng, Márta

2018-01-01

Abstract Barley chromosome 5H, carrying important QTLs for plant adaptation and tolerance to abiotic stresses, is extremely instable in the wheat genetic background and is eliminated in the early generations of wheat-barley crosses. A spontaneous wheat-barley 5HS-7DS.7DL translocation was previously obtained among the progenies of the Mv9kr1 x Igri hybrid. The present work reports on the transfer of the 5HS-7DS.7DL translocation into a modern wheat cultivar, Mv Bodri, in order to use it in the wheat breeding program. The comparison of the hybridization bands of DNA repeats HvT01, pTa71, (GAA)n and the barley centromere-specific (AGGGAG)n in Igri barley and the 5HS-7DS.7DL translocation, together with the visualization of the barley chromatin made it possible to determine the size of the introgressed barley segment, which was approximately 74% of the whole 5HS. Of the 29 newly developed PCR markers, whose source ESTs were selected from the Genome Zipper of barley chromosome 5H, 23 were mapped in the introgressed 1–0.26 FL 5HS bin, three were located in the missing C-0.26 FL region, while three markers were specific for 5HL. The translocation breakpoint was flanked by markers Hv7502 and Hv3949. A comparison of the parental wheat cultivars and the wheat-barley introgression lines indicated that the presence of the translocation improved tillering ability in the Mv9kr1 and Mv Bodri genetic background. The similar or better yield components under high- or low-input cultivation environments, respectively, indicated that the 5HS-7DS.7DL translocation had little or no negative effect on yield components, making it a promising genotype to improve wheat genetic diversity. These results promise to accelerate functional genomic studies on barley chromosome 5H and to support pre-breeding and breeding research on wheat. PMID:29889875

Quantifying rooting at depth in a wheat doubled haploid population with introgression from wild emmer.

PubMed

Clarke, Christina K; Gregory, Peter J; Lukac, Martin; Burridge, Amanda J; Allen, Alexandra M; Edwards, Keith J; Gooding, Mike J

2017-09-01

The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods. Roots of doubled haploid (DH) lines from a winter wheat ('Shamrock' × 'Shango') population were assessed using a seedling screen in moist paper rolls, in rhizotrons to the end of tillering, and in the field post-anthesis. A linkage map was produced using single nucleotide polymorphism markers to identify quantitative trait loci (QTLs) for rooting traits. Shamrock had greater root length density (RLD) at depth than Shango, in the field and within the rhizotrons. The DH population exhibited diversity for rooting traits within the three environments studied. QTLs were identified on chromosomes 5D, 6B and 7B, explaining variation in RLD post-anthesis in the field. Effects associated with the non-glaucous trait on RLD interacted significantly with depth in the field, and some of this interaction mapped to 2BS. The effect of genotype was strongly influenced by the method of root assessment, e.g. glaucousness expressed in the field was negatively associated with root length in the rhizotrons, but positively associated with length in the seedling screen. To our knowledge, this is the first study to identify QTLs for rooting at depth in field-grown wheat at mature growth stages. Within the population studied here, our results are consistent with the hypothesis that some of the variation in rooting is associated with recent introgression from wild emmer. The expression of genetic effects differed between the methods of root assessment. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company.

An introgression on wheat chromosome 4DL in RL6077 (Thatcher*6/PI 250413) confers adult plant resistance to stripe rust and leaf rust (Lr67).

PubMed

Hiebert, Colin W; Thomas, Julian B; McCallum, Brent D; Humphreys, D Gavin; DePauw, Ronald M; Hayden, Matthew J; Mago, Rohit; Schnippenkoetter, Wendelin; Spielmeyer, Wolfgang

2010-10-01

Adult plant resistance (APR) to leaf rust and stripe rust derived from the wheat (Triticum aestivum L.) line PI250413 was previously identified in RL6077 (=Thatcher*6/PI250413). The leaf rust resistance gene in RL6077 is phenotypically similar to Lr34 which is located on chromosome 7D. It was previously hypothesized that the gene in RL6077 could be Lr34 translocated to another chromosome. Hybrids between RL6077 and Thatcher and between RL6077 and 7DS and 7DL ditelocentric stocks were examined for first meiotic metaphase pairing. RL6077 formed chain quadrivalents and trivalents relative to Thatcher and Chinese Spring; however both 7D telocentrics paired only as heteromorphic bivalents and never with the multivalents. Thus, chromosome 7D is not involved in any translocation carried by RL6077. A genome-wide scan of SSR markers detected an introgression from chromosome 4D of PI250413 transferred to RL6077 through five cycles of backcrossing to Thatcher. Haplotype analysis of lines from crosses of Thatcher × RL6077 and RL6058 (Thatcher*6/PI58548) × RL6077 showed highly significant associations between introgressed markers (including SSR marker cfd71) and leaf rust resistance. In a separate RL6077-derived population, APR to stripe rust was also tightly linked with cfd71 on chromosome 4DL. An allele survey of linked SSR markers cfd71 and cfd23 on a set of 247 wheat lines from diverse origins indicated that these markers can be used to select for the donor segment in most wheat backgrounds. Comparison of RL6077 with Thatcher in field trials showed no effect of the APR gene on important agronomic or quality traits. Since no other known Lr genes exist on chromosome 4DL, the APR gene in RL6077 has been assigned the name Lr67.

Multilocus Detection of Wolf x Dog Hybridization in Italy, and Guidelines for Marker Selection

PubMed Central

Randi, Ettore; Hulva, Pavel; Fabbri, Elena; Galaverni, Marco; Galov, Ana; Kusak, Josip; Bigi, Daniele; Bolfíková, Barbora Černá; Smetanová, Milena; Caniglia, Romolo

2014-01-01

Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past generation backcrosses is always uncertain, and a larger number of ancestry-informative markers is needed. PMID:24466077

Multilocus detection of wolf x dog hybridization in italy, and guidelines for marker selection.

PubMed

Randi, Ettore; Hulva, Pavel; Fabbri, Elena; Galaverni, Marco; Galov, Ana; Kusak, Josip; Bigi, Daniele; Bolfíková, Barbora Černá; Smetanová, Milena; Caniglia, Romolo

2014-01-01

Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past generation backcrosses is always uncertain, and a larger number of ancestry-informative markers is needed.

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

PubMed Central

2014-01-01

Background Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy. Conclusions The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources. PMID:24739206

Chromosomal Location and Comparative Genomics Analysis of Powdery Mildew Resistance Gene Pm51 in a Putative Wheat-Thinopyrum ponticum Introgression Line

PubMed Central

Zhang, Xiaojun; Li, Xin; Guo, Huijuan; Gong, Wenping; Jia, Juqing; Qiao, Linyi; Ren, Yongkang; Yang, Zujun; Chang, Zhijian

2014-01-01

Powdery mildew (PM) is a very destructive disease of wheat (Triticum aestivum L.). Wheat-Thinopyrum ponticum introgression line CH7086 was shown to possess powdery mildew resistance possibly originating from Th. ponticum. Genomic in situ hybridization and molecular characterization of the alien introgression failed to identify alien chromatin. To study the genetics of resistance, CH7086 was crossed with susceptible genotypes. Segregation in F2 populations and F2:3 lines tested with Chinese Bgt race E09 under controlled conditions indicated that CH7086 carries a single dominant gene for powdery mildew resistance. Fourteen SSR and EST-PCR markers linked with the locus were identified. The genetic distances between the locus and the two flanking markers were 1.5 and 3.2 cM, respectively. Based on the locations of the markers by nullisomic-tetrasomic and deletion lines of ‘Chinese Spring’, the resistance gene was located in deletion bin 2BL-0.89-1.00. Conserved orthologous marker analysis indicated that the genomic region flanking the resistance gene has a high level of collinearity to that of rice chromosome 4 and Brachypodium chromosome 5. Both resistance specificities and tests of allelism suggested the resistance gene in CH7086 was different from previously reported powdery mildew resistance genes on 2BL, and the gene was provisionally designated PmCH86. Molecular analysis of PmCH86 compared with other genes for resistance to Bgt in the 2BL-0.89-1.00 region suggested that PmCH86 may be a new PM resistance gene, and it was therefore designated as Pm51. The closely linked flanking markers could be useful in exploiting this putative wheat-Thinopyrum translocation line for rapid transfer of Pm51 to wheat breeding programs. PMID:25415194

Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

PubMed Central

Dunn, Barbara; Paulish, Terry; Stanbery, Alison; Piotrowski, Jeff; Koniges, Gregory; Kroll, Evgueny; Louis, Edward J.; Liti, Gianni; Sherlock, Gavin; Rosenzweig, Frank

2013-01-01

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species. PMID:23555283

Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

USDA-ARS?s Scientific Manuscript database

Background: Potato (Solanum tuberosum) is the world’s most important vegetable crop and central to global food security. Cultivated potato is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Numerous wild potato species serve as a resource for introgress...

Can Pierce’s disease resistance introgressed into Vitis vinifera be translocated from a resistant rootstock to a susceptible scion?

USDA-ARS?s Scientific Manuscript database

The goal of this research is to evaluate the potential of a non-transgenic, PD-resistant Vitis vinifera selection used as an experimental rootstock to confer systemic resistance to PD-susceptible V. vinifera scions. Source of PD-susceptible plant material was the wine grape variety ‘Chardonnay’, kno...

Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed wild steelhead trout using a 57K SNP array

USDA-ARS?s Scientific Manuscript database

Natural-origin steelhead in the Pacific Northwest USA are threatened by a number of factors including habitat destruction, disease, decline in marine survival and a potential erosion of genetic viability due to introgression from hatchery strains. The major goal of this study was to use a recently ...

Methodology for creating alloplasmic soybean lines by using Glycine tomentella as a maternal parent

USDA-ARS?s Scientific Manuscript database

Soybean breeders have not exploited the diversity of the 26 wild perennial species of the subgenus Glycine Willd. that are distantly related to soybean [G. max (L.) Merr.]. The objectives of this study were to introgress cytoplasmic and genetic diversity from G. tomentella PI 441001 (2n=78) into the...

Gene expression profiling describes the genetic regulation of Meloidogyne arenaria resistance in Arachis hypogaea and reveals a candidate gene for resistance

USDA-ARS?s Scientific Manuscript database

Resistance to root-knot nematode was introgressed into cultivated peanut Arachis hypogaea from a wild peanut relative, A. cardenasii and previously mapped to chromosome A09. The highly resistant recombinant inbred RIL 46 and moderately resistant RIL 48 were selected from a population with cv. Gregor...

Marker-assisted NIL development of an Oryza sativa x Oryza rufipogon cross using SSRs, InDels and SNPs

USDA-ARS?s Scientific Manuscript database

A set of near isogenic lines (NILs) with introgressions from O. rufipogon (IRGC 105491) in the genetic background of an elite US variety, cv Jefferson, were developed to confirm the performance of six yield-enhancing QTLs identified in a previous study. Approximately 200 SSRs were used to evaluate ...

Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

USDA-ARS?s Scientific Manuscript database

In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 elements in whole, unmilled rice (Oryza sativa L.) grain were identified. Two rice mapping populations, the ‘Lemont’ x ‘TeQing’ recombinant inbred lines (LT-RILs), and the TeQing-into-Lemont backcross introgression lin...

Introgression of a new stem rust resistance gene from Aegilops markgrafii into wheat

USDA-ARS?s Scientific Manuscript database

In a prior study, we reported that an Alcedo/Aegilops markgrafii disomic addition line, AIII(D) (2n=44), was resistant to three races of the Ug99 lineage and five North American races of stem rust pathogen in wheat and the resistance originated from the alien chromosome. In this study, our objectiv...

Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams

Treesearch

Kevin S. McKelvey; Michael K. Young; Taylor M. Wilcox; Daniel M. Bingham; Kristine L. Pilgrim; Michael K. Schwartz

2016-01-01

Introgressive hybridization between native and introduced species is a growing conservation concern. For native cutthroat trout and introduced rainbow trout in western North America, this process is thought to lead to the formation of hybrid swarms and the loss of monophyletic evolutionary lineages. Previous studies of this phenomenon, however, indicated that...

Targeted introgression of stem rust Ug99 resistance from wheatgrasses into pasta and bread wheat

USDA-ARS?s Scientific Manuscript database

In the past 50 years, a number of stem rust resistance (Sr) genes have been transferred from several wheat-related grasses into durum (i.e. pasta) and bread wheat through chromosome translocations and additions. To utilize these genes for controlling the Ug99 races of the stem rust pathogen, we ini...

Genetic effects of nine Gossypium barbadense L. chromosome substitution lines in topcrosses with five elite Upland cotton G. hirsutum L. cultivars

USDA-ARS?s Scientific Manuscript database

Crosses between Gossypium barbadense L. and Upland (G. hirsutum L.) have produced limited success in introgressing fiber quality genes into Upland cotton. Chrosome substitution lines (CSL) have chromosomes or arms from G. barbadense, line 3-79, substituted for the corresponding chromosome or arm in ...

Can Pierce’s disease resistance introgressed into Vitis vinifera be translocated from a resistant rootstock to a susceptible scion?

USDA-ARS?s Scientific Manuscript database

The goal of this research is to evaluate the potential of a non-transgenic, PD resistant Vitis vinifera selection used as an experimental rootstock to confer systemic resistance to PD susceptible V. vinifera scions. Source of PD susceptible plant material will be the wine grape variety ‘Chardonnay’,...

Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.)

USDA-ARS?s Scientific Manuscript database

Rice (Oryza sativa L.) kernel fissuring increases breakage during milling and decreases the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to...

Genotyping-by-sequencing to re-map QTL for type II Fusarium head blight and leaf rust resistance in a wheat-tall wheatgrass introgression recombinant inbred population

USDA-ARS?s Scientific Manuscript database

Fusarium graminaerum (Fusarium head blight; FHB) and Puccinia recondita Roberge ex Desmaz. f. sp. tritici Eriks. & E. Henn (leaf rust; LR) are two major fungal pathogens threatening the wheat crop; consequently identifying resistance genes from various sources is always of importance to wheat breede...

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Treesearch

Kasey K. Pham; Andrew L. Hipp; Paul S. Manos; Richard C. Cronn

2017-01-01

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect...

Introgression of leginsulin, a cysteine-rich protein, and high-protein trait from an Asian soybean plant introduction genotype into a North American experimental soybean line

USDA-ARS?s Scientific Manuscript database

Soybean is an important protein source for both humans and animals. However, soybean proteins are relatively poor in the sulfur-containing amino acids, cysteine and methionine. Improving the content of endogenous proteins rich in sulfur containing amino acids could enhance the nutritive value of soy...

Can Pierce’s disease PdR1 resistance introgressed into Vitis vinifera be translocated from a resistant rootstock to a susceptible scion?

USDA-ARS?s Scientific Manuscript database

The goal of this research is to evaluate the potential of a non-transgenic, PD resistant Vitis vinifera selection used as an experimental rootstock to confer systemic resistance to PD susceptible V. vinifera scions. Source of PD susceptible plant material was the wine grape variety ‘Chardonnay’, kno...

Targeted discovery of single-nucleotide polymorphisms in an unmarked wheat chromosomal region containing the Hessian fly resistance gene H33

USDA-ARS?s Scientific Manuscript database

The highly effective Hessian fly-resistance gene, H33, was introgressed from durum wheat into common wheat and genetically mapped to chromosome 3AS, in previous research. However, H33 located to a region that is well-known to be devoid of molecular markers, with the closest flanking simple sequence ...

Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl19 in confection sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC1F2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed...

Genotyping-by-sequencing uncovers the introgression alien segments associated with Sclerotinia basal stalk rot resistance from wild species—I. Helianthus argophyllus and H. petiolaris

USDA-ARS?s Scientific Manuscript database

Basal stalk rot (BSR), caused by Sclerotinia Sclerotiorum, is a devastating disease in sunflower worldwide. The progress of breeding for Sclerotinia BSR resistance has been hampered due to the lack of effective sources of resistance for cultivated sunflower. Our objective was to transfer BSR resista...

Genetics and mapping of a novel downy mildew resistance gene, Pl18, introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

Sunflower downy mildew is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflowe...

Quantitative trait locus mapping of drought and salt tolerance in as introgressed recombinant inbred line population of upland cotton under the greenhouse and feild conditions

USDA-ARS?s Scientific Manuscript database

Drought and salt tolerances are complex traits and controlled by multiple genes, environmental factors and their interactions. Drought and salt stresses can result in more than 50% yield loss in Upland cotton (Gossypium hirsutum L.). G. barbadense L. (the source of Pima cotton) carries desirable tra...

California golden trout and climate change: Is their stream habitat vulnerable to climate warming?

Treesearch

Kathleen R. Matthews

2010-01-01

The California golden trout (CGT) Oncorhynchus mykiss aguabonita is one of the few native high-elevation fish in the Sierra Nevada. They are already in trouble because of exotic trout, genetic introgression, and degraded habitat, and now face further stress from climate warming. Their native habitat on the Kern Plateau meadows mostly in the Golden...

Effectiveness of the Ty-3 Introgression for Conferring Resistance in Recombinant Inbred Lines of Tomato to Bipartite Begomoviruses in Guatemala

USDA-ARS?s Scientific Manuscript database

Management of begomovirus-incited diseases on tomatoes in Guatemala continues to be a challenge and there continues to be a need to better understand the genetics of resistance to begomoviruses. In this study, the resistant line, Gh13, was crossed with the susceptible line, HUJ-VF, that lacked the ...

Hybridization and introgression between the exotic Siberian elm, Ulmus pumila, and the native Field elm, U. minor, in Italy

USDA-ARS?s Scientific Manuscript database

In response to the first Dutch elm disease (DED) pandemic, Siberian elm, Ulmus pumila, was planted to replace the native elm, U. minor, in Italy. The potential for hybridization between these two species is high and repeated hybridization could result in the genetic swamping of the native species an...

Frequent fire protects shortleaf pine (Pinus echinata) from introgression by loblolly pine (P. taeda).

Treesearch

John F Stewart; Rodney E Will; Kevin M Robertson; Dana Nelson

2014-01-01

Across much of the globe, fire is a major disturbance agent of forest and grassland communities. The removal of fire from previously fire-maintained ecosystems, which has occurred in many areas, changes species composition, favoring later less fire tolerant species over fire-adapted ones. A recent measured increase in the rate of hybridization between the fire-adapted...

Genetic introgression of ethylene-suppressed, long shelf-life transgenic tomatoes with higher-polyamines trait overcomes many unintended effects due to reduced ethylene on metabolome

USDA-ARS?s Scientific Manuscript database

Ethylene regulates a myriad physiological and biochemical processes in ripening fruits and is accepted as the ripening hormone for the climacteric fruits. However, its effects on metabolome and resulting fruit quality are not yet fully understood, particularly when some of the ripening-associated bi...

Rainbow trout (Oncorhynchus mykiss) invasion and the spread of hybridization with native westslope cutthroat trout (Oncorhynchus clarkii lewisi)

USGS Publications Warehouse

Boyer, M.C.; Muhlfeld, C.C.; Allendorf, F.W.

2008-01-01

We analyzed 13 microsatellite loci to estimate gene flow among westslope cutthroat trout, Oncorhynchus clarkii lewisi, populations and determine the invasion pattern of hybrids between native O. c. lewisi and introduced rainbow trout, Oncorhynchus mykiss, in streams of the upper Flathead River system, Montana (USA) and British Columbia (Canada). Fourteen of 31 sites lacked evidence of O. mykiss introgression, and gene flow among these nonhybridized O. c. lewisi populations was low, as indicated by significant allele frequency divergence among populations (?ST = 0.076, ?ST = 0.094, P < 0.001). Among hybridized sites, O. mykiss admixture declined with upstream distance from a site containing a hybrid swarm with a predominant (92%) O. mykiss genetic contribution. The spatial distribution of hybrid genotypes at seven diagnostic microsatellite loci revealed that O. mykiss invasion is facilitated by both long distance dispersal from this hybrid swarm and stepping-stone dispersal between hybridized populations. This study provides an example of how increased straying rates in the invasive taxon can contribute to the spread of extinction by hybridization and suggests that eradicating sources of introgression may be a useful conservation strategy for protecting species threatened with genomic extinction. ?? 2008 NRC.

Hybridization following population collapse in a critically endangered antelope

PubMed Central

Vaz Pinto, Pedro; Beja, Pedro; Ferrand, Nuno; Godinho, Raquel

2016-01-01

Population declines may promote interspecific hybridization due to the shortage of conspecific mates (Hubb’s ‘desperation’ hypothesis), thus greatly increasing the risk of species extinction. Yet, confirming this process in the wild has proved elusive. Here we combine camera-trapping and molecular surveys over seven years to document demographic processes associated with introgressive hybridization between the critically endangered giant sable antelope (Hippotragus niger variani), and the naturally sympatric roan antelope (H. equinus). Hybrids with intermediate phenotypes, including backcrosses with roan, were confirmed in one of the two remnant giant sable populations. Hybridization followed population depletion of both species due to severe wartime poaching. In the absence of mature sable males, a mixed herd of sable females and hybrids formed and grew progressively over time. To prevent further hybridization and recover this small population, all sable females were confined to a large enclosure, to which sables from the other remnant population were translocated. Given the large scale declines in many animal populations, hybridization and introgression associated with the scarcity of conspecific mates may be an increasing cause of biodiversity conservation concern. In these circumstances, the early detection of hybrids should be a priority in the conservation management of small populations. PMID:26732144

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture.

PubMed

Jinam, Timothy A; Phipps, Maude E; Aghakhanian, Farhang; Majumder, Partha P; Datar, Francisco; Stoneking, Mark; Sawai, Hiromi; Nishida, Nao; Tokunaga, Katsushi; Kawamura, Shoji; Omoto, Keiichi; Saitou, Naruya

2017-08-01

Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Simulating evolutionary responses of an introgressed insect resistance trait for ecological effect assessment of transgene flow: a model for supporting informed decision-making in environmental risk assessment

PubMed Central

Meier, Matthias S; Trtikova, Miluse; Suter, Matthias; Edwards, Peter J; Hilbeck, Angelika

2013-01-01

Predicting outcomes of transgene flow from arable crops requires a system perspective that considers ecological and evolutionary processes within a landscape context. In Europe, the arable weed Raphanus raphanistrum is a potential hybridization partner of oilseed rape, and the two species are ecologically linked through the common herbivores Meligethes spp. Observations in Switzerland show that high densities of Meligethes beetles maintained by oilseed rape crops can lead to considerable damage on R. raphanistrum. We asked how increased insect resistance in R. raphanistrum – as might be acquired through introgression from transgenic oilseed rape – would affect seed production under natural herbivore pressure. In simulation experiments, plants protected against Meligethes beetles produced about twice as many seeds as unprotected plants. All stages in the development of reproductive structures from buds to pods were negatively affected by the herbivore, with the transition from buds to flowers being the most vulnerable. We conclude that resistance to Meligethes beetles could confer a considerable selective advantage upon R. raphanistrum in regions where oilseed rape is widely grown. PMID:23467842

Genetic and demographic implications of aquaculture in white sturgeon (Acipenser transmontanus)conservation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jager, Yetta

2005-01-01

This study uses a genetic individual-based model of white sturgeon (Acipenser transmontanus) populations in a river to examine the genetic and demographic trade-offs associated with operating a conservation hatchery. Simulation experiments evaluated three management practices: (i) setting quotas to equalize family contributions in an effort to prevent genetic swamping, (ii) an adaptive management scheme that interrupts stocking when introgression exceeds a specified threshold, and (iii) alternative broodstock selection strategies that influence domestication. The first set of simulations, designed to evaluate equalizing the genetic contribution of families, did not show the genetic benefits expected. The second set of simulations showed thatmore » simulated adaptive management was not successful in controlling introgression over the long term, especially with uncertain feedback. The third set of simulations compared the effects of three alternative broodstock selection strategies on domestication for hypothetical traits controlling early density-dependent survival. Simulated aquaculture selected for a density-tolerant phenotype when broodstock were taken from a genetically connected population. Using broodstock from an isolated population (i.e., above an upstream barrier or in a different watershed) was more effective at preventing domestication than using wild broodstock from a connected population.« less

Interspecific Introgression in Cetaceans: DNA Markers Reveal Post-F1 Status of a Pilot Whale

PubMed Central

Miralles, Laura; Lens, Santiago; Rodríguez-Folgar, Antonio; Carrillo, Manuel; Martín, Vidal; Mikkelsen, Bjarni; Garcia-Vazquez, Eva

2013-01-01

Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus) are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region) and eight nuclear loci (microsatellites) as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain), one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals. PMID:23990883

An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family.

PubMed Central

Liu, Zhanjiang; Karsi, Attila; Li, Ping; Cao, Dongfeng; Dunham, R

2003-01-01

Catfish is the major aquaculture species in the United States. The hybrid catfish produced by crossing channel catfish females with blue catfish males exhibit a number of desirable production traits, but their mass production has been difficult. To introduce desirable genes from blue catfish into channel catfish through introgression, a genetic linkage map is helpful. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP). A total of 607 AFLP markers were analyzed using 65 primer combinations and an interspecific backcross resource family. A total of 418 AFLP markers were assigned to 44 linkage groups. Among the remaining 189 markers, 101 were not used because of significant segregation distortion, 29 were unlinked, and 59 were eliminated because they span very large distances. The 418 AFLP markers covered 1593 cM Kosambi. The AFLP markers showed a high level of clustering that appears to be related to certain primer combinations. This linkage map will serve as the basis for mapping a greater number of markers to provide a map with high enough resolution for it to be useful for selective breeding programs using introgression. PMID:14573480

Genetic basis of hybrid male sterility among three closely related species of Drosophila.

PubMed

Mishra, Paras Kumar; Singh, B N

2005-05-01

The genetic basis of hybrid male sterility among three closely related species, Drosophila bipectinata, D. parabipectinata and D. malerkotliana has been investigated by using backcross analysis methods. The role of Y chromosome, major hybrid sterility (MHS) genes (genetic factors) and cytoplasm (non-genetic factor) have been studied in the hybrids of these three species. In the species pair, bipectinata--parabipectinata, Y chromosome introgression of parabipectinata in the genomic background of bipectinata and the reciprocal Y chromosome introgression were unsuccessful as all males in second backcross generation were sterile. Neither MHS genes nor cytoplasm was found important for sterility. This suggests the involvement of X-Y, X-autosomes or polygenic interactions in hybrid male sterility. In bipectinata--malerkotliana and parabipectinata--malerkotliana species pairs, Y chromosome substitution in reciprocal crosses did not affect male fertility. Backcross analyses also show no involvement of MHS genes or cytoplasm in hybrid male sterility in these two species pairs. Therefore, X- autosome interaction or polygenic interaction is supposed to be involved in hybrid male sterility in these two species pairs. These findings also provide evidence that even in closely related species, genetic interactions underlying hybrid male sterility may vary.

Genetic architecture of autosome-mediated hybrid male sterility in Drosophila.

PubMed

Marín, I

1996-04-01

Several estimators have been developed for assessing the number of sterility factors in a chromosome based on the sizes of fertile and sterile introgressed fragments. Assuming that two factors are required for producing sterility, simulations show that one of these, twice the inverse of the relative size of the largest fertile fragment, provides good average approximations when as few as five fertile fragments are analyzed. The estimators have been used for deducing the number of factors from previous data on several pairs of species. A particular result contrasts with the authors' interpretations: instead of the high number of sterility factors suggested, only a few per autosome are estimated in both reciprocal crosses involving Drosophila buzzatii and D. koepferae. It has been possible to map these factors, between three and six per chromosome, in the autosomes 3 and 4 of these species. Out of 203 introgressions of different fragments or combinations of fragments, the outcome of at least 192 is explained by the mapped zones. These results suggest that autosome-mediated sterility in the male hybrids of these species is mediated by a few epistatic factors, similarly to X-mediated sterility in the hybrids of other Drosophila species.

Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome.

PubMed

Tao, Yun; Zeng, Zhao-Bang; Li, Jian; Hartl, Daniel L; Laurie, Cathy C

2003-08-01

Hybrid male sterility (HMS) is a rapidly evolving mechanism of reproductive isolation in Drosophila. Here we report a genetic analysis of HMS in third-chromosome segments of Drosophila mauritiana that were introgressed into a D. simulans background. Qualitative genetic mapping was used to localize 10 loci on 3R and a quantitative trait locus (QTL) procedure (multiple-interval mapping) was used to identify 19 loci on the entire chromosome. These genetic incompatibilities often show dominance and complex patterns of epistasis. Most of the HMS loci have relatively small effects and generally at least two or three of them are required to produce complete sterility. Only one small region of the third chromosome of D. mauritiana by itself causes a high level of infertility when introgressed into D. simulans. By comparison with previous studies of the X chromosome, we infer that HMS loci are only approximately 40% as dense on this autosome as they are on the X chromosome. These results are consistent with the gradual evolution of hybrid incompatibilities as a by-product of genetic divergence in allopatric populations.

Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome.

PubMed Central

Tao, Yun; Zeng, Zhao-Bang; Li, Jian; Hartl, Daniel L; Laurie, Cathy C

2003-01-01

Hybrid male sterility (HMS) is a rapidly evolving mechanism of reproductive isolation in Drosophila. Here we report a genetic analysis of HMS in third-chromosome segments of Drosophila mauritiana that were introgressed into a D. simulans background. Qualitative genetic mapping was used to localize 10 loci on 3R and a quantitative trait locus (QTL) procedure (multiple-interval mapping) was used to identify 19 loci on the entire chromosome. These genetic incompatibilities often show dominance and complex patterns of epistasis. Most of the HMS loci have relatively small effects and generally at least two or three of them are required to produce complete sterility. Only one small region of the third chromosome of D. mauritiana by itself causes a high level of infertility when introgressed into D. simulans. By comparison with previous studies of the X chromosome, we infer that HMS loci are only approximately 40% as dense on this autosome as they are on the X chromosome. These results are consistent with the gradual evolution of hybrid incompatibilities as a by-product of genetic divergence in allopatric populations. PMID:12930748

Early detection of nonnative alleles in fish populations: When sample size actually matters

USGS Publications Warehouse

Croce, Patrick Della; Poole, Geoffrey C.; Payne, Robert A.; Gresswell, Bob

2017-01-01

Reliable detection of nonnative alleles is crucial for the conservation of sensitive native fish populations at risk of introgression. Typically, nonnative alleles in a population are detected through the analysis of genetic markers in a sample of individuals. Here we show that common assumptions associated with such analyses yield substantial overestimates of the likelihood of detecting nonnative alleles. We present a revised equation to estimate the likelihood of detecting nonnative alleles in a population with a given level of admixture. The new equation incorporates the effects of the genotypic structure of the sampled population and shows that conventional methods overestimate the likelihood of detection, especially when nonnative or F-1 hybrid individuals are present. Under such circumstances—which are typical of early stages of introgression and therefore most important for conservation efforts—our results show that improved detection of nonnative alleles arises primarily from increasing the number of individuals sampled rather than increasing the number of genetic markers analyzed. Using the revised equation, we describe a new approach to determining the number of individuals to sample and the number of diagnostic markers to analyze when attempting to monitor the arrival of nonnative alleles in native populations.

Identification of novel mouse genes conferring posthypoxic pauses

PubMed Central

Gillombardo, C. Barton; Yamauchi, Motoo; Adams, Mark D.; Dostal, Jesse; Chai, Sam; Moore, Michael W.; Donovan, Lucas M.; Han, Fang

2012-01-01

Although central to the susceptibility of adult diseases characterized by abnormal rhythmogenesis, characterizing the genes involved is a challenge. We took advantage of the C57BL/6J (B6) trait of hypoxia-induced periodic breathing and its absence in the C57BL/6J-Chr 1A/J/NaJ chromosome substitution strain to test the feasibility of gene discovery for this abnormality. Beginning with a genetic and phenotypic analysis of an intercross study between these strains, we discovered three quantitative trait loci (QTLs) on mouse chromosome 1, with phenotypic effects. Fine-mapping reduced the genomic intervals and gene content, and the introgression of one QTL region back onto the C57BL/6J-Chr 1A/J/NaJ restored the trait. mRNA expression of non-synonymous genes in the introgressed region in the medulla and pons found evidence for differential expression of three genes, the highest of which was apolipoprotein A2, a lipase regulator; the apo a2 peptide fragment (THEQLTPLVR), highly expressed in the liver, was expressed in low amounts in the medulla but did not correlate with trait expression. This work directly demonstrates the impact of elements on mouse chromosome 1 in respiratory rhythmogenesis. PMID:22539170

Integrative Taxonomy of Southeast Asian Snail-Eating Turtles (Geoemydidae: Malayemys) Reveals a New Species and Mitochondrial Introgression

PubMed Central

Ihlow, Flora; Vamberger, Melita; Flecks, Morris; Hartmann, Timo; Cota, Michael; Makchai, Sunchai; Meewattana, Pratheep; Dawson, Jeffrey E.; Kheng, Long; Rödder, Dennis; Fritz, Uwe

2016-01-01

Based on an integrative taxonomic approach, we examine the differentiation of Southeast Asian snail-eating turtles using information from 1863 bp of mitochondrial DNA, 12 microsatellite loci, morphology and a correlative species distribution model. Our analyses reveal three genetically distinct groups with limited mitochondrial introgression in one group. All three groups exhibit distinct nuclear gene pools and distinct morphology. Two of these groups correspond to the previously recognized species Malayemys macrocephala (Chao Phraya Basin) and M. subtrijuga (Lower Mekong Basin). The third and genetically most divergent group from the Khorat Basin represents a previously unrecognized species, which is described herein. Although Malayemys are extensively traded and used for religious release, only few studied turtles appear to be translocated by humans. Historic fluctuations in potential distributions were assessed using species distribution models (SDMs). The Last Glacial Maximum (LGM) projection of the predictive SDMs suggests two distinct glacial distribution ranges, implying that the divergence of M. macrocephala and M. subtrijuga occurred in allopatry and was triggered by Pleistocene climate fluctuations. Only the projection derived from the global circulation model MIROC reveals a distinct third glacial distribution range for the newly discovered Malayemys species. PMID:27050302

Introgression of wild alleles into the tetraploid peanut crop to improve water use efficiency, earliness and yield.

PubMed

Dutra, Wellison F; Guerra, Yrlânia L; Ramos, Jean P C; Fernandes, Pedro D; Silva, Carliane R C; Bertioli, David J; Leal-Bertioli, Soraya C M; Santos, Roseane C

2018-01-01

The introduction of genes from wild species is a practice little adopted by breeders for the improvement of commercial crops, although it represents an excellent opportunity to enrich the genetic basis and create new cultivars. In peanut, this practice is being increasingly adopted. In this study we present results of introgression of wild alleles from the wild species Arachis duranensis and A. batizocoi improving photosynthetic traits and yield in a set of lines derived from the cross of an induced allotetraploid and cultivated peanut with selection under water stress. The assays were carried out in greenhouse and field focusing on physiological and agronomic traits. A multivariate model (UPGMA) was adopted in order to classify drought tolerant lines. Several lines showed improved levels of tolerance, with values similar to or greater than the tolerant control. Two BC1F6 lines (53 P4 and 96 P9) were highlighted for good drought-related traits, earliness and pod yield, having better phenotypic profile to the drought tolerant elite commercial cultivar BR1. These lines are good candidates for the creation of peanut cultivars suitable for production in semiarid environments.

Biological invasions, climate change and genomics

PubMed Central

Chown, Steven L; Hodgins, Kathryn A; Griffin, Philippa C; Oakeshott, John G; Byrne, Margaret; Hoffmann, Ary A

2015-01-01

The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species’ geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved. PMID:25667601

Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution.

PubMed

Schwarzer, Julia; Swartz, Ernst Roelof; Vreven, Emmanuel; Snoeks, Jos; Cotterill, Fenton Peter David; Misof, Bernhard; Schliewen, Ulrich Kurt

2012-11-07

The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.

POPULATION GENETICS OF THE MOSQUITO CULEX PIPIENS PALLENS REVEALS SEX-LINKED ASYMMETRIC INTROGRESSION BY CULEX QUINQUEFASCIATUS

PubMed Central

Fonseca, Dina M.; Smith, Julie L.; Kim, Heung-Chol; Mogi, Motoyoshi

2009-01-01

The Culex pipiens complex in Asia includes a temperate subspecies, Culex pipiens pallens, of uncertain taxonomic status. The shape of the male genitalia suggests it is a hybrid between Cx. pipiens and Cx. quinquefasciatus. We studied populations of Cx. p. pallens in Japan, Korea, and China and compared them to local populations of Cx. quinquefasciatus and Cx. p. pipiens. We examined variation in a nuclear intron in the acetylcholinesterase-2 gene [ACE] and eight microsatellite loci. We found a distinct microsatellite signature for Cx. p. pallens indicating restricted gene flow between Eastern and Western populations of Cx. pipiens, supporting the existence of two subspecies. Furthermore, a multilocus genotype analysis revealed current hybridization between Cx. p. pallens and Cx. quinquefasciatus in southern Japan, Republic of Korea, and China but not in Hokkaido, in northern Japan. Surprisingly, however, we found that the sex-linked ACE locus in chromosome I has introgressed asymmetrically through the males such that all male Cx. p. pallens have a copy of the Cx. quinquefasciatus ACE locus. This result highlights some of the potential consequences of hybridization between local and introduced species to disease transmission worldwide. PMID:19584006

Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley

PubMed Central

Wang, Yonggang; Ren, Xifeng; Sun, Dongfa; Sun, Genlou

2016-01-01

The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm. PMID:27786300

Hybridization rapidly reduces fitness of a native trout in the wild

USGS Publications Warehouse

Muhlfeld, C.C.; Kalinowski, S.T.; McMahon, T.E.; Taper, M.L.; Painter, S.; Leary, R.F.; Allendorf, F.W.

2009-01-01

Human-mediated hybridization is a leading cause of biodiversity loss worldwide. How hybridization affects fitness and what level of hybridization is permissible pose difficult conservation questions with little empirical information to guide policy and management decisions. This is particularly true for salmonids, where widespread introgression among non-native and native taxa has often created hybrid swarms over extensive geographical areas resulting in genomic extinction. Here, we used parentage analysis with multilocus microsatellite markers to measure how varying levels of genetic introgression with non-native rainbow trout (Oncorhynchus mykiss) affect reproductive success (number of offspring per adult) of native westslope cutthroat trout (Oncorhynchus clarkii lewisi) in the wild. Small amounts of hybridization markedly reduced fitness of male and female trout, with reproductive success sharply declining by approximately 50 per cent, with only 20 per cent admixture. Despite apparent fitness costs, our data suggest that hybridization may spread due to relatively high reproductive success of first-generation hybrids and high reproductive success of a few males with high levels of admixture. This outbreeding depression suggests that even low levels of admixture may have negative effects on fitness in the wild and that policies protecting hybridized populations may need reconsideration. ?? 2009 The Royal Society.

Marker-free transgenic (MFT) near-isogenic introgression lines (NIILs) of 'golden' indica rice (cv. IR64) with accumulation of provitamin A in the endosperm tissue.

PubMed

Baisakh, Niranjan; Rehana, Sayda; Rai, Mayank; Oliva, Norman; Tan, Jing; Mackill, David J; Khush, Gurdev S; Datta, Karabi; Datta, Swapan K

2006-07-01

We have developed near-isogenic introgression lines (NIILs) of an elite indica rice cultivar (IR64) with the genes for beta-carotene biosynthesis from dihaploid (DH) derivatives of golden japonica rice (cv. T309). A careful analysis of the DH lines indicated the integration of the genes of interest [phytoene synthase (psy) and phytoene desaturase (crtI)] and the selectable marker gene (hygromycin phosphotransferase, hph) in two unlinked loci. During subsequent crossing, progenies could be obtained carrying only the locus with psy and crtI, which was segregated independently from the locus containing the hph gene during meiotic segregation. The NIILs (BC(2)F(2)) showed maximum similarity with the recurrent parent cultivar IR64. Further, progenies of two NIILs were devoid of any fragments beyond the left or right border, including the chloramphenicol acetyltransferase (cat) antibiotic resistance gene of the transformation vector. Spectrophotometric readings showed the accumulation of up to 1.06 microg total carotenoids, including beta-carotene, in 1 g of the endosperm. The accumulation of beta-carotene was also evident from the clearly visible yellow colour of the polished seeds.

The threat of increasing hybridization of an endangered plant species, Purshia subintegra, in the Verde Valley, Arizona

Treesearch

Joanne E. Baggs; Joyce Maschinski

2001-01-01

The existence of the endangered shrub Purshia subintegra may be threatened by hybridization with the more common P. stansburiana. In the Verde Valley, the range of the rare P. subintegra overlaps with the range of P. stansburiana, allowing introgression to occur. Although P. subintegra and P. stansburiana have many distinguishing characteristics, there are plants in...

Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage".

PubMed

Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

2013-03-29

Based on nuclear and mitochondrial DNA, Hailer et al. (Reports, 20 April 2012, p. 344) suggested early divergence of polar bears from a common ancestor with brown bears and subsequent introgression. Our population genetic analysis that traces each of the genealogies in the independent nuclear loci does not support the evolutionary model proposed by the authors.

Triallelic SNPs for estimating cattle introgression, inbreeding, and determining parentage in North American yak

USDA-ARS?s Scientific Manuscript database

The current population of yaks in the U.S. is estimated to exceed 5,000 and was derived from about 150 animals imported in the 20th Century. During the expansion of the U.S. herd, some yaks were allowed to hybridize with cattle, although it is not clear to what extent. Our aim was to use next genera...

Pest resistance and agronomic performance of Upland cotton lines following eight generations of introgression of the BNL3279_105 DNA marker from Gossypium barbadense GB713

USDA-ARS?s Scientific Manuscript database

The BNL3279 primers give unique DNA markers that are closely linked with resistance to reniform nematodes in Gossypium longicalx, Gossypium barbadense GB713, and Gossypium aridum. Plants that had been selected and advanced based on reniform nematode bioassays for each of five or six generations of ...

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis)

USDA-ARS?s Scientific Manuscript database

In previous work, using near isogenic line (NIL) populations in which segments of the tesosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot resistance. We identified...

Pyramiding Sclerotinia head rot and stalk rot resistances into elite sunflower breeding lines with the aid of DNA markers

USDA-ARS?s Scientific Manuscript database

Work was conducted in 2008 to determine the stalk rot resistance of RILs from the RHA 280 x RHA 801 population, as well as to begin introgression of previously identified QTL for head rot resistance into elite sunflower germplasm lines. The stalk rot RILs and their testcrosses with cms HA 89 were t...

Agronomic and physiological performance of Teqing x Lemont introgression rice (Oryza sativa L.) lines under limited irrigation system

USDA-ARS?s Scientific Manuscript database

Rice is a staple food for almost half of the world. Most rice in the world, including the USA, is produced under a flooded paddy system that makes rice one of the most irrigated grain crops on earth. With many water resources being depleted due to high irrigation demands, it has become essential to ...

The Interactive Effects of Transgenically Overexpressed 1Ax1 with Various HMW-GS Combinations on Dough Quality by Introgression of Exogenous Subunits into an Elite Chinese Wheat Variety

PubMed Central

Zhang, Jian; Lei, Qian; Meng, Dandan; Ma, Fengyun; Hu, Wei; Chen, Mingjie; Chang, Junli; Wang, Yuesheng; Yang, Guangxiao; He, Guangyuan

2013-01-01

Seed storage proteins in wheat endosperm, particularly high-molecular-weight glutenin subunits (HMW-GS), are primary determinants of dough properties, and affect both end-use quality and grain utilization of wheat (Triticum aestivum L). In order to investigate the interactive effects between the transgenically overexpressed 1Ax1 subunit with different HMW-GS on dough quality traits, we developed a set of 8 introgression lines (ILs) overexpressing the transgenic HMW-glutenin subunit 1Ax1 by introgression of this transgene from transgenic line B102-1-2/1 into an elite Chinese wheat variety Chuanmai107 (C107), using conventional crossing and backcrossing breeding technique. The donor C107 strain lacks 1Ax1 but contains the HMW-GS pairs 1Dx2+1Dy12 and 1Bx7+1By9. The resultant ILs showed robust and stable expression of 1Ax1 even after five generations of self-pollination, and crossing/backcrossing three times. In addition, overexpression of 1Ax1 was compensated by the endogenous gluten proteins. All ILs exhibited superior agronomic performance when compared to the transgenic parent line, B102-1-2/1. Mixograph results demonstrated that overexpressed 1Ax1 significantly improved dough strength, resistance to extension and over-mixing tolerance, in the targeted wheat cultivar C107. Further, comparisons among the ILs showed the interactive effects of endogenous subunits on dough properties when 1Ax1 was overexpressed: subunit pair 17+18 contributed to increased over-mixing tolerance of the dough; expression of the Glu-D1 allele maintained an appropriate balance between x-type and y-type subunits and thereby improved dough quality. It is consistent with ILs C4 (HMW-GS are 1, 17+18, 2+12) had the highest gluten index and Zeleny sedimentation value. This study demonstrates that wheat quality could be improved by using transgenic wheat overexpressing HMW-GS and the feasibility of using such transgenic lines in wheat quality breeding programs. PMID:24167625

Shoal bass hybridization in the Chattahoochee River Basin near Atlanta, Georgia

USGS Publications Warehouse

Taylor, Andrew T.; Tringali, Michael D.; O'Rourke, Patrick M.; Long, James M.

2018-01-01

The shoal bass (Micropterus cataractae) is a sportfish endemic to the Apalachicola-Chattahoochee-Flint Basin of the southeastern United States. Introgression with several non-native congeners poses a pertinent threat to shoal bass conservation, particularly in the altered habitats of the Chattahoochee River. Our primary objective was to characterize hybridization in shoal bass populations near Atlanta, Georgia, including a population inhabiting Big Creek and another in the main stem Chattahoochee River below Morgan Falls Dam (MFD). A secondary objective was to examine the accuracy of phenotypic identifications below MFD based on a simplified suite of characters examined in the field. Fish were genotyped with 16 microsatellite DNA markers, and results demonstrated that at least four black bass species were involved in introgressive hybridization. Of 62 fish genotyped from Big Creek, 27% were pure shoal bass and 65% represented either F1 hybrids of shoal bass x smallmouth bass (M. dolomieu) or unidirectional backcrosses towards shoal bass. Of 29 fish genotyped below MFD and downstream at Cochran Shoals, 45% were pure shoal bass. Six hybrid shoal bass included both F1 hybrids and backcrosses with non-natives including Alabama bass (M. henshalli), spotted bass (M. punctulatus), and smallmouth bass. Shoal bass alleles comprised only 21% of the overall genomic composition in Big Creek and 31% below MFD (when combined with Cochran Shoals). Phenotypic identification below MFD resulted in an overall correct classification rate of 86% when discerning pure shoal bass from all other non-natives and hybrids. Results suggest that although these two shoal bass populations feature some of the highest introgression rates documented, only a fleeting opportunity may exist to conserve pure shoal bass in both populations. Continued supplemental stocking of pure shoal bass below MFD appears warranted to thwart increased admixture among multiple black bass taxa, and a similar stocking program could benefit the Big Creek population. Further, selective removal of non-natives and hybrids, which appears to be practical with phenotypic identification, may provide increased benefits towards conserving genetic integrity of these shoal bass populations.

Pm55, a developmental-stage and tissue-specific powdery mildew resistance gene introgressed from Dasypyrum villosum into common wheat.

PubMed

Zhang, Ruiqi; Sun, Bingxiao; Chen, Juan; Cao, Aizhong; Xing, Liping; Feng, Yigao; Lan, Caixia; Chen, Peidu

2016-10-01

Powdery mildew resistance gene Pm55 was physically mapped to chromosome arm 5VS FL 0.60-0.80 of Dasypyrum villosum . Pm55 is present in T5VS·5AL and T5VS·5DL translocations, which should be valuable resources for wheat improvement. Powdery mildew caused by Blumeria graminis f. sp. tritici is a major wheat disease worldwide. Exploiting novel genes effective against powdery mildew from wild relatives of wheat is a promising strategy for controlling this disease. To identify novel resistance genes for powdery mildew from Dasypyrum villosum, a wild wheat relative, we evaluated a set of Chinese Spring-D. villosum disomic addition and whole-arm translocation lines for reactions to powdery mildew. Based on the evaluation data, we concluded that the D. villosum chromosome 5V controls post-seedling resistance to powdery mildew. Subsequently, three introgression lines were developed and confirmed by molecular and cytogenetic analysis following ionizing radiation of the pollen of a Chinese Spring-D. villosum 5V disomic addition line. A homozygous T5VS·5AL translocation line (NAU421) with good plant vigor and full fertility was further characterized using sequential genomic in situ hybridization, C-banding, and EST-STS marker analysis. A dominant gene permanently named Pm55 was located in chromosome bin 5VS 0.60-0.80 based on the responses to powdery mildew of all wheat-D. villosum 5V introgression lines evaluated at both seeding and adult stages. This study demonstrated that Pm55 conferred growth-stage and tissue-specific dependent resistance; therefore, it provides a novel resistance type for powdery mildew. The T5VS·5AL translocation line with additional softness loci Dina/Dinb of D. villosum provides a possibility of extending the range of grain textures to a super-soft category. Accordingly, this stock is a new source of resistance to powdery mildew and may be useful in both resistance mechanism studies and soft wheat improvement.

Shoal Bass hybridization below Morgan Falls Dam.

USGS Publications Warehouse

Taylor, Andrew T.; Tringali, Michael D.; O'Rourke, Patrick M.; Long, James M.

2018-01-01

The shoal bass (Micropterus cataractae) is a sportfish endemic to the Apalachicola-Chattahoochee-Flint Basin of the southeastern United States. Introgression with several non-native congeners poses a pertinent threat to shoal bass conservation, particularly in the altered habitats of the Chattahoochee River. Our primary objective was to characterize hybridization in shoal bass populations near Atlanta, Georgia, including a population inhabiting Big Creek and another in the main stem Chattahoochee River below Morgan Falls Dam (MFD). A secondary objective was to examine the accuracy of phenotypic identifications below MFD based on a simplified suite of characters examined in the field. Fish were genotyped with 16 microsatellite DNA markers, and results demonstrated that at least four black bass species were involved in introgressive hybridization. Of 62 fish genotyped from Big Creek, 27% were pure shoal bass and 65% represented either F1 hybrids of shoal bass x smallmouth bass (M. dolomieu) or unidirectional backcrosses towards shoal bass. Of 29 fish genotyped below MFD and downstream at Cochran Shoals, 45% were pure shoal bass. Six hybrid shoal bass included both F1 hybrids and backcrosses with non-natives including Alabama bass (M. henshalli), spotted bass (M. punctulatus), and smallmouth bass. Shoal bass alleles comprised only 21% of the overall genomic composition in Big Creek and 31% below MFD (when combined with Cochran Shoals). Phenotypic identification below MFD resulted in an overall correct classification rate of 86% when discerning pure shoal bass from all other non-natives and hybrids. Results suggest that although these two shoal bass populations feature some of the highest introgression rates documented, only a fleeting opportunity may exist to conserve pure shoal bass in both populations. Continued supplemental stocking of pure shoal bass below MFD appears warranted to thwart increased admixture among multiple black bass taxa, and a similar stocking program could benefit the Big Creek population. Further, selective removal of non-natives and hybrids, which appears to be practical with phenotypic identification, may provide increased benefits towards conserving genetic integrity of these shoal bass populations.

High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population.

PubMed

Yang, Yi; Shen, Yusen; Li, Shunda; Ge, Xianhong; Li, Zaiyun

2017-01-01

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed ( Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses ( B. rapa ssp. chinesis × O. violaceus ) × B. napus . In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs ( cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09 , and cqSL.C09 ) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica).

PubMed

Angelone, Samer; Jowers, Michael J; Molinar Min, Anna Rita; Fandos, Paulino; Prieto, Paloma; Pasquetti, Mario; Cano-Manuel, Francisco Javier; Mentaberre, Gregorio; Olvera, Jorge Ramón López; Ráez-Bravo, Arián; Espinosa, José; Pérez, Jesús M; Soriguer, Ramón C; Rossi, Luca; Granados, José Enrique

2018-05-08

Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions. We tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Previous studies based on large sample sizes taken from its principal populations have revealed that the Iberian ibex has a remarkably small MHC DRB1 diversity (only six remnant alleles) as a result of recent population bottlenecks and a marked demographic decline that has led to the extinction of two recognized subspecies. Extending on the geographic range to include non-studied isolated Iberian ibex populations, we sequenced a new MHC DRB1 in what seemed three small isolated populations in Southern Spain (n = 132). The findings indicate a higher genetic diversity than previously reported in this important gene. The newly discovered allele, MHC DRB1*7, is identical to one reported in the domestic goat C. aegagrus hircus. Whether or not this is the result of ancient polymorphisms maintained by balancing selection or, alternatively, introgressions from domestic goats through hybridization needs to be clarified in future studies. However, hybridization between Iberian ibex and domestic goats has been reported in Spain and the fact that the newly discovered allele is only present in one of the small isolated populations and not in the others suggests introgression. The new discovered allele is not expected to increase fitness in C. pyrenaica since it generates the same protein as the existing MHC DRB1*6. Analysis of a microsatellite locus (OLADRB1) near the new MHC DRB1*7 gene reveals a linkage disequilibrium between these two loci. The allele OLADRB1, 187 bp in length, was unambiguously linked to the MHC DRB1*7 allele. This enabled us to perform a DRB-STR matching method for the recently discovered MHC allele. This finding is critical for the conservation of the Iberian ibex since it directly affects the identification of the units of this species that should be managed and conserved separately (Evolutionarily Significant Units).

Exploring New Alleles Involved in Tomato Fruit Quality in an Introgression Line Library of Solanum pimpinellifolium

PubMed Central

Barrantes, Walter; López-Casado, Gloria; García-Martínez, Santiago; Alonso, Aranzazu; Rubio, Fernando; Ruiz, Juan J.; Fernández-Muñoz, Rafael; Granell, Antonio; Monforte, Antonio J.

2016-01-01

We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the “Moneymaker” cultivar in order to evaluate the accession’s breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of “Moneymaker,” which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic traits. This difference in QTL stability may be due to a predominant additive gene action for QTLs involved in fruit weight, whereas epistatic and genetic background interactions are most likely important for the other traits. PMID:27582742

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

PubMed Central

2012-01-01

Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking. PMID:22448748

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

PubMed

Uwimana, Brigitte; Smulders, Marinus J M; Hooftman, Danny A P; Hartman, Yorike; van Tienderen, Peter H; Jansen, Johannes; McHale, Leah K; Michelmore, Richard W; Visser, Richard G F; van de Wiel, Clemens C M

2012-03-26

After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.

Mapping of the potato leafroll virus resistance gene, Rlretb, from Solanum etuberosum identifies interchromosomal translocations among its E-genome chromosomes 4 and 9 relative to the A-genome of Solanum L. sect. Petota

USDA-ARS?s Scientific Manuscript database

Gene Rlretb, derived from the potato species Solanum etuberosum, confers resistance to potato leafroll virus (PLRV). Mapping of this gene would aid in developing marker-assisted selection protocols to facilitate its introgression into cultivated potato. One RFLP marker and 45 cleaved amplified pol...

Hybridization and introgression of the two strains of Hokkaikdo gypsy moths as invasions by alien species

Treesearch

Yasutomo Higashiura; Michio Ishihara; Hirofumi Yamaguchi; Nanako Ono; Shin-ichi Tokishita; Hideo Yamagata; Takema Fukatsu

2007-01-01

Male-killing refers to the death of male embryos or larvae, and is well known in a variety of organisms, such as plants, mites, and insects (Hurst et al. 1997). We have found male-killing by about 10 percent females in a Bibai, Hokkaido, Japan, population of the gypsy moth, Lymantria dispar L., and have found maternal inheritance of the trait (...

Pineapple [Ananas comosus (L.) Merr].

PubMed

Gangopadhyay, Gaurab; Mukherjee, Kalyan K

2015-01-01

The efficacy of Agrobacterium-mediated pineapple transformation technique has been improved (mean percentage of transgenic micro-shoots regenerated from initial callus explants up to 20.6%) using a novel encapsulation-based, antibiotic selection procedure. The detailed protocol using a standard plant transformation vector (pCAMBIA1304) as reported in an 'elite' Indian variety (Queen) of pineapple [Ananas comosus (L.) Merr] can be applied to other varieties of pineapple for introgression of target genes.

Occurrence of shortleaf x loblolly pine hybrids in shortleaf pine orchards: Implications for ecosystem restoration

Treesearch

John F. Stewart; Rodney Will; Barbara S. Crane; C. Dana Nelson

2016-01-01

Shortleaf pine (Pinus echinata Mill.) is an important conifer in much of the southeastern United States. However, the species and its associated ecosystems are in decline, and recent evidence about hybridization with loblolly pine (Pinus taeda L.) raises concerns that the species may be at risk of further losses due to introgression. Although shortleaf pine is not...

The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea.

PubMed

Ng, Nathaniel S R; Wilton, Peter R; Prawiradilaga, Dewi Malia; Tay, Ywee Chieh; Indrawan, Mochamad; Garg, Kritika M; Rheindt, Frank E

2017-09-01

The role of Pleistocene Ice Age in tropical diversification is poorly understood, especially in archipelagos, in which glaciation-induced sea level fluctuations may lead to complicated changes in land distribution. To assess how Pleistocene land bridges may have facilitated gene flow in tropical archipelagos, we investigated patterns of diversification in the rarely-collected rusty-bellied fantail Rhipidura teysmanni (Passeriformes: Rhipiduridae) complex from Wallacea using a combination of bioacoustic traits and whole-genome sequencing methods (dd-RADSeq). We report a biogeographic leapfrog pattern in the vocalizations of these birds, and uncover deep genomic divergence among island populations despite the presence of intermittent land connections between some. We demonstrate how rare instances of genetic introgression have affected the evolution of this species complex, and document the presence of double introgressive mitochondrial sweeps, highlighting the dangers of using only mitochondrial DNA in evolutionary research. By applying different tree inference approaches, we demonstrate how concatenation methods can give inaccurate results when investigating divergence in closely-related taxa. Our study highlights high levels of cryptic avian diversity in poorly-explored Wallacea, elucidates complex patterns of Pleistocene climate-mediated diversification in an elusive montane songbird, and suggests that Pleistocene land bridges may have accounted for limited connectivity among montane Wallacean biota. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south-western Ethiopian montane rainforests

PubMed Central

Aerts, Raf; Berecha, Gezahegn; Gijbels, Pieter; Hundera, Kitessa; Glabeke, Sabine; Vandepitte, Katrien; Muys, Bart; Roldán-Ruiz, Isabel; Honnay, Olivier

2013-01-01

The montane rainforests of SW Ethiopia are the primary centre of diversity of Coffea arabica and the origin of all Arabica coffee cultivated worldwide. This wild gene pool is potentially threatened by forest fragmentation and degradation, and by introgressive hybridization with locally improved coffee varieties. We genotyped 703 coffee shrubs from unmanaged and managed coffee populations, using 24 microsatellite loci. Additionally, we genotyped 90 individuals representing 23 Ethiopian cultivars resistant to coffee berry disease (CBD). We determined population genetic diversity, genetic structure, and admixture of cultivar alleles in the in situ gene pool. We found strong genetic differentiation between managed and unmanaged coffee populations, but without significant differences in within-population genetic diversity. The widespread planting of coffee seedlings including CBD-resistant cultivars most likely offsets losses of genetic variation attributable to genetic drift and inbreeding. Mixing cultivars with original coffee genotypes, however, leaves ample opportunity for hybridization and replacement of the original coffee gene pool, which already shows signs of admixture. In situ conservation of the wild gene pool of C. arabica must therefore focus on limiting coffee production in the remaining wild populations, as intensification threatens the genetic integrity of the gene pool by exposing wild genotypes to cultivars. PMID:23798974

Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

PubMed

Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

2016-01-01

Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

PubMed

Winfield, Mark O; Allen, Alexandra M; Burridge, Amanda J; Barker, Gary L A; Benbow, Harriet R; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; King, Julie; West, Claire; Griffiths, Simon; King, Ian; Bentley, Alison R; Edwards, Keith J

2016-05-01

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Transfer of useful variability of high grain iron and zinc from Aegilops kotschyi into wheat through seed irradiation approach.

PubMed

Verma, Shailender Kumar; Kumar, Satish; Sheikh, Imran; Malik, Sachin; Mathpal, Priyanka; Chugh, Vishal; Kumar, Sundip; Prasad, Ramasare; Dhaliwal, Harcharan Singh

2016-01-01

To transfer the 2S chromosomal fragment(s) of Aegilops kotschyi (2S(k)) into the bread wheat genome which could lead to the biofortification of wheat with high grain iron and zinc content. Wheat-Ae. kotschyi 2A/2S(k) substitution lines with high grain iron and zinc content were used to transfer the gene/loci for high grain Fe and Zn content into wheat using seed irradiation approach. Bread wheat plants derived from 40 krad-irradiated seeds showed the presence of univalents and multivalents during meiotic metaphase-I. Genomic in situ hybridization analysis of seed irradiation hybrid F2 seedlings showed several terminal and interstitial signals indicated the introgression of Ae. kotschyi chromosome segments. This proves the efficacy of seed radiation hybrid approach in gene transfer experiments. All the radiation-treated hybrid plants with high grain Fe and Zn content were analyzed with wheat group 2 chromosome-specific polymorphic simple sequence repeat markers to identify the introgression of small alien chromosome fragment(s). Radiation-induced hybrids showed more than 65% increase in grain iron and 54% increase in Zn contents with better harvest index than the elite wheat cultivar WL711 indicating effective and compensating translocations of 2S(k) fragments into wheat genome.