Tandem selection for fusiform rust sisease resistance to develop a clonal elite breeding population of loblolly pine

Treesearch

Steve McKeand; Saul Garcia; Josh Steiger; Jim Grissom; Ross Whetten; Fikret Isik

2012-01-01

The elite breeding populations of loblolly pine (Pinus taeda L.) in the North Carolina State University Cooperative Tree Improvement Program are intensively managed for short-term genetic gain. Fusiform rust disease, caused by the fungus Cronartium quercuum f. sp. fusiforme, is the most economically...

Parameter-based stochastic simulation of selection and breeding for multiple traits

Treesearch

Jennifer Myszewski; Thomas Byram; Floyd Bridgwater

2006-01-01

To increase the adaptability and economic value of plantations, tree improvement professionals often manage multiple traits in their breeding programs. When these traits are unfavorably correlated, breeders must weigh the economic importance of each trait and select for a desirable aggregate phenotype. Stochastic simulation allows breeders to test the effects of...

Comparison of Pinus taeda L. whole-tree wood property calibrations using diffuse reflectance near infrared spectra obtained using a variety of sampling options

Treesearch

P. David Jones; Laurence R. Schimleck; Richard F. Daniels; Alexander Clark; Robert C. Purnell

2008-01-01

A necessary objective for tree-breeding programs, with a focus on wood quality, is the measurement of wood properties on a whole-tree basis, however, the time and cost involved limits the numbers of trees sampled. Near infrared (NIR) spectroscopy provides an alternative and recently, it has been demonstrated that calibrations based on milled increment cores and whole-...

Advances in Japanese pear breeding in Japan

PubMed Central

Saito, Toshihiro

2016-01-01

The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan’s history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars ‘Chojuro’ and ‘Nijisseiki’ around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars ‘Niitaka’ and ‘Shinko’ were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including ‘Kosui’, ‘Hosui’, and ‘Akizuki’, which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, ‘Gold Nijisseiki’ has become a leading cultivar. Moreover, ‘Nansui’ from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress. PMID:27069390

Application of Genomic Technologies to the Breeding of Trees

PubMed Central

Badenes, Maria L.; Fernández i Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J.

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species. PMID:27895664

Application of Genomic Technologies to the Breeding of Trees.

PubMed

Badenes, Maria L; Fernández I Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

Genomics-assisted breeding in fruit trees.

PubMed

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Genomics-assisted breeding in fruit trees

PubMed Central

Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

Genetic evaluation of the Association of Zoos and Aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2011-01-01

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered species that has been bred in captivity since the 1970s. In 1992, the Tree Kangaroo Species Survival Plan(®) (TKSSP) was established to coordinate the captive management of Association of Zoos and Aquariums (AZA) D. matschiei. The TKSSP makes annual breeding recommendations primarily based on the mean kinship (MK) strategy. Captive breeding programs often use the MK strategy to preserve genetic diversity in small populations-to avoid the negative consequences of inbreeding and retain their adaptive potential. The ability of a captive breeding program to retain the population's genetic diversity over time can be evaluated by comparing the genetic diversity of the captive population to wild populations. We analyzed DNA extracted from blood and fecal samples from AZA (n = 71), captive (n = 28), and wild (n = 22) D. matschiei using eight microsatellite markers and sequenced the partial mitochondrial DNA control region gene. AZA D. matschiei had a similar expected heterozygosity (H(e) = 0.595 ± 0.184) compared with wild D. matschiei (H(e) = 0.628 ± 0.143), but they had different allelic frequencies (F(ST) = 0.126; P < 0.001). AZA D. matschiei haplotype diversity was almost two times lower than wild D. matschiei Ĥ = 0.740 ± 0.063. These data will assist management of AZA D. matschiei and serve as a baseline for AZA and wild D. matschiei genetic diversity values that could be used to monitor future changes in their genetic diversity. © 2010 Wiley Periodicals, Inc.

Breeding graft-compatible Douglas-fir rootstocks (Pseudotsuga menziesii (Mirb.) Franco).

Treesearch

D.L. Copes

1999-01-01

A study encompassing 24 years was conducted to determine if a breeding program could produce highly graft-compatible rootstocks. Twenty-seven trees of apparent high graft compatibility were selected and crossed to produce 226 control-pollinated families. Seedlings were grown, field planted, and grafted with test scions. Graft unions from field tests were evaluated...

Blight-resistant American chestnut trees: selection of progeny from a breeding program

Treesearch

Shiv Hiremath; Kirsten Lehtoma; Fred Hebard

2007-01-01

Introduction of the fungus Cryphonectria parasitica into North America in early 1900s resulted in the demise of the American chestnut, which was once the most dominant forest tree in the eastern United States. While the American chestnut (Castanea dentate) is susceptible, its counterpart from Asia, the Chinese chestnut, is...

Using DNA Markers to Distinguish Among Chestnut Species and Hybrids

Treesearch

Thomas L. Kubisiak

1999-01-01

Identification of American chestnut trees in the wild for inclusion in breeding programs is currently done using morphological traits. Distinguishing traits include leafshape, stipule size, presence or absence of leaf and stem trichomes, and stem color. Application of these traits is reasonably clear if the trees are pure American chestnut, but identitication of...

A SNP resource for douglas-fir: de novo transcriptome assembly and SNP detection and validation

Treesearch

Glenn R. Howe; Jianbin Yu; Brian Knaus; Richard Cronn; Scott Kolpak; Peter Dolan; W. Walter Lorenz; Jeffrey F.D. Dean

2013-01-01

Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauco) are native to North America, the coastal variety is...

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.

PubMed

Howe, Glenn T; Yu, Jianbin; Knaus, Brian; Cronn, Richard; Kolpak, Scott; Dolan, Peter; Lorenz, W Walter; Dean, Jeffrey F D

2013-02-28

Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

PubMed Central

2013-01-01

Background Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change. PMID:23445355

Walnut genetic improvement at the start of a new century

Treesearch

Keith E. Woeste; James R. McKenna

2004-01-01

Since the early 1960s, researchers in programs to improve black walnut for timber have struggled to meet some basic breeding objectives. Promising avenues of research had been identified by the early 1950s, and conventional methods to breed forest trees were widely adopted as suitable for walnut. Progress has been slow however, due to practical problems related to...

Inter- and intraspecific grafting and breeding of five-needle pines

Treesearch

Clifford E. Ahlgren

1970-01-01

The forest tree improvement work at the Center was started in 1949 with the introduction of some of Dr. Riker's grafted eastern white pine selections. Subsequently a program of selecting, grafting, breeding and testing for resistance was begun. The work was initiated at Basswood Lake (15 miles NE of Ely, Minnesota) rather than elsewhere on a more accessible site...

A Strategy for the Third Breeding Cycle of Loblolly Pine in the Southeastern U.S.

Treesearch

S.E. McKeand; F.E. Bridgwater

1998-01-01

A strategy for the North Carolina State University - Industry Cooperative Tree Improvement Program's third-cycle breeding for loblolly pine (Pinus taeda L.) was developed to provide genetic gain in the short-term as well as to maintain genetic diversity so that long-term genetic gains will also be possible. Our strategy will be to manage a...

Variation in Fiber Length of Eastern Cottonwood in the Lower Mississippi Valley

Treesearch

James R. Wilcox; Robert E. Farmer

1968-01-01

In the research reported here, variation in fiber length within and between trees of Populus deltoides Bartr. was studied to obtain data essential to a breeding program. Samples were obtained by taking increment cores from trees growing in natural stands in Louisiana, Mississippi, and Tennessee. Most of the variation proved to be associated with...

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

PubMed Central

DuVal, Ashley; Gezan, Salvador A.; Mustiga, Guiliana; Stack, Conrad; Marelli, Jean-Philippe; Chaparro, José; Livingstone, Donald; Royaert, Stefan; Motamayor, Juan C.

2017-01-01

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program. PMID:29250097

Conserving and managing the trees of the future: genetic resources for Pacific Northwest forests.

Treesearch

Sally Duncan

2003-01-01

Genetic resource management has historically called for altering the genetic structure of plant populations through selection for traits of interest such as rapid growth. Although this is still a principal component of tree breeding programs in the Pacific Northwest, managing genetic resources now also brings a clear focus on retaining a broad diversity within and...

Genetic improvement of shortleaf pine on the Mark Twain, Ouachita, and Ozark National Forests

Treesearch

Charly Studyvin; David Gwaze

2007-01-01

A genetic conservation and breeding program for shortleaf pine (Pinus echinata Mill.) was initiated in the 1960s by the Mark Twain National Forest in Missouri. Superior trees were selected from natural stands throughout the Forest. Fifty of the top-ranked superior trees were grafted into a first generation seed orchard at the Ouachita National Forest...

Predicting extractives content of Eucalyptus bosistoana F. Muell. Heartwood from stem cores by near infrared spectroscopy

NASA Astrophysics Data System (ADS)

Li, Yanjie; Altaner, Clemens

2018-06-01

Time and resource are the restricting factors for the wider use of chemical information of wood in tree breeding programs. NIR offers an advantage over wet-chemical analysis in these aspects and is starting to be used for tree breeding. This work describes the development of a NIR-based assessment of extractive content in heartwood of E. bosistoana, which does not require milling and conditioning of the samples. This was achieved by applying the signal processing algorithms (external parameter orthogonalisation (EPO) and significance multivariate correlation (sMC)) to spectra obtained from solid wood cores, which were able to correct for moisture content, grain direction and sample form. The accuracy of extractive content predictions was further improved by variable selection, resulting in a root mean square error of 1.27%. Considering the range of extractive content in E. bosistoana heartwood of 1.3 to 15.0%, the developed NIR calibration has the potential to be used in an E. bosistoana breeding program or to assess the special variation in extractive content throughout a stem.

Cooperative advanced-generation breeding and testing of coastal Douglas-fir and western hemlock—strategy and implementation.

Treesearch

K. J.S. Jayawickrama; G.R. Johnson; T. Ye

2005-01-01

As in many temperate regions of the world, forest tree improvement got underway in the Pacific Northwest of the USA in the 1950s, with a number of companies and agencies starting independent tree improvement programs. Booth-Kelly Lumber Co., Crown Zellerbach Corp., the Industrial Forestry Association, Port Blakely Mill Co., Simpson Timber Co., Timber Service Co., the...

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

PubMed Central

Cornille, Amandine; Feurtey, Alice; Gélin, Uriel; Ropars, Jeanne; Misvanderbrugge, Kristine; Gladieux, Pierre; Giraud, Tatiana

2015-01-01

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe. PMID:25926882

Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops

PubMed Central

van Nocker, Steve; Gardiner, Susan E

2014-01-01

Woody perennial plants, including trees that produce fruits and nuts of horticultural value, typically have long breeding cycles, and development and introduction of improved cultivars by plant breeders may require many breeding cycles and dozens of years. However, recent advances in biotechnologies and genomics have the potential to accelerate cultivar development greatly in all crops. This mini-review summarizes approaches to reduce the number and the duration of breeding cycles for horticultural tree crops, and outlines the challenges that remain to implement these into efficient breeding pipelines. PMID:26504538

Sycamore produces viable seed after six years

Treesearch

A. F. Ike

1966-01-01

In the early stages of any tree improvement program it is desirable to know how soon progenies of selected parents can themselves be included in a breeding program. How soon will they produce viable pollen and seed? In the case of sycamore (Platanus occidentalis L.), the information is meager: the Woody- Plant Seed Manual lists the minimum commercial seedbearing age...

Camcore: Thirty-five years of Mesoamerican pine gene conservation

Treesearch

J.L. Lopez; W.S. Dvorak; G.R. Hodge

2017-01-01

Camcore is an international tree breeding and conservation program with headquarters at North Carolina State University. Camcore was founded in 1980 as a cooperative, non-profit organization to identify and save the dwindling natural populations of pines in the highland regions of Guatemala in Central America. Funded by the private sector, the program has played an...

Tree-breeding technique: some effects of continuous bagging

Treesearch

Jonathan W. Wright

1951-01-01

In tree-breeding operations, it is standard practice to protect the tree flowers with vegetable parchment or sausage-casing bags during the pollination period so no unwanted pollen can get to them. Since the bags often damage the tree, they are usually removed as soon as the pollination period ends - within 2 or 3 weeks.

Summary of tree-breeding experiments by The Northeastern Forest Experiment Station 1947-1950

Treesearch

Jonathan W. Wright

1953-01-01

The tree-breeding work of the Northeastern Forest Experiment Station has its roots in a project started in 1924 by the Oxford Paper Company of Rumford, Maine, to develop fast-growing poplars that would be suitable for pulpwood. The initial tree-breeding work in this project was done by A. B. Stout and Ernst J. Schreiner, most of it at the New York Botanical Garden and...

Joint proceedings, Second Genetics Workshop of the Society of American Foresters and Seventh Lake States Forest Tree Improvement Conference, October 21-23, 1965.

Treesearch

NCFES

1966-01-01

Included are (1) 22 technical papers (by researchers from many sections of the United States and Canada) pertaining to selection and progeny testing, radiation genetics, intraspecific variation, natural and artificial hybridization, breeding systems, breeding methodology and specialized tree breeding techniques, and applied breeding and allied fields; (2) concise...

The American Chestnut Foundation breeding program

Treesearch

F.V. Hebard

2012-01-01

Chestnut blight, incited by Cryphonectria parasistica, devastated American chestnut (Castanea dentata (Borkh.) Marsh) in the first half of the 20th century, killing approximately 4 billion dominant and codominant trees. Millions of small sprouts still persist throughout the botanical range of C. dentata. Most are not infected...

Citrus cyopreservation: viability of diverse taxa and histological observations

USDA-ARS?s Scientific Manuscript database

Diverse citrus cultivars maintained clonally within gene banks serve as valuable resources for research and breeding programs worldwide. These critical collections are kept as trees within field, screenhouse, or greenhouse collections. These ex situ collections are at risk of being lost due to unfor...

Managing the rate of increase in average co-ancestry in a rolling front tree breeding strategy.

PubMed

Kerr, R J; McRae, T A; Dutkowski, G W; Tier, B

2015-04-01

In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long- and short-term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by the STBA (Pinus radiata and Eucalyptus globulus) is the long interval (up to 7 years) between when an individual is mated and when its progeny is first assessed in field trials and performance data included in the national performance database. Mate selection methods must therefore recognize the large pool of unmeasured progeny generated over recent years of crossing. In addition, the substantial delay between when an individual is selected in a field trial and when it is clonally copied into a mating facility (breeding arboretum) means that selection and mating must occur as a two-step process. In this article, we describe modifications to preselection and mate selection algorithms that allow unmeasured progeny (juveniles) to be recognized. We also demonstrate that the addition of hypothetical new progeny to the juvenile pool is important for computing the increase in average co-ancestry in the population. Methods outlined in this article may have relevance to animal breeding programmes where between mating and progeny measurement, new rounds of mating are initiated. © 2015 Blackwell Verlag GmbH.

Seasonal changes in adrenocortical responses to acute stress in Eurasian tree sparrow (Passer montanus) on the Tibetan Plateau: comparison with house sparrow (P. domesticus) in North America and with the migratory P. domesticus in Qinghai Province.

PubMed

Li, Dongming; Wang, Gang; Wingfield, John C; Zhang, Zhi; Ding, Changqing; Lei, Fumin

2008-08-01

Seasonal modulation of the adrenocortical response to stress appears to be ubiquitous in arctic-breeding and temperate-zone-breeding birds, but has not been well investigated in alpine-breeding species at mid-latitude. We examined the adrenocortical response to acute stress (capture, handling and restraint) in populations of Eurasian tree sparrow (Passer montanus) among seasons and migratory house sparrow (P. domesticus bactrianus) in pre-breeding on the Qinghai-Xizang Plateau (the Tibetan Plateau). A population of house sparrow (Passer domesticus domesticus) was also sampled in lowland Phoenix, Arizona during breeding and wintering stages. In Eurasian tree sparrows, baseline corticosterone (CORT) does not differ among life history stages, but stress-induced CORT level (maximal CORT, total and corrected integrated CORT) is significantly higher in late breeding stage than those in early breeding and prebasic molt stages. In house sparrows, stress-induced CORT level does not differ between sites and life history stages, but baseline CORT is significantly lower in pre-breeding from Qinghai compared with those in breeding and wintering stages from Phoenix. Interestingly, both baseline CORT and maximal CORT do not differ between the populations of Eurasian tree sparrow and house sparrow in early/pre-breeding stage although tree sparrow is resident species whereas house sparrow is migratory in Qinghai. Our results suggest that the extreme environment of the Tibetan Plateau does not have significant effects on adrenocortical responses to acute stress in Eurasian tree sparrows and house sparrows, which may be a result of masking by human activities. These invasive human commensals may have a unique HPA axis response to different environments because they can take advantage of human food sources and shelter (i.e. buildings).

Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana).

PubMed

Lenz, Patrick R N; Beaulieu, Jean; Mansfield, Shawn D; Clément, Sébastien; Desponts, Mireille; Bousquet, Jean

2017-04-28

Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, which is especially relevant for the genetic improvement of boreal conifers characterized by long breeding cycles. In the present study, we tested GS in an advanced-breeding population of the boreal black spruce (Picea mariana [Mill.] BSP) for growth and wood quality traits, and concurrently examined factors affecting GS model accuracy. The study relied on 734 25-year-old trees belonging to 34 full-sib families derived from 27 parents and that were established on two contrasting sites. Genomic profiles were obtained from 4993 Single Nucleotide Polymorphisms (SNPs) representative of as many gene loci distributed among the 12 linkage groups common to spruce. GS models were obtained for four growth and wood traits. Validation using independent sets of trees showed that GS model accuracy was high, related to trait heritability and equivalent to that of conventional pedigree-based models. In forward selection, gains per unit of time were three times higher with the GS approach than with conventional selection. In addition, models were also accurate across sites, indicating little genotype-by-environment interaction in the area investigated. Using information from half-sibs instead of full-sibs led to a significant reduction in model accuracy, indicating that the inclusion of relatedness in the model contributed to its higher accuracies. About 500 to 1000 markers were sufficient to obtain GS model accuracy almost equivalent to that obtained with all markers, whether they were well spread across the genome or from a single linkage group, further confirming the implication of relatedness and potential long-range linkage disequilibrium (LD) in the high accuracy estimates obtained. Only slightly higher model accuracy was obtained when using marker subsets that were identified to carry large effects, indicating a minor role for short-range LD in this population. This study supports the integration of GS models in advanced-generation tree breeding programs, given that high genomic prediction accuracy was obtained with a relatively small number of markers due to high relatedness and family structure in the population. In boreal spruce breeding programs and similar ones with long breeding cycles, much larger gain per unit of time can be obtained from genomic selection at an early age than by the conventional approach. GS thus appears highly profitable, especially in the context of forward selection in species which are amenable to mass vegetative propagation of selected stock, such as spruces.

Performance of Seven Tree Breeding Strategies Under Conditions of Inbreeding Depression.

PubMed

Wu, Harry X; Hallingbäck, Henrik R; Sánchez, Leopoldo

2016-01-06

In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term. Copyright © 2016 Wu et al.

Performance of Seven Tree Breeding Strategies Under Conditions of Inbreeding Depression

PubMed Central

Wu, Harry X.; Hallingbäck, Henrik R.; Sánchez, Leopoldo

2016-01-01

In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term. PMID:26739644

Cost and accuracy of advanced breeding trial designs in apple

PubMed Central

Harshman, Julia M; Evans, Kate M; Hardner, Craig M

2016-01-01

Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions. How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program. Designs of field trials of advanced apple candidates in which reduced number of locations, the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program. The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy. Critical percentage difference, response to selection, and correlated response were used to examine changes in accuracy of trait evaluations. For the quality traits evaluated, accuracy and response to selection were not substantially reduced for most trial designs. Risk management influences the decision to change trial design, and some designs had greater risk associated with them. Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design. The methods outlined in this analysis would be well suited to other horticultural crop breeding programs. PMID:27019717

Predicting age-age genetic correlations in tree-breeding programs: a case study of Pinus taeda L.

Treesearch

D.P. Gwaze; F.E. Bridgwater; T.D. Byram; J.A. Woolliams; C.G. Williams

2000-01-01

A meta-analysis of 520 parents and 51,439 individuals was used to develop two equations for predicting age-age genetic correlations in Pinus taeda L. Genetic and phenotypic family mean correlations and heritabilities were estimated for ages ranging from 2 to 25 years on 31...

DNA fingerprinting sets for four southern pines

Treesearch

Craig Echt; Sedley Josserand

2018-01-01

DNA markers can provide valuable genetic information for forest tree research, breeding, conservation, and restoration programs. When properly evaluated, selected sets of DNA markers can be used to efficiently get information about genetic diversity in regions, forests, or stands, or in seed lots and orchards. Selected markers also can be used to determine parentage or...

Increased wood-fiber production: technology, economics, and ecology

Treesearch

William R. Bentley

1973-01-01

Forest tree improvement is a form of technological change, and it should be viewed as such. The economic objective of technological change is to increase productivity per dollar invested. This is accomplished through selection and breeding for increased growth rates or reduced losses to insects and disease. Programs which yield improved planting stock make forest...

An unusually large number of eggs laid by a breeding red-cockaded woodpecker female

Treesearch

Richard N. Conner; Daniel Saenz; James R. McCormick

2001-01-01

The Red-cockaded Woodpecker (Picoides borealis) is a cooperatively breeding species that typically uses a single cavity for nesting (Ligon 1970, Walters et al. 1988). A single tree, or aggregation of cavity trees, termed the cluster, is inhabited by a group of woodpeckers that includes a single breeding pair and up to several helpers, which are...

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

PubMed

Vouraki, Sotiria; Gelasakis, Athanasios I; Alexandri, Panoraia; Boukouvala, Evridiki; Ekateriniadou, Loukia V; Banos, Georgios; Arsenos, Georgios

2018-01-01

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought

PubMed Central

Ludovisi, Riccardo; Tauro, Flavia; Salvati, Riccardo; Khoury, Sacha; Mugnozza Scarascia, Giuseppe; Harfouche, Antoine

2017-01-01

Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F2 partially inbred population (termed here ‘POP6’), whose F1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature (Tc) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype variability under drought stress conditions. Tc derived from aerial thermal imagery presented a good correlation with ground-truth stomatal conductance (gs) in both segmentation techniques. Interestingly, the HTFP approach was instrumental to detect drought-tolerant response in 25% of the population. This study shows the potential of UAV-based thermal imaging for field phenomics of poplar and other tree species. This is anticipated to have tremendous implications for accelerating forest tree genetic improvement against abiotic stress. PMID:29021803

UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought.

PubMed

Ludovisi, Riccardo; Tauro, Flavia; Salvati, Riccardo; Khoury, Sacha; Mugnozza Scarascia, Giuseppe; Harfouche, Antoine

2017-01-01

Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F 2 partially inbred population (termed here 'POP6'), whose F 1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature ( T c ) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype variability under drought stress conditions. T c derived from aerial thermal imagery presented a good correlation with ground-truth stomatal conductance ( g s ) in both segmentation techniques. Interestingly, the HTFP approach was instrumental to detect drought-tolerant response in 25% of the population. This study shows the potential of UAV-based thermal imaging for field phenomics of poplar and other tree species. This is anticipated to have tremendous implications for accelerating forest tree genetic improvement against abiotic stress.

The South Florida Avocado Breeding Program at USDA-Agricultural Research Service Subtropical Horticulture Research Station (USDA-ARS SHRS)

USDA-ARS?s Scientific Manuscript database

USDA-ARS SHRS is part of the USDA National Germplasm Repository system and houses collections of tropical and subtropical fruit trees such as mango, lychee, and avocado. In addition to maintaining the germplasm collections, our mission is to also identify genetic diversity in the collections, to ev...

Making history: Field testing of blight-resistant American chestnut (Castanea dentata) in the Southern Region

Treesearch

Stacy L. Clark; Scott E. Schlarbaum; A.M. Saxton; Fred V. Hebard

2011-01-01

The American chestnut (Castanea dentata Marsh. Borkh.) was decimated by an exotic fungus (chestnut blight [Cryphonectria parasitica Murr. Bar]) in the early part of the 20th century. The American Chestnut Foundation (TACF) uses a back-cross breeding program to produce a tree that is predicted to be American chestnut in character...

A red-cockaded woodpecker group with two simultaneous nest trees

Treesearch

Richard N. Conner; James M. McCormick; Richard R. Schaefer; Daniel Saenz; D. Craig Rudolph

2001-01-01

During a study of red cockaded woodpecker (P icoides borealis) nesting in eastern Texas, we discovered a single breeding pair of woodpeckers with two simultaneous nests in nest trees that were 24 m apart. Incubation of eggs in each nest tree was at least 13 d and may have been as long as 16 d. The breeding male incubated and fed a nestling in one...

Developing publicly acceptable tree health policy: public perceptions of tree-breeding solutions to ash dieback among interested publics in the UK.

PubMed

Jepson, Paul R; Arakelyan, Irina

2017-07-01

The UK needs to develop effective policy responses to the spread of tree pathogens and pests. This has been given the political urgency following the media and other commentary associated with the arrival of a disease that causes 'dieback' of European Ash ( Fraxinus excelsior ) - a tree species with deep cultural associations. In 2014 the UK government published a plant biosecurity strategy and linked to this invested in research to inform policy. This paper reports the findings of a survey of informed UK publics on the acceptability of various potential strategies to deal with ash dieback, including "no action". During the summer of 2015, we conducted a face-to-face survey of 1152 respondents attending three major countryside events that attract distinct publics interested in the countryside: landowners & land managers; naturalists and gardeners. We found that UK publics who are likely to engage discursively and politically (through letter writing, petitions etc.) with the issue of ash dieback a) care about the issue, b) want an active response, c) do not really distinguish between ash trees in forestry or ecological settings, and d) prefer traditional breeding solutions. Further that e) younger people and gardeners are open to GM breeding techniques, but f) the more policy-empowered naturalists are more likely to be anti-GM. We suggest that these findings provide three 'steers' for science and policy: 1) policy needs to include an active intervention component involving the breeding of disease-tolerant trees, 2) that the development of disease tolerance using GM-technologies could be part of a tree-breeding policy, and 3) there is a need for an active dialogue with publics to manage expectations on the extent to which science and policy can control tree disease or, put another way, to build acceptability for the prospect that tree diseases may have to run their course.

Intra-annual variation in habitat choice by an endemic woodpecker: Implications for forest management and conservation

NASA Astrophysics Data System (ADS)

Garcia-del-Rey, Eduardo; Fernández-Palacios, José María; Muñoz, Pascual Gil

2009-09-01

The Canary Islands great spotted woodpecker Dendrocopos major canariensis is an endemic bird restricted to the Pinus canariensis forests of Tenerife and Gran Canaria. Classification tree models were applied to explore the relationship of the occurrence of this picid and habitat variables between two contrasting periods (breeding vs. non-breeding seasons) and for the entire annual cycle. During the reproductive period the availability of mature trees (DBH > 60 cm), and snags (dead trees), for nesting and roosting, characterize the breeding territory. Outside the breeding season the choice of locations was driven by a tree cover larger than 28.5% and the presence of trees taller than 8.5 m on average, a pattern explained by the availability of pine seeds in the cones of well-developed canopies, and less so by predation risk. Overall, during the annual cycle, well-developed canopy sites influenced the presence of this picidae (tree cover > 38%) and on more open sites (<38%) the presence of mature trees (DBH> 60 cm) became the second most important predictor of occurrence. We suggest that food abundance and availability could be the ultimate factor explaining the intra-annual variation observed, with the availability of snags being an important factor during nesting. In the range of this endemic, we recommend selective cuts in pine plantations, to allow the trees to set seed and improve their crops, minimizing the elimination of snags, and killing some large pine trees if the priority is to expand the distributional range of the woodpecker.

Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

PubMed Central

Ndiaye, Ndèye Penda; Sow, Adama; Dayo, Guiguigbaza-Kossigan; Ndiaye, Saliou; Sawadogo, Germain Jerôme; Sembène, Mbacké

2015-01-01

Aim: In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama). Methods: Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software. Results: A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. Conclusions: The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival. PMID:27047188

Founding concepts for tree breeding and research

Treesearch

Hyun Kang

1983-01-01

Forestry research is a multidisciplinary venture and is typically a long-term effort with relatively low funding. The success of forestry research and tree breeding depends greatly on the coordination among forestry practitioners, research managers, and researchers. To coordinate they must have a common understanding of the research process. Therefore, the common...

Common families across test series—how many do we need?

Treesearch

G.R. Johnson

2004-01-01

In order to compare families that are planted on different sites, many forest tree breeding programs include common families in their different series of trials. Computer simulation was used to examine how many common families were needed in each series of progeny trials in order to reliably compare families across series. Average gain and its associated variation...

Rootstock effects on fruit quality among 'Ray Ruby' grapefruit trees grown in the Indian River district of Florida

USDA-ARS?s Scientific Manuscript database

The objective of this experiment was to compare fruit quality parameters of ‘Ray Ruby’ grapefruit grown on seven rootstocks. Four recent releases from the USDA rootstock breeding program, US-852, US-897, US-942 and US-812 (all Citrus reticulata x P. trifoliata hybrids), X639 (C. reticulata x P. tri...

The efficiency of introduced pisolithus tinctorius inoculum on backcrossed chestnut germination and survival

Treesearch

Jenise M. Bauman; Carolyn H. Keiffer; Shiv Hiremath

2012-01-01

American chestnut was eliminated as a canopy tree from the Appalachian region of North America with the introduction of chestnut blight in the early 1900s. Breeding programs initiated in the 1980s have produced seedling lines that display the pure American morphology with potential resistance to chestnut blight. More work is required to assess their field performance...

"Super" Spruce Seedlings Continue Superior Growth for 18 Years

Treesearch

Hans Nienstaedt

1981-01-01

White spruce seedlings--20, 19, 18, and 17 inches tall--were selected among 2-2 transplants; controls from the same beds averaged 7.7 inches tall. After 18 years in the field, the selected seedlings continued to have a 30 percent height growth advantage over the controls. This note discusses how to incorporate super spruce seedlings into a tree breeding program....

Modeling hormonal control of cambium proliferation.

PubMed

Oles, Vladyslav; Panchenko, Alexander; Smertenko, Andrei

2017-01-01

Rise of atmospheric CO2 is one of the main causes of global warming. Catastrophic climate change can be avoided by reducing emissions and increasing sequestration of CO2. Trees are known to sequester CO2 during photosynthesis, and then store it as wood biomass. Thus, breeding of trees with higher wood yield would mitigate global warming as well as augment production of renewable construction materials, energy, and industrial feedstock. Wood is made of cellulose-rich xylem cells produced through proliferation of a specialized stem cell niche called cambium. Importance of cambium in xylem cells production makes it an ideal target for the tree breeding programs; however our knowledge about control of cambium proliferation remains limited. The morphology and regulation of cambium are different from those of stem cell niches that control axial growth. For this reason, translating the knowledge about axial growth to radial growth has limited use. Furthermore, genetic approaches cannot be easily applied because overlaying tissues conceal cambium from direct observation and complicate identification of mutants. To overcome the paucity of experimental tools in cambium biology, we constructed a Boolean network CARENET (CAmbium REgulation gene NETwork) for modelling cambium activity, which includes the key transcription factors WOX4 and HD-ZIP III as well as their potential regulators. Our simulations predict that: (1) auxin, cytokinin, gibberellin, and brassinosteroids act cooperatively in promoting transcription of WOX4 and HD-ZIP III; (2) auxin and cytokinin pathways negatively regulate each other; (3) hormonal pathways act redundantly in sustaining cambium activity; (4) individual cambium cells can have diverse molecular identities. CARENET can be extended to include components of other signalling pathways and be integrated with models of xylem and phloem differentiation. Such extended models would facilitate breeding trees with higher wood yield.

Leaf litter of invasive Chinese tallow (Triadica sebifera) negatively affects hatching success of an aquatic breeding anuran, the southern leopard frog (Lithobates sphenocephalus)

Treesearch

C.K. Adams; D. Saenz

2012-01-01

Chinese tallow (Triadica sebifera (L.) Small) is an aggressive invasive tree species that can be abundant in parts of its non-native range. This tree species has the capability of producing monocultures, by outcompeting native trees, which can be in or near wetlands that are utilized by breeding amphibians. Existing research suggests that leaf litter from invasive...

Buteo Nesting Ecology: Evaluating Nesting of Swainson's Hawks in the Northern Great Plains.

PubMed

Inselman, Will M; Datta, Shubham; Jenks, Jonathan A; Jensen, Kent C; Grovenburg, Troy W

2015-01-01

Swainson's hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson's hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson's hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%-42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson's hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson's hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson's hawks arriving to the breeding grounds.

Tree Planting at the Bent Creek Experimental Forest

Treesearch

John C. Barber

1953-01-01

Foresters everywhere are becoming increasingly conscious of the potentialities of tree selection and breeding. In the quest for suitable breeding material, many of the plantations of the past are assuming importance, for each plantation of introduced species may provide information on its adaptability to a certain area and the desirable and undesirable traits which...

The red-cockaded woodpecker cavity tree: A very special pine

Treesearch

Richard N. Conner; D. Craig Rudolph; Daniel Saenz; Robert H. Johnson

2004-01-01

The adaptation of red-cockaded woodpeckers (Picoides borealis) to fire-maintained southern pine ecosystems has included the development of behaviors that permit the species to use living pines for their cavity trees. Their adaptation to pine ecosystems has also involved a major adjustment in the species' breeding system to cooperative breeding,...

Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population

PubMed Central

Tisné, Sébastien; Pomiès, Virginie; Riou, Virginie; Syahputra, Indra; Cochard, Benoît; Denis, Marie

2017-01-01

Multi-parental populations are promising tools for identifying quantitative disease resistance loci. Stem rot caused by Ganoderma boninense is a major threat to palm oil production, with yield losses of up to 80% prompting premature replantation of palms. There is evidence of genetic resistance sources, but the genetic architecture of Ganoderma resistance has not yet been investigated. This study aimed to identify Ganoderma resistance loci using an oil palm multi-parental population derived from nine major founders of ongoing breeding programs. A total of 1200 palm trees of the multi-parental population was planted in plots naturally infected by Ganoderma, and their health status was assessed biannually over 25 yr. The data were treated as survival data, and modeled using the Cox regression model, including a spatial effect to take the spatial component in the spread of Ganoderma into account. Based on the genotypes of 757 palm trees out of the 1200 planted, and on pedigree information, resistance loci were identified using a random effect with identity-by-descent kinship matrices as covariance matrices in the Cox model. Four Ganoderma resistance loci were identified, two controlling the occurrence of the first Ganoderma symptoms, and two the death of palm trees, while favorable haplotypes were identified among a major gene pool for ongoing breeding programs. This study implemented an efficient and flexible QTL mapping approach, and generated unique valuable information for the selection of oil palm varieties resistant to Ganoderma disease. PMID:28592650

PCBs and DDE in Tree Swallow (Tachycineta bicolor) Eggs and Nestlings from an Estuarine PCB Superfund Site, New Bedford Harbor, MA, U.S.A.

EPA Science Inventory

While breeding tree swallows (Tachycineta bicolor) have been used as biomonitors for freshwater sites, we report the first use of this species to assess the transfer of breeding ground contaminants from an estuarine system. Eggs and nestlings were collected from nest boxes locat...

Influence of fine-scale habitat structure on nest-site occupancy, laying date and clutch size in Blue Tits Cyanistes caeruleus

NASA Astrophysics Data System (ADS)

Amininasab, Seyed Mehdi; Vedder, Oscar; Schut, Elske; de Jong, Berber; Magrath, Michael J. L.; Korsten, Peter; Komdeur, Jan

2016-01-01

Most birds have specific habitat requirements for breeding. The vegetation structure surrounding nest-sites is an important component of habitat quality, and can have large effects on avian breeding performance. We studied 13 years of Blue Tit Cyanistes caeruleus population data to determine whether characteristics of vegetation structure predict site occupancy, laying date and number of eggs laid. Measurements of vegetation structure included the density of English Oak Quercus robur, European Beech Fagus sylvatica, and other deciduous, coniferous and non-coniferous evergreen trees, within a 20-m radius of nest-boxes used for breeding. Trees were further sub-divided into specific classes of trunk circumferences to determine the densities for different maturity levels. Based on Principal Component Analysis (PCA), we reduced the total number of 17 measured vegetation variables to 7 main categories, which we used for further analyses. We found that the occupancy rate of sites and the number of eggs laid correlated positively with the proportion of deciduous trees and negatively with the density of coniferous trees. Laying of the first egg was advanced with a greater proportion of deciduous trees. Among deciduous trees, the English Oak appeared to be most important, as a higher density of more mature English Oak trees was associated with more frequent nest-box occupancy, a larger number of eggs laid, and an earlier laying start. Furthermore, laying started earlier and more eggs were laid in nest-boxes with higher occupancy rates. Together, these findings highlight the role of deciduous trees, particularly more mature English Oak, as important predictors of high-quality preferred habitat. These results aid in defining habitat quality and will facilitate future studies on the importance of environmental quality for breeding performance.

Genomics of pear and other Rosaceae fruit trees

PubMed Central

Yamamoto, Toshiya; Terakami, Shingo

2016-01-01

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry. PMID:27069399

Genomics of pear and other Rosaceae fruit trees.

PubMed

Yamamoto, Toshiya; Terakami, Shingo

2016-01-01

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.

Changing nest placement of Hawaiian Common Amakihi during the breeding cycle

USGS Publications Warehouse

van Riper, Charles; Kern, M. D.; Sogge, M. K.

1993-01-01

We studied the nesting behavior of the Common Amakihi (Hemignathus virens) from 1970-1981 on the island of Hawaii to determine if the species alters nest placement over a protracted 9-month breeding season. Birds preferentially chose the southwest quadrant of trees in which to build nests during all phases of the breeding season. It appeared that ambient temperature (Ta) was a contributing factor to differential nest placement between early and late phases of the annual breeding cycle. When Ta is low during the early (December-March) breeding period, Common Amakihi selected exposed nesting locations that benefitted them with maximum solar insolation. However, in the later phase of the breeding period (April-July) when Ta was much higher, renesting birds selected nest sites deeper in the canopy in significantly taller trees. This is one of the few documented examples in which a species changes location of nest during a breeding season, thus allowing exploitation of temporally differing microclimatic conditions.

Declines in the breeding population of Vaux's Swifts in northeastern Oregon.

Treesearch

Evelyn L. Bull

2003-01-01

I investigated trends in the breeding population of Vaux's Swift (Chaetura vauxi) in northeastern Oregon by revisiting in 2003 39 stands of trees that contained swifts in 1991. In 2003 the number of swifts in these stands was significantly fewer, with only 46% of the stands still containing swifts. Only 29% of the 58 nest and roost trees the...

Persimmon breeding in Japan for pollination-constant non-astringent (PCNA) type with marker-assisted selection

PubMed Central

Sato, Akihiko; Yamada, Masahiko

2016-01-01

Oriental persimmon (Diospyros kaki) originated in Eastern Asia, and many indigenous cultivars have been developed in China, Japan, and Korea. These cultivars are classified into four groups based on their natural astringency loss on the tree and seed formation: pollination-constant non-astringent (PCNA), pollination-variant non-astringent (PVNA), pollination-constant astringent (PCA), and pollination-variant astringent (PVA). PCNA is the most desirable type because the fruit can be eaten without any postharvest treatment; therefore, one of the goals of our persimmon breeding programs is to release superior PCNA cultivars. The PCNA genotype is recessive to the other three non-PCNA genotypes, and PCNA-type F1 offspring are obtained exclusively from crosses among PCNA genotypes. Moreover, the number of superior PCNA cross-parents have been limited. In the late 1980s, inbreeding depression became obvious, especially in terms of fruit size, tree vigor, and productivity. To mitigate the inbreeding, a backcross program using PCNA [(non-PCNA × PCNA) × PCNA] was started in 1990. This process, however, was inefficient because only 15% of the offspring were PCNA, and all offspring had to be grown to the fruiting stage. Therefore, molecular markers linked to the PCNA locus were developed for discriminating PCNA offspring. A molecular marker linked to Chinese PCNA has also been developed. PMID:27069391

Multivariate analysis in a genetic divergence study of Psidium guajava.

PubMed

Nogueira, A M; Ferreira, M F S; Guilhen, J H S; Ferreira, A

2014-12-18

The family Myrtaceae is widespread in the Atlantic Forest and is well-represented in the Espírito Santo State in Brazil. In the genus Psidium of this family, guava (Psidium guajava L.) is the most economically important species. Guava is widely cultivated in tropical and subtropical countries; however, the widespread cultivation of only a small number of guava tree cultivars may cause the genetic vulnerability of this crop, making the search for promising genotypes in natural populations important for breeding programs and conservation. In this study, the genetic diversity of 66 guava trees sampled in the southern region of Espírito Santo and in Caparaó, MG, Brazil were evaluated. A total of 28 morphological descriptors (11 quantitative and 17 multicategorical) and 18 microsatellite markers were used. Principal component, discriminant and cluster analyses, descriptive analyses, and genetic diversity analyses using simple sequence repeats were performed. Discrimination of accessions using molecular markers resulted in clustering of genotypes of the same origin, which was not observed using morphological data. Genetic diversity was detected between and within the localities evaluated, regardless of the methodology used. Genetic differentiation among the populations using morphological and molecular data indicated the importance of the study area for species conservation, genetic erosion estimation, and exploitation in breeding programs.

Persimmon breeding in Japan for pollination-constant non-astringent (PCNA) type with marker-assisted selection.

PubMed

Sato, Akihiko; Yamada, Masahiko

2016-01-01

Oriental persimmon (Diospyros kaki) originated in Eastern Asia, and many indigenous cultivars have been developed in China, Japan, and Korea. These cultivars are classified into four groups based on their natural astringency loss on the tree and seed formation: pollination-constant non-astringent (PCNA), pollination-variant non-astringent (PVNA), pollination-constant astringent (PCA), and pollination-variant astringent (PVA). PCNA is the most desirable type because the fruit can be eaten without any postharvest treatment; therefore, one of the goals of our persimmon breeding programs is to release superior PCNA cultivars. The PCNA genotype is recessive to the other three non-PCNA genotypes, and PCNA-type F1 offspring are obtained exclusively from crosses among PCNA genotypes. Moreover, the number of superior PCNA cross-parents have been limited. In the late 1980s, inbreeding depression became obvious, especially in terms of fruit size, tree vigor, and productivity. To mitigate the inbreeding, a backcross program using PCNA [(non-PCNA × PCNA) × PCNA] was started in 1990. This process, however, was inefficient because only 15% of the offspring were PCNA, and all offspring had to be grown to the fruiting stage. Therefore, molecular markers linked to the PCNA locus were developed for discriminating PCNA offspring. A molecular marker linked to Chinese PCNA has also been developed.

Buteo Nesting Ecology: Evaluating Nesting of Swainson’s Hawks in the Northern Great Plains

PubMed Central

Inselman, Will M.; Datta, Shubham; Jenks, Jonathan A.; Jensen, Kent C.; Grovenburg, Troy W.

2015-01-01

Swainson’s hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson’s hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson’s hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, S Dist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%–42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson’s hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson’s hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson’s hawks arriving to the breeding grounds. PMID:26327440

Breeding bird response to juniper woodland expansion

USGS Publications Warehouse

Rosenstock, Steven S.; van Riper, Charles

2001-01-01

In recent times, pinyon (Pinus spp.)-juniper (Juniperus spp.) woodlands have expanded into large portions of the Southwest historically occupied by grassland vegetation. From 1997-1998, we studied responses of breeding birds to one-seed juniper (J. monosperma) woodland expansion at 2 grassland study areas in northern Arizona. We sampled breeding birds in 3 successional stages along a grassland-woodland gradient: un-invaded grassland, grassland undergoing early stages of juniper establishment, and developing woodland. Species composition varied greatly among successional stages and was most different between endpoints of the gradient. Ground-nesting grassland species predominated in uninvaded grassland but declined dramatically as tree density increased. Tree- and cavity-nesting species increased with tree density and were most abundant in developing woodland. Restoration of juniper-invaded grasslands will benefit grassland-obligate birds and other wildlife.

Prediction of insemination outcomes in Holstein dairy cattle using alternative machine learning algorithms.

PubMed

Shahinfar, Saleh; Page, David; Guenther, Jerry; Cabrera, Victor; Fricke, Paul; Weigel, Kent

2014-02-01

When making the decision about whether or not to breed a given cow, knowledge about the expected outcome would have an economic impact on profitability of the breeding program and net income of the farm. The outcome of each breeding can be affected by many management and physiological features that vary between farms and interact with each other. Hence, the ability of machine learning algorithms to accommodate complex relationships in the data and missing values for explanatory variables makes these algorithms well suited for investigation of reproduction performance in dairy cattle. The objective of this study was to develop a user-friendly and intuitive on-farm tool to help farmers make reproduction management decisions. Several different machine learning algorithms were applied to predict the insemination outcomes of individual cows based on phenotypic and genotypic data. Data from 26 dairy farms in the Alta Genetics (Watertown, WI) Advantage Progeny Testing Program were used, representing a 10-yr period from 2000 to 2010. Health, reproduction, and production data were extracted from on-farm dairy management software, and estimated breeding values were downloaded from the US Department of Agriculture Agricultural Research Service Animal Improvement Programs Laboratory (Beltsville, MD) database. The edited data set consisted of 129,245 breeding records from primiparous Holstein cows and 195,128 breeding records from multiparous Holstein cows. Each data point in the final data set included 23 and 25 explanatory variables and 1 binary outcome for of 0.756 ± 0.005 and 0.736 ± 0.005 for primiparous and multiparous cows, respectively. The naïve Bayes algorithm, Bayesian network, and decision tree algorithms showed somewhat poorer classification performance. An information-based variable selection procedure identified herd average conception rate, incidence of ketosis, number of previous (failed) inseminations, days in milk at breeding, and mastitis as the most effective explanatory variables in predicting pregnancy outcome. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

PubMed

Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

2014-12-12

Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P < 0.0001). Sampled demes sites (1- 7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (Rxy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

Identification of Ganoderma Disease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population.

PubMed

Tisné, Sébastien; Pomiès, Virginie; Riou, Virginie; Syahputra, Indra; Cochard, Benoît; Denis, Marie

2017-06-07

Multi-parental populations are promising tools for identifying quantitative disease resistance loci. Stem rot caused by Ganoderma boninense is a major threat to palm oil production, with yield losses of up to 80% prompting premature replantation of palms. There is evidence of genetic resistance sources, but the genetic architecture of Ganoderma resistance has not yet been investigated. This study aimed to identify Ganoderma resistance loci using an oil palm multi-parental population derived from nine major founders of ongoing breeding programs. A total of 1200 palm trees of the multi-parental population was planted in plots naturally infected by Ganoderma , and their health status was assessed biannually over 25 yr. The data were treated as survival data, and modeled using the Cox regression model, including a spatial effect to take the spatial component in the spread of Ganoderma into account. Based on the genotypes of 757 palm trees out of the 1200 planted, and on pedigree information, resistance loci were identified using a random effect with identity-by-descent kinship matrices as covariance matrices in the Cox model. Four Ganoderma resistance loci were identified, two controlling the occurrence of the first Ganoderma symptoms, and two the death of palm trees, while favorable haplotypes were identified among a major gene pool for ongoing breeding programs. This study implemented an efficient and flexible QTL mapping approach, and generated unique valuable information for the selection of oil palm varieties resistant to Ganoderma disease. Copyright © 2017 Tisné et al.

Effects of clearcutting, patch cutting, and low-density shelterwoods on breeding birds and tree regeneration in New Hampshire northern hardwoods

Treesearch

Mariko Yamasaki; Christine A. Costello; William B. Leak

2014-01-01

Clearcutting is an effective regeneration practice for northern hardwoods in New England. However, in esthetically sensitive areas forest managers sometimes use methods that soften the visual impact, such as smaller clearcuts (patch cuts) or low-density shelterwoods. It is unclear if these methods produce the same effects as clearcuts on tree regeneration and breeding...

Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region.

PubMed

Liao, Yuying; Mo, Guodong; Sun, Junli; Wei, Fengying; Liao, Dezhong Joshua

2016-05-01

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

PubMed Central

Bink, Marco CAM; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program. PMID:27806077

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.

PubMed

Bartholomé, Jérôme; Bink, Marco Cam; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.

Breeding biology and nest-site selection of red-tailed hawks in an altered desert grassland

USGS Publications Warehouse

Hobbs, R.J.; DeStefano, S.; Halvorson, W.L.

2006-01-01

Red-tailed Hawks (Buteo jamaicensis) have expanded their range as trees have invaded formerly-open grasslands. Desert grasslands of southern Arizona have been invaded by mesquite trees (Prosopis velutina) since Anglo-American settlement and now support a large population of Red-tailed Hawks. We studied a population of Red-tailed Hawks in an altered desert grassland in southern Arizona. Our objectives were to determine what environmental characteristics influence Red-tailed Hawk habitat selection in mesquite-invaded desert grasslands and to evaluate the habitat quality of these grasslands for Red-tailed Hawks based on nesting density, nest success, and productivity. Red-tailed Hawks had 86% (95% C.I. = 73-99) nest success and 1.82 young per breeding pair (95% C.I. = 1.41-2.23). Nesting density was 0.15 (95% CI = 0.08-0.21) breeding pairs/km2 and the mean nearest-neighbor distance was 1.95 km (95% C.I. = 1.74-2.16). Red-tailed Hawks selected nest-sites with taller nest-trees and greater tree height and cover than were available at random. Mesquite trees in desert grasslands provide abundant potential nesting structures for Red-tailed Hawks. ?? 2006 The Raptor Research Foundation, Inc.

Genomic selection in forage breeding: designing an estimation population

USDA-ARS?s Scientific Manuscript database

The benefits of genomic selection to livestock, crops and forest tree breeding can be extended to forage grasses and legumes. The main benefits expected are increased selection accuracy and reduced costs per unit of genotype evaluated and breeding cycle length. Aiming at designing a training populat...

Removal of Competition Bias from Forest Genetics Experiments

Treesearch

D. T. Cooper; Robert B. Ferguson

1977-01-01

Estimates of genetic gains and of juvenile-mature correlations in small-plot breeding experiments may be inflated because trees that grow rapidly early continue to be the largest trees, and trees that begin slowly usually stay small. A procedure which takes missing trees, relative sizes and distances between competing trees, and the intensity of competition into...

Accelerating the domestication of forest trees in a changing world.

PubMed

Harfouche, Antoine; Meilan, Richard; Kirst, Matias; Morgante, Michele; Boerjan, Wout; Sabatti, Maurizio; Scarascia Mugnozza, Giuseppe

2012-02-01

In light of impending water and arable land shortages, population growth and climate change, it is more important than ever to examine how forest tree domestication can be accelerated to sustainably meet future demands for wood, biomass, paper, fuel and biomaterials. Because of long breeding cycles, tree domestication cannot be rapidly achieved through traditional genetic improvement methods alone. Integrating modern genetic and genomic techniques with conventional breeding will expedite tree domestication. Breeders will only embrace these technologies if they are cost-effective and readily accessible, and forest landowners will only adopt end-products that meet with regulatory approval and public acceptance. All parties involved must work together to achieve these objectives for the benefit of society. Copyright © 2011 Elsevier Ltd. All rights reserved.

Frequencies of genes for coat colour and horns in Nordic cattle breeds

PubMed Central

Kantanen, Juha; Olsaker, Ingrid; Brusgaard, Klaus; Eythorsdottir, Emma; Holm, Lars-Erik; Lien, Sigbjørn; Danell, Birgitta; Adalsteinsson, Stefan

2000-01-01

Gene frequencies of coat colour and horn types were assessed in 22 Nordic cattle breeds in a project aimed at establishing genetic profiles of the breeds under study. The coat colour loci yielding information on genetic variation were: extension, agouti, spotting, brindle, dun dilution and colour sided. The polled locus was assessed for two alleles. A profound variation between breeds was observed in the frequencies of both colour and horn alleles, with the older breeds generally showing greater variation in observed colour, horn types and segregating alleles than the modern breeds. The correspondence between the present genetic distance matrix and previous molecular marker distance matrices was low (r = 0.08 – 0.12). The branching pattern of a neighbour-joining tree disagreed to some extent with the molecular data structure. The current data indicates that 70% of the total genetic variation could be explained by differences between the breeds, suggesting a much greater breed differentiation than typically found at protein and microsatellite loci. The marked differentiation of the cattle breeds and observed disagreements with the results from the previous molecular data in the topology of the phylogenetic trees are most likely a result of selection on phenotypic characters analysed in this study. PMID:14736370

Nesting habitat and productivity of Swainson's Hawks in southeastern Arizona

USGS Publications Warehouse

Nishida, Catherine; Boal, Clint W.; DeStefano, Stephen; Hobbs, Royden J.

2013-01-01

We studied Swainson's Hawks (Buteo swainsoni) in southeastern Arizona to assess the status of the local breeding population. Nest success (≥1 young fledged) was 44.4% in 1999 with an average of 1.43 ± 0.09 (SE) young produced per successful pair. Productivity was similar in 2000, with 58.2% nesting success and 1.83 ± 0.09 fledglings per successful pair. Mesquite (Prosopis velutina) and cottonwood (Populus fremontii) accounted for >50% of 167 nest trees. Nest trees were taller than surrounding trees and random trees, and overall there was more vegetative cover at nest sites than random sites. This apparent requirement for cover around nest sites could be important for management of the species in Arizona. However, any need for cover at nest sites must be balanced with the need for open areas for foraging. Density of nesting Swainson's Hawks was higher in agriculture than in grasslands and desert scrub. Breeding pairs had similar success in agricultural and nonagricultural areas, but the effect of rapid and widespread land-use change on breeding distribution and productivity continues to be a concern throughout the range of the species.

Tree and root architecture of Malus sieversii seedlings for rootstock breeding

USDA-ARS?s Scientific Manuscript database

The foundation of a successful apple orchard is in large part the rootstock used to establish the trees in that orchard. Apple rootstocks can impart several important architectural tree characters to the scion, among which are reduction in tree size and early production of flowers/fruit. It is pro...

Pollen dispersion of some forest trees

Treesearch

Jonathan W. Wright

1952-01-01

The distance the pollen of forest trees travels is of practical and theoretical importance not only in tree breeding, but also in silviculture. For example, one way to produce elite or hybrid tree seed where vegetative propagation is impractical is by the establishment of "seed orchards" or natural-crossing plots. The success of such orchards will depend...

'Jones hybrid' hickory: a case study in Carya curation.

PubMed

Grauke, L J; Mendoza-Herrera, M Azucena; Stelly, David M; Klein, Patricia E

2016-01-01

'Jones Hybrid' hickory is an accession in the National Collection of Genetic Resources for Pecans and Hickories for which information about origin, identity and characteristics is very incomplete. Phenotypic and genetic profiles, when examined in the context of historic literature, provide evidence that the accession in question is 'Siers' a cultivar of Carya  ×  laneyi (an interspecific hybrid between C. ovata and C. cordiformis ). The accession has traits that make it interesting in the pecan breeding program, with potential for both rootstock and scion development. The tall, slender tree form of 'Jones Hybrid' is a trait that could be valuable in commercial pecan cultivars, allowing increased tree densities and reducing the need for expensive hedging operations. Tree size reduction is a goal to be pursued in scion selection and rootstock development, with each goal requiring assessment of reproductive potential of the accession.

Exploring public perceptions of solutions to tree diseases in the UK: Implications for policy-makers.

PubMed

Jepson, Paul; Arakelyan, Irina

2017-10-01

Tree diseases are on the increase in many countries and the implications of their appearance can be political, as well as ecological and economic. Preventative policy approaches to tree diseases are difficult to formulate because dispersal pathways for pest and pathogens are numerous, poorly known and likely to be beyond human management control. Genomic techniques could offer the quickest and most predictable approach to developing a disease tolerant native ash. The population of European Ash ( Fraxinus Excelsi or) has suffered major losses in the last decade, due to the onset of Hymenoscyphus fraxineus (previously called Chalara Fraxinea ) commonly known in the UK as ash dieback. This study presents evidence on the public acceptability of tree-breed solutions to the spread of Chalara , with the main aim to provide science and policy with an up-stream 'steer' on the likely public acceptability of different tree breeding solutions. The findings showed that whilst there was a firm anti-GM and ' we shouldn't tamper with nature ' attitude among UK publics, there was an equally firm and perhaps slightly larger pragmatic attitude that GM (science and technology) should be used if there is a good reason to do so, for example if it can help protect trees from disease and help feed the world. The latter view was significantly stronger among younger age groups (Millennials), those living in urban areas and when the (GM)modified trees were destined for urban and plantation, rather than countryside settings. Overall, our findings suggest that the UK government could consider genomic solutions to tree breeding with more confidence in the future, as large and influential publics appear to be relaxed about the use of genomic techniques to increase tolerance of trees to disease.

Genetic Map of Mango: A Tool for Mango Breeding

PubMed Central

Kuhn, David N.; Bally, Ian S. E.; Dillon, Natalie L.; Innes, David; Groh, Amy M.; Rahaman, Jordon; Ophir, Ron; Cohen, Yuval; Sherman, Amir

2017-01-01

Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color. PMID:28473837

Evaluating and improving rootstocks for apple cultivation

USDA-ARS?s Scientific Manuscript database

The foundations of a productive and healthy orchard are the rootstocks that provide anchorage, water and nutrients essential to the above ground portions of the trees. The utilization of composite trees has increased the efficiency of breeding productive apple trees by dividing the selection of sci...

Myrciaria dubia, an Amazonian fruit: population structure and its implications for germplasm conservation and genetic improvement.

PubMed

Nunes, C F; Setotaw, T A; Pasqual, M; Chagas, E A; Santos, E G; Santos, D N; Lima, C G B; Cançado, G M A

2017-03-22

Myrciaria dubia (camu-camu) is an Amazon tree that produces a tart fruit with high vitamin C content. It is probably the fruit with the highest vitamin C content among all Brazilian fruit crops and it can be used to supplement daily vitamin C dose. This property has attracted the attention of consumers and, consequently, encouraged fruit farmers to produce it. In order to identify and select potential accessions for commercial exploitation and breeding programs, M. dubia has received considerable research attention. The identification and characterization of genetic diversity, as well as identification of the population structure of accessions preserved in germplasm banks are fundamental for the success of any breeding program. The objective of this study was to evaluate the genetic variability of 10 M. dubia populations obtained from the shores of Reis Lake, located in the municipality of Caracaraí, Roraima, Brazil. Fourteen polymorphic inter simple sequence repeat (ISSR) markers were used to study the population genetic diversity, which resulted in 108 identified alleles. Among the 14 primers, GCV, UBC810, and UBC827 produced the highest number of alleles. The study illustrated the suitability and efficiency of ISSR markers to study the genetic diversity of M. dubia accessions. We also revealed the existence of high genetic variability among both accessions and populations that can be exploited in future breeding programs and conservation activities of this species.

Computational approaches for the classification of seed storage proteins.

PubMed

Radhika, V; Rao, V Sree Hari

2015-07-01

Seed storage proteins comprise a major part of the protein content of the seed and have an important role on the quality of the seed. These storage proteins are important because they determine the total protein content and have an effect on the nutritional quality and functional properties for food processing. Transgenic plants are being used to develop improved lines for incorporation into plant breeding programs and the nutrient composition of seeds is a major target of molecular breeding programs. Hence, classification of these proteins is crucial for the development of superior varieties with improved nutritional quality. In this study we have applied machine learning algorithms for classification of seed storage proteins. We have presented an algorithm based on nearest neighbor approach for classification of seed storage proteins and compared its performance with decision tree J48, multilayer perceptron neural (MLP) network and support vector machine (SVM) libSVM. The model based on our algorithm has been able to give higher classification accuracy in comparison to the other methods.

Forest Tree Improvement Research in the South and Southeast

Treesearch

Keith W. Dorman

1966-01-01

The Committee on Southern Forest Tree improvement has directed its Subcommittee on Tree Selection and Breeding to summarize the projects by agencies doing forest tree improvement research in the South and Southeast. This area corresponds roughly to what is known as the southern pine region. The project summaries and the consolidated report were to be patterned after...

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

PubMed

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele.

PubMed

Takeshima, S-N; Miyasaka, T; Matsumoto, Y; Xue, G; Diaz, V de la Barra; Rogberg-Muñoz, A; Giovambattista, G; Ortiz, M; Oltra, J; Kanemaki, M; Onuma, M; Aida, Y

2015-01-01

Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Population-Wide Failure to Breed in the Clark's Nutcracker (Nucifraga columbiana).

PubMed

Schaming, Taza D

2015-01-01

In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark's nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark's nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark's nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark's nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.

Geographic variation in foraging ecologies of breeding and nonbreeding birds in oak woodlands

Treesearch

William M. Block

1990-01-01

I studied geographic variation in the foraging ecology of four breeding and four non breeding species in three oak (Quercus spp.) woodlands of California. Variations were evident for all species. Variations in tree-species use, foraging tactics, substrates, and behaviors were species-specific. For example, White-breasted Nuthatches (Sitta carolinensis) used...

Practical breeding of cottonwood in the north-central region

Treesearch

Carl A. Mohn

1973-01-01

More than 20 years ago Scott Pauley (1949) designated the genus Populus as the "guinea pig of forest-tree breeding. This designation is still appropriate as evidenced by the steady, almost overwhelming, stream of publications related to the genetics and breeding of poplars. A good indication of the scope and depth of genetic work with poplars...

Allozyme markers in forest genetic conservation

Treesearch

Constance I. Millar; R. D. Westfall

1992-01-01

Genetic diversity is important in tree-breeding, in managing rare and endangered tree species, and in maintaining healthy populations of widespread native tree species. Allozymes are useful in determining genetic relationships among species, where they can be used to assess affiliations of rare taxa and predict relative endangerment among species. Because allozymes...

Frankixalus, a New Rhacophorid Genus of Tree Hole Breeding Frogs with Oophagous Tadpoles

PubMed Central

Biju, S. D.; Mahony, Stephen; Kamei, Rachunliu G.; Thomas, Ashish; Shouche, Yogesh; Raxworthy, Christopher J.; Meegaskumbura, Madhava; Bocxlaer, Ines Van

2016-01-01

Despite renewed interest in the biogeography and evolutionary history of Old World tree frogs (Rhacophoridae), this family still includes enigmatic frogs with ambiguous phylogenetic placement. During fieldwork in four northeastern states of India, we discovered several populations of tree hole breeding frogs with oophagous tadpoles. We used molecular data, consisting of two nuclear and three mitochondrial gene fragments for all known rhacophorid genera, to investigate the phylogenetic position of these new frogs. Our analyses identify a previously overlooked, yet distinct evolutionary lineage of frogs that warrants recognition as a new genus and is here described as Frankixalus gen. nov. This genus, which contains the enigmatic ‘Polypedates’ jerdonii described by Günther in 1876, forms the sister group of a clade containing Kurixalus, Pseudophilautus, Raorchestes, Mercurana and Beddomixalus. The distinctiveness of this evolutionary lineage is also corroborated by the external morphology of adults and tadpoles, adult osteology, breeding ecology, and life history features. PMID:26790105

Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers.

PubMed

Cappa, Eduardo P; El-Kassaby, Yousry A; Muñoz, Facundo; Garcia, Martín N; Villalba, Pamela V; Klápště, Jaroslav; Marcucci Poltri, Susana N

2018-06-01

We investigated the impact of combining the pedigree- and genomic-based relationship matrices in a multiple-trait individual-tree mixed model (a.k.a., multiple-trait combined approach) on the estimates of heritability and on the genomic correlations between growth and stem straightness in an open-pollinated Eucalyptus grandis population. Additionally, the added advantage of incorporating genomic information on the theoretical accuracies of parents and offspring breeding values was evaluated. Our results suggested that the use of the combined approach for estimating heritabilities and additive genetic correlations in multiple-trait evaluations is advantageous and including genomic information increases the expected accuracy of breeding values. Furthermore, the multiple-trait combined approach was proven to be superior to the single-trait combined approach in predicting breeding values, in particular for low-heritability traits. Finally, our results advocate the use of the combined approach in forest tree progeny testing trials, specifically when a multiple-trait individual-tree mixed model is considered. Copyright © 2018 Elsevier B.V. All rights reserved.

Breeding bird use of and nesting success in exotic Russian olive in New Mexico

Treesearch

Scott H. Stoleson; Deborah M. Finch

2001-01-01

The exotic tree, Russian olive (Elaeagnus angustifolia), has invaded riparian zones throughout much of the western Unites States. Although promoted as a useful species for wildlife because of its abundant edible fruit, evidence for its value to breeding birds remains sparse. We compared relative rates of usage, nest success, and cowbird parasitism of birds breeding in...

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

PubMed Central

Montenegro, M; Llambí, S; Castro, G; Barlocco, N; Vadell, A; Landi, V; Delgado, JV; Martínez, A

2015-01-01

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (FIS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances DA showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity. PMID:25983624

Population-Wide Failure to Breed in the Clark’s Nutcracker (Nucifraga columbiana)

PubMed Central

Schaming, Taza D.

2015-01-01

In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark’s nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark’s nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark’s nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark’s nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences. PMID:25970294

Pre- and post-experimental manipulation assessments confirm the increase in number of birds due to the addition of nest boxes.

PubMed

Cuatianquiz Lima, Cecilia; Macías Garcia, Constantino

2016-01-01

Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. We assessed whether the availability of tree cavities influenced the number of SCNs in two temperate forest types, and evaluated the change in number of SCNs after adding nest boxes. First, we counted all cavities within each of our 25-m radius sampling points in mature and young forest plots during 2009. We then added nest boxes at standardised locations during 2010 and 2011 and conducted fortnightly bird counts (January-October 2009-2011). In 2011 we added two extra plots of each forest type, where we also conducted bird counts. Prior to adding nest boxes, counts revealed more SCNs in mature than in young forest. Following the addition of nest boxes, the number of SCNs increased significantly in the points with nest boxes in both types of forest. Counts in 2011 confirmed the increase in number of birds due to the addition of nest boxes. Given the likely benefits associated with a richer bird community we propose that, as is routinely done in some countries, forest management programs preserve old tree stumps and add nest boxes to forest plantations in order to increase bird numbers and bird community diversity.

Productivity and breeding habitat of loggerhead shrikes in a southwestern urban environment

USGS Publications Warehouse

Boal, C.W.; Estabrook, T.S.; Duerr, A.E.

2003-01-01

Declines in loggerhead shrike (Lanius ludovicianus) populations have been associated in part with habitat loss and degradation, including that resulting from urbanization. We monitored the productivity and examined nesting habitat of loggerhead shrikes nesting in an urban environment in Tucson, Arizona. We located 22 breeding pairs in 1997 and 26 breeding pairs in 1998, with a 72% breeding area reoccupancy between years. Mean fledgling numbers were 2.28/ nesting attempt and 3.11/successful nest. Although some pairs initially failed and renested, 91% and 73% of shrike pairs successfully fledged young in 1997 and 1998, respectively. Mayfield estimates of nesting success were 78% in 1997 and 65% in 1998. Nest sites were characterized by more trees >3 m in height, taller nest trees than those randomly available, and a greater proportion of bare ground surface than at random sites. Shrike breeding territories had lower proportions of residential and commercial development and greater proportions of open areas with low-growing vegetation than randomly available. Some shrikes nested in school playgrounds, residential front yards, and parking lots, if adjacent open space was available.

Use of Hardwood Tree Species by Birds Nesting in Ponderosa Pine Forests

Treesearch

Kathryn L. Purcell; Douglas A. Drynan

2008-01-01

We examined the use of hardwood tree species for nesting by bird species breeding in ponderosa pine (Pinus ponderosa) forests in the Sierra National Forest, California. From 1995 through 2002, we located 668 nests of 36 bird species nesting in trees and snags on four 60-ha study sites. Two-thirds of all species nesting in trees or snags used...

Insect outbreak shifts the direction of selection from fast to slow growth rates in the long-lived conifer Pinus ponderosa.

PubMed

de la Mata, Raul; Hood, Sharon; Sala, Anna

2017-07-11

Long generation times limit species' rapid evolution to changing environments. Trees provide critical global ecosystem services, but are under increasing risk of mortality because of climate change-mediated disturbances, such as insect outbreaks. The extent to which disturbance changes the dynamics and strength of selection is unknown, but has important implications on the evolutionary potential of tree populations. Using a 40-y-old Pinus ponderosa genetic experiment, we provide rare evidence of context-dependent fluctuating selection on growth rates over time in a long-lived species. Fast growth was selected at juvenile stages, whereas slow growth was selected at mature stages under strong herbivory caused by a mountain pine beetle ( Dendroctonus ponderosae ) outbreak. Such opposing forces led to no net evolutionary response over time, thus providing a mechanism for the maintenance of genetic diversity on growth rates. Greater survival to mountain pine beetle attack in slow-growing families reflected, in part, a host-based life-history trade-off. Contrary to expectations, genetic effects on tree survival were greatest at the peak of the outbreak and pointed to complex defense responses. Our results suggest that selection forces in tree populations may be more relevant than previously thought, and have implications for tree population responses to future environments and for tree breeding programs.

Use of generalized regression tree models to characterize vegetation favoring Anopheles albimanus breeding.

PubMed

Hernandez, J E; Epstein, L D; Rodriguez, M H; Rodriguez, A D; Rejmankova, E; Roberts, D R

1997-03-01

We propose the use of generalized tree models (GTMs) to analyze data from entomological field studies. Generalized tree models can be used to characterize environments with different mosquito breeding capacity. A GTM simultaneously analyzes a set of predictor variables (e.g., vegetation coverage) in relation to a response variable (e.g., counts of Anopheles albimanus larvae), and how it varies with respect to a set of criterion variables (e.g., presence of predators). The algorithm produces a treelike graphical display with its root at the top and 2 branches stemming down from each node. At each node, conditions on the value of predictors partition the observations into subgroups (environments) in which the relation between response and criterion variables is most homogeneous.

Tadpoles of Early Breeding Amphibians are Negatively Affected by Leaf Litter From Invasive Chinese Tallow Trees

NASA Astrophysics Data System (ADS)

Leonard, N. E.

2005-05-01

As wetlands are invaded by Chinese tallow trees (Triadica sebifera), native trees are displaced and detrital inputs to amphibian breeding ponds are altered. I used a mesocosm experiment to examine the effect of Chinese tallow leaf litter on the survival to, size at, and time to metamorphosis of amphibian larvae. Fifty 1000-L cattle watering tanks were treated with 1500 g dry weight of one of five leaf litter treatments: Chinese tallow, laurel oak (Quercus laurifolia), water tupelo (Nyssa aquatica), slash pine (Pinus elliottii), or a 3:1:1:1 mixture. Each tank received 45 tadpoles of Pseudacris feriarum, Bufo terrestris, and Hyla cinerea in sequence according to their natural breeding phonologies. Every Pseudacris feriarum and Bufo terrestris tadpole exposed to Chinese tallow died prior to metamorphosis. Hyla cinerea survival in tanks with tallow-only was significantly lower than that observed for all other leaf treatments. Hyla cinerea tadpoles from tallow-only and mixed-leaf treatments were larger at metamorphosis and transformed faster than those in tanks with native leaves only. These results suggest that Chinese tallow leaf litter may negatively affect tadpoles of early breeding frogs and that Chinese tallow invasion may change the structure of amphibian communities in temporary ponds.

Invasive parasites, habitat change and heavy rainfall reduce breeding success in Darwin's finches.

PubMed

Cimadom, Arno; Ulloa, Angel; Meidl, Patrick; Zöttl, Markus; Zöttl, Elisabet; Fessl, Birgit; Nemeth, Erwin; Dvorak, Michael; Cunninghame, Francesca; Tebbich, Sabine

2014-01-01

Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance)is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.

Better trees through systematic breeding

Treesearch

Robert Z. Callaham

1957-01-01

Today I would like to tell you briefly about the efforts of forest geneticists to improve the quality of forest trees. What do we mean by quality? Here, the consumer has the first word. The trees we produce are primarily for timber production, and the timber growing and wood-using industries give us our guidelines. Nevertheless, many of the characteristics sought by...

Tree genetic and improvement research at the University of Minnesota

Treesearch

Scott S. Pauley

1970-01-01

The School of Forestry's Tree Improvement Research Project was initiated in 1955. Studies in this area during the past fourteen years have been designed to accumulate information on genetic diversity in native and exotic tree species and isolate genetically superior lines for direct use in Minnesota forest plantings or for further selective breeding. Nursery...

Technological advances in temperate hardwood tree improvement including breeding and molecular marker applications

Treesearch

Paula M. Pijut; Keith E. Woeste; G. Vengadesan

2007-01-01

Hardwood forests and plantations are an important economic resource for the forest products industry worldwide and to the international trade of lumber and logs. Hardwood trees are also planted for ecological reasons, for example, wildlife habitat, native woodland restoration, and riparian buffers. The demand for quality hardwood from tree plantations will continue to...

Leafing-out date not indicative of growth rate in hybrid poplars

Treesearch

Harold F. Ford; Edward I. Sucoff

1961-01-01

In breeding trees for rapid growth, testing the progeny usually requires many years. To shorten the testing period, geneticists have tried to find characteristics in juvenile trees that would indicate mature-tree performance. With hybrid poplars (Populus spp.), work at the Northeastern Forest Experiment Station has shown that the thickness of bark on...

Somatic embryogenesis and cryostorage for conservation and restoration of threatened forest trees

Treesearch

S.A. Merkle; A.R. Tull; H.J. Gladfelter; P.M. Montello; J.E. Mitchell; C. Ahn; R.D. McNeill

2017-01-01

Threats to North American forest trees from exotic pests and pathogens or habitat loss, make it imperative that every available tool be employed for conservation and restoration of these at risk species. One such tool, in vitro propagation, could greatly enhance conservation of forest tree genetic material and selection and breeding of resistant or...

Gene-assisted selection: applications of association genetics for forest tree breeding

Treesearch

Philip L. Wilcox; Craig E. Echt; Rowland D. Burdon

2007-01-01

This chapter describes application of association genetics in forest tree species for the purposes of selection. We use the term gene-assisted selection (GAS) to denote application of marker-trait associations determined via association genetics, which we anticipate will be based on poly morph isms associated with expressed genes. The salient features of forest trees...

Genetic data analysis for plant and animal breeding

USDA-ARS?s Scientific Manuscript database

This book is an advanced textbook covering the application of quantitative genetics theory to analysis of actual data (both trait and DNA marker information) for breeding populations of crops, trees, and animals. Chapter 1 is an introduction to basic software used for trait data analysis. Chapter 2 ...

Predicting breeding bird occurrence by stand- and microhabitat-scale features in even-aged stands in the Central Appalachians

USGS Publications Warehouse

McDermott, M.E.; Wood, P.B.; Miller, G.W.; Simpson, B.T.

2011-01-01

Spatial scale is an important consideration when managing forest wildlife habitat, and models can be used to improve our understanding of these habitats at relevant scales. Our objectives were to determine whether stand- or microhabitat-scale variables better predicted bird metrics (diversity, species presence, and abundance) and to examine breeding bird response to clearcut size and age in a highly forested landscape. In 2004-2007, vegetation data were collected from 62 even-aged stands that were 3.6-34.6. ha in size and harvested in 1963-1990 on the Monongahela National Forest, WV, USA. In 2005-2007, we also surveyed birds at vegetation plots. We used classification and regression trees to model breeding bird habitat use with a suite of stand and microhabitat variables. Among stand variables, elevation, stand age, and stand size were most commonly retained as important variables in guild and species models. Among microhabitat variables, medium-sized tree density and tree species diversity most commonly predicted bird presence or abundance. Early successional and generalist bird presence, abundance, and diversity were better predicted by microhabitat variables than stand variables. Thus, more intensive field sampling may be required to predict habitat use for these species, and management may be needed at a finer scale. Conversely, stand-level variables had greater utility in predicting late-successional species occurrence and abundance; thus management decisions and modeling at this scale may be suitable in areas with a uniform landscape, such as our study area. Our study suggests that late-successional breeding bird diversity can be maximized long-term by including harvests >10. ha in size into our study area and by increasing tree diversity. Some harvesting will need to be incorporated regularly, because after 15 years, the study stands did not provide habitat for most early successional breeding specialists. ?? 2010 Elsevier B.V.

Life-history dependent relationships between body condition and immunity, between immunity indices in male Eurasian tree sparrows.

PubMed

Zhao, Yuliang; Li, Mo; Sun, Yanfeng; Wu, Wei; Kou, Guanqun; Guo, Lingling; Xing, Danning; Wu, Yuefeng; Li, Dongming; Zhao, Baohua

2017-08-01

In free-living animals, recent evidence indicates that innate, and acquired, immunity varies with annual variation in the demand for, and availability of, food resources. However, little is known about how animals adjust the relationships between immunity and body condition, and between innate and acquired immunity to optimize survival over winter and reproductive success during the breeding stage. Here, we measured indices of body condition (size-corrected mass [SCM], and hematocrit [Hct]), constitutive innate immunity (plasma total complement hemolysis activity [CH 50 ]) and acquired immunity (plasma immunoglobulin A [IgA]), plus heterophil/lymphocyte (H/L) ratios, in male Eurasian tree sparrows (Passer montanus) during the wintering and the breeding stages. We found that birds during the wintering stage had higher IgA levels than those from the breeding stage. Two indices of body condition were both negatively correlated with plasma CH 50 activities, and positively with IgA levels in wintering birds, but this was not the case in the breeding birds. However, there was no correlation between CH 50 activities and IgA levels in both stages. These results suggest that the relationships between body condition and immunity can vary across life-history stage, and there are no correlations between innate and acquired immunity independent of life-history stage, in male Eurasian tree sparrows. Therefore, body condition indices predict immunological state, especially during the non-breeding stage, which can be useful indicators of individual immunocompetences for understanding the variations in innate and acquired immunity in free-living animals. Copyright © 2017 Elsevier Inc. All rights reserved.

Growth, survival, and competitive ability of chestnut (Castanea Mill.) seedlings planted across a gradient of light levels

Treesearch

Cornelia C. Pinchot; Scott E. Schlarbaum; Stacy L. Clark; Arnold M. Saxton; Ami M. Sharp; Callie J. Schweitzer; Frederick V. Hebard

2017-01-01

There has been an increased interest in tree breeding for resistance to exotic pests and pathogens, however relatively little research has focused on the reintroduction of these tree species. Understanding the durability of resistance in field settings and the field performance of improved trees is critical for successful species reintroduction. To evaluate methods for...

A comparison of the breeding ecology of birds nesting in boxes and tree cavities

Treesearch

Kathryn L. Purcell; Jared Verner; Lewis W. Oring

1997-01-01

We compared laying date, nesting success, clutch size, and productivity of four bird species that nest in boxes and tree cavities to examine whether data from nest boxes are comparable with data from tree cavities. Western Bluebirds (Sialia mexicana) gained the most advantage from nesting in boxes. They initiated egg laying earlier, had higher nesting success, lower...

Restoration of chestnuts as a timber crop in Connecticut

Treesearch

S.L. Anagnostakis; C.C. Pinchot

2014-01-01

American chestnut trees were an important source of timber in Connecticut until chestnut blight disease reduced them to understory shrubs. Breeding begun in 1930 has now produced trees with enough resistance to initiate field trials in the forest. Biological control by hypovirulence viruses is being used in the plots in an effort to keep native trees alive. If native...

Effects of green-tree retention on abundance and guild composition of corticolous arthropods

Treesearch

Juraj Halaj; Charles B. Halpern; Hoonbok Yi

2009-01-01

We studied the effects of varying levels and patterns of green-tree retention on the community composition of bark-dwelling arthropods. Arthropods were sampled with crawl traps installed on 280 live trees and 260 snags (all Douglas-fir) at three locations (experimental blocks) in the western Cascade Range of Oregon and Washington. Sampling coincided with the breeding...

Importance of breeding season and maternal investment in studies of sex-ratio adjustment: a case study using tree swallows

PubMed Central

Baeta, Renaud; Bélisle, Marc; Garant, Dany

2012-01-01

The control of primary sex-ratio by vertebrates has become a major focus in biology in recent years. Evolutionary theory predicts that a differential effect of maternal characteristics on the fitness of sons and daughters is an important route, whereby selection is expected to favour a bias towards the production of one sex. However, despite experimental evidence for adaptive brood sex-ratio manipulation, support for this prediction remains a major challenge in vertebrates where inconsistencies between correlative studies are frequently reported. Here, we used a large dataset (2215 nestlings over 3 years) from a wild population of tree swallows (Tachycineta bicolor) and show that variations in breeding conditions affect female sex allocation in this species. Our results also suggest that such variation in sex allocation, owing to breeding season heterogeneity, modifies the relationships between maternal characteristics and maternal investment. Indeed, we detect a positive effect of maternal age on brood sex-ratio when age also affects offspring condition (in a low-quality breeding season). Our results indicate that including measures of both breeding season quality and maternal investment will help to better understand sex allocation patterns. PMID:22130173

Realized gain from breeding Eucalyptus grandis in Florida

Treesearch

George Meskimen

1983-01-01

E. grandis is in the fourth generation of selection in southwest Florida. The breeding strategy combines a provenance trial, genetic base population, seedling seed orchard, and progeny test in a single plantation where all families are completely randomized in single-tree plots. That planting configuration closely predicted the magnitude of genetic...

Conservation priorities for tree crop wild relatives in the United States

USDA-ARS?s Scientific Manuscript database

Our native crop wild relatives have proved useful as genetic resources in breeding more productive, nutritious, and resilient crops. Their utilization is expected only to increase with better information on the species and improving breeding tools, but may well be constrained by their limited repres...

Genetically engineered trees for plantation forests: key considerations for environmental risk assessment

PubMed Central

Häggman, Hely; Raybould, Alan; Borem, Aluizio; Fox, Thomas; Handley, Levis; Hertzberg, Magnus; Lu, Meng-Zu; Macdonald, Philip; Oguchi, Taichi; Pasquali, Giancarlo; Pearson, Les; Peter, Gary; Quemada, Hector; Séguin, Armand; Tattersall, Kylie; Ulian, Eugênio; Walter, Christian; McLean, Morven

2013-01-01

Forests are vital to the world's ecological, social, cultural and economic well-being yet sustainable provision of goods and services from forests is increasingly challenged by pressures such as growing demand for wood and other forest products, land conversion and degradation, and climate change. Intensively managed, highly productive forestry incorporating the most advanced methods for tree breeding, including the application of genetic engineering (GE), has tremendous potential for producing more wood on less land. However, the deployment of GE trees in plantation forests is a controversial topic and concerns have been particularly expressed about potential harms to the environment. This paper, prepared by an international group of experts in silviculture, forest tree breeding, forest biotechnology and environmental risk assessment (ERA) that met in April 2012, examines how the ERA paradigm used for GE crop plants may be applied to GE trees for use in plantation forests. It emphasizes the importance of differentiating between ERA for confined field trials of GE trees, and ERA for unconfined or commercial-scale releases. In the case of the latter, particular attention is paid to characteristics of forest trees that distinguish them from shorter-lived plant species, the temporal and spatial scale of forests, and the biodiversity of the plantation forest as a receiving environment. PMID:23915092

Pre- and post-experimental manipulation assessments confirm the increase in number of birds due to the addition of nest boxes

PubMed Central

Cuatianquiz Lima, Cecilia

2016-01-01

Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. We assessed whether the availability of tree cavities influenced the number of SCNs in two temperate forest types, and evaluated the change in number of SCNs after adding nest boxes. First, we counted all cavities within each of our 25-m radius sampling points in mature and young forest plots during 2009. We then added nest boxes at standardised locations during 2010 and 2011 and conducted fortnightly bird counts (January–October 2009–2011). In 2011 we added two extra plots of each forest type, where we also conducted bird counts. Prior to adding nest boxes, counts revealed more SCNs in mature than in young forest. Following the addition of nest boxes, the number of SCNs increased significantly in the points with nest boxes in both types of forest. Counts in 2011 confirmed the increase in number of birds due to the addition of nest boxes. Given the likely benefits associated with a richer bird community we propose that, as is routinely done in some countries, forest management programs preserve old tree stumps and add nest boxes to forest plantations in order to increase bird numbers and bird community diversity. PMID:26998410

Apple rootstocks: history, physiology, management and breeding

USDA-ARS?s Scientific Manuscript database

For more than two millennia superior fruit tree genotypes have been grafted onto rootstocks to maintain the genetic identity of the desirable scions. Until the 20th century most fruit trees were grafted onto seedling rootstocks. Following the classification, evaluation and propagation of clonal root...

Insect outbreak shifts the direction of selection from fast to slow growth rates in the long-lived conifer Pinus ponderosa

PubMed Central

Sala, Anna

2017-01-01

Long generation times limit species’ rapid evolution to changing environments. Trees provide critical global ecosystem services, but are under increasing risk of mortality because of climate change-mediated disturbances, such as insect outbreaks. The extent to which disturbance changes the dynamics and strength of selection is unknown, but has important implications on the evolutionary potential of tree populations. Using a 40-y-old Pinus ponderosa genetic experiment, we provide rare evidence of context-dependent fluctuating selection on growth rates over time in a long-lived species. Fast growth was selected at juvenile stages, whereas slow growth was selected at mature stages under strong herbivory caused by a mountain pine beetle (Dendroctonus ponderosae) outbreak. Such opposing forces led to no net evolutionary response over time, thus providing a mechanism for the maintenance of genetic diversity on growth rates. Greater survival to mountain pine beetle attack in slow-growing families reflected, in part, a host-based life-history trade-off. Contrary to expectations, genetic effects on tree survival were greatest at the peak of the outbreak and pointed to complex defense responses. Our results suggest that selection forces in tree populations may be more relevant than previously thought, and have implications for tree population responses to future environments and for tree breeding programs. PMID:28652352

Mangrove habitat partitioning by Ucides cordatus (Ucididae): effects of the degree of tidal flooding and tree-species composition during its life cycle

NASA Astrophysics Data System (ADS)

Wunderlich, A. C.; Pinheiro, M. A. A.

2013-06-01

Environmental factors strongly affect mangrove crabs, and some factors modulate population structure and habitat partitioning during the crabs' life cycle. However, the effect of these environmental factors on habitat selection by mangrove crabs is still unknown. We evaluated habitat selection by the mangrove crab Ucides cordatus in mangrove forests with different degrees of predominance of Rhizophora mangle, Laguncularia racemosa or Avicennia schaueriana, two tidal flooding levels (less- and more-flooded), and two biological periods (breeding and non-breeding seasons). Sampling was conducted in four mangrove forests with different influences of these biotic and abiotic parameters. We used the data for sex ratio to explain environmental partitioning by this species. Females predominated in R. mangle mangroves, independently of the biological period (breeding or non-breeding seasons), and males predominated only in the less-flooded L. racemosa mangroves. The flooding level affected the sex ratio of U. cordatus, with a predominance of males in less-flooded mangroves, independently of the biological period; and a gender balance in the more-flooded mangroves only during the breeding season. Outside the breeding season, the largest specimens were recorded in the R. mangle mangroves, but in the breeding season, the largest crabs were recorded in the L. racemosa mangroves with a higher level of flooding. These results suggest that tree-species composition and tidal flooding level can have a significant effect on the habitat partitioning of sexes and sizes of the mangrove crab U. cordatus both during and outside the breeding season.

Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate.

PubMed

MacLachlan, Ian R; Yeaman, Sam; Aitken, Sally N

2018-02-01

Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca  ×  Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average -7%, range -24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%-86%). Clines in growth with temperature-related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration-related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold-related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry-phenotype-climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using AGF prescriptions similar to those of natural populations.

Institute of forest tree breeding: Improvement and gene conservation of iconic tree species in the 21st Century

Treesearch

C. Dana Nelson; Jennifer L. Koch

2017-01-01

Our nation’s forests and forest trees are undergoing unprecedented stress from invasive pathogens and pests, climate change, land fragmentation, and urbanization. Some of these stresses are acute, either regionally or locally, and are having significant negative impacts on regional and local economies and ecosystems. Managing and improving the genetic resources of...

Genome sequence of the olive tree, Olea europaea.

PubMed

Cruz, Fernando; Julca, Irene; Gómez-Garrido, Jèssica; Loska, Damian; Marcet-Houben, Marina; Cano, Emilio; Galán, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez-Fernández, Manuel; García, Jose Luis; Gut, Ivo G; Vargas, Pablo; Alioto, Tyler S; Gabaldón, Toni

2016-06-27

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip.

PubMed

Cañas-Álvarez, J J; González-Rodríguez, A; Munilla, S; Varona, L; Díaz, C; Baro, J A; Altarriba, J; Molina, A; Piedrafita, J

2015-11-01

The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

Genome-editing technologies and their potential application in horticultural crop breeding

PubMed Central

Xiong, Jin-Song; Ding, Jing; Li, Yi

2015-01-01

Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

Outlook for blight-resistant American chestnut trees

Treesearch

Paul H. Sisco

2009-01-01

Culminating 20 years of breeding efforts, in spring 2008, The American Chestnut Foundation (TACF) delivered its first 500 chestnuts to the USDA Forest Service for testing on National Forest lands. The expectation is that these seedlings will be more resistant to chestnut blight (Cryphonectria parasitica) than are pure American chestnut trees (

Breeding potential of elite Pee Dee germplasm in Upland cotton breeding programs

USDA-ARS?s Scientific Manuscript database

Successful plant breeding programs begin with parental line selection. Effective parental line selection is facilitated when the breeding potential of candidate parental lines is known. Using topcross families involving germplasm representing eight US public cotton breeding programs, we evaluated th...

Nest sites and reproductive success of the Barred Owls (Strix varia) in Michigan

Treesearch

Sergej Postupalsky; Joseph M. Papp; Lewis Scheller

1997-01-01

During 1976-1995 we monitored 114 Barred Owl (Strix varia) breeding attempts in northern Michigan. We describe nest sites and report reproductive success for different types of nest sites. Most natural nest sites were tree cavities caused by decay at places where a limb or tree top had broken off. The mean d.b.h. of cavity trees (N = 18) was 48 cm...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.21 General... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...) A person wishing to obtain a permit under this subpart or approval of cooperative breeding programs...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.21 General... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...) A person wishing to obtain a permit under this subpart or approval of cooperative breeding programs...

Genetically engineered trees for plantation forests: key considerations for environmental risk assessment.

PubMed

Häggman, Hely; Raybould, Alan; Borem, Aluizio; Fox, Thomas; Handley, Levis; Hertzberg, Magnus; Lu, Meng-Zu; Macdonald, Philip; Oguchi, Taichi; Pasquali, Giancarlo; Pearson, Les; Peter, Gary; Quemada, Hector; Séguin, Armand; Tattersall, Kylie; Ulian, Eugênio; Walter, Christian; McLean, Morven

2013-09-01

Forests are vital to the world's ecological, social, cultural and economic well-being yet sustainable provision of goods and services from forests is increasingly challenged by pressures such as growing demand for wood and other forest products, land conversion and degradation, and climate change. Intensively managed, highly productive forestry incorporating the most advanced methods for tree breeding, including the application of genetic engineering (GE), has tremendous potential for producing more wood on less land. However, the deployment of GE trees in plantation forests is a controversial topic and concerns have been particularly expressed about potential harms to the environment. This paper, prepared by an international group of experts in silviculture, forest tree breeding, forest biotechnology and environmental risk assessment (ERA) that met in April 2012, examines how the ERA paradigm used for GE crop plants may be applied to GE trees for use in plantation forests. It emphasizes the importance of differentiating between ERA for confined field trials of GE trees, and ERA for unconfined or commercial-scale releases. In the case of the latter, particular attention is paid to characteristics of forest trees that distinguish them from shorter-lived plant species, the temporal and spatial scale of forests, and the biodiversity of the plantation forest as a receiving environment. © 2013 ILSI Research Foundation. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data.

PubMed

Tapio, I; Värv, S; Bennewitz, J; Maleviciute, J; Fimland, E; Grislis, Z; Meuwissen, T H E; Miceikiene, I; Olsaker, I; Viinalass, H; Vilkki, J; Kantanen, J

2006-12-01

Northern European indigenous cattle breeds are currently endangered and at a risk of becoming extinct. We analyzed variation at 20 microsatellite loci in 23 indigenous, 3 old imported, and 9 modern commercial cattle breeds that are presently distributed in northern Europe. We measured the breeds' allelic richness and heterozygosity, and studied their genetic relationships with a neighbor-joining tree based on the Chord genetic distance matrix. We used the Weitzman approach and the core set diversity measure of Eding et al. (2002) to quantify the contribution of each breed to the maximum amount of genetic diversity and to identify breeds important for the conservation of genetic diversity. We defined 11 breeds as a "safe set" of breeds (not endangered) and estimated a reduction in genetic diversity if all nonsafe (endangered) breeds were lost. We then calculated the increase in genetic diversity by adding one by one each of the nonsafe breeds to the safe set (the safe-set-plus-one approach). The neighbor-joining tree grouped the northern European cattle breeds into Black-and-White type, Baltic Red, and Nordic cattle groups. Väne cattle, Bohus Poll, and Danish Jersey had the highest relative contribution to the maximum amount of genetic diversity when the diversity was quantified by the Weitzman diversity measure. These breeds not only showed phylogenetic distinctiveness but also low within-population variation. When the Eding et al. method was applied, Eastern Finncattle and Lithuanian White Backed cattle contributed most of the genetic variation. If the loss of the nonsafe set of breeds happens, the reduction in genetic diversity would be substantial (72%) based on the Weitzman approach, but relatively small (1.81%) based on the Eding et al. method. The safe set contained only 66% of the observed microsatellite alleles. The safe-set-plus-one approach indicated that Bohus Poll and Väne cattle contributed most to the Weitzman diversity, whereas the Eastern Finncattle contribution was the highest according to the Eding et al. method. Our results indicate that both methods of Weitzman and Eding et al. recognize the importance of local populations as a valuable resource of genetic variation.

Chemical Relationship On Detection Of Ganoderma Disease On Oil Palm Tree System

NASA Astrophysics Data System (ADS)

Imran, S. N. M.; Baharudin, F.; Ali, M. F.; Rahiman, M. H. F.

2018-04-01

Detection of fungal disease is the major issues in agricultural management and production. This disease would attack the plantation area and damaging the based root or the stem tissue of the trees. In oil palm industry, Basal Stem Rot (BSR) is the major disease in Malaysia that caused by a fungal named Ganoderma Boninense species. Since agricultural areas in Malaysia are the great factors that contribute in the economic sector, therefore the prevention and controlling this disease situation are needed to reduce the extent of the infection. These plant diseases are mostly being caused by the inflectional disease form such as viruses, viroids, bacteria, protozoa and even parasitic plants. It also could included mites and vertebrate or small insects that consume the plant tissues. Studies focused more on the breeding and relationship of the disease in the stumps, roots and soil system if oil palm trees by identifying the heavy metal; Phosphorus, copper, Iron, Manganese, Potassium and Zinc characteristic. Samples were taken from various types of physical appearance of the trees. It shows the relationship of the fungal disease breeding between oil palm trees and the heavy metals does affect the tree’s system.

Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED

USDA-ARS?s Scientific Manuscript database

The complete genomic sequences of apple (Malus × domestica Borkh), peach (Prunus persica (L.) Batsch), and diploid strawberry (Fragaria vesca L.) – one member of each of the three main fruit-producing branches of the Rosaceae family tree – were available in 2010. Despite this achievement, virtually ...

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes

USDA-ARS?s Scientific Manuscript database

Background: Apple tree breeding is slow and difficult due to long generation times, self incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose stead...

Seed zones and breeding zones for sugar pine in southwestern Oregon.

Treesearch

Robert K. Campbell; Albert I. Sugano

1987-01-01

Provisional seed zones and breeding zones were developed for sugar pine (Pinus lambertiana Dougl.) in southwestern Oregon. Zones are based on a map of genetic variation patterns obtained by evaluating genotypes of trees from 142 locations in the region. Genotypes controlling growth vigor and growth rhythm were assessed in a common garden. Within...

Breeding birds of even- and uneven-aged pine forests of eastern Texas

Treesearch

Ronald E. Thill; Nancy E. Koerth

2005-01-01

While single-tree selection, uneven-aged management is being used increasingly on southern national forests as an alternative to clearcutting and planting of pine, its effects on wildlife are largely unknown. We compared breeding season bird abundance, species richness, diversity, and composition among uneven-aged stands and six seral stages of even-aged stands in...

The pines of the Eddy Arboretum

Treesearch

John Duffield

1949-01-01

The Eddy Arboretum at Placerville, California, contains more than 90 species, varieties, and hybrids of pines, and is therefore of great interest to horticulturists. The Arboretum was established in 1925 as a source of breeding stock for the Eddy Tree Breeding Station, founded in the same year by Mr. James G. Eddy of Seattle. In 1934 Mr. Eddy presented the Arboretum...

Conservation priorities for tree crop wild relatives in the United States

Treesearch

Colin K. Khoury; Stephanie L. Greene; Karen A. Williams; Chrystian C. Sosa; Chris Richards

2017-01-01

Crop wild relatives native to the United States have proved useful as genetic resources in breeding more productive, nutritious, and resilient crops. Their utilization is expected to increase with better information about the species and improving breeding tools. But this utilization may be constrained by their limited representation in genebanks and the ongoing loss...

The potential of breeding for enhanced inducibility in Pinus pinaster and Pinus radiata

Treesearch

Rafael Zas; Alejandro Solla; Xoaquin Moreira; Luis Sampedro

2012-01-01

Most resistance mechanisms against pests and pathogens in pine trees involve the production of chemical defenses. These defenses are not cost free and the production of secondary metabolisms is generally inversely related with other plant fitness correlates, such as growth. The existence of these negative genetic correlations imposes an important obstacle for breeding...

Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora.

PubMed

Leroy, Thierry; De Bellis, Fabien; Legnate, Hyacinthe; Musoli, Pascal; Kalonji, Adrien; Loor Solórzano, Rey Gastón; Cubry, Philippe

2014-06-01

The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum-Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.

Breeding next generation tree fruits: technical and legal challenges

PubMed Central

Dalla Costa, Lorenza; Malnoy, Mickael; Gribaudo, Ivana

2017-01-01

The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of ‘green’ biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome. Grapevine, the most important fruit crop in the world from an economical point of view, is a peculiar case for NPBTs because of the load of cultural aspects, varietal traditions and consumer demands, which hinder the use of classical breeding techniques and, furthermore, the application of genetic engineering to wine grape cultivars. Here we explore the technical challenges which may hamper the application of cisgenesis and genome editing to this perennial plant, in particular focusing on the bottlenecks of the Agrobacterium-mediated gene transfer. In addition, strategies to eliminate undesired sequences from the genome and to choose proper target sites are discussed in light of peculiar features of this species. Furthermore is reported an update of the international legislative frameworks regulating NPBT products which shows conflicting positions and, in the case of the European Union, a prolonged lack of regulation. PMID:29238598

Impact of Supplementary Feeding on Reproductive Success of White Storks

PubMed Central

Hilgartner, Roland; Stahl, Daniel; Zinner, Dietmar

2014-01-01

European white stork (Ciconia ciconia) populations have been object to several conservation measures such as reintroduction programs, habitat improvement or supplementary feeding in the last decades. Although recent white stork censuses revealed an upward trend of most of the western populations, evaluations of the relative importance of certain conservation measures are still scarce or even lacking. In our study we analyzed the effect of supplementary feeding on the reproductive success of white storks in conjunction with other factors such as weather or nest site characteristics. We present data of 569 breeding events at 80 different nest sites located in variable distances to an artificial feeding site at Affenberg Salem (south-western Germany) collected from 1990–2012. A multilevel Poisson regression revealed that in our study population (1) reproductive success was negatively affected by monthly precipitation in April, May and June, (2) pairs breeding on power poles had a lower reproductive success than pairs breeding on platforms or trees and (3) reproductive success was significantly higher in pairs breeding in close distance to the feeding site. The number of fledglings per nest decreased by 8% per kilometer distance to the feeding site. Our data suggest that supplementary feeding increases fledgling populations which may be a tool to attenuate population losses caused by factors such as habitat deterioration or unfavorable conditions in wintering habitats. PMID:25119566

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the Director... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Approval of cooperative breeding programs...

Reproductive traits affect the rescue of valuable and endangered multipurpose tropical trees

PubMed Central

Sinébou, Viviane; Quinet, Muriel; Ahohuendo, Bonaventure C.; Jacquemart, Anne-Laure

2016-01-01

Conservation strategies are urgently needed in Tropical areas for widely used tree species. Increasing numbers of species are threatened by overexploitation and their recovery might be poor due to low reproductive success and poor regeneration rates. One of the first steps in developing any conservation policy should be an assessment of the reproductive biology of species that are threatened by overexploitation. This work aimed to study the flowering biology, pollination and breeding system of V. doniana, a multipurpose threatened African tree, as one step in assessing the development of successful conservation strategies. To this end, we studied (1) traits directly involved in pollinator attraction like flowering phenology, flower numbers and morphology, and floral rewards; (2) abundance, diversity and efficiency of flower visitors; (3) breeding system, through controlled hand-pollination experiments involving exclusion of pollinators and pollen from different sources; and (4) optimal conditions for seed germination. The flowering phenology was asynchronous among inflorescences, trees and sites. The flowers produced a large quantity of pollen and nectar with high sugar content. Flowers attracted diverse and abundant visitors, counting both insects and birds, and efficient pollinators included several Hymenoptera species. We detected no spontaneous self-pollination, indicating a total dependence on pollen vectors. Vitex doniana is self-compatible and no inbreeding depression occurred in the first developmental stages. After extraction of the seed from the fruit, seed germination did not require any particular conditions or pre-treatments and the seeds showed high germination rates. These pollination and breeding characteristics as well as germination potential offer the required conditions to develop successful conservation strategies. Protection, cultivation and integration in agroforestry systems are required to improve the regeneration of the tree. PMID:27354660

Reproductive traits affect the rescue of valuable and endangered multipurpose tropical trees.

PubMed

Sinébou, Viviane; Quinet, Muriel; Ahohuendo, Bonaventure C; Jacquemart, Anne-Laure

2016-01-01

Conservation strategies are urgently needed in Tropical areas for widely used tree species. Increasing numbers of species are threatened by overexploitation and their recovery might be poor due to low reproductive success and poor regeneration rates. One of the first steps in developing any conservation policy should be an assessment of the reproductive biology of species that are threatened by overexploitation. This work aimed to study the flowering biology, pollination and breeding system of V. doniana, a multipurpose threatened African tree, as one step in assessing the development of successful conservation strategies. To this end, we studied (1) traits directly involved in pollinator attraction like flowering phenology, flower numbers and morphology, and floral rewards; (2) abundance, diversity and efficiency of flower visitors; (3) breeding system, through controlled hand-pollination experiments involving exclusion of pollinators and pollen from different sources; and (4) optimal conditions for seed germination. The flowering phenology was asynchronous among inflorescences, trees and sites. The flowers produced a large quantity of pollen and nectar with high sugar content. Flowers attracted diverse and abundant visitors, counting both insects and birds, and efficient pollinators included several Hymenoptera species. We detected no spontaneous self-pollination, indicating a total dependence on pollen vectors. Vitex doniana is self-compatible and no inbreeding depression occurred in the first developmental stages. After extraction of the seed from the fruit, seed germination did not require any particular conditions or pre-treatments and the seeds showed high germination rates. These pollination and breeding characteristics as well as germination potential offer the required conditions to develop successful conservation strategies. Protection, cultivation and integration in agroforestry systems are required to improve the regeneration of the tree. Published by Oxford University Press on behalf of the Annals of Botany Company.

A founder project: marketing the domestication baseline for forest trees

Treesearch

C. G. Williams; Floyd E. Bridgwater; C. Dana Nelson

2004-01-01

One of the most apparent benefits of forest genomics programmes is to provide genotypic information on the original selections of tree improvement programmes worldwide. In many breeding programmes, brances from these selections were grafted onto seedlings and the grafted seedlings composed the first seed orchards for planting programmes. with advanced generation...

Provenance research: investigation of genetic diversity associated with geography

Treesearch

Robert Z. Callaham

1963-01-01

Provenance in forestry refers to the population of trees growing at n particular place of origin. Provenance research defines the genetic and environmental components of phenotypic variation associated with geographic source. Information on provenance is important in assuring sources of seed to give well-adapted, productive trees and in directing breeding of...

Chapter 6: Characteristics of Marbled Murrelet Nest Trees and Nesting Stands

Treesearch

Thomas E. Hamer; S. Kim Nelson

1995-01-01

We summarize the characteristics of 61 tree nests and nesting stands of the Marbled Murrelet ( Brachyramphus marmoratus ) located from 1974 to 1993 in Alaska, British Columbia, Washington, Oregon, and California. Evidence of breeding 30-60 km inland was common in California, Oregon, and Washington. Nesting greater distances from the coast may have...

Generation of American elm trees with tolerance to Dutch elm disease through controlled crosses and selection

Treesearch

James M. Slavicek; Kathleen S. Knight

2012-01-01

The goal of our research and development efforts is to generate new and/or improved selections of the American elm (Ulmus americana L.) with tolerance/resistance to Dutch elm disease (DED). The approaches we are taking for this effort include: 1) controlled breeding using known DED -tolerant selections, 2) controlled breeding using DED-tolerant...

Seed zones and breeding zones for white pine in the Cascade Range of Washington and Oregon.

Treesearch

Robert K. Campbell; Albert I. Sugano

1989-01-01

Provisional seed zones and breeding zones were developed for white pine (Pinus monticola Dougl. ex D. Don) in the Cascade Range of western Washington and Oregon. Recommendations were based on genetic variation patterns obtained by evaluating genotypes of trees from 115 locations. Genotypes controlling growth vigor and growth rhythm were assessed in...

Breeding season concerns and response to forest management: Can forest management produce more breeding birds? Ornitologia Neotropical

Treesearch

J.L. Larkin; P.B. Wood; T.J. Boves; J. Sheehan; D.A. Buehler

2012-01-01

Cerulean Warblers (Setophaga cerulea), one of the fastest declining avian species in North America, are associated with heterogeneous canopies in mature hardwood forests. However, the age of most second and third-growth forests in eastern North American is not sufficient for natural tree mortality to maintain structurally diverse canopies. Previous research suggests...

[Breeding ecology of Chinese Bulbul in the urban environment of Hangzhou, China].

PubMed

Lan, Si-Si; Zhang, Qin; Huang, Qin; Chen, Shui-Hua

2013-06-01

The Chinese Bulbul, Pycnonotus sinensis, is one of the most abundant and widely distributed birds of south China, settling even in dense urban areas. From March-July 2012, we surveyed the Chinese Bulbul in the urban environment of Hangzhou, China, to gain a clearer perspective on their breeding ecology. Totally, 117 nests were found, mainly on the trees of Osmanthus fragrans (84.6%, n=117) in residential areas,street tree strips, and green belt. Our results include several noteworthy observations: nest height from the ground was 3.16±0.91 m (n=117); egg-laying begins in early April with peak times from April 11-25; and the nesting period was 11.85±1.12 days (n=47). In terms of fertility and reproduction, we also observed that the average incubation period was 11.34±1.12 days (n=32); average clutch size was 3.37±0.48 eggs (n=103); hatching success 68.3%, fledging rate 52.1%, and the total breeding success 35.58% (n=117). The main causes of breeding failure included egg and fledgling predation, as well as human disturbance.

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture.

PubMed

Migault, Vincent; Pallas, Benoît; Costes, Evelyne

2016-01-01

In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a 'Starkrimson' × 'Granny Smith' cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.

Patterns of molecular genetic variation among cat breeds.

PubMed

Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

2008-01-01

Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

Radioactive contamination of nest materials of the Eurasian Tree Sparrow Passer montanus due to the Fukushima nuclear accident: The significance in the first year.

PubMed

Matsui, Shin; Kasahara, Satoe; Morimoto, Gen; Mikami, Osamu K; Watanabe, Mamoru; Ueda, Keisuke

2015-11-01

The 2011 Fukushima nuclear accident contaminated large areas of eastern and northeastern Japan, releasing vast amounts of radiation. Here we investigated radioactive contamination of the nest materials of the Eurasian Tree Sparrow Passer montanus from the breeding season of 2011 directly after the accident to the next breeding season of 2012 at two sites. In Tokyo (222 km southwest of the plant), ambient dose rates in the nestboxes were lower than those in Ibaraki (175 km southwest of the plant), where the levels of 2011 were higher than those of 2012. Further, the amount of radioactive Cs in each nest increased with the increase in nest weight, with a higher increment at Ibaraki than at Tokyo. These data suggested higher nest contamination levels in the breeding season directly after a nuclear accident than in later seasons, and an increment of nest contamination levels via nest materials of birds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase.

PubMed

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross 'Olivière' x 'Arbequina' were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase

PubMed Central

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross ‘Olivière’ x ‘Arbequina’ were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding. PMID:26062090

Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding.

PubMed

Holliday, Jason A; Aitken, Sally N; Cooke, Janice E K; Fady, Bruno; González-Martínez, Santiago C; Heuertz, Myriam; Jaramillo-Correa, Juan-Pablo; Lexer, Christian; Staton, Margaret; Whetten, Ross W; Plomion, Christophe

2017-02-01

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology. © 2016 John Wiley & Sons Ltd.

Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping.

PubMed

Durand, Jean-Baptiste; Allard, Alix; Guitton, Baptiste; van de Weg, Eric; Bink, Marco C A M; Costes, Evelyne

2017-01-01

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γ g ) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γ g and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

Avian guild structure and habitat associations in suburban bird communities

Treesearch

Richard M. ​DeGraaf; James M. Wentworth

1986-01-01

Breeding bird communities were compared in three suburbs: a 70-year-old area of large houses along streets shaded by mature trees (MT), primarily oaks (Quercus) and elms (Ulmus); a 15-year-old area built upon open agricultural land with young maple (Acer) street trees (YT); and a 15-year-old area on which...

'HoneySweet' - a transgenic plum pox virus resistant plum - from laboratory and experimental field plots to regulatory approval

USDA-ARS?s Scientific Manuscript database

Genetic engineering (GE) has the potential to revolutionize fruit tree breeding. It is an approach that can target specific genetic improvements and allow for the development of novel, useful traits. While GE does not provide a panacea for all of the difficulties associated with fruit tree breedin...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for zoological breeding or display...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for zoological breeding or display...

Tree stocking affects winter bird densities across a gradient of savanna, woodland, and forest in the Missouri Ozarks

Treesearch

Sarah W. Kendrick; Frank R., III Thompson

2013-01-01

Savanna and woodland were historically prevalent in the midwestern United States, and managers throughout the area are currently attempting to restore these communities. Better knowledge of the responses of breeding and non-breeding birds to savanna and woodland restoration is needed to inform management.We surveyed abundance of winter resident birds across a gradient...

Woody landscape plant breeding in Minnesota (45°N): It's not all about cold hardiness

Treesearch

S.C. ​Hokanson; V.M. Whitaker; J.M. Bradeen; M.C. Long; S.K. Krebs; R.A. Blanchette; J. Juzwik; K. Zuzek; S. McNamara

2010-01-01

The Woody Landscape Plant Breeding project at the University of Minnesota has been in existence since 1954. The project was initiated largely to develop an extended palette of cold-hardy woody landscape plants for northern landscapes. Since its inception, it has been responsible for the release of 49 woody plant cultivars including large stature shade trees, small...

Effectiveness of a detached‐leaf assay as a proxy for stem inoculations in backcrossed chestnut (Castanea) blight resistance breeding populations

Treesearch

N. R. LaBonte; J.R. McKenna; K. Woeste

2016-01-01

A recently developed detached-leaf blight resistance assay has generated interest because it could reduce the amount of time needed to evaluate backcrossed hybrid trees in the American chestnut blight resistance breeding programme. We evaluated the leaf inoculation technique on a sample of advanced progeny from the Indiana state chapter American Chestnut Foundation...

Reconsidering Tree Fruit as Candidate Crops Through the Use of Rapid Cycle Crop Breeding Technologies

NASA Technical Reports Server (NTRS)

Graham, Gary Thomas

2014-01-01

Tree fruit, although desirable from a crew nutrition and menu diversity perspective, have long been dismissed as candidate crops based on their long juvenile phase, large architecture, low short-term harvest index, and dormancy requirements. Recent developments in Rapid Cycle Crop Breeding (RCCB) have overcome these historical limitations, opening the door to a new era in candidate crop research. Researchers at the United States Department of Agriculture (USDA) have developed FT-construct (Flowering Locus T) dwarf plum lines that have a very short juvenile phase, vine-like architecture, and no obligate dormancy period. In a collaborative research effort, NASA and the USDA are evaluating the performance of these FT-lines under controlled environment conditions relevant to spaceflight.

Breeding birds and vegetation structure in western North Dakota wooded draws

USGS Publications Warehouse

Faanes, C.A.

1987-01-01

Populations and distribution of breeding birds occupying wooded draws were studied in a five-county region of western North Dakota during June 1982. Wooded draw vegetation was dominated by green ash, which occurred in 96% of the draws sampled. Chokecherry and juneberry were the most frequent shrub species. I recorded 49 bird species in the 30 draws censused. Rufous-sided towhee, brown-headed cowbird, house wren, and American goldfinch were the most numerous bird species present. Significant correlations were found between (1) the number of live trees and bird species evenness, (2) density of dead trees and bird species diversity and richness, (3) density of shrubs with bird species evenness, and (4) foliage volume in the high ground layer and bird species evenness.

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

PubMed Central

2013-01-01

Background Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees. Results Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified. Conclusions Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services. PMID:23317283

Effects of Supplementary Feeding on the Breeding Ecology of the Buff-Throated Partridge in a Tibetan Sacred Site, China.

PubMed

Yang, Nan; Moermond, Timothy C; Lloyd, Huw; Xu, Yu; Dou, Liang; Zhang, Kai; Yue, Bisong; Ran, Jianghong

2016-01-01

Our goal was to document effects of year-round supplemental feeding on breeding ecology of the Buff-throated Partridge, Tetraophasis szechenyii, within a Tibetan sacred site. We evaluated effects of supplemental feeding used as religious/cultural practices which could potentially aid conservation of endangered phasianids. We compared fed breeding groups to neighboring nonfed groups. Fed groups initiated first clutches significantly earlier than nonfed groups. Earlier laying groups within fed and nonfed groups showed significantly lower hatching rates than later groups; however, fed groups showed significantly higher hatching rates than nonfed groups laying in the same period. Earlier laying increased opportunities to renest. All six fed groups with clutch failures renested compared to only one of five nonfed groups with clutch failures. Fed female breeders showed significantly greater investment in their young with larger clutches and larger eggs, which likely increased survivability of early hatchlings. We observed no predation on birds at feeding sites and recorded only four cases of predation on incubating females, which showed no detectable difference between fed and nonfed groups. Ground-nesting birds typically face high risks of predation. Ten of the 48 groups nested in trees, which occurs in few phasianid species. Tree nests showed significantly higher hatching rates compared to ground nests; however, we found no significant difference in tree nesting between fed and nonfed groups. This partridge is one of four gallinaceous species with cooperative breeding. Breeding groups with helpers had significantly greater reproductive success than single pairs, and fed female breeders with helpers laid bigger eggs than single pairs. Comparing annual reproductive output per group, fed groups not only produced significantly more independent young (≥ 150 days post-hatching), their young hatched significantly earlier, which likely have greater reproductive value over later hatched young of nonfed groups. Supplemental feeding year-round is likely what enabled the successes of the fed partridges.

Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

PubMed Central

Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

2015-01-01

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

PubMed

Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

2005-01-01

In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

Hybrid poplar planting in the Lake States

Treesearch

Paul O. Rudolf

1948-01-01

Poplars are among our fastest growing trees. Many of them are also relatively easy to grow from cuttings and to hybridize by means of cut flower-bearing twigs. Their wood is in demand for pulpwood, veneer for match and crate production, boxboards, and other uses. For these reasons there has been interest in many countries in selecting and breeding poplars. The tree...

Asian longhorned beetle (Coleoptera: Cerambycidae), an introduced pest of maple and other hardwood trees in North America and Europe

Treesearch

P.S. Meng; K. Hoover; M.A. Keena

2015-01-01

The Asian longhorned beetle, Anoplophora glabripennis (Motschulsky), threatens urban and forest hardwood trees both where introduced and in parts of its native range. Native to Asia, this beetle has hitchhiked several times in infested wood packaging used in international trade, and has established breeding populations in five U.S. states, Canada,...

Bird populations in logged and unlogged western larch/Douglas-fir forest in northwestern Montana

Treesearch

Bret W. Tobalske; Raymond C. Shearer; Richard L. Hutto

1991-01-01

Of 32 species of abundant breeding birds, populations of 10 species differed significantly between small cutting units and adjacent uncut forest. Foliage foragers and tree gleaners were less abundant in cutting units, while flycatching species and ground foragers were more common there. Of nesting guilds, conifer tree nesters were least abundant in cutting units, and...

Habitat suitability and nest survival of white-headed woodpeckers in unburned forests of Oregon

Treesearch

Jeff P. Hollenbeck; Vicki Saab; Richard W. Frenzel

2011-01-01

We evaluated habitat suitability and nest survival of breeding white-headed woodpeckers (Picoides albolarvatus) in unburned forests of central Oregon, USA. Daily nest-survival rate was positively related to maximum daily temperature during the nest interval and to density of large-diameter trees surrounding the nest tree. We developed a niche-based habitat suitability...

Management practices associated with conception rate and service rate of lactating Holstein cows in large, commercial dairy herds.

PubMed

Schefers, J M; Weigel, K A; Rawson, C L; Zwald, N R; Cook, N B

2010-04-01

Data from lactating Holstein cows in herds that participate in a commercial progeny testing program were analyzed to explain management factors associated with herd-average conception and service rates on large commercial dairies. On-farm herd management software was used as the source of data related to production, reproduction, culling, and milk quality for 108 herds. Also, a survey regarding management, facilities, nutrition, and labor was completed on 86 farms. A total of 41 explanatory variables related to management factors and conditions that could affect conception and service rate were considered in this study. Models explaining conception and service rates were developed using a machine learning algorithm for constructing model trees. The most important explanatory variables associated with conception rate were the percentage of repeated inseminations between 4 and 17 d post-artificial insemination, stocking density in the breeding pen, length of the voluntary waiting period, days at pregnancy examination, and somatic cell score. The most important explanatory variables associated with service rate were the number of lactating cows per breeding technician, use of a resynchronization program, utilization of soakers in the holding area during the summer, and bunk space per cow in the breeding pen. The aforementioned models explained 35% and 40% of the observed variation in conception rate and service rate, respectively, and underline the association of herd-level management factors not strictly related to reproduction with herd reproductive performance. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Relative abundance of tree hole-breeding mosquitoes in Boone County, Missouri, USA, with emphasis on the vector potential of Aedes triseriatus for canine heartworm, Dirofilaria immitis (Spirurida: Filariidae).

PubMed

Debboun, Mustapha; Green, Theodore J; Rueda, Leopoldo M; Hall, Robert D

2005-09-01

Aedes (Protomacleaya) triseriatus currently shares its habitat in the USA with the introduced species Aedes (Finlaya) japonicus and Aedes (Stegomyia) albopictus. In the late 1980s, before the introduction of these 2 species, Ae. triseriatus was the dominant tree hole- and artificial container-breeding mosquito in central Missouri. Aedes triseriatus represented 89% of the mosquito immatures collected from water-filled tree holes and artificial containers at 3 forested field sites in central Missouri, from May to October, 1986 to 1988. Laboratory-reared female Ae. triseriatus were able to support larval development of Dirofilaria immitis (canine heartworm) to the infective 3rd larval stage. A blood meal from a microfilaremic Collie-mix dog was sufficient to infect adult female mosquitoes, indicating that Ae. triseriatus is a possible vector of canine heartworm in central Missouri. Confirmation of the vector status of this species depends on the yet-to-be observed transmission of D. immitis by Ae. triseriatus in the field, possibly by experimental infection of dogs by wild-caught mosquitoes. Defining the role of this species in epizootic outbreaks could contribute toward accurate risk assessment as the abundance of Ae. triseriatus increases and decreases in response to the success of Ae. albopictus, Ae. japonicus, or other introduced container-breeding mosquitoes.

Plastid genome sequence of an ornamental and editable fruit tree of Rosaceae, Prunus mume.

PubMed

Wang, Shuo; Gao, Cheng-Wen; Gao, Li-Zhi

2016-11-01

Here we assembled and analyzed the complete chloroplast genome of Prunus mume, a popular ornamental and editable fruit tree of Rosaceae. The cp genome exhibited a circular DNA molecule of 157 712 bp with a typical quadripartite structure consisted of two inverted repeat regions (IRa and IRb) of 26 394 bp separated by large (LSC) and small (SSC) single-copy regions of 85 861 and 19 063 bp, respectively. It encoded 112 unique genes, 19 of which were duplicated in the IR regions, giving a total of 131 genes. Eighteen of these genes harbored one or two introns. GC content was 38.9%, and coding regions accounted for 51.3% of the genome. Phylogenetic analysis showed that P. mume clustered with P. persica and P. kansuensis in the genus Punus. This newly determined chloroplast genome will enhance modern breeding programs for the purpose of genetic improvement of this valuable plant.

Schemes for Oestrus Synchronization Protocols and Controlled Breeding Programs in Cattle

NASA Astrophysics Data System (ADS)

Sabo, Y. G.; Sandabe, U. K.; Maina, V. A.; Balla, H. G.

Today prostaglandin and progesterone has been found widely used in several schemes of oestrus synchronization and controlled breeding program. Several controlled breeding program, have been developed for synchronizing groups of all open or lactating cows within a breeding group with or without ovarian palpation. Such programs are reviewed in this article which involves extending the luteal phase by treatment with exogenous progesterone such as: progesterone treatment regimes using syncro-mate-B, progesterone releasing intravaginal device, melengesterol acetate-select and melegestrol acetate plus prostaglandin. Also reviewed in the program is the termination of the luteal phase by treatment with prostaglandin or its analogues. These includes, controlled breeding without ovarian palpation such as, the 7-days program; 11-days program, target breeding, ovsynch program, Heat synch, Cosynch and pre synch-ovsynch program. In our opinion full potential of progesterone and prostaglandin for the detection of oestrus and timed artificial insemination should be utilized. This reduces the much labour input employed in previous years. The practitioner of the livestock herd health must-develop strategies for the delivery of this technology to livestock farmers, its use and limitations.

Molecular characterization of Syrian date palm cultivars using plasmid-like DNA markers.

PubMed

Haider, N; Nabulsi, I

2012-02-01

Date palm (Phoenix dactylifera L.) is one of the most important domesticated fruit trees in the Near East and North African countries. This tree has been, for several decades, in serious threat of being completely destroyed by the "Bayoud" disease caused by Fusarium oxysporum f. sp. albedinis. In this study, 18 Syrian date palm cultivars and four male trees were analyzed according to the identity of mitochondrial plasmid-like DNAs. A PCR strategy that employs plasmid-like DNAs-specific primer pair was used. These primers amplify a product of either 373-bp or 265-bp that corresponds to the S-(Bayoud-susceptible) or the R-plasmid (Bayoud-resistant), respectively. Generated data revealed that only six cultivars ('Medjool', 'Ashrasi', 'Gish Rabi', 'Khineze', and yellow- and red-'Kabkab') have the S-plasmid, suggesting their susceptibility to the fusariosis, while the remaining 12 cultivars and the four male trees contain the R-plasmid, suggesting their resistance to the fusariosis. The PCR process applied here has been proved efficient for the rapid screening for the presence of the S and R DNAs in Syrian date palm. PCR markers developed in this study could be useful for the screening of date palm lines growing in the field. The availability of such diagnostic tool for plasmid characterization in date palm would also be of great importance in establishing propagation and breeding programs of date palm in Syria.

Mapping vulnerability of spruce-fir stands in the Northeast to spruce budworm attack

Treesearch

Thomas F. McLintock

1949-01-01

Once again a spruce budworm epidemic threatens to destroy large volumes of timber in the Northeast. One defense against the budworm is to cut and utilize trees in those stands in which the budworms are most apt to feed and breed. In this report the author presents three practical methods of determining what trees or stands should be cut first.

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation.

PubMed

Shinada, Hiroshi; Yamamoto, Toshio; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Matsuba, Shuichi; Fujino, Kenji

2014-04-01

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

The effects of experimental lake acidification on the reproductive success of tree swallows

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

St. Louis, V.L.

1992-01-01

The effects of lake acidification on reproductive success of tree swallows (Tachycineta bicolor) breeding near experimentally acidified and unmanipulated reference lakes at the Experimental Lake Area (ELA) were studied. Tree swallows are aerial insectivores that commonly breed near water and forage on emergent insects. Predictions suggest that avian food abundance and quality may be altered due to acidification. Breeding swallows foraged on chironomids emerging at their nest-site lakes before searching for food elsewhere. Among the calcium-rich items consumed by the swallows, fish bones were most numerous, followed by crayfish exoskeleton, clam shell, and bird eggshell. We found significantly fewer calcium-richmore » items in the stomachs of nestlings from acid lakes than in those from reference lakes. Chironomid species were significantly more abundant in acid lakes, while the Chironominae were less numerous. Biomass of emerging chironomids either increased significantly following acidification, or was not different from that of reference lakes. Concentrations of Al, Ca, Mn, and Zn were on average higher in chironomids from a number of the acid lakes than in chironomids from reference lakes. Calcium concentrations in chironomids from the most acid lake were significantly lower, suggesting that Ca may be difficult to sequester at low pH levels. Hepatic concentrations of metallothioneins in tree swallow nestlings were negatively correlated with pH of the nest-site lake. Additive concentrations of Cu and Zn in the liver were correlated with liver MT concentrations, but Cd was not. Near acidified lakes, eggs were smaller in certain dimensions, hatching success was lower, certain nestling body characters were smaller, nestling wing length was shorter, and growth functions were different than near unmanipulated reference lakes. Clearly even non-aquatic organisms are affected by acidification of freshwater ecosystems.« less

A Ranking Approach to Genomic Selection.

PubMed

Blondel, Mathieu; Onogi, Akio; Iwata, Hiroyoshi; Ueda, Naonori

2015-01-01

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual's breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used. In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value. We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental results suggest that tree-based ensemble methods including McRank, Random Forests and Gradient Boosting Regression Trees achieve excellent ranking accuracy. RKHS regression and RankSVM also achieve good accuracy when used with an RBF kernel. Traditional regression methods such as Bayesian lasso, wBSR and BayesC were found less suitable for ranking. Pearson correlation was found to correlate poorly with NDCG. Our study suggests two important messages. First, ranking methods are a promising research direction in GS. Second, NDCG can be a useful evaluation measure for GS.

[Graft hybridization and the specificity of heredity in fruit trees].

PubMed

Liu, Yong-Sheng; Li, Bao-Yin; Li, Gui-Rong; Zhou, Xiu-Mei

2004-09-01

Emphatically discusses the relationship between graft hybridization and the specificity of heredity in fruit trees on the basis of introducing the recent achievements in plant graft hybridization. We propose that genetic materials in rootstock being translocated and integrated into the genome of the germ cells and embryonic cells in scion are the main reasons why the majority of the hybrid seedlings have wild properties and the heredity of fruit trees violate Mendel's laws of heredity. The potential of graft hybridization in fruit breeding are also discussed.

[Genetic engineering of forest woody plants].

PubMed

Mashkina, O S; Butorina, A K

2003-03-01

The present state of genetic engineering (GE) of forest woody plants is considered with special reference to the materials of the International Conference "Wood, Breeding, Biotechnology and Industrial Expectations" held in France in June, 2001. Main tree species subjected to GE are listed, aims of constructing transgenic plants discussed, and methods described. Major achievements in the field are considered along with the problems associated with the employment of GE in the breeding of forest woody plants.

Flowers & Weeds.

ERIC Educational Resources Information Center

Flannery, Maura C.

1996-01-01

Describes the topics and teaching strategies employed in an Issues in Biology course. Discusses flowers, plant breeding, potatoes and tomatoes, the chocolate tree, weeds, Arabidopis, gene transfers, and plant genes/human genes. Contains 22 references. (JRH)

Differential interspecific incompatibility in Populus breeding

Treesearch

A. Assibi Mahama; Ronald S., Jr. Zalesny; Richard B. Hall

2006-01-01

Interspecific hybrids of Populus are valuable in tree production systems. Hybrid vigor is achieved for various traits and is useful for transferring disease and pest resistance. Incompatibility, however, sometimes precludes such combinations.

Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values.

PubMed

Granleese, Tom; Clark, Samuel A; Swan, Andrew A; van der Werf, Julius H J

2015-09-14

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs. Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection. All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively. Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space.

Breeding and Selection of New Switchgrass Varieties for Increased Biomass Production

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

Taliaferro, C.M.

2003-05-27

Switchgrass breeding and genetics research was conducted from 1992-2002 at the Oklahoma State University as part of the national DOE-Bioenergy Feedstock Development Program (BFDP) effort to develop the species as a bioenergy feedstock crop. The fundamental objective of the program was to implement and conduct a breeding program to increase biomass yield capability in switchgrass and develop cultivars for the central and southern United States. Supporting research objectives included: (1) switchgrass germplasm collection, characterization, and enhancement; (2) elucidation of cytogenetic and breeding behavior; and (3) identification of best breeding procedures.

Extensive female-mediated gene flow and low phylogeography among seventeen goat breeds in southwest China.

PubMed

Zhao, Wei; Zhong, Tao; Wang, Lin Jie; Li, Li; Zhang, Hong Ping

2014-08-01

Indigenous Chinese goat mtDNA is highly diverse but lacks geographic specificity; however, whether gene flow or gene exchange contributed to this remains unknown. We reanalyzed a consensus fragment of 481 bp in the D-loop region from 339 individuals. The network and neighbor-joining tree revealed three divergent maternal haplogroups (A, B1, and B2) in 17 local breeds. Although high polymorphism resulting in 198 different haplotypes was observed (h = 0.984 ± 0.002; π = 0.0336 ± 0.0008), neither the distribution of haplotypes nor PCA analysis revealed any obvious geographic structure in the local breeds. Extensive gene flow was widely detected among breeds from southwest China. High levels of gene exchange were detected between Qianbei Brown goats and the other breeds, indicating either more contribution or introgression to their gene pools. This study will be helpful in understanding the phylogeography and gene flow among the goat breeds of southwest China.

Factors determining presence of passerines breeding within White Stork Ciconia ciconia nests

NASA Astrophysics Data System (ADS)

Zbyryt, Adam; Jakubas, Dariusz; Tobolka, Marcin

2017-10-01

Nests of White Stork Ciconia ciconia are commonly used by various passerines as nesting sites. In this study, we investigated factors determining presence and number of pairs of species breeding within White Stork nests in an extensive farmland in NE Poland. In 133 (57%) out of 233 White Stork nests, we found at least one breeding pair of passerine bird. These were from three species: House Sparrows Passer domesticus (68% of 133 nests with co-breeding), Tree Sparrows Passer montanus (65%), and Starlings Sturnus vulgaris (30%). The probability of breeding passerines within White Stork nests increased with increasing nest thickness, and was significantly higher in currently occupied nests. Sparrows were more likely to breed in White Stork nests located on electricity poles, situated closer to settlements and surrounded mainly by arable fields where meadows were not prevalent. In this paper, we show that White Stork nests are favorable nesting sites for passerines, as they are well insulated and provide an anti-predatory shield.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

PubMed Central

Browett, Sam; McHugo, Gillian; Richardson, Ian W.; Magee, David A.; Park, Stephen D. E.; Fahey, Alan G.; Kearney, John F.; Correia, Carolina N.; Randhawa, Imtiaz A. S.; MacHugh, David E.

2018-01-01

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland. PMID:29520297

Transformation of fruit trees. Useful breeding tool or continued future prospect?

PubMed

Petri, César; Burgos, Lorenzo

2005-02-01

Regeneration and transformation systems using mature plant material of woody fruit species have to be achieved as a necessary requirement for the introduction of useful genes into specific cultivars and the rapid evaluation of resulting horticultural traits. Although the commercial production of transgenic annual crops is a reality, commercial genetically-engineered fruit trees are still far from common. In most woody fruit species, transformation and regeneration of commercial cultivars are not routine, generally being limited to a few genotypes or to seedlings. The future of genetic transformation as a tool for the breeding of fruit trees requires the development of genotype-independent procedures, based on the transformation of meristematic cells with high regeneration potential and/or the use of regeneration-promoting genes. The public concern with the introduction of antibiotic resistance into food and the restrictions due to new European laws that do not allow deliberate release of plants transformed with antibiotic-resistance genes highlight the development of methods that avoid the use of antibiotic-dependent selection or allow elimination of marker genesfrom the transformed plant as a research priority in coming years.

Precocious flowering in trees: the FLOWERING LOCUS T gene as a research and breeding tool in Populus.

PubMed

Zhang, Huanling; Harry, David E; Ma, Cathleen; Yuceer, Cetin; Hsu, Chuan-Yu; Vikram, Vikas; Shevchenko, Olga; Etherington, Elizabeth; Strauss, Steven H

2010-06-01

Expression of FLOWERING LOCUS T (FT) and its homologues has been shown to accelerate the onset of flowering in a number of plant species, including poplar (Populus spp.). The application of FT should be of particular use in forest trees, as it could greatly accelerate and enable new kinds of breeding and research. Recent evidence showing the extent to which FT is effective in promoting flowering in trees is discussed, and its effectiveness in poplar is reported. Results using one FT gene from Arabidopsis and two from poplar, all driven by a heat-inducible promoter, transformed into two poplar genotypes are also described. Substantial variation in flowering response was observed depending on the FT gene and genetic background. Heat-induced plants shorter than 30 cm failed to flower as well as taller plants. Plants exposed to daily heat treatments lasting 3 weeks tended to produce fewer abnormal flowers than those in heat treatments of shorter durations; increasing the inductive temperature from 37 degrees C to 40 degrees C produced similar benefits. Using optimal induction conditions, approximately 90% of transgenic plants could be induced to flower. When induced FT rootstocks were grafted with scions that lacked FT, flowering was only observed in rootstocks. The results suggest that a considerable amount of species- or genotype-specific adaptation will be required to develop FT into a reliable means for shortening the generation cycle for breeding in poplar.

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

Persian walnut breeding in California

Treesearch

Charles A. Leslie; Gale H. McGranahan

2004-01-01

For over 50 years the University of California Davis Walnut Breeding Program has worked to address the needs of California walnut growers by identifying genetic approaches to problems and developing improved cultivars. The breeding program is a cooperative endeavor that draws on the efforts and resources of university researchers and facilities, USDA germplasm programs...

Reproductive and resource benefits to large female body size in a mammal with female-biased sexual size dimorphism

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

Fokidis, H.B., T.S. Risch and T.C. Glenn

Factors underlying the evolution of female-biased sexual size dimorphism in mammals are poorly understood. In an effort to better understand these factors we tested whether larger female southern flying squirrels, Glaucomys volans, gained reproductive advantages (larger litters or more male mates) and direct resource benefits, such as larger home ranges or access to more food (i.e. mast-producing trees). As dimorphism can vary with age in precocial breeding species, we compared females during their first reproduction and during a subsequent breeding attempt. Females were not significantly larger or heavier than males at first reproduction, but became about 7% heavier and 22%more » larger than males at subsequent breeding. Larger females produced larger litters and had home ranges containing a greater proportion of upland hardwood trees. Female body size was not associated with either multiple male mating or home range size, but females with larger home ranges had higher indexes of body condition. Females in precocial breeding flying squirrels initiate reproduction before sexual size dimorphism is evident, and thus, may be allocating resources to both reproduction and growth simultaneously, or delaying growth entirely. Larger females produce more pups and have access to more food resources. Thus, selection for increased female size may partly explain how female-biased sexual size dimorphism is maintained in this species.« less

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

PubMed Central

Manunza, A.; Cardoso, T. F.; Noce, A.; Martínez, A.; Pons, A.; Bermejo, L. A.; Landi, V.; Sànchez, A.; Jordana, J.; Delgado, J. V.; Adán, S.; Capote, J.; Vidal, O.; Ugarte, E.; Arranz, J. J.; Calvo, J. H.; Casellas, J.; Amills, M.

2016-01-01

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. PMID:27272025

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK.

PubMed

Manunza, A; Cardoso, T F; Noce, A; Martínez, A; Pons, A; Bermejo, L A; Landi, V; Sànchez, A; Jordana, J; Delgado, J V; Adán, S; Capote, J; Vidal, O; Ugarte, E; Arranz, J J; Calvo, J H; Casellas, J; Amills, M

2016-06-07

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.

Global impact of accelerated plant breeding: Evidence from a meta-analysis on rice breeding.

PubMed

Lenaerts, Bert; de Mey, Yann; Demont, Matty

2018-01-01

Rice breeders in Asia and elsewhere in the world have long overlooked trying to shorten the time it takes to develop new varieties. Plant breeders have proposed a technique called Rapid Generation Advance (RGA) as a way to accelerate the results of public rice breeding programs. However, little is known about RGA's potential impact. Here, we present the first results of a global impact study of RGA. More specifically, we calculated the multiplicator effects of RGA on the research benefits generated by conventional rice breeding programs and applied them to a meta-analysis of selected impact studies in the literature. These insights are a first crucial step in developing a targeted approach for disseminating RGA technology among rice breeders to accelerate the impact of their public rice breeding programs around the world. We show that the additional benefits due to time savings are considerable and offer some insights into the economics of breeding. Our results confirm that the adoption of accelerated breeding would lead to substantial advantages to rice breeding programs and the earlier variety release leads to significant economic benefits to society. This can be important to policy makers when reshaping their public breeding methods and optimising their return on research investments in breeding.

AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

PubMed

Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

2016-04-01

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

PubMed Central

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios. PMID:25750652

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs.

PubMed

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.

Characterization of resistance to pine wood nematode infection in Pinus thunbergii using suppression subtractive hybridization.

PubMed

Hirao, Tomonori; Fukatsu, Eitaro; Watanabe, Atsushi

2012-01-24

Pine wilt disease is caused by the pine wood nematode, Bursaphelenchus xylophilus, which threatens pine forests and forest ecosystems worldwide and causes serious economic losses. In the 40 years since the pathogen was identified, the physiological changes occurring as the disease progresses have been characterized using anatomical and biochemical methods, and resistant trees have been selected via breeding programs. However, no studies have assessed the molecular genetics, e.g. transcriptional changes, associated with infection-induced physiological changes in resistant or susceptible trees. We constructed seven subtractive suppression hybridization (SSH) cDNA libraries using time-course sampling of trees inoculated with pine wood nematode at 1, 3, or 7 days post-inoculation (dpi) in susceptible trees and at 1, 3, 7, or 14 dpi in resistant trees. A total of 3,299 sequences was obtained from these cDNA libraries, including from 138 to 315 non-redundant sequences in susceptible SSH libraries and from 351 to 435 in resistant SSH libraries. Using Gene Ontology hierarchy, those non-redundant sequences were classified into 15 subcategories of the biological process Gene Ontology category and 17 subcategories of the molecular function category. The transcriptional components revealed by the Gene Ontology classification clearly differed between resistant and susceptible libraries. Some transcripts were discriminative: expression of antimicrobial peptide and putative pathogenesis-related genes (e.g., PR-1b, 2, 3, 4, 5, 6) was much higher in susceptible trees than in resistant trees at every time point, whereas expression of PR-9, PR-10, and cell wall-related genes (e.g., for hydroxyproline-rich glycoprotein precursor and extensin) was higher in resistant trees than in susceptible trees at 7 and 14 dpi. Following inoculation with pine wood nematode, there were marked differences between resistant and susceptible trees in transcript diversity and the timing and level of transcripts expressed in common; in particular, expression of stress response and defense genes differed. This study provided new insight into the differences in the physiological changes between resistant and susceptible trees that have been observed in anatomical and biochemical studies.

Simulated selection responses for breeding programs including resistance and resilience to parasites in Creole goats.

PubMed

Gunia, M; Phocas, F; Gourdine, J-L; Bijma, P; Mandonnet, N

2013-02-01

The Creole goat is a local breed used for meat production in Guadeloupe (French West Indies). As in other tropical countries, improvement of parasite resistance is needed. In this study, we compared predicted selection responses for alternative breeding programs with or without parasite resistance and resilience traits. The overall breeding goal included traits for production, reproduction, and parasite resilience and resistance to ensure a balanced selection outcome. The production traits were BW and dressing percentage (DP). The reproduction trait was fertility (FER), which was the number of doe kiddings per mating. The resistance trait was worm fecal egg count (FEC), which is a measurement of the number of gastro-intestinal parasite eggs found in the feces. The resilience trait was the packed cell volume (PCV), which is a measurement of the volume of red blood cells in the blood. Dressing percentage, BW, and FEC were measured at 11 mo of age, which is the mating or selling age. Fertility and PCV were measured on females at each kidding period. The breeding program accounting for the overall breeding goal and a selection index including all traits gave annual selection responses of 800 g for BW, 3.75% for FER, 0.08% for DP, -0.005 ln(eggs/g) for FEC, and 0.28% for PCV. The expected selection responses for BW and DP in this breeding program were reduced by 2% and 6%, respectively, compared with a breeding program not accounting for FEC and PCV. The overall breeding program, proposed for the Creole breed, offers the best breeding strategy in terms of expected selection responses, making it possible to improve all traits together. It offers a good balance between production and adaptation traits and may present some interest for the selection of other goat breeds in the tropics.

The chapter breeding program of the American Chestnut Foundation

Treesearch

Sara Fitzsimmons; Kendra Gurney; William White; Katy McCune

2012-01-01

A unique feature of the American Chestnut Foundation breeding program is the use of volunteers to conduct most of the regional breeding that will help increase genetic diversity and preserve local adaptation in the products of our program. This effort is coordinated by the four authors of this abstract, who are employees of the Foundation. The Foundation has...

Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds

PubMed Central

Reist-Marti, Sabine B; Abdulai, Awudu; Simianer, Henner

2006-01-01

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries. PMID:16451794

The fine-scale genetic structure of the two-spotted spider mite in a commercial greenhouse.

PubMed

Uesugi, R; Kunimoto, Y; Osakabe, Mh

2009-02-01

The fine-scale genetic structure of Tetranychus urticae Koch was studied to estimate local gene flow within a rose tree habitat in a commercial greenhouse using seven microsatellite markers. Two beds of rose trees with different population densities were selected and 18 consecutive quadrats of 1.2 m length were sequentially established in each bed. Heterozygote deficiency was positive within quadrats, which was most likely a result of the Wahlund effect because the mites usually form small breeding colonies. Low population density and frequent inbreeding could also accelerate genetic differentiation among the breeding colonies. A short-range (2.4-3.6 m) positive autocorrelation and clear genetic cline among quadrat populations was detected within a bed. This suggests that gene flow was limited to a short range even if population density was substantially increased. Therefore, large-scale dispersal such as aerial dispersal contributed very little to gene flow in the greenhouse.

Potential benefits of genomic selection on genetic gain of small ruminant breeding programs.

PubMed

Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Elsen, J M

2013-08-01

In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the reference population and genomic selection gave the best results when nref > 1,000 individuals for dairy breeds and nref > 2,000 individuals for meat breed. Genetic correlation between meat and maternal traits had a large impact on the genetic gain of both traits. Changes in AGG due to correlation were greatest for low heritable maternal traits. As a general rule, AGG was increased both by optimizing selection designs and including genomic information.

Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

PubMed Central

Delplancke, Malou; Alvarez, Nadir; Espíndola, Anahí; Joly, Hélène; Benoit, Laure; Brouck, Elise; Arrigo, Nils

2012-01-01

Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean. PMID:25568053

Low effect of young afforestations on bird communities inhabiting heterogeneous Mediterranean cropland

PubMed Central

Rey Benayas, José M.; Carrascal, Luis M.

2015-01-01

Afforestation programs such as the one promoted by the EU Common Agricultural Policy have spread tree plantations on former cropland. These afforestations attract generalist forest and ubiquitous species but may cause severe damage to open habitat species, especially birds of high conservation value. We investigated the effects of young (<20 yr) tree plantations dominated by pine P. halepensis on bird communities inhabiting the adjacent open farmland habitat in central Spain. We hypothesize that pine plantations located at shorter distances from open fields and with larger surface would affect species richness and conservation value of bird communities. Regression models controlling for the influence of land use types around plantations revealed positive effects of higher distance to pine plantation edge on community species richness in winter, and negative effects on an index of conservation concern (SPEC) during the breeding season. However, plantation area did not have any effect on species richness or community conservation value. Our results indicate that the effects of pine afforestation on bird communities inhabiting Mediterranean cropland are diluted by heterogeneous agricultural landscapes. PMID:26664801

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

PubMed

Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

2014-04-04

Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling and trait-associated transcript analysis using an apple F1 population readily identified genes physically linked to powdery mildew disease resistance and woolly apple aphid resistance loci. This result was especially useful in apple, where extreme levels of heterozygosity make the development of reliable DNA markers quite difficult. The results suggest that this approach could prove effective in crops with complicated genetics, or for which few genomic information resources are available.

Pollution ecology of breeding great blue herons in the Columbia Basin, Oregon and Washington

USGS Publications Warehouse

Blus, L.J.; Henny, C.J.; Kaiser, T.E.

1980-01-01

Approximately 40 pairs of Great Blue Herons (Ardea herodias) formerly nested in trees on or near Blalock Island about 95 km downstream from Richland, Washington, in the Columbia River (Nehls 1972 ). In conjunction with construction of the John Day Lock and Dam and before creating Lake Umatilla in 1968, large trees along the shoreline, including those in the heronry on Blalock Island, were removed except for about six cottonwood trees (Populus sp.) that were left standing near the south bank of the river (David Lenhart, pers. comm.). As a mitigation procedure, the Umatilla National Wildlife Refuge (Umatilla) was established in 1967. The herons subsequently established a secondary heronry in the six cottonwoods; 20 pairs were present in 1971 (Nehls 1972). The inundated trees died and deteriorated; only two trees with eight nests remained in 1976 (Henny and Kurtz 1978), and we found just two nests in one tree in 1978. With a decrease in traditional nesting sites, the birds nested on islands in big sagebrush (Artemisia tridentata), on channel markers in the Columbia River, and on nesting platforms constructed for Canada Geese (Branta canadensis). The purpose of this paper is to describe the breeding biology of Great Blue Herons at Umatilla and the McNary Recreation Area (McNary) in 1978 and the relationship of organochlorine residues in eggs to eggshell thickness and reproductive success. The primary reason for conducting this study was to determine if the heptachlor seed treatment that was severely affecting Canada Geese at Umatilla (Blus et al. 1979) was also a hazard to Great Blue Herons. At the same time we also investigated possible effects of other organochlorines on the herons.

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

PubMed Central

Beaulieu, J; Doerksen, T; Clément, S; MacKay, J; Bousquet, J

2014-01-01

Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach. PMID:24781808

Identification of key ancestors of modern germplasm in a breeding program of maize.

PubMed

Technow, F; Schrag, T A; Schipprack, W; Melchinger, A E

2014-12-01

Probabilities of gene origin computed from the genomic kinships matrix can accurately identify key ancestors of modern germplasms Identifying the key ancestors of modern plant breeding populations can provide valuable insights into the history of a breeding program and provide reference genomes for next generation whole genome sequencing. In an animal breeding context, a method was developed that employs probabilities of gene origin, computed from the pedigree-based additive kinship matrix, for identifying key ancestors. Because reliable and complete pedigree information is often not available in plant breeding, we replaced the additive kinship matrix with the genomic kinship matrix. As a proof-of-concept, we applied this approach to simulated data sets with known ancestries. The relative contribution of the ancestral lines to later generations could be determined with high accuracy, with and without selection. Our method was subsequently used for identifying the key ancestors of the modern Dent germplasm of the public maize breeding program of the University of Hohenheim. We found that the modern germplasm can be traced back to six or seven key ancestors, with one or two of them having a disproportionately large contribution. These results largely corroborated conjectures based on early records of the breeding program. We conclude that probabilities of gene origin computed from the genomic kinships matrix can be used for identifying key ancestors in breeding programs and estimating the proportion of genes contributed by them.

Keys to the Larval and Adult Mosquitoes of Espiritu Santo (New Hebrides) with Notes on Their Bionomics

DTIC Science & Technology

1946-01-01

coconut halves and husks , bamboo stumps, and artificial containers such as tin cans, sagging tent covers, tarpaulins, and wooden frames holding...The larvae are occasionally found with hebrideus breeding in water held in wooden frames or coconut husks , but they are also found in tree holes...HEBRIDEUS EDW. Larvae: This is a common larva found in tree holes, coconut husks and shells, sagging tents and tarpulins, wooden frames, rain

PCBs and DDE in tree swallow (Tachycineta bicolor) eggs and nestlings from an estuarine PCB superfund site, New Bedford Harbor, MA, U.S.A.

USGS Publications Warehouse

Jayaraman, Saro; Nacci, Diane E.; Champlin, Denise M.; Pruell, Richard J.; Rocha, Kenneth J.; Custer, Christine M.; Custer, Thomas W.; Cantwell, Mark

2009-01-01

While breeding tree swallows (Tachycineta bicolor) have been used as biomonitors for freshwater sites, we report the first use of this species to assess contaminant bioaccumulation from estuarine breeding grounds into these aerial insectivores. Eggs and nestlings were collected from nest boxes in a polychlorinated biphenyl (PCB) contaminated estuary, the New Bedford Harbor Superfund site (NBH, Massachusetts, USA), and a reference salt marsh, Fox Hill (FH, Jamestown, Rhode Island, USA). Sediments, eggs, and nestlings were compared on a ng g−1 wet weight basis for total PCBs and DDE (1,1-bis-(4-chlorophenyl)-2,2-dichloroethene), metabolite of DDT (1,1,1-trichloro-2,2-bis-(p-chlorophenyl)ethane). NBH samples contained high concentrations of PCBs compared to FH for sediment (36,500 and 0.2), eggs (11,200 and 323), and nestlings (16,800 and 26). PCB homologue patterns linked tree swallow contamination to NBH sediment. NBH samples were also contaminated with DDE compared to FH for sediment (207 and 0.9) and nestlings (235 and 30) but not for eggs (526 and 488), suggesting both NBH and nonbreeding ground sources for DDE. The relationships between sediment and tree swallow egg and nestling PCBs were similar to those reported for freshwater sites. Like some highly contaminated freshwater sites, NBH PCB bioaccumulation had little apparent effect on reproductive success.

PCBs and DDE in tree swallow (Tachycineta bicolor) eggs and nestlings from an estuarine PCB superfund site, New Bedford Harbor, MA, U.S.A.

PubMed

Jayaraman, Saro; Nacci, Diane E; Champlin, Denise M; Pruell, Richard J; Rocha, Kenneth J; Custer, Christine M; Custer, Thomas W; Cantwell, Mark

2009-11-01

While breeding tree swallows (Tachycineta bicolor) have been used as biomonitors for freshwater sites, we report the first use of this species to assess contaminant bioaccumulation from estuarine breeding grounds into these aerial insectivores. Eggs and nestlings were collected from nest boxes in a polychlorinated biphenyl (PCB) contaminated estuary, the New Bedford Harbor Superfund site (NBH, Massachusetts, USA), and a reference salt marsh, Fox Hill (FH, Jamestown, Rhode Island, USA). Sediments, eggs, and nestlings were compared on a ng g(-1) wet weight basis for total PCBs and DDE (1,1-bis-(4-chlorophenyl)-2,2-dichloroethene), metabolite of DDT (1,1,1-trichloro-2,2-bis-(p-chlorophenyl)ethane). NBH samples contained high concentrations of PCBs compared to FH for sediment (36,500 and 0.2), eggs (11,200 and 323), and nestlings (16,800 and 26). PCB homologue patterns linked tree swallow contamination to NBH sediment. NBH samples were also contaminated with DDE compared to FH for sediment (207 and 0.9) and nestlings (235 and 30) but not for eggs (526 and 488), suggesting both NBH and nonbreeding ground sources for DDE. The relationships between sediment and tree swallow egg and nestling PCBs were similar to those reported for freshwater sites. Like some highly contaminated freshwater sites, NBH PCB bioaccumulation had little apparent effect on reproductive success.

Larval breeding sites of Lutzomyia longipalpis (Diptera: Psychodidae) in visceral leishmaniasis endemic urban areas in Southeastern Brazil.

PubMed

Casanova, Cláudio; Andrighetti, Maria T M; Sampaio, Susy M P; Marcoris, Maria L G; Colla-Jacques, Fernanda E; Prado, Angelo P

2013-01-01

The scarcity of information on the immature stages of sand flies and their preferred breeding sites has resulted in the focus of vectorial control on the adult stage using residual insecticide house-spraying. This strategy, along with the treatment of human cases and the euthanasia of infected dogs, has proven inefficient and visceral leishmaniasis continues to expand in Brazil. Identifying the breeding sites of sand flies is essential to the understanding of the vector's population dynamic and could be used to develop novel control strategies. In the present study, an intensive search for the breeding sites of Lutzomyia longipalpis was conducted in urban and peri-urban areas of two municipalities, Promissão and Dracena, which are endemic for visceral leishmaniasis in São Paulo State, Brazil. During an exploratory period, a total of 962 soil emergence traps were used to investigate possible peridomiciliary breeding site microhabitats such as: leaf litter under tree, chicken sheds, other animal sheds and uncovered debris. A total of 160 sand flies were collected and 148 (92.5%) were L. longipalpis. In Promissão the proportion of chicken sheds positive was significantly higher than in leaf litter under trees. Chicken shed microhabitats presented the highest density of L. longipalpis in both municipalities: 17.29 and 5.71 individuals per square meter sampled in Promissão and Dracena respectively. A contagious spatial distribution pattern of L. longipalpis was identified in the emergence traps located in the chicken sheds. The results indicate that chicken sheds are the preferential breeding site for L. longipalpis in the present study areas. Thus, control measures targeting the immature stages in chicken sheds could have a great effect on reducing the number of adult flies and consequently the transmission rate of Leishmania (Leishmania) infantum chagasi.

Larval Breeding Sites of Lutzomyia longipalpis (Diptera: Psychodidae) in Visceral Leishmaniasis Endemic Urban Areas in Southeastern Brazil

PubMed Central

Casanova, Cláudio; Andrighetti, Maria T. M.; Sampaio, Susy M. P.; Marcoris, Maria L. G.; Colla-Jacques, Fernanda E.; Prado, Ângelo P.

2013-01-01

Background The scarcity of information on the immature stages of sand flies and their preferred breeding sites has resulted in the focus of vectorial control on the adult stage using residual insecticide house-spraying. This strategy, along with the treatment of human cases and the euthanasia of infected dogs, has proven inefficient and visceral leishmaniasis continues to expand in Brazil. Identifying the breeding sites of sand flies is essential to the understanding of the vector's population dynamic and could be used to develop novel control strategies. Methodology/Principal finding In the present study, an intensive search for the breeding sites of Lutzomyia longipalpis was conducted in urban and peri-urban areas of two municipalities, Promissão and Dracena, which are endemic for visceral leishmaniasis in São Paulo State, Brazil. During an exploratory period, a total of 962 soil emergence traps were used to investigate possible peridomiciliary breeding site microhabitats such as: leaf litter under tree, chicken sheds, other animal sheds and uncovered debris. A total of 160 sand flies were collected and 148 (92.5%) were L. longipalpis. In Promissão the proportion of chicken sheds positive was significantly higher than in leaf litter under trees. Chicken shed microhabitats presented the highest density of L. longipalpis in both municipalities: 17.29 and 5.71 individuals per square meter sampled in Promissão and Dracena respectively. A contagious spatial distribution pattern of L. longipalpis was identified in the emergence traps located in the chicken sheds. Conclusion The results indicate that chicken sheds are the preferential breeding site for L. longipalpis in the present study areas. Thus, control measures targeting the immature stages in chicken sheds could have a great effect on reducing the number of adult flies and consequently the transmission rate of Leishmania (Leishmania) infantum chagasi. PMID:24069494

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds.

PubMed

Guo, H W; Li, C; Wang, X N; Li, Z J; Sun, G R; Li, G X; Liu, X J; Kang, X T; Han, R L

2017-10-01

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

Inference of population splits and mixtures from genome-wide allele frequency data.

PubMed

Pickrell, Joseph K; Pritchard, Jonathan K

2012-01-01

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

Successful crossings with early flowering transgenic poplar: interspecific crossings, but not transgenesis, promoted aberrant phenotypes in offspring.

PubMed

Hoenicka, Hans; Lehnhardt, Denise; Nilsson, Ove; Hanelt, Dieter; Fladung, Matthias

2014-10-01

In forest tree species, the reproductive phase is reached only after many years or even decades of juvenile growth. Different early flowering systems based on the genetic transfer of heat-shock promoter driven flowering-time genes have been proposed for poplar; however, no fertile flowers were reported until now. Here, we studied flower and pollen development in both HSP::AtFT and wild-type male poplar in detail and developed an optimized heat treatment protocol to obtain fertile HSP::AtFT flowers. Anthers from HSP::AtFT poplar flowers containing fertile pollen grains showed arrested development in stage 12 instead of reaching phase 13 as do wild-type flowers. Pollen grains could be isolated under the binocular microscope and were used for intra- and interspecific crossings with wild-type poplar. F1-seedlings segregating the HSP::AtFT gene construct according to Mendelian laws were obtained. A comparison between intra- and interspecific crossings revealed that genetic transformation had no detrimental effects on F1-seedlings. However, interspecific crossings, a broadly accepted breeding method, produced 47% seedlings with an aberrant phenotype. The early flowering system presented in this study opens new possibilities for accelerating breeding of poplar and other forest tree species. Fast breeding and the selection of transgene-free plants, once the breeding process is concluded, can represent an attractive alternative even under very restrictive regulations. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Evolutionary genomics of dog domestication.

PubMed

Wayne, Robert K; vonHoldt, Bridgett M

2012-02-01

We review the underlying principles and tools used in genomic studies of domestic dogs aimed at understanding the genetic changes that have occurred during domestication. We show that there are two principle modes of evolution within dogs. One primary mode that accounts for much of the remarkable diversity of dog breeds is the fixation of discrete mutations of large effect in individual lineages that are then crossed to various breed groupings. This transfer of mutations across the dog evolutionary tree leads to the appearance of high phenotypic diversity that in actuality reflects a small number of major genes. A second mechanism causing diversification involves the selective breeding of dogs within distinct phenotypic or functional groups, which enhances specific group attributes such as heading or tracking. Such progressive selection leads to a distinct genetic structure in evolutionary trees such that functional and phenotypic groups cluster genetically. We trace the origin of the nuclear genome in dogs based on haplotype-sharing analyses between dogs and gray wolves and show that contrary to previous mtDNA analyses, the nuclear genome of dogs derives primarily from Middle Eastern or European wolves, a result more consistent with the archeological record. Sequencing analysis of the IGF1 gene, which has been the target of size selection in small breeds, further supports this conclusion. Finally, we discuss how a black coat color mutation that evolved in dogs has transformed North American gray wolf populations, providing a first example of a mutation that appeared under domestication and selectively swept through a wild relative.

Floral biology, breeding system and pollination ecology of an endangered tree Tetracentron sinense Oliv. (Trochodendraceae).

PubMed

Gan, Xiaohong; Cao, Lingling; Zhang, Xia; Li, Huaichun

2013-12-01

Tetracentron sinense Oliv. is an endangered tree mainly distributed in south-central China. The breeding system and pollination ecology of T. sinense are unclear. With a conservation perspective, the floral biology, breeding system and pollination ecology of Tetracentron sinense Oliv. were investigated, in order to discuss the endangered factors related to pollination, and to provide important information for its conservation. Our results revealed four important aspects of the reproductive biology of T. sinense. 1) T. sinense usually flowers by the beginning of June, and the flowering period of the population is about two months, and the florescence of florets lasted for 15 to 24 days with delicate fragrance. 2) The pollen/ovule ratio is 720 ± 28, and the outcrossing index is three. Artificial pollination experiments showed that T. sinense is self-compatible, with facultative xenogamy and no indication of agamospermy. 3) The pollination syndrome is ambophily, and self-pollination plays an important role in fruit production if wind and insect pollination is unavailable. 4) Insect pollinators were predominantly represented by Coleoptera, Diptera and Hymenoptera. Syrphid fly and bees were the main effective pollinators. The results suggested that T. sinense exhibits a mixed-mating system, and autogamy in its breeding system may provide reproductive assurance for the population maintenance. During flowering and pollination in natural population, the decrease of population density and harsh environmental condition might be one of crucial reasons resulting in endanger for this species.

Breeding resistance to butternut canker disease

Treesearch

James McKenna; Keith Woeste; Michael Ostry

2012-01-01

Butternut (Juglans cinerea L.) is being killed throughout its native range by an exotic fungus Ophiognomonia clavigignenti-juglandacearum (Ocj). In recent years, many disease-free trees have been determined to be complex hybrids with an admixture of Japanese walnut (J. ailantifolia)....

Resistance to Dutch Elm Disease Reduces Presence of Xylem Endophytic Fungi in Elms (Ulmus spp.)

PubMed Central

Martín, Juan A.; Witzell, Johanna; Blumenstein, Kathrin; Rozpedowska, Elzbieta; Helander, Marjo; Sieber, Thomas N.; Gil, Luis

2013-01-01

Efforts to introduce pathogen resistance into landscape tree species by breeding may have unintended consequences for fungal diversity. To address this issue, we compared the frequency and diversity of endophytic fungi and defensive phenolic metabolites in elm (Ulmus spp.) trees with genotypes known to differ in resistance to Dutch elm disease. Our results indicate that resistant U. minor and U. pumila genotypes exhibit a lower frequency and diversity of fungal endophytes in the xylem than susceptible U. minor genotypes. However, resistant and susceptible genotypes showed a similar frequency and diversity of endophytes in the leaves and bark. The resistant and susceptible genotypes could be discriminated on the basis of the phenolic profile of the xylem, but not on basis of phenolics in the leaves or bark. As the Dutch elm disease pathogen develops within xylem tissues, the defensive chemistry of resistant elm genotypes thus appears to be one of the factors that may limit colonization by both the pathogen and endophytes. We discuss a potential trade-off between the benefits of breeding resistance into tree species, versus concomitant losses of fungal endophytes and the ecosystem services they provide. PMID:23468900

A pre-breeding screening program for transgenic boars based on fluorescence in situ hybridization assay.

PubMed

Bou, Gerelchimeg; Sun, Mingju; Lv, Ming; Zhu, Jiang; Li, Hui; Wang, Juan; Li, Lu; Liu, Zhongfeng; Zheng, Zhong; He, Wenteng; Kong, Qingran; Liu, Zhonghua

2014-08-01

For efficient transgenic herd expansion, only the transgenic animals that possess the ability to transmit transgene into next generation are considered for breeding. However, for transgenic pig, practically lacking a pre-breeding screening program, time, labor and money is always wasted to maintain non-transgenic pigs, low or null transgenic transmission pigs and the related fruitless gestations. Developing a pre-breeding screening program would make the transgenic herd expansion more economical and efficient. In this technical report, we proposed a three-step pre-breeding screening program for transgenic boars simply through combining the fluorescence in situ hybridization (FISH) assay with the common pre-breeding screening workflow. In the first step of screening, combined with general transgenic phenotype analysis, FISH is used to identify transgenic boars. In the second step of screening, combined with conventional semen test, FISH is used to detect transgenic sperm, thus to identify the individuals producing high quality semen and transgenic sperm. In the third step of screening, FISH is used to assess the in vitro fertilization embryos, thus finally to identify the individuals with the ability to produce transgenic embryos. By this three-step screening, the non-transgenic boars and boars with no ability to produce transgenic sperm or transgenic embryos would be eliminated; therefore only those boars could produce transgenic offspring are maintained and used for breeding and herd expansion. It is the first time a systematic pre-breeding screening program is proposed for transgenic pigs. This program might also be applied in other transgenic large animals, and provide an economical and efficient strategy for herd expansion.

Selective breeding of food sized rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

Selective breeding of food size rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

A simple language to script and simulate breeding schemes: the breeding scheme language

USDA-ARS?s Scientific Manuscript database

It is difficult for plant breeders to determine an optimal breeding strategy given that the problem involves many factors, such as target trait genetic architecture and breeding resource availability. There are many possible breeding schemes for each breeding program. Although simulation study may b...

Ecohealth System Dynamic Model as a Planning Tool for the Reduction of Breeding Sites

NASA Astrophysics Data System (ADS)

Respati, T.; Raksanagara, A.; Djuhaeni, H.; Sofyan, A.; Shandriasti, A.

2017-03-01

Dengue is still one of major health problem in Indonesia. Dengue transmission is influenced by dengue prevention and eradication program, community participation, housing environment and climate. The complexity of the disease coupled with limited resources necessitates different approach for prevention methods that include factors contribute to the transmission. One way to prevent the dengue transmission is by reducing the mosquito’s breeding sites. Four factors suspected to influence breeding sites are dengue prevention and eradication program, community participation, housing environment, and weather condition. In order to have an effective program in reducing the breeding site it is needed to have a model which can predict existence of the breeding sites while the four factors under study are controlled. The objective of this study is to develop an Ecohealth model using system dynamic as a planning tool for the reduction of breeding sites to prevent dengue transmission with regard to dengue prevention and eradication program, community participation, housing environment, and weather condition. The methodology is a mixed method study using sequential exploratory design. The study comprised of 3 stages: first a qualitative study to 14 respondents using in-depth interview and 6 respondents for focus group discussion. The results from the first stage was used to develop entomology and household survey questionnaires for second stage conducted in 2036 households across 12 sub districts in Bandung City. Ecohealth system dynamic model was developed using data from first and second stages. Analyses used are thematic analysis for qualitative data; spatial, generalized estimating equation (GEE) and structural equation modeling for quantitative data; also average mean error (AME) and average variance error (AVE) for dynamic system model validation. System dynamic model showed that the most effective approach to eliminate breeding places was by ensuring the availability of basic sanitation for all houses. Weather factors such as precipitation can be compensated with the eradication of breeding sites activities which is conducted as scheduled and at the same time for the whole areas. Conclusion of this study is that dengue prevention and eradication program, community participation, and housing environment contributed to breeding places elimination influenced the existence of the breeding sites. The availability of basic sanitation and breeding places eradication program done timely and collectively are the most effective approach to eradicate breeding sites. Ecohealth dynamic system model can be used as a tool for the planning of breeding sites eradication program to prevent disease transmissions at city level.

Genetic transformation in citrus: Thinking outside the box

USDA-ARS?s Scientific Manuscript database

Conventional breeding methods to incorporate resistance in citrus are very slow, due to extended juvenility from seedling trees and multiple generations needed to incorporate resistance from distant relatives. Use of transgenic methods may provide disease resistance in less time. Published protocols...

7 CFR 761.2 - Abbreviations and definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., vegetable, forage, tree farming, nursery crops, nuts, aquaculture species, and other plant and animal..., reptiles, or aquatic plants) raised in a controlled or selected environment of which the applicant has... farm machinery, equipment, vehicles, foundation and breeding livestock herds and flocks, including...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 761.2 - Abbreviations and definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., tree farming, nursery crops, nuts, aquaculture species, and other plant and animal production, as..., reptiles, or aquatic plants) raised in a controlled or selected environment of which the applicant has... machinery, equipment, vehicles, foundation and breeding livestock herds and flocks, including replacements...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina).

PubMed

González, Máximo; Maldonado, Jonathan; Salazar, Erika; Silva, Herman; Carrasco, Basilio

2016-09-01

Japanese plum (Prunus salicina L.) is a fruit tree of the Rosaceae family, which is an economically important stone fruit around the world. Currently, Japanese plum breeding programs combine traditional breeding and plant physiology strategies with genetic and genomic analysis. In order to understand the flavonoid pathway regulation and to develop molecular markers associated to the fuit skin color (EST-SSRs), we performed a next generation sequencing based on Illumina Hiseq2000 platform. A total of 22.4 GB and 21 GB raw data were obtained from 'Lamoon' and 'Angeleno' respectively, corresponding to 85,404,726 raw reads to 'Lamoon' and 79,781,666 to 'Angeleno'. A total of 139,775,975 reads were filtered after removing low-quality reads and trimming the adapter sequences. De novo transcriptome assembly was performed using CLC Genome Workbench software and a total of 54,584 unique contigs were generated, with an N50 of 1343 base pair (bp) and a mean length of 829 bp. This work contributed with a specific Japanese plum skin transcriptome, providing two libraries of contrasting fruit skin color phenotype (yellow and red) and increasing substantially the GB of raw data available until now for this specie.

Development of a transgenic early flowering pear (Pyrus communis L.) genotype by RNAi silencing of PcTFL1-1 and PcTFL1-2.

PubMed

Freiman, Aviad; Shlizerman, Lyudmila; Golobovitch, Sara; Yablovitz, Zeev; Korchinsky, Raia; Cohen, Yuval; Samach, Alon; Chevreau, Elisabeth; Le Roux, Pierre-Marie; Patocchi, Andrea; Flaishman, Moshe A

2012-06-01

Trees require a long maturation period, known as juvenile phase, before they can reproduce, complicating their genetic improvement as compared to annual plants. 'Spadona', one of the most important European pear (Pyrus communis L.) cultivars grown in Israel, has a very long juvenile period, up to 14 years, making breeding programs extremely slow. Progress in understanding the molecular basis of the transition to flowering has revealed genes that accelerate reproductive development when ectopically expressed in transgenic plants. A transgenic line of 'Spadona', named Early Flowering-Spadona (EF-Spa), was produced using a MdTFL1 RNAi cassette targeting the native pear genes PcTFL1-1 and PcTFL1-2. The transgenic line had three T-DNA insertions, one assigned to chromosome 2 and two to chromosome 14 PcTFL1-1 and PcTFL1-2 were completely silenced, and EF-Spa displayed an early flowering phenotype: flowers developed already in tissue culture and on most rooted plants 1-8 months after transfer to the greenhouse. EF-Spa developed solitary flowers from apical or lateral buds, reducing vegetative growth vigor. Pollination of EF-Spa trees generated normal-shaped fruits with viable F1 seeds. The greenhouse-grown transgenic F1 seedlings formed shoots and produced flowers 1-33 months after germination. Sequence analyses, of the non-transgenic F1 seedlings, demonstrated that this approach can be used to recover seedlings that have no trace of the T-DNA. Thus, the early flowering transgenic line EF-Spa obtained by PcTFL1 silencing provides an interesting tool to accelerate pear breeding.

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.

PubMed

Brito, Luiz F; Kijas, James W; Ventura, Ricardo V; Sargolzaei, Mehdi; Porto-Neto, Laercio R; Cánovas, Angela; Feng, Zeny; Jafarikia, Mohsen; Schenkel, Flávio S

2017-03-14

The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean H O and H E was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures F EH , F VR , F LEUT , F ROH and F PED was 0.129, -0.012, -0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds' development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed F ST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats.

Tissue Mercury Concentrations and Survival of Tree Swallow Embryos, Nestlings and Young Adult Females on a Contaminated Site.

PubMed

Taylor, Capwell E; Cristol, Daniel A

2015-10-01

Tree swallows nesting on mercury-contaminated sites along the South River in Virginia, USA were monitored for reproductive success. The bodies of nestlings found deceased in their nest boxes were collected, along with blood and feather samples from the adult parents and surviving siblings. We also measured hatching and fledging success of the clutches and the annual recapture rate of adults. We found that the body feathers of deceased nestlings contained significantly higher concentrations of mercury (12.89 ± 8.42 μg/g, n = 15) than those of nestlings that survived to fledge (7.41 ± 4.79 μg/g, n = 15). However, mothers of more successful clutches (>75 % hatching) did not differ in mercury concentrations from females with less successful clutches (<50 % hatching). Additionally, adult females breeding for the first time that returned to breed the following year did not differ in blood mercury from females of the same age that bred once but never returned. Our results suggest that mercury had its greatest effect on these songbirds during the nestling stage, whereas for embryos or first-time breeding females, other factors likely played larger roles in mortality.

Habitat selection by breeding red-winged blackbirds

USGS Publications Warehouse

Albers, P.H.

1978-01-01

Habitat preferences of breeding Red-winged Blackbirds in an agricultural area were determined by comparing population density, landscape characteristics, and vegetational descriptions. Observations were made throughout the breeding season. Preferred breeding habitats of Red-wings, in order of preference, were wetlands, hayfields, old fields, and pastures. Males and females occupied old fields and wetlands first, then hayfields, and finally, pastures. Cutting of hayfields caused territorial abandonment by both sexes within 48 h. The apparent movement of displaced females from cut hayfields to uncut hayfields suggests that habitat fidelity of females is strong after the breeding effort has begun. Breeding Red-wings exhibited general preferences for trees, large amounts of habitat edge, erect old vegetation, and sturdy, tall, and dense vegetation. Vegetative forms and species, such as upland grasses, broad- and narrow-leafed monocots in wetlands, and forbs were important to the Red-wing at various times during the breeding season. Landscape and vegetational preferences of breeding adults were easier to observe early in the breeding season (March through May) than later. Vegetational growth and increases in the size of the breeding population probably make these preferences more difficult to detect. Territory size was poorly correlated with landscape and vegetational characteristics in uplands but strongly correlated with broad- and narrow-leafed mono cots and vegetative height in wetlands. Wetland territories were smaller than upland territories. Territories increased in size during the middle and late portions of the breedi g season. Habitat selection by the Red-winged Blackbird can best be studied by evaluating vegetative preferences throughout the breeding season.

Variation and inheritance pattern in cone and seed characteristics of Scots pine (Pinus sylvestris L.) for evaluation of genetic diversity.

PubMed

Sevik, Hakan; Topaçoğlu, Osman

2015-09-01

Scots pine (Pinus sylvestris L.) is one of the most common and important forest tree species in Turkey due to usefulness of its wood to many commercial uses. This species is classified as one of the economically important tree species for Turkish Forestry in the "National Tree Breeding and Seed Production Program". The objective of the present study was to investigate variation and inheritance pattern in cone and seed characteristics of Scots pine and to evaluate variation in cone and seed characters within and among clones and grafts. The results showed that maximum CV among the clones was found for SWe (21.95), FS (16.99) and CWe (16.88). According to the results of SAS, variation between the clones is averaged at 19.2% and variation within the clones is averaged at 24.4 %. Variation between the clones ranged from 3.6% (SW) to 34.5% (TC) and variation within the clones ranged from 12.3% (SW) to 38.1% (WL). For CW, AL, AW, WW and TC, genetic variation among clones was higher than within clones. When the results of study like compared with results obtained from natural populations, it was seen that genetic variability in seed orchard which was subjected to study was quite low. This case may have dangerous results for the future of forests.

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

Yellow-Billed Cuckoo Distribution, Abundance, and Habitat Use Along the Lower Colorado and Tributaries, 2006 Annual Report

USGS Publications Warehouse

Johnson, Matthew J.; Holmes, Jennifer A.; Calvo, Christopher; Samuels, Ivan; Krantz, Stefani; Sogge, Mark K.

2007-01-01

Executive Summary This 2006 annual report details the first season of a 2-year study documenting western yellow-billed cuckoo (Coccyzus americanus occidentalis) distribution, abundance, and habitat use throughout the Lower Colorado River Multi-Species Conservation Plan boundary area. We conducted cuckoo surveys at 55 sites within 17 areas, between 11 June and 13 September. The 243 visits across all sites yielded 180 yellow-billed cuckoo detections. Cuckoos were detected at 27 of the 55 sites, primarily at the Bill Williams River National Wildlife Refuge AZ sites (n = 117 detections) and the Grand Canyon National Park-Lake Mead National Recreation Area AZ delta sites (n = 29 detections). There were also cuckoos at the Gila River-Colorado River Confluence, AZ (n = 9), Overton Wildlife Management, NV area (n = 7), and Limitrophe Division North, AZ (n = 6); however, at these sites the numbers were much lower and very few of these birds were considered to be paired or breeding. The greatest number of detections (n = 79) occurred during the second survey period (3-23 July). In 2006, we confirmed five breeding events, including one nesting observation and sightings of four juveniles; all confirmed breeding was at the Bill Williams River NWR and Grand Canyon NP-Lake Mead NRA delta sites. The breeding status of most of our detections were unknown, however, we observed 17 adult cuckoos carrying nest material or food and 40 cuckoo detections were detected while counter-calling occurred in same area during repeated surveys. We used playback recordings to survey for western yellow-billed cuckoos. Compared to simple point counts or surveys, this method increases the number of detections of this secretive, elusive species. It has long been suspected that cuckoos have a fairly low response rate, and that the standard survey method of using playback recordings may fail to detect all birds present in an area. In 2006, we found that the majority (72%) of cuckoo detections were solicited through playback at all study sites. The number of solicited detections peaked during the first half of July and then declined as the breeding season progressed, while the number of unsolicited detections (cuckoos heard calling before playback was initiated) remained fairly constant. The majority (64%) of cuckoo detections, solicited or unsolicited, were aural; 27 percent were both heard and seen and nine percent were visual detections only. Cuckoos in areas with the largest populations had the highest rate of vocalizations before playback or after the first broadcast. In contrast, more than half the responses at sites with fewer cuckoos (with < 10 detections per site) first occurred after three or more playback recordings. This type of baseline information will be used to help refine the survey protocol for 2007, and to create hypotheses that can serve as the foundation for a full-scale evaluation and optimization of this survey technique. Our preliminary analysis of vegetation data from occupied and unoccupied sites in 2006 focused on general patterns in the distribution and abundance of woody species. The density and composition of woody riparian vegetation varied considerably among the study areas. Much of the variation in tree density was due to the patterns of abundance of trees in the smallest size class (< 8 cm dbh). The dominant tree species at the cuckoo survey sites were cottonwood, willow, and tamarisk. Tamarisk was the most common tree, due to the abundance of small (< 8 cm dbh) individuals. When occupied and unoccupied sites were compared, occupied sites tended to have higher average canopy cover, attributable to higher average cover of the mid and low canopy. The dominant canopy at occupied sites most often consisted of cottonwood or willow trees. In addition, occupied sites in most areas had lower than average total tree density whereas unoccupied sites were denser than average. When densities of trees in different size classes were com

Microsatellite-based phylogeny of Indian domestic goats

PubMed Central

Rout, Pramod K; Joshi, Manjunath B; Mandal, Ajoy; Laloe, D; Singh, Lalji; Thangaraj, Kumarasamy

2008-01-01

Background The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones. Results The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The DA measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution. Conclusion Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information. PMID:18226239

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2012 CFR

2012-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Permits for cooperative breeding. 15.24...

FT overexpression induces precocious flowering and normal reproductive development in Eucalyptus.

PubMed

Klocko, Amy L; Ma, Cathleen; Robertson, Sarah; Esfandiari, Elahe; Nilsson, Ove; Strauss, Steven H

2016-02-01

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1-5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

PubMed

Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

2016-03-01

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. © 2015 John Wiley & Sons Ltd.

Nest temperature fluctuations in a cavity nester, the southern ground-hornbill.

PubMed

Combrink, L; Combrink, H J; Botha, A J; Downs, C T

2017-05-01

Southern ground-hornbills Bucorvus leadbeateri inhabit savanna and bushveld regions of South Africa. They nest in the austral summer, which coincides with the wet season and hottest daytime temperatures in the region. They are secondary cavity nesters and typically nest in large cavities in trees, cliffs and earth banks, but readily use artificial nest boxes. Southern ground-hornbills are listed as Endangered in South Africa, with reintroductions into suitable areas highlighted as a viable conservation intervention for the species. Nest microclimate, and the possible implications this may have for the breeding biology of southern ground-hornbills, have never been investigated. We used temperature dataloggers to record nest cavity temperature and ambient temperature for one artificial and 11 natural southern ground-hornbill tree cavity nests combined, spanning two breeding seasons. Mean hourly nest temperature, as well as mean minimum and mean maximum nest temperature, differed significantly between southern ground-hornbill nests in both breeding seasons. Mean nest temperature also differed significantly from mean ambient temperature for both seasons. Natural nest cavities provided a buffer against the ambient temperature fluctuations. The artificial nest provided little insulation against temperature extremes, being warmer and cooler than the maximum and minimum local ambient temperatures, respectively. Nest cavity temperature was not found to have an influence on the breeding success of the southern ground-hornbill groups investigated in this study. These results have potentially important implications for southern ground-hornbill conservation and artificial nest design, as they suggest that the birds can tolerate greater nest cavity temperature extremes than previously thought. Copyright © 2017 Elsevier Ltd. All rights reserved.

Songbird use of floodplain and upland forests along the Upper Mississippi River corridor during spring migration

USGS Publications Warehouse

Kirsch, Eileen M.; Heglund, Patricia J.; Gray, Brian R.; Mckann, Patrick

2013-01-01

The Upper Mississippi River is thought to provide important stopover habitat for migrating landbirds because of its north-south orientation and floodplain forests. The river flows through the Driftless Area of southwestern Wisconsin and southeastern Minnesota where forests are plentiful, yet forests of the floodplain and Driftless Area uplands differ greatly in landscape setting, tree species composition, and topography. We compared landbird assemblages in these upland and floodplain forests over three springs, 2005–2007, using line-transect surveys at randomly selected areas in and within 16 km of the floodplain. We found more species of both transient and locally breeding migrants per survey in floodplain than in upland forest. Detections of transient neotropical migrants did not differ statistically by habitat. Detections of locally breeding neotropical and temperate-zone migrants and transient temperate-zone migrants were greater in floodplain than in upland forest. Between floodplain and upland forest, assemblages of locally breeding species, including neotropical and temperate-zone migrants (of which some individuals were in transit), differed substantially, but assemblages of transients (including both neotropical and temperate-zone migrants) did not differ as much. Only two species of transient migrants had clear affinities for floodplain forest, and none had an affinity for upland forest, whereas most locally breeding migrants had an affinity for either upland or floodplain forest. Within each spring, however, detections of transient neotropical migrants shifted from being greater in floodplain to greater in upland forests. This intraseasonal shift may be related to the phenology of certain tree species.

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds.

PubMed

MacNeil, M D; Cronin, M A; Blackburn, H D; Richards, C M; Lockwood, D R; Alexander, L J

2007-06-01

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.

Population genetics of commercial and feral honey bees in Western Australia.

PubMed

Chapman, Nadine C; Lim, Julianne; Oldroyd, Benjamin P

2008-04-01

Due to the introduction of exotic honey bee (Apis mellifera L.) diseases in the eastern states, the borders of the state of Western Australia were closed to the import of bees for breeding and other purposes > 25 yr ago. To provide genetically improved stock for the industry, a closed population breeding program was established that now provides stock for the majority of Western Australian beekeepers. Given concerns that inbreeding may have resulted from the closed population breeding structure, we assessed the genetic diversity within and between the breeding lines by using microsatellite and mitochondrial markers. We found that the breeding population still maintains considerable genetic diversity, despite 25 yr of selective breeding. We also investigated the genetic distance of the closed population breeding program to that of beekeepers outside of the program, and the feral Western Australian honey bee population. The feral population is genetically distinct from the closed population, but not from the genetic stock maintained by beekeepers outside of the program. The honey bees of Western Australia show three mitotypes, originating from two subspecies: Apis mellifera ligustica (mitotypes C1 and M7b) and Apis mellifera iberica (mitotype M6). Only mitotypes C1 and M6 are present in the commercial populations. The feral population contains all three mitotypes.

Selecting loblolly pine parents for seed orchards to minimize the cost of producing pulp

Treesearch

W.J. Lowe; T.D. Byram; F.E. Bridgwater

1999-01-01

Southern pine cooperative breeding programs currently emphasize genetic improvement of growth rates. When a deployment population, typically a seed orchard, is established, there is an opportunity to emphasize traits other than growth rate to maximize the profit of individual cooperators in the breeding program. The authors studied a southeast Texas breeding population...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

Techniques for monitoring pileated woodpeckers.

Treesearch

Evelyn L Bull; Richard S. Holthausen; Marie G. Henjum

1990-01-01

Methods of locating pileated woodpeckers (Dryocopus pileatus) are described, including imitating pileated woodpecker vocalizations, identifying nest and roost trees, and finding foraging signs. Populations of pileated woodpeckers can be monitored by using (1) density of breeding pairs, (2) reproduction, and (3) presence or absence of birds. The...

Efficacy of a mermithid nematode Romanomermis iyengari (Welch) (Nematoda: Mermithidae) in controlling tree hole-breeding mosquito Aedes albopictus (Skuse) (Diptera: Culicidae) in a rubber plantation area of Kerala, India.

PubMed

Paily, K P; Chandhiran, K; Vanamail, P; Kumar, N Pradeep; Jambulingam, P

2013-03-01

In rubber plantations, tree holes are one of the major types of breeding habitats of Aedes mosquitoes which transmit dengue and chikungunya. A mermithid nematode, Romanomermis iyengari, was evaluated in tree holes for its efficacy in controlling Aedes albopictus. Infection of mosquito larvae by the nematode was determined through microscopic examination on the next day of application, and evaluation of immature density of mosquito was done on the seventh day. After application of the infective stage of the nematode in a host-parasite ratio of 1:3 or 1:4, the infection rates on the different larval instars of mosquito were similar, 85.7-95.8 % in first to third instars and 79.3 % in fourth instar larvae or 100 and 92.9 %, respectively. Parasite burden varied from 1.1 to 2.4, respectively, among first and third instar larvae applied at 1:3. At 1:4, the parasite burden was between 1.6 (fourth instar) and 4 (second instar). The increase in parasite burden due to parasite density was significant in all the larval instars (P < 0.05). High parasite burden is detrimental to parasite recycling as it can cause premature mortality of the host. Hence, the dosage of 1:3 could be considered as suitable for rubber tree hole habitats. In the nematode-applied tree holes, there was a significant level (P < 0.05) of reduction in the immature density of A. albopictus, especially late instars and pupae, confirming the efficacy of R. iyengari in infecting the mosquito and controlling pupal emergence.

Attack pattern and reproductive ecology of Tomicus brevipilosus (Coleoptera: Curculionidae) on Pinus yunnanensis in Southwestern China.

PubMed

Chen, Peng; Lu, Jun; Haack, Robert A; Ye, Hui

2015-01-01

Tomicus brevipilosus (Eggers) (Coleoptera: Curculionidae, Scolytinae) was recently discovered as a new pest of Yunnan pine (Pinus yunnanensis Franchet) in Yunnan Province in southwestern China. However, little was known on its reproductive biology and pattern of trunk attack on Yunnan pine. The objectives of this study were to better understand the reproductive biology of T. brevipilosus by investigating the seasonality of trunk attacks by parent adults for the purpose of reproduction (i.e., breeding attacks) and the within-tree pattern of these attacks. Our results showed that T. brevipilosus breeding attacks in P. yunnanensis generally started in early March and ended in early June in Anning County, Yunnan. T. brevipilosus exhibited two general patterns of infestation. From early March to mid-April, T. brevipilosus bred preferentially in the trunks of Yunnan pine trees that were already infested by Tomicus yunnanensis Kirkendall and Faccoli and Tomicus minor (Hartig), colonizing spaces along the trunk (mostly in the mid- and lower trunk) that were not already occupied by the other two Tomicus species. Later, from about mid-April to early June, when there were no Yunnan pine trees newly infested by T. yunnanensis and T. minor, T. brevipilosus attacked Yunnan pine by itself, infesting the lower parts of the trunk first and then infesting progressively upward along the trunk into the crown. Infestation by T. brevipilosus extends the total period that P. yunnanensis trees are under attack by Tomicus beetles in southwestern China, which helps explain why Yunnan pine has suffered high levels of tree mortality in recent decades. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

KSC-07pd0875

NASA Image and Video Library

2007-04-11

KENNEDY SPACE CENTER, FLA. -- A palm warbler looks for seeds among the branches of a tree on Kennedy Space Center. Palm warblers breed far to the north in Canada, and winter primarily in the southern United States and northern Caribbean. They breed in bogs, open boreal coniferous forest, and partly open situations with scattered trees and heavy undergrowth, usually near water. They are found in migration and winter in a variety of woodland, second growth and thicket habitats, on the ground in savanna and open fields, and in mangroves. Their diet consists of insects, some seeds and fruits in fall and winter. KSC shares a boundary with the Merritt Island Wildlife Nature Refuge. The refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles. In addition, the Refuge supports 19 endangered or threatened wildlife species on Federal or State lists, more than any other single refuge in the U.S. Photo credit: NASA/Dimitri Gerondidakis

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans.

PubMed

Ceh, E; Dovc, P

2014-08-01

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour-joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects. © 2014 Blackwell Verlag GmbH.

Epidemiology of tree-hole breeding mosquitoes in the tropical rainforest of Imo State, south-east Nigeria.

PubMed

Anosike, Jude C; Nwoke, Bertram E B; Okere, Anthony N; Oku, Ene E; Asor, Joe E; Emmy-Egbe, Ifeyinwa O; Adimike, Desmond A

2007-01-01

The study of tree-hole breeding mosquitoes was carried out in the tropical rainforest of Imo State Nigeria (two rural areas and two forest reserves in some parts of Orlu Senatorial Zone) between May-October 2002. Using standard entomological procedures, two macrohabitats (natural tree-holes and bamboo traps) and two microhabitats (leaf axils of cocoyams/pineapples and leaf axils of plantain/banana) were sampled for various mosquito species. Mosquitoes were recovered from all the various biotypes sampled. Types of mosquitoes species encountered, their relative abundance, as well as genera varied significantly during the study (p<0.05). Four genera of mosquitoes: Aedes, Culex, Anopheles and Toxorhynchites were recovered while 16 species of mosquitoes encountered include: Aedes aegypti, Ae. africanus, Ae. simpsoni, Ae. albopictus, Ae. stokesi, Ae. taylori, Ae. apicoargenteus, Culex quinquefasciatus, Cx. nebulosus, Cx. trigripes, Cx. decens, Anopheles gambiae, An. funiestus, An. coustani and Toxorhynchites viridibasis. Most of the mosquitoes showed oviposition preferences for one or more habitats. The presence of Ae. africanus, Ae. simpsoni and Ae. aegypti indicate that the study areas were at risk of yellow fever epidemic. The presence of Anopheles and Culex species ensured endemicity of malaria and filariasis, while the recovery of Ae. albopictus in this region suggests a possible outbreak of dengue fever in future if not properly controlled.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes

PubMed Central

2014-01-01

Background Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Results Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Conclusions Gene expression profiling and trait-associated transcript analysis using an apple F1 population readily identified genes physically linked to powdery mildew disease resistance and woolly apple aphid resistance loci. This result was especially useful in apple, where extreme levels of heterozygosity make the development of reliable DNA markers quite difficult. The results suggest that this approach could prove effective in crops with complicated genetics, or for which few genomic information resources are available. PMID:24708064

Habitat suitability—density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)

PubMed Central

Moreno, Ángel C.; Delgado, Alejandro; Suárez, Víctor; Trujillo, Domingo

2017-01-01

Background Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs. Methods We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994. Results The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July–September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195–430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic. Discussion Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abundance during the reproductive season. The outcomes of these models can be used for the identification of potential areas for the reintroduction of the species in other suitable pine forests and to inform forest management practices. PMID:28924498

Epigenetic regulation of adaptive responses of forest tree species to the environment

PubMed Central

Bräutigam, Katharina; Vining, Kelly J; Lafon-Placette, Clément; Fossdal, Carl G; Mirouze, Marie; Marcos, José Gutiérrez; Fluch, Silvia; Fraga, Mario Fernández; Guevara, M Ángeles; Abarca, Dolores; Johnsen, Øystein; Maury, Stéphane; Strauss, Steven H; Campbell, Malcolm M; Rohde, Antje; Díaz-Sala, Carmen; Cervera, María-Teresa

2013-01-01

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change. PMID:23467802

Characterization of casein gene complex and genetic diversity analysis in Indian goats.

PubMed

Rout, P K; Kumar, A; Mandal, A; Laloe, D; Singh, S K; Roy, R

2010-04-01

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

PubMed

Wang, G Z; Chen, S S; Chao, T L; Ji, Z B; Hou, L; Qin, Z J; Wang, J M

2017-05-01

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

Genetic map of mango: a tool for mango breeding

USDA-ARS?s Scientific Manuscript database

Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop, affectionately labeled the “King of Fruit”. Mango is an allotetraploid with 40 chromosomes and the size of the diploid genome is ~439 Mb. Most of the current commercial cultivars are select...

Post-breeding bird responses to canopy tree retention, stand size, and edge in regenerating Appalachian hardwood stands

USGS Publications Warehouse

McDermott, Molly E.; Wood, Petra B.

2011-01-01

Avian use of even-aged timber harvests is likely affected by stand attributes such as size, amount of edge, and retained basal area, all characteristics that can easily be manipulated in timber harvesting plans. However, few studies have examined their effects during the post-breeding period. We studied the impacts of clearcut, low-leave two-age, and high-leave two-age harvesting on post-breeding birds using transect sampling and mist-netting in north-central West Virginia. In our approach, we studied the effects of these harvest types as well as stand size and edge on species characteristic of both early-successional and mature forest habitats. In 2005–2006, 13 stands ranging from 4 to 10 years post-harvest and 4–21 ha in size were sampled from late June through mid-August. Capture rates and relative abundance were similar among treatments for generalist birds. Early-successional birds had the lowest capture rates and fewer species (∼30% lower), and late-successional birds reached their highest abundance and species totals (double the other treatments) in high-leave two-age stands. Area sensitivity was evident for all breeding habitat groups. Both generalist and late-successional bird captures were negatively related to stand size, but these groups showed no clear edge effects. Mean relative abundance decreased to nearly zero for the latter group in the largest stands. In contrast, early-successional species tended to use stand interiors more often and responded positively to stand size. Capture rates for this group tripled as stand size increased from 4 to 21 ha. Few birds in the forest periphery responded to harvest edge types despite within-stand edge effects evident for several species. To create suitable habitat for early-successional birds, large, non-linear openings with a low retained basal area are ideal, while smaller harvests and increased residual tree retention would provide habitat for more late-successional birds post-breeding. Although our study has identified habitat use patterns for different species in timber harvests, understanding habitat-specific bird survival is needed to help determine the quality of silvicultural harvests for post-breeding birds.

Advances and Challenges in Genomic Selection for Disease Resistance.

PubMed

Poland, Jesse; Rutkoski, Jessica

2016-08-04

Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens, becomes a tractable and powerful approach in breeding programs.

Study on natural breeding sites of sand flies (Diptera: Phlebotominae) in areas of Leishmania transmission in Colombia.

PubMed

Vivero, Rafael José; Torres-Gutierrez, Carolina; Bejarano, Eduar E; Peña, Horacio Cadena; Estrada, Luis Gregorio; Florez, Fernando; Ortega, Edgar; Aparicio, Yamileth; Muskus, Carlos E

2015-02-22

The location of the microhabitats where immature phlebotomine sand flies of the genus Lutzomyia develop is one of the least-known aspects of this group of medically important insects. For this reason strategies of source reduction approach for their control have not been possible in contrast to other insect vectors (such as mosquitoes), because their juvenile stages in terrestrial microhabitats is difficult to detect. Direct examination of soil samples, incubation of substrates and the use of emergence traps were the methods used to identify juvenile stages in 160 soil samples from urban and forest habitats within the foci of Leishmania transmission in Colombia. Immatures collected were identified subsequent from the rearing and emergence of adults using taxonomic keys or the analysis of the mitochondrial marker cytochrome oxidase I. Plant species associated with the natural breeding sites were identified and physicochemical properties of the soils were analyzed. A total of 38 (23.7%) sampling sites were identified as breeding sites, 142 phlebotomine sand flies were identified, belonging to 13 species of the genus Lutzomyia and two of Brumptomyia. The greatest numbers of immature were found within the tabular roots (51 immature sand flies from eight positive sites) and bases of trees (35 immature sand flies from 11 sites). The characterization and presence of the tree species (mainly Ceiba pentadra, Anacardium excelsum, Pseudosamanea guachapale) and the physicochemical properties (relative humidity and carbon/nitrogen ratio) of the soils associated with these breeding sites are significant factors in explaining the diversity and abundance of phlebotomine sand flies. Immature phlebotomine sand flies of the genus Lutzomyia in Colombia can be found in a wide variety of breeding sites rich in organic matter, high relative humidity and are associated with a typical vegetation of each locality. These results provide new perspectives for the study of the ecology of the genus Lutzomyia in Colombia and the development of vector control strategies.

Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.

PubMed

Pembleton, Luke W; Inch, Courtney; Baillie, Rebecca C; Drayton, Michelle C; Thakur, Preeti; Ogaji, Yvonne O; Spangenberg, German C; Forster, John W; Daetwyler, Hans D; Cogan, Noel O I

2018-06-02

Exploitation of data from a ryegrass breeding program has enabled rapid development and implementation of genomic selection for sward-based biomass yield with a twofold-to-threefold increase in genetic gain. Genomic selection, which uses genome-wide sequence polymorphism data and quantitative genetics techniques to predict plant performance, has large potential for the improvement in pasture plants. Major factors influencing the accuracy of genomic selection include the size of reference populations, trait heritability values and the genetic diversity of breeding populations. Global diversity of the important forage species perennial ryegrass is high and so would require a large reference population in order to achieve moderate accuracies of genomic selection. However, diversity of germplasm within a breeding program is likely to be lower. In addition, de novo construction and characterisation of reference populations are a logistically complex process. Consequently, historical phenotypic records for seasonal biomass yield and heading date over a 18-year period within a commercial perennial ryegrass breeding program have been accessed, and target populations have been characterised with a high-density transcriptome-based genotyping-by-sequencing assay. Ability to predict observed phenotypic performance in each successive year was assessed by using all synthetic populations from previous years as a reference population. Moderate and high accuracies were achieved for the two traits, respectively, consistent with broad-sense heritability values. The present study represents the first demonstration and validation of genomic selection for seasonal biomass yield within a diverse commercial breeding program across multiple years. These results, supported by previous simulation studies, demonstrate the ability to predict sward-based phenotypic performance early in the process of individual plant selection, so shortening the breeding cycle, increasing the rate of genetic gain and allowing rapid adoption in ryegrass improvement programs.

Can functional hologenomics aid tackling current challenges in plant breeding?

PubMed

Nogales, Amaia; Nobre, Tânia; Valadas, Vera; Ragonezi, Carla; Döring, Matthias; Polidoros, Alexios; Arnholdt-Schmitt, Birgit

2016-07-01

Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A computational approach to animal breeding.

PubMed

Berger-Wolf, Tanya Y; Moore, Cristopher; Saia, Jared

2007-02-07

We propose a computational model of mating strategies for controlled animal breeding programs. A mating strategy in a controlled breeding program is a heuristic with some optimization criteria as a goal. Thus, it is appropriate to use the computational tools available for analysis of optimization heuristics. In this paper, we propose the first discrete model of the controlled animal breeding problem and analyse heuristics for two possible objectives: (1) breeding for maximum diversity and (2) breeding a target individual. These two goals are representative of conservation biology and agricultural livestock management, respectively. We evaluate several mating strategies and provide upper and lower bounds for the expected number of matings. While the population parameters may vary and can change the actual number of matings for a particular strategy, the order of magnitude of the number of expected matings and the relative competitiveness of the mating heuristics remains the same. Thus, our simple discrete model of the animal breeding problem provides a novel viable and robust approach to designing and comparing breeding strategies in captive populations.

Improving Charging-Breeding Simulations with Space-Charge Effects

NASA Astrophysics Data System (ADS)

Bilek, Ryan; Kwiatkowski, Ania; Steinbrügge, René

2016-09-01

Rare-isotope-beam facilities use Highly Charged Ions (HCI) for accelerators accelerating heavy ions and to improve measurement precision and resolving power of certain experiments. An Electron Beam Ion Trap (EBIT) is able to create HCI through successive electron impact, charge breeding trapped ions into higher charge states. CBSIM was created to calculate successive charge breeding with an EBIT. It was augmented by transferring it into an object-oriented programming language, including additional elements, improving ion-ion collision factors, and exploring the overlap of the electron beam with the ions. The calculation is enhanced with the effects of residual background gas by computing the space charge due to charge breeding. The program assimilates background species, ionizes and charge breeds them alongside the element being studied, and allows them to interact with the desired species through charge exchange, giving fairer overview of realistic charge breeding. Calculations of charge breeding will be shown for realistic experimental conditions. We reexamined the implementation of ionization energies, cross sections, and ion-ion interactions when charge breeding.

Comparison of breeding bird and vegetation communities in primary and secondary forests of Great Smoky Mountains National Park

USGS Publications Warehouse

Simons, Theodore R.; Shriner, Susan A.; Farnsworth, George L.

2006-01-01

We compared breeding bird communities and vegetation characteristics at paired point locations in primary (undisturbed) and mature secondary forest (70-100 years old) sites in Great Smoky Mountains National Park, USA to understand how sites logged prior to creation of the park compare to undisturbed sites following 70 years of protection from human disturbance. We found that bird and vegetation communities are currently similar, but retain some differences in species composition. Rank abundance curves for primary and secondary forest bird communities showed very similar patterns of species dominance. Species composition was also similar on the two sites which shared 24 of the 25 most frequently recorded species. Nonetheless, comparisons of density estimates derived from distance sampling showed three bird species were more abundant on primary forest sites and that one bird species was significantly more abundant on secondary forest sites. Notably, comparisons based on raw counts (unadjusted for potential differences in detectability) produced somewhat different results. Analyses of vegetation samples for the paired sites also showed relative similarity, but with some differences between primary and secondary forests. Primary forest sites had more large trees (trees greater than 50 cm diameter at breast height) and late successional species. Primary forest sites had a denser tall shrub layer while secondary forest sites had a denser canopy layer. Nonetheless, tree species richness, basal area of live trees and number of standing snags did not differ between primary and secondary forest sites. Results indicate that breeding bird communities on sites within the park that were logged commercially 70 years ago are currently quite similar to bird communities on sites with no history of human disturbance. Similarities between the bird communities on previously disturbed and undisturbed sites in Great Smoky Mountains National Park may exceed those on more fragmented landscapes because large patches of primary forest, adjacent to commercially logged sites, remained in the park when it was established in 1935. These patches of primary forest may have served as source areas for commercially logged sites.

Reproductive ecology of the Maui Parrotbill

USGS Publications Warehouse

Simon, John C.; Pratt, T.K.; Berlin, Kim E.; Kowalsky, James R.

2000-01-01

The endangered Maui Parrotbill (Pseudonestor xanthophrys) is an excavating, insectivorous Hawaiian honeycreeper endemic to the high elevation rain forests of east Maui, Hawaii. From March 1994 to June 1997, we studied various aspects of their breeding ecology. We color-banded 18 individuals, located and monitored 9 active nests, and took behavioral data during 440 hrs of nest observation. Both members of a pair maintained a year-round, all-purpose territory that included nest sites and food resources. Maui Parrotbill were monogamous within and between years; we found no evidence of polyandry, polygyny, or helpers at the nest. Nests were cup-shaped, composed mainly of lichen interlaced with small twigs, and positioned in the outer canopy forks of mature ohia (Metrosideros polymorpha) trees. Modal clutch size was one. Females performed most nest construction and all incubation and brooding; males provisioned females and assisted in feeding nestlings after their fourth day. Fledglings depended on parental care for 5-8 months, during which their bill strength increased and foraging skills improved. We calculated the overall nest success rate by the Mayfield Method as 0.42 for the 1995/1996 and 1996/1997 breeding seasons combined. Nest failure and fledgling disappearance coincided with events of high rainfall. Their breeding ecology most closely resembled the Akiapolaau (Hemignathus munroi), another excavating, insectivorous Hawaiian honeycreeper found on Hawaii Island. As with the Akiapolaau, the threat of extinction is persistent and results from both the constraints of inherent life history traits and artificial ecological changes. We advocate the protection and expansion of habitable forest areas and an ongoing program to monitor and mitigate the effects of invasive species.

Tanoak resistance: can it be used to sustain populations?

Treesearch

Katherine J. Hayden; Alex Lundquist; Douglas J. Schmidt; Richard A. Sniezko; Susan J. Frankel; Matteo. Garbelotto

2010-01-01

Tanoak (Lithocarpus densiflorus) trees are among Phytophthora ramorum’s most susceptible hosts. Extensive mortality in this species has led researchers to question whether selective breeding for resistance can be used to sustain populations; the answer depends on the extent and heritability of pathogen resistance within the...

Silvicultural and logistical considerations associated with the pending reintroduction of American chestnut

Treesearch

Douglass F. Jacobs

2010-01-01

Traditional breeding for blight resistance has led to the potential to restore American chestnut (Castanea dentata (Marsh.) Borkh.) to Eastern United States forests using a blight resistant hybrid chestnut tree. With prospects of pending wide-scale reintroduction, restoration strategies based on ecological and biological characteristics of the...

Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm

USDA-ARS?s Scientific Manuscript database

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in...

Emerald ash borer survival in firewood

Treesearch

Robert A. Haack; Toby R. Petrice

2005-01-01

The emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), is native to Asia and was first discovered in Michigan and Ontario in 2002. As of October 2004, EAB was only found to breed in ash (Fraxinus) trees in North America. EAB is spreading naturally through adult flight as well as artificially through...

Frontalin interrupts attraction of Ips pini (Coleoptera; Scolytidae) to ipsdienol

Treesearch

Daniel R. Miller

2001-01-01

The pine engraver, Ips pini (Say), breeds in the phloem tissue of dead, dying, or downed pines, occasionally attacking standing live trees when populations build up to significant levels following logging activities or infestations by the mountain pine beetle, Dendroctonus ponderosae Hopkins, (Furniss and Carolin 1980). In British...

Bird community relationships to succession in green ash (Fraxinus pennsylvanica) woodlands

Treesearch

Mark A. Rumble; John E. Gobeille

1998-01-01

We studied the relationship between breeding birds and seral stages of green ash (Fraxinus pennsylvanica) woodlands in central South Dakota between 1990 and 1992. Stands of early seral green ash undergoing primary succession had few small trees with western snowberry (Symphoricarpos occidentalis) in the understory. Some early seral...

Typification of infrageneric names in Ulmus L.

USDA-ARS?s Scientific Manuscript database

The elms (the genus Ulmus) are one of the most important tree crops for the $4.7billion per year U.S. nursery industry, but utilization of these plants has been limited in recent decades by introduced diseases, especially Dutch elm disease. Research and breeding for disease resistance have been base...

Red-cockaded woodpecker foraging behavior

Treesearch

D. Craig Rudolph; Richard N. Conner; Richard R. Schaefer; Nancy E. Koerth

2007-01-01

We studied Red-cockaded Woodpeckers (Picoides borealis) to examine the effect of status and gender on foraging behavior. Foraging behavior of breeding pairs extended beyond separation by foraging height to include zones (bole, trunk in crown, primary limb, secondary limb) of the tree used and foraging methods (scaling, probing, excavating). Helper...

Inbreeding depression in selfs of redwood

Treesearch

W. J. Libby; B. G. McCutchan; C. I. Millar

1981-01-01

Given the polyploid chromosome constitution of Sequoia sempervirens, there was reason to question whether it would exhibit inbreeding depression. Preliminary results from studies of self and related outcross families are reported as a guide to the selection of trees for redwood seed orchards and breeding-orchards. The data indicate that, compared to...

Transcriptome architecture across tissues in the pig

PubMed Central

Ferraz, André LJ; Ojeda, Ana; López-Béjar, Manel; Fernandes, Lana T; Castelló, Anna; Folch, Josep M; Pérez-Enciso, Miguel

2008-01-01

Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome. PMID:18416811

Benefits of prophylactic gastropexy for dogs at risk of gastric dilatation-volvulus.

PubMed

Ward, Michael P; Patronek, Gary J; Glickman, Lawrence T

2003-09-12

The lifetime probability of death from gastric dilation-volvulus (GDV) for five dog breeds was estimated based on published breed-specific longevity and GDV incidence. These breeds were Great Dane, Irish Setter, Rottweiler, Standard Poodle and Weimaraner. Lifetime risk (95% CI) of GDV in these breeds ranged from 3.9% (0-11.2%) for Rottweiler to 36.7% (25.2-44.6%) for Great Dane. A decision-tree analysis for prophylactic gastropexy--using lifetime probability of death from GDV and expected cost savings for veterinary services as outcome measures--was undertaken to determine the preferred course of action in several dog breeds. Prophylactic gastropexy was the preferred choice of action for all breeds examined, with the reduction in mortality (versus no gastropexy) ranging from 2.2-fold (Rottweiler) to 29.6-fold (Great Dane). Assuming a prophylactic gastropexy costs US$ 400, the procedure was cost-effective when the lifetime risk of GDV was > or = 34%. The maximum and minimum estimated breakeven costs for the gastopexy procedure ranged from US$ 20 (Rottweiler) to US$ 435 (Great Dane). The cost-effectiveness of prophylactic gastropexy was most sensitive to the cost of treating GDV (US$ 1500). Prophylactic gastropexy raises ethical issues that need to be considered by veterinarians and dog breeders.

Need and prospects for using tracer techniques in fruit breeding

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

Zagaja, S.W.

1975-01-01

Compared with staple food crops and fodder crops, the commercial value of fruits depends more on their quality than on their productivity. Modified screening techniques are therefore required for fruit crop improvement. The following are areas of fruit crop improvement in which tracer techniques could be used to speed up the progress: assessment of rootstocks and particularly their effect on vigour of growth and productivity of the trees; assessment of mutants productivity; assessment of adaptability to various habitats of fruit tree cultivars and rootstocks; and juvenility studies on fruit trees, aimed at shortening the juvenile stage. On each of thesemore » subjects background information is provided and suggestions are made concerning the scope of research. (auth)« less

Historical use of cultivars as parents in Florida and Louisiana sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum L. spp. hybrids) growers depend on breeding programs for new, high-yielding cultivars that have resistance to abiotic and biotic stresses, so breeders continually seek out widely adapted, high yielding germplasm to be used as parents for their programs. Cultivars are sometimes u...

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Influence of the variation of geometrical and topological traits on light interception efficiency of apple trees: sensitivity analysis and metamodelling for ideotype definition

PubMed Central

Da Silva, David; Han, Liqi; Faivre, Robert; Costes, Evelyne

2014-01-01

Background and Aims The impact of a fruit tree's architecture on its performance is still under debate, especially with regard to the definition of varietal ideotypes and the selection of architectural traits in breeding programmes. This study aimed at providing proof that a modelling approach can contribute to this debate, by using in silico exploration of different combinations of traits and their consequences on light interception, here considered as one of the key parameters to optimize fruit tree production. Methods The variability of organ geometrical traits, previously described in a bi-parental population, was used to simulate 1- to 5-year-old apple trees (Malus × domestica). Branching sequences along trunks observed during the first year of growth of the same hybrid trees were used to initiate the simulations, and hidden semi-Markov chains previously parameterized were used in subsequent years. Tree total leaf area (TLA) and silhouette to total area ratio (STAR) values were estimated, and a sensitivity analysis was performed, based on a metamodelling approach and a generalized additive model (GAM), to analyse the relative impact of organ geometry and lateral shoot types on STAR. Key Results A larger increase over years in TLA mean and variance was generated by varying branching along trunks than by varying organ geometry, whereas the inverse was observed for STAR, where mean values stabilized from year 3 to year 5. The internode length and leaf area had the highest impact on STAR, whereas long sylleptic shoots had a more significant effect than proleptic shoots. Although the GAM did not account for interactions, the additive effects of the geometrical factors explained >90% of STAR variation, but much less in the case of branching factors. Conclusions This study demonstrates that the proposed modelling approach could contribute to screening architectural traits and their relative impact on tree performance, here viewed through light interception. Even though trait combinations and antagonism will need further investigation, the approach opens up new perspectives for breeding and genetic selection to be assisted by varietal ideotype definition. PMID:24723446

Short- and long-term implications of clearcut and two-age silviculture for conservation of breeding forest birds in the central Appalachians, USA

USGS Publications Warehouse

McDermott, M.E.; Wood, P.B.

2009-01-01

Two-age (deferment or leave tree) harvesting is used increasingly in even-aged forest management, but long-term responses of breeding avifauna to retention of residual canopy trees have not been investigated. Breeding bird surveys completed in 1994-1996 in two-age and clearcut harvests in the central Appalachian Mountains of West Virginia, USA allowed us to document long-term changes in these stands. In 2005 and 2006, we conducted point counts in mature unharvested forest stands and in 19-26 year-old clearcut and two-age harvests from the original study and in younger clearcut and two-age stands (6-10 years old). We found differences in breeding bird metrics among these five treatments and temporal differences in the original stands. Although early-successional species are typically absent from group selection cuts, they were almost as common in young two-age stands as clearcuts, supporting two-age harvests as an alternative to clearcutting. Although older harvests had lower species richness and diversity, they were beginning to provide habitat for some species of late-successional forest songbirds that were absent or uncommon in young harvests. Overall, late-successional forest-interior species were more flexible in their use of different seral stages; several species used both age classes and harvest types in addition to mature forest, which may reflect the lack of edges in our heavily-forested landscape. Consequently, two-age management provides habitat for a diverse group of species as these stands mature and may be an ecologically sustainable alternative to clearcutting in landscapes where brown-headed cowbirds (Molothrus ater) are uncommon. ?? 2008 Elsevier Ltd.

Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil.

PubMed

Brasil, B S A F; Coelho, E G A; Drummond, M G; Oliveira, D A A

2013-11-18

The Brazilian cattle population is mainly composed of breeds of zebuine origin and their American derivatives. Comprehensive knowledge about the genetic diversity of these populations is fundamental for animal breeding programs and the conservation of genetic resources. This study aimed to assess the phylogenetic relationships, levels of genetic diversity, and patterns of taurine/zebuine admixture among 9 commercial cattle breeds raised in Brazil. Analysis of DNA polymorphisms was performed on 2965 animals using the 11 microsatellite markers recommended by the International Society of Animal Genetics. High genetic diversity was detected in all breeds, even though significant inbreeding was observed within some. Differences among the breeds accounted for 14.72% of the total genetic variability, and genetic differentiation was higher among taurine than among zebuine cattle. Of note, Nelore cattle presented with high levels of admixture, which is consistent with the history of frequent gene flow during the establishment of this breed in Brazil. Furthermore, significant genetic variability was partitioned within the commercial cattle breeds formed in America, which, therefore, comprise important resources of genetic diversity in the tropics. The genetic characterization of these important Brazilian breeds may now facilitate the development of management and breeding programs for these populations.

Thermal conditions within tree cavities in ponderosa pine (Pinus ponderosa) forests: potential implications for cavity users.

PubMed

Vierling, Kerri T; Lorenz, Teresa J; Cunningham, Patrick; Potterf, Kelsi

2018-04-01

Tree cavities provide critical roosting and breeding sites for multiple species, and thermal environments in these cavities are important to understand. Our objectives were to (1) describe thermal characteristics in cavities between June 3 and August 9, 2014, and (2) investigate the environmental factors that influence cavity temperatures. We placed iButtons in 84 different cavities in ponderosa pine (Pinus ponderosa) forests in central Washington, and took hourly measurements for at least 8 days in each cavity. Temperatures above 40 °C are generally lethal to developing avian embryos, and ~ 18% of the cavities had internal temperatures of ≥ 40 °C for at least 1 h of each day. We modeled daily maximum cavity temperature, the amplitude of daily cavity temperatures, and the difference between the mean internal cavity and mean ambient temperatures as a function of several environmental variables. These variables included canopy cover, tree diameter at cavity height, cavity volume, entrance area, the hardness of the cavity body, the hardness of the cavity sill (which is the wood below the cavity entrance which forms the barrier between the cavity and the external environment), and sill width. Ambient temperature had the largest effect size for maximum cavity temperature and amplitude. Larger trees with harder sills may provide more thermally stable cavity environments, and decayed sills were positively associated with maximum cavity temperatures. Summer temperatures are projected to increase in this region, and additional research is needed to determine how the thermal environments of cavities will influence species occupancy, breeding, and survival.

Thermal conditions within tree cavities in ponderosa pine (Pinus ponderosa) forests: potential implications for cavity users

NASA Astrophysics Data System (ADS)

Vierling, Kerri T.; Lorenz, Teresa J.; Cunningham, Patrick; Potterf, Kelsi

2017-11-01

Tree cavities provide critical roosting and breeding sites for multiple species, and thermal environments in these cavities are important to understand. Our objectives were to (1) describe thermal characteristics in cavities between June 3 and August 9, 2014, and (2) investigate the environmental factors that influence cavity temperatures. We placed iButtons in 84 different cavities in ponderosa pine (Pinus ponderosa) forests in central Washington, and took hourly measurements for at least 8 days in each cavity. Temperatures above 40 °C are generally lethal to developing avian embryos, and 18% of the cavities had internal temperatures of ≥ 40 °C for at least 1 h of each day. We modeled daily maximum cavity temperature, the amplitude of daily cavity temperatures, and the difference between the mean internal cavity and mean ambient temperatures as a function of several environmental variables. These variables included canopy cover, tree diameter at cavity height, cavity volume, entrance area, the hardness of the cavity body, the hardness of the cavity sill (which is the wood below the cavity entrance which forms the barrier between the cavity and the external environment), and sill width. Ambient temperature had the largest effect size for maximum cavity temperature and amplitude. Larger trees with harder sills may provide more thermally stable cavity environments, and decayed sills were positively associated with maximum cavity temperatures. Summer temperatures are projected to increase in this region, and additional research is needed to determine how the thermal environments of cavities will influence species occupancy, breeding, and survival.

Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

PubMed Central

Misra, Raj Shekhar; Boonkorkaew, Patchareeya; Thanomchit, Kanokwan

2017-01-01

The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance. PMID:28658282

Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

PubMed

Rochus, Christina M; Johansson, Anna M

2017-01-01

Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

Extending RosBREED in the Pacific Northwest for strawberry processing traits: year 1

USDA-ARS?s Scientific Manuscript database

In an effort to implement marker-assisted breeding in Rosaceae, many traits need to be characterized in diverse germplasm. The USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project includes breeding programs of four Rosaceae crops (apple, peach, cherry, and strawberry). Phenotyping ea...

PALLAS BARLEY, A VARIETY PRODUCED BY IONIZING RADIATION: ITS SIGNIFICANCE FOR PLANT BREEDING AND EVOLUTION

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

Borg, G.; Froier, K.f Gustafsson, A.

1959-10-31

Results are reported from plant breeding programs in which mutations induced in barley by irradiation resulted in the development of a variety with characteristics superior to the parents. Good results were also reported in the development of superior varieties of oil rape, white mustard, and pea plants. The usefulness of radiation-induced mutations in plant breeding programs is discussed. (C.H.)

Genetic characterization of Russian honey bee stock selected for improved resistance to Varroa destructor.

PubMed

Bourgeois, A Lelania; Rinderer, Thomas E

2009-06-01

Maintenance of genetic diversity among breeding lines is important in selective breeding and stock management. The Russian Honey Bee Breeding Program has strived to maintain high levels of heterozygosity among its breeding lines since its inception in 1997. After numerous rounds of selection for resistance to tracheal and varroa mites and improved honey production, 18 lines were selected as the core of the program. These lines were grouped into three breeding blocks that were crossbred to improve overall heterozygosity levels of the population. Microsatellite DNA data demonstrated that the program has been successful. Heterozygosity and allelic richness values are high and there are no indications of inbreeding among the three blocks. There were significant levels of genetic structure measured among the three blocks. Block C was genetically distinct from both blocks A and B (F(ST) = 0.0238), whereas blocks A and B did not differ from each other (F(ST) = 0.0074). The same pattern was seen for genic (based on numbers of alleles) differentiation. Genetic distance, as measured by chord distance, indicates that all of the 18 lines are equally distant, with minimal clustering. The data indicate that the overall design of the breeding program has been successful in maintaining high levels of diversity and avoiding problems associated with inbreeding.

Genetic effects of chronic habitat fragmentation in a wind-pollinated tree

PubMed Central

Jump, Alistair S.; Peñuelas, Josep

2006-01-01

Habitat fragmentation poses a serious threat to plants through genetic changes associated with increased isolation and reduced population size. However, the longevity of trees, combined with effective seed or pollen dispersal, can enhance their resistance to these effects. The European beech (Fagus sylvatica) dominates forest over large regions of Europe. We demonstrate that habitat fragmentation in this species has led to genetic bottlenecks and the disruption of the species' breeding system, leading to significantly elevated levels of inbreeding, population divergence, and reduced genetic diversity within populations. These results show that, in contrast with the findings of previous studies, forest fragmentation has a negative genetic impact, even in this widespread, wind-pollinated tree. The identification of significant effects of forest fragmentation in beech demonstrates that trees are not at reduced risk from environmental change. This should be accounted for in the management of remaining natural and seminatural forest throughout the world. PMID:16698935

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

PubMed Central

Pierce, Magretha D.; Dzama, Kennedy; Muchadeyi, Farai C.

2018-01-01

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs. PMID:29868114

Methods for shorebird surveys in the Arctic

Treesearch

Jonathan Bart; Susan L. Earnst

2005-01-01

A substantial effort is being made to develop a longterm monitoring program for shorebirds in North American (Brown et al. 2000, Donaldson et al. 2001, Bart et al. this volume). The current program, PRISM (Program for Regional and International Shorebird Monitoring), has four segments: arctic and boreal breeding surveys, temperate breeding surveys, temperate non-...

Integrating molecular tools and conventional approaches in the Oregon State University hazelnut breeding program

Treesearch

Shawn A. Mehlenbacher

2012-01-01

The Oregon State University (OSU) hazelnut breeding program, initiated in 1969, continues to develop new cultivars for the hazelnut industry that combine suitability to the blanched kernel market with resistance to eastern filbert blight (EFB) caused by Anisogramma anomala. Oregon's hazelnut growers support the program through the Oregon...

Trees wanted--dead or alive! Host selection and population dynamics in tree-killing bark beetles.

PubMed

Kausrud, Kyrre L; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between "endemic" and "epidemic" regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.

Population structure of four Thai indigenous chicken breeds.

PubMed

Mekchay, Supamit; Supakankul, Pantaporn; Assawamakin, Anunchai; Wilantho, Alisa; Chareanchim, Wanwisa; Tongsima, Sissades

2014-03-27

In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Waterbird nest density and nest survival in rice fields of southwestern Louisiana

USGS Publications Warehouse

Pierluissi, S.; King, Sammy L.; Kaller, Michael D.

2010-01-01

Rice fields in southwestern Louisiana provide breeding habitat for several waterbird species; however, little is known about nest density, nest survival and the importance of landscape context of rice fields in determining breeding activity. In 2004, 42 rice fields were searched for nests, and 40 were searched in 2005. Land uses surrounding rice fields, including irrigation canals, trees, crawfish ponds, rice, fallow and soybean fields, were examined to determine influence on nest density and survival. Nest densities were 13.5-16.0 nests/km2 for Purple Gallinules (Porphyrio martinica), 3.0-13.7 nests/km2 for Fulvous Whistling Ducks (Dendrocygna bicolor), 2.6-2.8 nests/km2 for Common Moorhens (Gallinula chloropus), 0.3-0.92 nests/km2 for Least Bitterns (Ixobrychus exilisi) and 0-0.6 nests/km2 for Mottled Ducks (Anas fulvigula). Nest survival was 52-79% for Purple Gallinules and 39-43% for Fulvous Whistling Ducks. Apparent nest success of Common Moorhens was 73-75%, 83% for Least Bitterns and 33% for Mottled Ducks. Purple Gallinule and Common Moorhen nest densities were highest in fields with a larger proportion of irrigation canals surrounding rice fields. Purple Gallinule nest densities were greater in fields devoid of trees and landscapes dominated by rice fields and pasture, rather than landscapes containing soybean fields and residential areas. Fulvous Whistling Duck nest densities were higher in agriculturally-dominated landscapes with few trees.

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs

PubMed Central

Pérez, Ana G.; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties (“Picual” and “Arbequina”) used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile. PMID:29535752

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs.

PubMed

Pérez, Ana G; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties ("Picual" and "Arbequina") used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile.

Branching out to residential lands: Missions and strategies of five tree distribution programs in the U.S.

Treesearch

Vi D. Nguyen; Lara A. Roman; Dexter H. Locke; Sarah K. Mincey; Jessica R. Sanders; Erica Smith Fichman; Mike Duran-Mitchell; Sarah Lumban Tobing

2017-01-01

Residential lands constitute a major component of existing and possible tree canopy in many cities in the United States. To expand the urban forest on these lands, some municipalities and nonprofit organizations have launched residential yard tree distribution programs, also known as tree giveaway programs. This paper describes the operations of five tree distribution...

[Nesting habitat characterization for Amazona oratrix (Psittaciformes: Psittacidae) in the Central Pacific, Mexico].

PubMed

Monterrubio-Rico, Tiberio C; Álvarez-Jara, Margarito; Tellez-Garcia, Loreno; Tena-Morelos, Carlos

2014-09-01

The nesting requirements of the Yellow-headed Parrot (Amazona oratrix) are poorly understood, despite their broad historical distribution, high demand for pet trade and current endangered status. Information concerning their nesting requirements is required in order to design specific restoration and conser- vation actions. To assess this, we studied their nesting ecology in the Central Pacific, Michoacan, Mexico during a ten year period. The analyzed variables ranged from local scale nest site characteristics such as nesting tree species, dimensions, geographic positions, diet and nesting forest patches structure, to large scale features such as vegetation use and climatic variables associated to the nesting tree distributions by an ecological niche model using Maxent. We also evaluated the parrot tolerance to land management regimes, and compared the Pacific nest trees with 18 nest trees recorded in an intensively managed private ranch in Tamaulipas, Gulf of Mexico. Parrots nested in tall trees with canopy level cavities in 92 nest-trees recorded from 11 tree species. The 72.8% of nesting occurred in trees of Astronium graveolens, and Enterolobium cyclocarpum which qualified as key- stone trees. The forests where the parrots nested, presented a maximum of 54 tree species, 50% of which were identified as food source; besides, these areas also had a high abundance of trees used as food supply. The lowest number of tree species and trees to forage occurred in an active cattle ranch, whereas the highest species rich- ness was observed in areas with natural recovery. The nesting cavity entrance height from above ground of the Pacific nesting trees resulted higher than those found in the Gulf of Mexico. We hypothesize that the differences may be attributed to Parrot behavioral differences adapting to differential poaching pressure and cavity avail- ability. Nesting trees were found in six vegetation types; however the parrots preferred conserved and riparian semi-deciduous forest for nesting, with fewer nests in deciduous forest, while nesting in transformed agricultural fields was avoided. The main climatic variables associated with the potential distribution of nests were: mean temperature of wettest quarter, mean diurnal temperature range, and precipitation of wettest month. Suitable cli- matic conditions for the potential presence of nesting trees were present in 61% of the region; however, most of the area consisted of tropical deciduous forests (55.8%), while semi-deciduous tropical forests covered only 17% of the region. These results indicated the importance to conserve semi-deciduous forests as breeding habitats for the Yellow-headed Parrot, and revealed the urgent need to implement conservation and restoration actions. These should include a total ban of land use change in tropical semi-deciduous forest areas, and for selective logging of all keystone tree species; besides, we recommend the establishment of wildlife sanctuaries in important nesting areas, and a series of tropical forest restoration programs in the Central Pacific coast.

Ips Bark Beetles in the South

Treesearch

Michael D. Conner; Robert C. Wilkinson

1983-01-01

Ips beetles usually attack weakened, dying, or recently felled trees and fresh logging debris. Large numbers Ips may build up when natural events such as lightning storms, ice storms, tornadoes, wildfires, and droughts create large amounts of pine suitable for the breeding of these beetles. Ips populations may also build up following forestry activities, such as...

Responses of Breeding Bird Communities to Forest Fragmentation

Treesearch

James F. Lynch

1987-01-01

Field studies in eastern North America indicate that local densities of most forest-dwelling bird species are directly or indirectly influenced by forest insularization. Relevant site variables among those measured include patch area and isolation, tree stature and density, and development of herbaceous and shrub understorey. In general, highly migratory species that...

Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.

USDA-ARS?s Scientific Manuscript database

Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ~4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification pr...

Associations among breeding birds and gambel oak in Southwestern ponderosa pine forests

Treesearch

Stephanie Jentsch; R. William Mannan; Brett G. Dickson; William M. Block

2008-01-01

Ponderosa pine (Pinus ponderosa) forests with Gambel oak (Quercus gambelii) are associated with higher bird abundance and diversity than are ponderosa pine forests lacking Gambel oak. Little is known, however, about specific structural characteristics of Gambel oak trees, clumps, and stands that may be important to birds in...

Genetic variation and seed zones of Douglas-fir in the Siskiyou National Forest.

Treesearch

Robert K. Campbell; Albert I. Sugano

1993-01-01

Provisional seed zones and breeding zones were developed for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Siskiyou National Forest in southwestern Oregon. Zones were based on maps of genetic variation patterns obtained by evaluating genotypes of trees from 260 locations in the region. Genotypes controlling growth vigor and growth...

Nursery performance of American and Chinese chestnuts and backcross generations in commercial tree nurseries

Treesearch

Stacy L. Clark; Scott E. Schlarbaum; Arnold M. Saxton; Fred V. Hebard

2012-01-01

The American chestnut [Castanea dentata (Marsh.) Borkh.] was decimated by an exotic fungus [Cryphonectria parasitica (Murr.) Barr] in the early 1900s. Breeding efforts with American and Chinese chestnuts (C. mollissima Blume) produced putatively blight-resistant progeny (BC3F3) in 2007. We compared two nut size...

Large-scale forest composition influences northern goshawk nesting in Wisconsin

Treesearch

Deahn M. Donner; Dean Anderson; Daniel Eklund; Matthew St.Pierre

2013-01-01

The northern goshawk (Accipiter gentilis atricapillus) is a woodland raptor that uses a variety of forest types for nesting across its breeding range, but strongly depends on older forests with large trees and open understories. Goshawks may select nesting locations by maximizing the convergence of nesting and foraging habitats. Insights into goshawk...

Genome size variation in elms (Ulmus spp.) and related genera

USDA-ARS?s Scientific Manuscript database

The elms (the genus Ulmus) are one of the most important tree crops for the $4.7-billion per year U.S. nursery industry. Utilization of these plants has been limited in recent decades by diseases introduced from the Old World, especially Dutch elm disease. Past research and breeding have been based ...

Nut cold hardiness as a factor influencing the restoration of American chestnut in northern latitudes and high elevations

Treesearch

Thomas M. Saielli; Paul G. Schaberg; Gary J. Hawley; Joshua M. Halman; Kendra M. Gurney

2012-01-01

American chestnut (Castanea dentata (Marsh.) Borkh.) was functionally removed as a forest tree by chestnut blight (caused by the fungal pathogen Cryphonectria parasitica (Murr.) Barr). Hybrid-backcross breeding between blight-resistant Chinese chestnut (Castanea mollissima Blume) and American chestnut is used to...

Cottonwood Leaf Beetle (Coleoptera: Chrysomelidae) Larval Performance on Eight Populus Clones

Treesearch

David R. Coyle; Joel D. McMillin; Richard B. Hall; Elwood R. Hart

2001-01-01

Abstract: The cottonwood leaf beetle, Chrysomela scripta F., is the most serious defoliator of young plantation-grown Populus in the eastern United States, yet there is a paucity of data on larval feeding performance across Populus clones used in tree breeding. Field experiments were conducted in 1998 and 1999...

Tetrazolium chloride as an indicator of pine pollen germinability

Treesearch

Stanton A. Cook; Robert G. Stanley

1960-01-01

Controlled pollination in forest tree breeding requires pollen of known germination capacity. Methods of determining pollen viability include germination in a hanging drop, in a moist atmosphere, on agar gel, or in a sugar solution (DUFFIELD, 1954; DILLON et al., 1957). Errors commonly arise in the application of these techniques because maximum...

Fault-Tree Compiler

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Boerschlein, David P.

1993-01-01

Fault-Tree Compiler (FTC) program, is software tool used to calculate probability of top event in fault tree. Gates of five different types allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language easy to understand and use. In addition, program supports hierarchical fault-tree definition feature, which simplifies tree-description process and reduces execution time. Set of programs created forming basis for reliability-analysis workstation: SURE, ASSIST, PAWS/STEM, and FTC fault-tree tool (LAR-14586). Written in PASCAL, ANSI-compliant C language, and FORTRAN 77. Other versions available upon request.

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection.

PubMed

Haberland, A M; König von Borstel, U; Simianer, H; König, S

2012-09-01

Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r(TI) ) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (= accuracy of GEBV) was fixed to a relatively low value of r(mg) = 0.5. For a low heritability trait (h(2) = 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r(TI) from 0.27 to 0.54. Including the conventional information source 'own performance' into the before mentioned index, additional SNP information increases r(TI) by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs.

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

PubMed

Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

2014-06-01

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

Addition of a breeding database in the Genome Database for Rosaceae

PubMed Central

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

Addition of a breeding database in the Genome Database for Rosaceae.

PubMed

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox.

7 CFR 760.504 - Eligible orchardists and nursery tree growers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 7 2014-01-01 2014-01-01 false Eligible orchardists and nursery tree growers. 760.504..., DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.504 Eligible orchardists and nursery tree growers. (a) To be eligible for TAP payments, the eligible orchardist...

7 CFR 760.504 - Eligible orchardists and nursery tree growers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 7 2013-01-01 2013-01-01 false Eligible orchardists and nursery tree growers. 760.504..., DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.504 Eligible orchardists and nursery tree growers. (a) To be eligible for TAP payments, the eligible orchardist...

7 CFR 760.504 - Eligible orchardists and nursery tree growers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 7 2012-01-01 2012-01-01 false Eligible orchardists and nursery tree growers. 760.504..., DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.504 Eligible orchardists and nursery tree growers. (a) To be eligible for TAP payments, the eligible orchardist...

7 CFR 760.504 - Eligible orchardists and nursery tree growers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Eligible orchardists and nursery tree growers. 760.504..., DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.504 Eligible orchardists and nursery tree growers. (a) To be eligible for TAP payments, the eligible orchardist...

Nest design in a changing world: great tit Parus major nests from a Mediterranean city environment as a case study.

PubMed

Lambrechts, Marcel M; Charmantier, Anne; Demeyrier, Virginie; Lucas, Annick; Perret, Samuel; Abouladzé, Matthieu; Bonnet, Michel; Canonne, Coline; Faucon, Virginie; Grosset, Stéphanie; le Prado, Gaëlle; Lidon, Frédéric; Noell, Thierry; Pagano, Pascal; Perret, Vincent; Pouplard, Stéphane; Spitaliéry, Rémy; Bernard, Cyril; Perret, Philippe; Blondel, Jacques; Grégoire, Arnaud

2017-12-01

Investigations of urbanization effects on birds have focused mainly on breeding traits expressed after the nest-building stage (e.g. first-egg date, clutch size, breeding success, and offspring characteristics). Urban studies largely ignored how and why the aspects of nest building might be associated with the degree of urbanization. As urban environments are expected to present novel environmental changes relative to rural environments, it is important to evaluate how nest-building behavior is impacted by vegetation modifications associated with urbanization. To examine nest design in a Mediterranean city environment, we allowed urban great tits ( Parus major ) to breed in nest boxes in areas that differed in local vegetation cover. We found that different measures of nest size or mass were not associated with vegetation cover. In particular, nests located adjacent to streets with lower vegetation cover were not smaller or lighter than nests in parks with higher vegetation cover. Nests adjacent to streets contained more pine needles than nests in parks. In addition, in nests adjacent to streets, nests from boxes attached to pine trees contained more pine needles than nests from boxes attached to other trees. We suggest that urban-related alterations in vegetation cover do not directly impose physical limits on nest size in species that are opportunistic in the selection of nesting material. However, nest composition as reflected in the use of pine needles was clearly affected by habitat type and the planted tree species present, which implies that rapid habitat change impacts nest composition. We do not exclude that urbanization might impact other aspects of nest building behaviour not covered in our study (e.g. costs of searching for nest material), and that the strengths of the associations between urbanization and nest structures might differ among study populations or species.

Perennial plants for biofuel production: bridging genomics and field research.

PubMed

Alves, Alexandre Alonso; Laviola, Bruno G; Formighieri, Eduardo F; Carels, Nicolas

2015-04-01

Development of dedicated perennial crops has been indicated as a strategic action to meet the growing demand for biofuels. Breeding of perennial crops,however, is often time- and resource-consuming. As genomics offers a platform from which to learn more about the relationships of genes and phenotypes,its operational use in the context of breeding programs through strategies such as genomic selection promises to foster the development of perennial crops dedicated to biodiesel production by increasing the efficiency of breeding programs and by shortening the length of the breeding cycles. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular genetic diversity and maternal origin of Chinese black-bone chicken breeds.

PubMed

Zhu, W Q; Li, H F; Wang, J Y; Shu, J T; Zhu, C H; Song, W T; Song, C; Ji, G G; Liu, H X

2014-04-29

Chinese black-bone chickens are valued for the medicinal properties of their meat in traditional Chinese medicine. We investigated the genetic diversity and systematic evolution of Chinese black-bone chicken breeds. We sequenced the DNA of 520 bp of the mitochondrial cyt b gene of nine Chinese black-bone chicken breeds, including Silky chicken, Jinhu black-bone chicken, Jiangshan black-bone chicken, Yugan black-bone chicken, Wumeng black-bone chicken, Muchuan black-bone chicken, Xingwen black-bone chicken, Dehua black-bone chicken, and Yanjin black-bone chicken. We found 13 haplotypes. Haplotype and nucleotide diversity of the nine black-bone chicken breeds ranged from 0 to 0.78571 and 0.00081 to 0.00399, respectively. Genetic diversity was the richest in Jinhu black-bone chickens and the lowest in Yanjin black-bone chickens. Analysis of phylogenetic trees for all birds constructed based on hyplotypes indicated that the maternal origin of black-bone chickens is predominantly from three subspecies of red jungle fowl. These results provide basic data useful for protection of black-bone chickens and help determine the origin of domestic chickens.

Fault-Tree Compiler Program

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1992-01-01

FTC, Fault-Tree Compiler program, is reliability-analysis software tool used to calculate probability of top event of fault tree. Five different types of gates allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language of FTC easy to understand and use. Program supports hierarchical fault-tree-definition feature simplifying process of description of tree and reduces execution time. Solution technique implemented in FORTRAN, and user interface in Pascal. Written to run on DEC VAX computer operating under VMS operating system.

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

PubMed

Lin, Zibei; Cogan, Noel O I; Pembleton, Luke W; Spangenberg, German C; Forster, John W; Hayes, Ben J; Daetwyler, Hans D

2016-03-01

Genomic selection (GS) provides an attractive option for accelerating genetic gain in perennial ryegrass () improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time). Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD) in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot). Genomic estimated breeding values (GEBVs) for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively). Higher accuracy of GEBVs was obtained for flowering time (up to 0.7), partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy. Copyright © 2016 Crop Science Society of America.

Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed.

PubMed

Herrero-Medrano, J M; Megens, H J; Crooijmans, R P; Abellaneda, J M; Ramis, G

2013-06-01

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems - microsatellites, SNPs and mtDNA - were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H(e) = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

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

PubMed Central

2013-01-01

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

Unraveling additive from nonadditive effects using genomic relationship matrices.

PubMed

Muñoz, Patricio R; Resende, Marcio F R; Gezan, Salvador A; Resende, Marcos Deon Vilela; de Los Campos, Gustavo; Kirst, Matias; Huber, Dudley; Peter, Gary F

2014-12-01

The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance and epistatic effects. Partitioning genetic variance into its additive and nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability of dense panels of molecular markers makes possible the use of additive- and dominance-realized genomic relationships for the estimation of variance components and the prediction of genetic values (G-BLUP). We evaluated height data from a multifamily population of the tree species Pinus taeda with a systematic series of models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance), using either pedigree- or marker-based information. We show that, compared with the pedigree, use of realized genomic relationships in marker-based models yields a substantially more precise separation of additive and nonadditive components of genetic variance. We conclude that the marker-based relationship matrices in a model including additive and nonadditive effects performed better, improving breeding value prediction. Moreover, our results suggest that, for tree height in this population, the additive and nonadditive components of genetic variance are similar in magnitude. This novel result improves our current understanding of the genetic control and architecture of a quantitative trait and should be considered when developing breeding strategies. Copyright © 2014 by the Genetics Society of America.

Analysis of the complete mitochondrial genome of the Zhedong White goose and characterization of NUMTs: Reveal domestication history of goose in China and Euro.

PubMed

Ren, Ting; Liang, Shiri; Zhao, Ayong; He, Ke

2016-02-10

To understand the phyletic evolution of geese, the complete mitogenome of the Zhedong goose was sequenced for the first time. It is composed of 37 genes and 1 control region, and the structure and arrangement of all genes sequenced are identical to those of other goose breeds. We confirmed the accuracy of the mitogenome sequence through RT-PCR and found numts from amplification in genomic DNA. Comparisons of the phylogenetic trees and sequences of geese that were suggested a clade of Chinese geese, except the Yili goose, were classified in the Euro clade. Several breed-specific mutations and Chinese breed-specific mutations were found. Our results suggest that Chinese geese evolved from the swan goose, splitting from their common ancestors at different times, which was consistent with studies before. Furthermore, numts in most genes of Zhedong goose clustered with European geese in the phylogenetic tree, suggesting that the haplotypes in the Euro clade might be more ancient. However, the mitogenome of the swan goose shows distinctive evolutionary positions in some genes, which suggest its unclear relationship with Chinese geese and European geese. The current study added to the understanding of the evolution of geese and provided evidence that the typing of numts is an encouraging way for the evolutionary study of geese and the mitochondrial genomes of geese deserve further investigation. Copyright © 2015 Elsevier B.V. All rights reserved.

`Akohekohe response to flower availability: seasonal abundance, foraging, breeding, and molt

USGS Publications Warehouse

Berlin, Kim E.; Simon, John C.; Pratt, T.K.; Kowalsky, James R.; Hatfield, J.S.; Scott, J.M.; Conant, S.; van Riper, Charles

2001-01-01

We studied the relationship of flower availability to the seasonality of life history events of the `Akohekohe (Palmeria dolei), a primarily nectarivorous and endangered Hawaiian honeycreeper from montane rain forests on Maui, Hawai`i. For comparison, we also investigated temporal bird density and foraging behavior of three other competing Hawaiian honeycreepers: `Apapane (Himatione sanguinea), `I`iwi (Vestiaria coccinea), and Hawai`i `Amakihi (Hemignathus virens). All species except `Amakihi fed primarily on nectar of `Ohi?a-lehua (Metrosideros polymorpha), which produced flowers year-round but had an annual flowering peak in January. Flowers of several subcanopy shrubs and trees were important components of the diet for all nectarivores, and these were available seasonally depending upon the species. `Akohekohe densities did not change temporally, suggesting a relatively stable population residing above 1,700 m. Monthly densities of `Apapane, `I`iwi, and Hawai`i `Amakihi were positively correlated with monthly `Ohi?a-lehua flower abundance, and 50-80% of these populations departed temporarily from our high-elevation site in July. There was a positive correlation with the timing of Akohekohe breeding and high abundance of `Ohi?a-lehua bloom. Molt followed breeding. From a conservation perspective, these results show that `Akohekohe maintain a relatively stable population above the mid-elevation zone of disease transmission, particularly during the fall when `Ohi?a-lehua bloom decreases and mosquitoes increase. `Akohekohe remain on their territories partly by switching their foraging to subcanopy trees and shrubs, most of which require protection from feral pigs (Sus scrofa).

Nesting tree characteristics of heronry birds of urban ecosystems in peninsular India: implications for habitat management

PubMed Central

Sinu, Palatty Allesh

2017-01-01

Abstract Wetland ecosystems, particularly the mangrove forest, are the primary wild habitat of heronry birds. However, urban ecosystems have become a favorite breeding habitat of these birds. To provide inputs into the habitat management for conservation of these birds, we investigated the quantitative and qualitative characteristics of nesting trees of heronry birds in the urban environment of the North Kerala region of peninsular India. Census on nesting trees was done in 3 major microhabitats of the urban ecosystem: avenues of national highways and towns, nonresidential plots, and residential areas apart from the mangrove islets in the peri-urban locality. The study found that 174 trees of 22 species hosted 1,928 heronry bird nests in the urban habitats; mangrove forests, although plentiful in the study area, hosted only about 20% of the total nests encountered in the study. Rain trees Samanea saman (43.7%) were the most available nesting tree. The greatest number of nests and nesting trees were encountered on the roads of urban areas, followed by nonresidential areas and residential areas. The differences in the observed frequencies of nesting trees in 3 microhabitats and in 3 types of roads (national highways > state highways > small pocket road) were significant. Canopy spread, girth size, and quality of the trees predicted the tree selection of the heronry birds in urban environments. Therefore, we recommend proper management and notification of the identified nesting trees as protected sites for the conservation of herorny birds. PMID:29492020

Nesting tree characteristics of heronry birds of urban ecosystems in peninsular India: implications for habitat management.

PubMed

Roshnath, Ramesh; Sinu, Palatty Allesh

2017-12-01

Wetland ecosystems, particularly the mangrove forest, are the primary wild habitat of heronry birds. However, urban ecosystems have become a favorite breeding habitat of these birds. To provide inputs into the habitat management for conservation of these birds, we investigated the quantitative and qualitative characteristics of nesting trees of heronry birds in the urban environment of the North Kerala region of peninsular India. Census on nesting trees was done in 3 major microhabitats of the urban ecosystem: avenues of national highways and towns, nonresidential plots, and residential areas apart from the mangrove islets in the peri-urban locality. The study found that 174 trees of 22 species hosted 1,928 heronry bird nests in the urban habitats; mangrove forests, although plentiful in the study area, hosted only about 20% of the total nests encountered in the study. Rain trees Samanea saman (43.7%) were the most available nesting tree. The greatest number of nests and nesting trees were encountered on the roads of urban areas, followed by nonresidential areas and residential areas. The differences in the observed frequencies of nesting trees in 3 microhabitats and in 3 types of roads (national highways > state highways > small pocket road) were significant. Canopy spread, girth size, and quality of the trees predicted the tree selection of the heronry birds in urban environments. Therefore, we recommend proper management and notification of the identified nesting trees as protected sites for the conservation of herorny birds.

Fatty Acid Profile and Unigene-Derived Simple Sequence Repeat Markers in Tung Tree (Vernicia fordii)

PubMed Central

Zhang, Lin; Jia, Baoguang; Tan, Xiaofeng; Thammina, Chandra S.; Long, Hongxu; Liu, Min; Wen, Shanna; Song, Xianliang; Cao, Heping

2014-01-01

Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Lack of fatty acid composition and molecular markers hinders biochemical, genetic and breeding research. The objectives of this study were to determine fatty acid profiles and develop unigene-derived simple sequence repeat (SSR) markers in tung tree. Fatty acid profiles of 41 accessions showed that the ratio of α-eleostearic acid was increasing continuously with a parallel trend to the amount of tung oil accumulation while the ratios of other fatty acids were decreasing in different stages of the seeds and that α-eleostearic acid (18∶3) consisted of 77% of the total fatty acids in tung oil. Transcriptome sequencing identified 81,805 unigenes from tung cDNA library constructed using seed mRNA and discovered 6,366 SSRs in 5,404 unigenes. The di- and tri-nucleotide microsatellites accounted for 92% of the SSRs with AG/CT and AAG/CTT being the most abundant SSR motifs. Fifteen polymorphic genic-SSR markers were developed from 98 unigene loci tested in 41 cultivated tung accessions by agarose gel and capillary electrophoresis. Genbank database search identified 10 of them putatively coding for functional proteins. Quantitative PCR demonstrated that all 15 polymorphic SSR-associated unigenes were expressed in tung seeds and some of them were highly correlated with oil composition in the seeds. Dendrogram revealed that most of the 41 accessions were clustered according to the geographic region. These new polymorphic genic-SSR markers will facilitate future studies on genetic diversity, molecular fingerprinting, comparative genomics and genetic mapping in tung tree. The lipid profiles in the seeds of 41 tung accessions will be valuable for biochemical and breeding studies. PMID:25167054

‘Norman’ southern highbush blueberry

USDA-ARS?s Scientific Manuscript database

‘Norman’ is the third cultivar released from the University of Arkansas blueberry breeding program, which began in the late 1970s and has involved cooperative efforts with the U.S. Department of Agriculture (USDA). Previous cultivars released from this breeding program were ‘Ozarkblue’ and ‘Summit’....

St. Paul's Pig Pack.

ERIC Educational Resources Information Center

Miller, Penny Folley

1982-01-01

Describes a guinea pig (cavy) breeding and management program developed as part of an elementary school science curriculum. Includes comments on show competitions (sponsored by the American Rabbit Breeders Association) to measure the success of the breeding program and to enable children to experience the business world. (Author/JN)

7 CFR 760.500 - Applicability.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 2008 Farm Bill). (b) Eligible orchardists and nursery tree growers will be compensated as specified in... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.500 Applicability. (a) This subpart establishes the terms and conditions under which the Tree Assistance Program (TAP) will be...

7 CFR 760.500 - Applicability.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 2008 Farm Bill). (b) Eligible orchardists and nursery tree growers will be compensated as specified in... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.500 Applicability. (a) This subpart establishes the terms and conditions under which the Tree Assistance Program (TAP) will be...

7 CFR 760.500 - Applicability.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 2008 Farm Bill). (b) Eligible orchardists and nursery tree growers will be compensated as specified in... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.500 Applicability. (a) This subpart establishes the terms and conditions under which the Tree Assistance Program (TAP) will be...

7 CFR 760.500 - Applicability.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 2008 Farm Bill). (b) Eligible orchardists and nursery tree growers will be compensated as specified in... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.500 Applicability. (a) This subpart establishes the terms and conditions under which the Tree Assistance Program (TAP) will be...

Dendroscope: An interactive viewer for large phylogenetic trees

PubMed Central

Huson, Daniel H; Richter, Daniel C; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula

2007-01-01

Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. PMID:18034891

Population genetic analysis of a medicinally significant Australian rainforest tree, Fontainea picrosperma C.T. White (Euphorbiaceae): biogeographic patterns and implications for species domestication and plantation establishment.

PubMed

Lamont, R W; Conroy, G C; Reddell, P; Ogbourne, S M

2016-02-29

Fontainea picrosperma, a subcanopy tree endemic to the rainforests of northeastern Australia, is of medicinal significance following the discovery of the novel anti-cancer natural product, EBC-46. Laboratory synthesis of EBC-46 is unlikely to be commercially feasible and consequently production of the molecule is via isolation from F. picrosperma grown in plantations. Successful domestication and plantation production requires an intimate knowledge of a taxon's life-history attributes and genetic architecture, not only to ensure the maximum capture of genetic diversity from wild source populations, but also to minimise the risk of a detrimental loss in genetic diversity via founder effects during subsequent breeding programs designed to enhance commercially significant agronomic traits. Here we report the use of eleven microsatellite loci (PIC = 0.429; P ID  = 1.72 × 10(-6)) to investigate the partitioning of genetic diversity within and among seven natural populations of F. picrosperma. Genetic variation among individuals and within populations was found to be relatively low (A = 2.831; H E  = 0.407), although there was marked differentiation among populations (PhiPT = 0.248). Bayesian, UPGMA and principal coordinates analyses detected three main genotypic clusters (K = 3), which were present at all seven populations. Despite low levels of historical gene flow (N m  = 1.382), inbreeding was negligible (F = -0.003); presumably due to the taxon's dioecious breeding system. The data suggests that F. picrosperma was previously more continuously distributed, but that rainforest contraction and expansion in response to glacial-interglacial cycles, together with significant anthropogenic effects have resulted in significant fragmentation. This research provides important tools to support plantation establishment, selection and genetic improvement of this medicinally significant Australian rainforest species.

Performance of genomic prediction within and across generations in maritime pine.

PubMed

Bartholomé, Jérôme; Van Heerwaarden, Joost; Isik, Fikret; Boury, Christophe; Vidal, Marjorie; Plomion, Christophe; Bouffier, Laurent

2016-08-11

Genomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue. A reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population size (status number) of 25 was first selected with simulated data. This reference population (n = 818) covered three generations (G0, G1 and G2) and was genotyped with 4436 single-nucleotide polymorphism (SNP) markers. We evaluated the effects on prediction accuracy of both the relatedness between the calibration and validation sets and validation on the basis of progeny performance. Pedigree-based (best linear unbiased prediction, ABLUP) and marker-based (genomic BLUP and Bayesian LASSO) models were used to predict breeding values for three different traits: circumference, height and stem straightness. On average, the ABLUP model outperformed genomic prediction models, with a maximum difference in prediction accuracies of 0.12, depending on the trait and the validation method. A mean difference in prediction accuracy of 0.17 was found between validation methods differing in terms of relatedness. Including the progenitors in the calibration set reduced this difference in prediction accuracy to 0.03. When only genotypes from the G0 and G1 generations were used in the calibration set and genotypes from G2 were used in the validation set (progeny validation), prediction accuracies ranged from 0.70 to 0.85. This study suggests that the training of prediction models on parental populations can predict the genetic merit of the progeny with high accuracy: an encouraging result for the implementation of GS in the maritime pine breeding program.

Inventory of montane-nesting birds in the Arctic Network of National Parks, Alaska

USGS Publications Warehouse

Tibbitts, T.L.; Ruthrauff, D.R.; Gill, Robert E.; Handel, Colleen M.

2006-01-01

The Alaska Science Center of the U.S. Geological Survey conducted an inventory of birds in montane areas of the four northern parks in the Arctic Network of National Parks, Alaska. This effort represents the first comprehensive assessment of breeding range and habitat associations for the majority of avian species in the Arctic Network. Ultimately, these data provide a framework upon which to design future monitoring programs.A stratified random sampling design was used to select sample plots (n = 73 plots) that were allocated in proportion to the availability of ecological subsections. Point counts (n = 1,652) were conducted to quantify abundance, distribution, and habitat associations of birds. Field work occurred over three years (2001 to 2003) during two-week-long sessions in late May through early June that coincided with peak courtship activity of breeding birds.Totals of 53 species were recorded in Cape Krusenstern National Monument, 91 in Noatak National Preserve, 57 in Kobuk Valley National Park, and 96 in Gates of the Arctic National Park and Preserve. Substantial proportions of species in individual parks are considered species of conservation concern (18 to 26%) or species of stewardship responsibility of the land managers in the region (8 to 18%). The most commonly detected passerines on point counts included Redpoll spp. (Carduelis flammea and C. hornemanni), Savannah Sparrow (Passerculus sandwichensis), and American Tree Sparrow (Spizella arborea). The most numerous shorebirds were American Golden-Plover (Pluvialis dominica), Wilson’s Snipe (Gallinago delicata), and Whimbrel (Numenius phaeopus). Most species were detected at low rates, reflecting the low breeding densities (and/or low detectabilities) of birds in the montane Arctic. Suites of species were associated with particular ranges of elevation and showed strong associations with particular habitat types.

Forest gene conservation programs in Alberta, Canada

Treesearch

Jodie Krakowski

2017-01-01

Provincial tree improvement programs in Alberta began in 1976. Early gene conservation focused on ex situ measures such as seed and clone banking, and research trials of commercial species with tree improvement programs. The gene conservation program now encompasses representative and unique populations of all native tree species in situ. The ex situ program aims to...

Date Palm Genetic Diversity Analysis Using Microsatellite Polymorphism.

PubMed

Khierallah, Hussam S M; Bader, Saleh M; Hamwieh, Alladin; Baum, Michael

2017-01-01

Date palm (Phoenix dactylifera L.) is considered one of the great socioeconomic resources in the Middle East and the Arab regions. The tree has been and still is at the center of the comprehensive agricultural development. The number of known date palm cultivars, distributed worldwide, is approximately 3000. The success of genetic diversity conservation or any breeding program depends on an understanding of the amount and distribution of the genetic variation already in existence in the genetic pool. Development of suitable DNA molecular markers for this tree may allow researchers to estimate genetic diversity, which will ultimately lead to the genetic conservation of date palm. Simple sequence repeats (SSRs) are DNA strands, consisting of tandemly repeated mono-, di-, tri-, tetra-, or penta-nucleotide units that are arranged throughout the genomes of most eukaryotic species. Microsatellite markers, developed from genomic libraries, belong to either the transcribed region or the non-transcribed region of the genome, and there is rarely available information on their functions. Microsatellite sequences are especially suited to distinguish closely related genotypes due to a high degree of variability making them ideally suitable in population studies and the identification of closely related cultivars. This chapter focuses on the methods employed to characterize date palm genotypes using SSR markers.

Two-stage selection in slash pine produces good gains in fusiform rust resistance

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

Sluder, E.R.

The best 6 of 21 progeny-tested first-generation slash pine selections were crossed in a half diallel to study inheritance patterns of their superior fusiform rust resistance (5 trees) and height (1 tree). Their six first-test progenies were duplicated and included in the study. These two groups of progenies, along with two commercial check lots, were planted on an Upper Coastal Plain and a Flatwoods site in Georgia. At age 10 yr, the 15 progenies in the half diallel averaged 23% rust-infected compared with 54% for the check lots. First-test progenies averaged 30% infected. For percentage infection, the six parents differedmore » in general combining ability (GCA) (0.01>P>0.001) on both test sites and in specific combining ability (0.05>P>0.01) on one site. GCA variation for height was significant (0.05>P>0.01) on one site. The parent selected for height had the highest breeding value for height at age 10 yr. These results show that resistance to the fusiform rust disease, a serious problem in management of the species, can be improved in slash pine. These 6 parents and their 15 progenies in the half-diallel cross are a good source of rust resistance genes for use in slash pine improvement programs.« less

The Fault Tree Compiler (FTC): Program and mathematics

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1989-01-01

The Fault Tree Compiler Program is a new reliability tool used to predict the top-event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, AND m OF n gates. The high-level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precisely (within the limits of double precision floating point arithmetic) within a user specified number of digits accuracy. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Equipment Corporation (DEC) VAX computer with the VMS operation system.

Genetic fingerprinting of potato varieties from the Northwest Potato Variety Development Program

USDA-ARS?s Scientific Manuscript database

The Northwest Potato Variety Development Program using conventional breeding has successfully released more than 40 improved varieties of potato since its inception in 1983. Potato breeders rely primarily on morphological and phenotypic data for selection and breeding of potato cultivars. With the a...

The potential of open learning in animal breeding.

PubMed

Lohuis, M M; Lohuis, C T; Petrongolo, R A

1999-07-01

Animal breeding education is presently facing many challenges. These include rapid changes in breeding knowledge and technology, resource and funding restrictions, and altering demographics of the learner and the animal breeding industry. These challenges can be met via an open learning educational format. This nontraditional approach is based on the needs of individual learners, not the interests of the teacher or the institution. An important feature of open learning is its appropriateness for the professional development audience. Delivery methods include interactive distance courses on the Web, computer-assisted learning, and team-based study. The Canadian dairy breeding industry has expressed the need for ongoing professional development to understand and adopt new animal breeding technologies. The University of Guelph responded by delivering a series of animal breeding short courses (Executive Certificate Program in Animal Breeding) to industry decision makers in 1997. A version modified specifically for farmers and breeding industry personnel was offered in 1998. Through the collaboration of experts from various agricultural institutions and the use of a learner-centered format, this professional development initiative was a pedagogical and financial success. This paper describes how the open learning approach differs from traditional university teaching. Using the University of Guelph example in animal breeding professional development, the framework for a successful open learning program will be examined. The best practices for effective adult education will also be identified and discussed within this case study.

The influence of silvicultural treatments and site conditions on American chestnut (Castanea dentata) seedling establishment in eastern Kentucky, USA

Treesearch

Chuck Rhoades; David Loftis; Jeffrey Lewis; Stacy Clark

2009-01-01

After more than 50 years of research and selective breeding, blight-resistant American chestnut (Castanea dentata) trees will soon be available for planting into the species' pre-blight range. Increased understanding of the regeneration requirements of pure American chestnut (C. dentata [Marsh.] Borkh.) will increase the...

Pine breeding in the United States

Treesearch

J. W. Duffield; Palmer Stockwell

1950-01-01

Trees fit into the general rule that (the plants and animals which nature gave us have not been considered quite good enough. For millions of years, it is true, nature has developed a breathtaking variety of forms, each wonderfully adapted to its surroundings. Changes in climate or the conformation of the earth's surface have caused the extinction of some forms...

Long-term effects of different forest regeneration methods on mature forest birds

Treesearch

Roger W. Perry; Julianna M.A. Jenkins; Ronald E. Thill; Frank R. Thompson

2018-01-01

Changes in forest structure that result from silviculture, including timber harvest, can positively or negatively affect bird species that use forests. Because many bird species associated with mature forests are facing population declines, managers need to know how timber harvesting affects species of birds that rely on mature trees or forests for breeding, foraging,...

New efforts in eastern cottonwood biomass production through breeding and clonal refinement

Treesearch

Jason W. Cromer; Randall J. Rousseau; B. Landis Herrin

2014-01-01

First generation biofuels (also known as traditional biofuels) primarily use corn to produce ethanol. Newer techniques and knowledge are now allowing ethanol production from renewable resources such as trees that have more complex molecular structures that inhibit access to sugars. Ethanol production is through an enzymatic process which uses cellulose, or pyrolosis...

Altitudinal genetic variation among Pinus oocarpa populations in Michoacan, Mexico: implications for seed zoning, conservation, tree breeding and global warming

Treesearch

Cuauhtemoc Saenz-Romero; R. Ricardo Guzman-Reyna; Gerald E. Rehfeldt

2006-01-01

Pinus oocarpa has a large natural distribution in the sub-tropical forests of Mexico. Populations, however, are rapidly disappearing particularly in the Michoacan State as native forests are converted to avocado (Persea sp.) orchards.We investigated the patterning of genetic variation among P. oocarpa populations...

75 FR 46859 - Lacey Act Implementation Plan; Definitions for Exempt and Regulated Articles

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

... plants of species grown on a commercial scale. As we propose to define them, these terms would apply to... cultivar. A plant (except a tree) that: (a) Has been developed through selective breeding or other means... concern, while exempting plants grown on a commercial scale. They are also designed to be consistent with...

Influence of habitat and number of nestlings on partial brood loss in red-cockaded woodpeckers

Treesearch

James R. McCormick; Richard N. Conner; D. Brent Burt; Daniel Saenz

2004-01-01

Partial brood loss in red-cockaded woodpeckers (Picoides borealis) was studied during 2 breeding seasons in eastern Texas. The timing of partial brood loss, group size, number of initial nestlings, number of birds fledged, and habitat characteristics of the group's cavity-tree cluster were examined for 37 woodpecker groups in loblolly- (

Breeding for disease resistance in Hevea spp. - status, potential threats, and possible strategies.

Treesearch

Chaendaekattu Narayanan; Kavitha K. Mydin

2012-01-01

Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg., a forest tree native to the tropical rain forests of Central and South America, has only been recently domesticated outside its natural range of distribution. Almost all of the commercially cultivated clones of H. brasiliensis represent a very narrow genetic base...

Progress in birch genetics and tree improvement

Treesearch

Knud E. Clausen; Peter W. Garrett

1969-01-01

Little interest has been shown in genetic improvement of our native birches until fairly recently, except for the birch breeding and testing begun by the Northeastern Forest Experiment Station in 1940. Before we can begin improvement of a particular species or genus, we need to know how much genetic variation is present and how various characteristics are inherited....

Exploration of a rare population of Chinese chestnut in North America: stand dynamics, health and genetic relationships

Treesearch

Amy C. Miller; Keith E. Woeste; Sandra L. Anagnostakis; Doutlass F. Jacobs

2014-01-01

With the transport of plants around the globe, exotic species can readily spread disease to their native relatives; however, they can also provide genetic resistance to those relatives through hybrid breeding programmes. American chestnut (Castanea dentata) was an abundant tree species in North America until its decimation by introduced chestnut...

Bark beetle management after a mass attack - some Swiss experiences

Treesearch

B. Forster; F. Meier; R. Gall

2003-01-01

In 1990 and 1999, heavy storms accompanied by the worst gales ever recorded in Switzerland, struck Europe and left millions of cubic metres of windthrown Norway spruce trees; this provided breeding material for the eight-toothed spruce bark beetle (Ips typographus L.) and led to mass attacks in subsequent years which resulted in the additional loss...

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

PubMed Central

Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

2018-01-01

Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

Genetic diversity analysis of tree peony germplasm using iPBS markers.

PubMed

Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

2015-07-06

We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties.

Diversity for chemical composition in a collection of different varietal types of tree tomato (Solanum betaceum Cav.), an Andean exotic fruit.

PubMed

Acosta-Quezada, Pablo G; Raigón, María D; Riofrío-Cuenca, Tania; García-Martínez, María D; Plazas, Mariola; Burneo, Juan I; Figueroa, Jorge G; Vilanova, Santiago; Prohens, Jaime

2015-02-15

We evaluated 23 tree tomato (Solanum betaceum) accessions from five cultivar groups and one wild relative (Solanum cajanumense) for 26 composition traits. For all traits we found highly significant differences (P<0.001) among the materials studied. The high diversity found within S. betaceum for composition traits was matched by a high diversity within each of the cultivar groups. We found that sucrose and citric acid were the most important soluble sugar and organic acid, respectively, in tree tomato. Fruit in the anthocyanin pigmented (purple) group had a carotenoid content similar to that in the yellow-orange cultivar groups. Total phenolic content was significantly correlated (r=0.8607) with antioxidant activity. Analyses of mineral content showed that tree tomato is a good source of K, Mg, and Cu. Multivariate principal components analysis (PCA) confirmed that an important diversity exists within each cultivar group. The results we have obtained indicate that the high diversity found within the tree tomato could be exploited for selection and breeding for developing the tree tomato as a commercial crop. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of new techniques of using irradiation in the genetic improvement of warm season grasses and an assessment of the genetic and cytogenetic effects. Progress report, November 1, 1977--October 31, 1978. [Pearl millet, Bermuda-grass, and coastcross

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

Hanna, W.W.; Burton, G.W.

1978-05-01

Progress is reported on plant breeding programs for the genetic improvement of warm season grasses using irradiation as a tool. Data are included from studies on alteration of the protein quantity and quality in pearl millet grain by irradiation and mutation breeding; the effects of nitrogen and genotype on pearl millet grain; the effects of seed size on quality in pearl millet; irradiation breeding of sterile triploid turf Bermuda grasses; irradiation breeding of sterile coastcross-1, a forage grass, to increase winter hardiness; use of irradiation to induce resistance to rust disease; and an economic assessment of irradiation-induced mutants for plantmore » breeding programs.« less

Urban Tree Risk Management:A Community Guide to Program Design and Implementation

Treesearch

Jill Pokorny; Joseph O' Brien; Richard Hauer; Gary Johnson; Jana Albers; Peter Bedker; Manfred Mielke

2003-01-01

Urban Tree Risk Management: A Community Guide to Program Design and Implementation is a fully illustrated, easy to read training manual written for community leaders, administrators, city foresters, parks and public works staff, and private tree care practitioners. The manual is designed to assist communities design, adopt and implement tree risk management programs,...

Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

PubMed

Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

2012-06-01

Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application.

i-Tree and urban FIA—what's the connection?

Treesearch

David J. Nowak

2015-01-01

The i-Tree program (www.itreetools.org) was developed to assess ecosystem services and values from trees and forests based on measured forest data. The i-Tree program is currently being integrated with FIA data to assess various ecosystem services and values from urban FIA data. This presentation will overview the history and use of i-Tree; the various tools of i-Tree...

Determinants of establishment survival for residential trees in Sacramento County, CA

Treesearch

Lara A. Roman; John J. Battles; Joe R. McBride

2014-01-01

Urban forests can provide ecosystem services that motivate tree planting campaigns, and tree survival is a key element of program success and projected benefits. We studied survival in a shade tree give-away program in Sacramento, CA, monitoring a cohort of young trees for five years on single-family residential properties. We used conditional inference trees to...

User's Manual for Total-Tree Multiproduct Cruise Program

Treesearch

Alexander Clark; Thomas M. Burgan; Richard C. Field; Peter E. Dress

1985-01-01

This interactive computer program uses standard tree-cruise data to estimate the weight and volume of the total tree, saw logs, plylogs, chipping logs, pulpwood, crown firewood, and logging residue in timber stands.Input is cumulative cruise data for tree counts by d.b.h. and height. Output is in tables: board-foot volume by d.b.h.; total-tree and tree-component...

Trees Wanted—Dead or Alive! Host Selection and Population Dynamics in Tree-Killing Bark Beetles

PubMed Central

Kausrud, Kyrre L.; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr.

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between “endemic” and “epidemic” regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics. PMID:21647433

Initial experiences utilizing exotic landrace germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

A critical objective of plant breeding programs is accessing new sources of genetic variation. In upland cotton, one of the relatively untapped sources of genetic variation is maintained in the USDA-ARS cotton germplasm collection and is the exotic landrace collection. Photoperiod sensitivity is a m...

Increased use of young bulls in dairy cattle breeding programs

USDA-ARS?s Scientific Manuscript database

Availability of genomic evaluations since 2008 has provided many benefits with regard to improving the rate of genetic gain in dairy cattle breeding programs, one of which is a greater accuracy for young animals. As a result, AI organizations have been aggressively promoting young bulls and producer...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental populations are typically unrepli...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicat...

Prevalence and inheritance of and selection for hip dysplasia in seven breeds of dogs in Sweden and benefit: cost analysis of a screening and control program.

PubMed

Swenson, L; Audell, L; Hedhammar, A

1997-01-15

To determine the prevalence and changes over time in the prevalence of hip dysplasia; to ascertain whether prevalence or severity of hip dysplasia was associated with sex of the dogs, age at which coxofemoral joint status was evaluated, or ancestral background; to determine the effects of selective breeding; and to conduct an economic evaluation of the hip dysplasia program operated by the Swedish Kennel Club. Analysis of radiographic evaluations of coxofemoral joint conformity. 83,229 dogs from 7 breeds registered by the Swedish Kennel Club. All radiographs were scrutinized by a single radiologist (LA), and coxofemoral joint conformation was classified as normal or dysplastic, with the degree of dysplasia classified as 1,2,3, or 4. Decreasing prevalence of hip dysplasia corresponding to selection of breeding stock and high heritabilities was found. Sex differences were documented in 3 of the breeds. This was interpreted as breed differences in the distribution of genes related to hip dysplasia. Economic analyses showed that costs of screening and registration of coxofemoral joints was less than the value of dogs estimated to have been saved from moderate, severe, or very severe hip dysplasia in 6 of the breeds. Documented effects of age suggest that all dogs should be screened at the same age, rather than screening a few dogs at an older, more revealing age. In screening and control programs based on an open registry with access to family records, decreasing prevalence of hip dysplasia can be expected, and related to selection of breeding stock.

Population structure of four Thai indigenous chicken breeds

PubMed Central

2014-01-01

Background In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Results Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds- Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken - the red jungle fowls (RJF), and two commercial chicken breeds - the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD= 0.341, LK= 0.357, DA=0.349 and CH= 0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The FST values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The FST values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. Conclusion These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens. PMID:24674423

Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection.

PubMed

Teixeira, Rita Teresa; Fortes, Ana Margarida; Bai, Hua; Pinheiro, Carla; Pereira, Helena

2018-02-01

The phenylpropanoid pathway impacts the cork quality development. In cork of bad quality, the flavonoid route is favored, whereas in good quality, cork lignin and suberin production prevails. Cork oaks develop a thick cork tissue as a protective shield that results of the continuous activity of a secondary meristem, the cork cambium, or phellogen. Most studies applied to developmental processes do not consider the cell types from which the samples were extracted. Here, laser microdissection (LM) coupled with transcript profiling using RNA sequencing (454 pyrosequencing) was applied to phellogen cells of trees producing low- and good quality cork. Functional annotation and functional enrichment analyses showed that stress-related genes are enriched in samples extracted from trees producing good quality cork (GQC). This process is under tight transcriptional (transcription factors, kinases) regulation and also hormonal control involving ABA, ethylene, and auxins. The phellogen cells collected from trees producing bad quality cork (BQC) show a consistent up-regulation of genes belonging to the flavonoid pathway as a response to stress. They also display a different modulation of cell wall genes resulting into a thinner cork layer, i.e., less meristematic activity. Based on the analysis of the phenylpropanoid pathway regulating genes, in GQC, the synthesis of lignin and suberin is promoted, whereas in BQC, the same pathway favors the biosynthesis of free phenolic compounds. This study provided new insights of how cell-specific gene expression can determine tissue and organ morphology and physiology and identified robust candidate genes that can be used in breeding programs aiming at improving cork quality.

Proteomic analysis of Pinus radiata needles: 2-DE map and protein identification by LC/MS/MS and substitution-tolerant database searching.

PubMed

Valledor, Luis; Castillejo, Maria A; Lenz, Christof; Rodríguez, Roberto; Cañal, Maria J; Jorrín, Jesús

2008-07-01

Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.

Application of Unmanned Aircraft Systems (UAS) for phenotypic mapping of white spruce genotypes along environmental gradients

NASA Astrophysics Data System (ADS)

D'Odorico, P.; Wong, C. Y.; Besik, A.; Earon, E.; Isabel, N.; Ensminger, I.

2017-12-01

Rapid climate change is expected to cause a mismatch between locally adapted tree populations and the optimal climatic conditions to which they have adapted. Plant breeding and reforestation programs will increasingly need to rely on high-throughput precision phenotyping tools for the selection of genotypes with increased drought and stress tolerance. In this work, we present the possibilities offered by Unmanned Aircraft Systems (UAS) carrying optical sensors to monitor and assess differences in performance among white spruce genotypes. While high-throughput precision phenotyping using UAS has gained traction in agronomic crop research during the last few years, to our knowledge it is still at its infancy in forestry applications. UAS surveys were performed at different times during the growing season over large white spruce common garden experiments established by the Canadian Forest Service at four different sites, each characterized by 2000 clonally replicated genotypes. Sites are distributed over a latitudinal gradient, in Ontario and Quebec, Canada. The UAS payload consisted of a custom-bands multispectral sensor acquiring radiation at wavelength at which the reflectance spectrum of vegetation is known to capture physiological change under disturbance and stress. Ground based tree-top spectral reflectances and leaf level functional traits were also acquired for validation purposes parallel to UAS surveys. We will discuss the potential and the challenges of using optical sensors on UAS to infer genotypic variation in tree response to stress events and show how spectral data can function as the link between large-scale phenotype and genotype data.

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.

PubMed

Lin, Zibei; Shi, Fan; Hayes, Ben J; Daetwyler, Hans D

2017-05-01

Heuristic genomic inbreeding controls reduce inbreeding in genomic breeding schemes without reducing genetic gain. Genomic selection is increasingly being implemented in plant breeding programs to accelerate genetic gain of economically important traits. However, it may cause significant loss of genetic diversity when compared with traditional schemes using phenotypic selection. We propose heuristic strategies to control the rate of inbreeding in outbred plants, which can be categorised into three types: controls during mate allocation, during selection, and simultaneous selection and mate allocation. The proposed mate allocation measure GminF allocates two or more parents for mating in mating groups that minimise coancestry using a genomic relationship matrix. Two types of relationship-adjusted genomic breeding values for parent selection candidates ([Formula: see text]) and potential offspring ([Formula: see text]) are devised to control inbreeding during selection and even enabling simultaneous selection and mate allocation. These strategies were tested in a case study using a simulated perennial ryegrass breeding scheme. As compared to the genomic selection scheme without controls, all proposed strategies could significantly decrease inbreeding while achieving comparable genetic gain. In particular, the scenario using [Formula: see text] in simultaneous selection and mate allocation reduced inbreeding to one-third of the original genomic selection scheme. The proposed strategies are readily applicable in any outbred plant breeding program.

A squirrel searches for food at KSC

NASA Technical Reports Server (NTRS)

1999-01-01

An Eastern gray squirrel pauses in its daily search for food in the Merritt Island National Wildlife Refuge, which shares a boundary with Kennedy Space Center. The Eastern gray squirrel is found in wooded, suburban, and urban areas statewide. It nests in tree hollows or leaf nests in treetops. It forages during the day, mainly early morning and late afternoon, both on the ground and in trees, living on a diet of acorns, nuts, fruits, berries, insects, and bird eggs. Food plants include cypress, buckeyes, elms, grapes, tulip trees, mulberries, and tupelo. It breeds in late winter or early spring and again in late spring or summer, bearing two to six young. The eastern gray squirrel chatters when disturbed. The 92,000-acre wildlife refuge is a habitat for more than 310 species of birds, 25 mammals, 117 fishes and 65 amphibians and reptiles.

Seasonal patterns in reproductive success of temperate-breeding birds: Experimental tests of the date and quality hypotheses.

PubMed

Harriman, Vanessa B; Dawson, Russell D; Bortolotti, Lauren E; Clark, Robert G

2017-04-01

For organisms in seasonal environments, individuals that breed earlier in the season regularly attain higher fitness than their late-breeding counterparts. Two primary hypotheses have been proposed to explain these patterns: The quality hypothesis contends that early breeders are of better phenotypic quality or breed on higher quality territories, whereas the date hypothesis predicts that seasonally declining reproductive success is a response to a seasonal deterioration in environmental quality. In birds, food availability is thought to drive deteriorating environmental conditions, but few experimental studies have demonstrated its importance while also controlling for parental quality. We tested predictions of the date hypothesis in tree swallows ( Tachycineta bicolor ) over two breeding seasons and in two locations within their breeding range in Canada. Nests were paired by clutch initiation date to control for parental quality, and we delayed the hatching date of one nest within each pair. Subsequently, brood sizes were manipulated to mimic changes in per capita food abundance, and we examined the effects of manipulations, as well as indices of environmental and parental quality, on nestling quality, fledging success, and return rates. Reduced reproductive success of late-breeding individuals was causally related to a seasonal decline in environmental quality. Declining insect biomass and enlarged brood sizes resulted in nestlings that were lighter, in poorer body condition, structurally smaller, had shorter and slower growing flight feathers and were less likely to survive to fledge. Our results provide evidence for the importance of food resources in mediating seasonal declines in offspring quality and survival.

Innate immunity is not related to the sex of adult Tree Swallows during the nestling period

USGS Publications Warehouse

Houdek, Bradley J.; Lombardo, Michael P.; Thorpe, Patrick A.; Hahn, D. Caldwell

2011-01-01

Evolutionary theory predicts that exposure to more diverse pathogens will result in the evolution of a more robust immune response. We predicted that during the breeding season the innate immune function of female Tree Swallows (Tachycineta bicolor) should be more effective than that of males because (1) the transmission of sexually transmitted microbes during copulation puts females at greater risk because ejaculates move from males to females, (2) females copulate with multiple males, exposing them to the potentially pathogenic microbes in semen, and (3) females spend more time in the nest than do males so may be more exposed to nest microbes and ectoparasites that can be vectors of bacterial and viral pathogens. In addition, elevated testosterone in males may suppress immune function. We tested our prediction during the 2009 breeding season with microbicidal assays in vitro to assess the ability of the innate immune system to kill Escherichia coli. The sexes did not differ in the ability of their whole blood to kill E. coli. We also found no significant relationships between the ability of whole blood to kill E. coli and the reproductive performance or the physical condition of males or females. These results indicate that during the nestling period there are no sexual differences in this component of the innate immune system. In addition, they suggest that there is little association between this component of innate immunity and the reproductive performance and physical condition during the nestling period of adult Tree Swallows.

Biotechnology of temperate fruit trees and grapevines.

PubMed

Laimer, Margit; Mendonça, Duarte; Maghuly, Fatemeh; Marzban, Gorji; Leopold, Stephan; Khan, Mahmood; Balla, Ildiko; Katinger, Hermann

2005-01-01

Challenges concerning fruit trees and grapevines as long lived woody perennial crops require adapted biotechnological approaches, if solutions are to be found within a reasonable time frame. These challenges are represented by the need for correct identification of genetic resources, with the foreseen use either in conservation or in breeding programmes. Molecular markers provide most accurate information and will be the major solution for questions about plant breeders rights. Providing healthy planting material and rapid detection of newly introduced pathogens by reliable methods involving serological and molecular biological tools will be a future challenge of increases importance, given the fact that plant material travels freely in the entire European Union. But also new breeding goals and transgenic solutions are part of the biotechnological benefits, e.g. resistance against biotic and abiotic stress factors, modified growth habits, modified nutritional properties and altered processing and storage qualities. The successful characterization of transgenic grapevines and stone fruit trees carrying genes of viral origin in different vectors constructed under ecological consideration, will be presented. Beyond technical feasibility, efficiency of resistance, environmental safety and Intellectual Property Rights, also public acceptance needs consideration and has been addressed in a specific project. The molecular determination of internal quality parameters of food can also be addressed by the use of biotechnological tools. Patient independent detection tools for apple allergens have been developed and should allow to compare fruits from different production systems, sites, and genotypes for their content of health threatening compounds.

Application of selection index calculations to determine selection strategies in genomic breeding programs.

PubMed

König, S; Swalve, H H

2009-10-01

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r(TI)), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r(TI) strongly depends on the accuracy of GEBV (r(mg)) and the heritability of the trait. For a desired r(TI) of 0.8, h(2) = 0.10, and r(mg) = 0.5, at least 57 additional daughters have to be included in the genetic evaluation. Daughter records of genotyped sires are not necessary for optimal scenarios where r(mg) is greater than or equal to r(TI). There still is a substantial need for phenotypic daughter records, especially for low-heritability functional traits and r(mg) < 0.7. Phenotypic records from genotyped potential bull dams have no relevance for increasing r(TI), even with a low value for r(mg) of 0.5. Hence, genomic breeding programs should focus on recording functional traits within progeny groups, preferably in cooperator herds. For low-heritability traits and with r(mg) > 0.7, the RSR of conventional breeding programs was only 10% of RSR from genomic breeding strategies. As shown in scenarios including 2 traits in the index as well as in the aggregate genotype, the availability of highly accurate GEBV for production traits and low-accuracy GEBV for functional traits increased the risk of widening the gap between selection responses in production and functionality. Counteractions are possible, such as via higher economic weights for low-heritability functional traits. Finally, an alternative selection strategy considering only 2 pathways of selection for genotyped male calves and for cow dams was evaluated. This strategy is competitive with a 4-pathway genomic breeding program if the fraction of selected male calves for the artificial insemination program is below 1% and if selection is focused on functionality, thus pointing to substantial insufficiencies caused by low reliabilities of breeding values for cows for such traits in conventional bull dam selection schemes.

Tilting at windmills: 20 years of Hippeastrum breeding

USDA-ARS?s Scientific Manuscript database

Hippeastrum Herbert, amaryllis, has yielded popular large-flowered hybrids over a 200-year breeding history, with the Netherlands and South Africa currently dominating the market. The USDA breeding program is now almost ten years old, built upon a ten-year previous history at the University of Flori...

A role for selective contraception of individuals in conservation.

PubMed

Cope, Holly R; Hogg, Carolyn J; White, Peter J; Herbert, Catherine A

2018-06-01

Contraception has an established role in managing overabundant populations and preventing undesirable breeding in zoos. We propose that it can also be used strategically and selectively in conservation to increase the genetic and behavioral quality of the animals. In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic diversity by managing the reproductive contribution of each individual and preventing genetically suboptimal breeding through the use of selective contraception. Reproductive suppression of selected individuals in conservation programs has further benefits of allowing animals to be housed as a group in extensive enclosures without interfering with breeding recommendations, which reduces adaptation to captivity and facilitates the expression of wild behaviors and social structures. Before selective contraception can be incorporated into a breeding program, the most suitable method of fertility control must be selected, and this can be influenced by factors such as species life history, age, ease of treatment, potential for reversibility, and desired management outcome for the individual or population. Contraception should then be implemented in the population following a step-by-step process. In this way, it can provide crucial, flexible control over breeding to promote the physical and genetic health and sustainability of a conservation dependent species held in captivity. For Tasmanian devils (Sarcophilus harrisii), black-flanked rock wallabies (Petrogale lateralis), and burrowing bettongs (Bettongia lesueur), contraception can benefit their conservation by maximizing genetic diversity and behavioral integrity in the captive breeding program, or, in the case of the wallabies and bettongs, by reducing populations to a sustainable size when they become locally overabundant. In these examples, contraceptive duration relative to reproductive life, reversibility, and predictability of the contraceptive agent being used are important to ensure the potential for individuals to reproduce following cessation of contraception, as exemplified by the wallabies when their population crashed and needed females to resume breeding. © 2017 Society for Conservation Biology.

Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange.

PubMed

Kabbaj, Hafssa; Sall, Amadou T; Al-Abdallat, Ayed; Geleta, Mulatu; Amri, Ahmed; Filali-Maltouf, Abdelkarim; Belkadi, Bouchra; Ortiz, Rodomiro; Bassi, Filippo M

2017-01-01

Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.

Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars.

PubMed

Campoy, José Antonio; Lerigoleur-Balsemin, Emilie; Christmann, Hélène; Beauvieux, Rémi; Girollet, Nabil; Quero-García, José; Dirlewanger, Elisabeth; Barreneche, Teresa

2016-02-24

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry. A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method. The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.

Biochemical identification of mallard-black duck hybrids through a breeding program and in nature

USGS Publications Warehouse

Morgan, R.P.; Meritt, D.W.; Block, S.B.; Cole, M.

1978-01-01

From 1974 to 1976, a breeding program was used to produce black duck-mallard hybrids for the evaluation of inheritance patterns of serum proteins and esterases. In addition to the initial crosses, a series of matings in 1975 and 1976 were designed to evaluate inheritance patterns in hybrid matings with either black duck or mallards. At the F1 level, hybrids were easily distinguished. However, mallard or black duck crosses with hybrids were detectable as hybrids in only 11.5 - 22.6% of the progeny using serum proteins, and 22.6 - 38.8% using serum esterases. Concurrent with the breeding program, a field survey indicated hybrid frequencies ranging from 4% to 28%.

Biomechanical differences in the stem straightening process among Pinus pinaster provenances. A new approach for early selection of stem straightness.

PubMed

Sierra-de-Grado, Rosario; Pando, Valentín; Martínez-Zurimendi, Pablo; Peñalvo, Alejandro; Báscones, Esther; Moulia, Bruno

2008-06-01

Stem straightness is an important selection trait in Pinus pinaster Ait. breeding programs. Despite the stability of stem straightness rankings in provenance trials, the efficiency of breeding programs based on a quantitative index of stem straightness remains low. An alternative approach is to analyze biomechanical processes that underlie stem form. The rationale for this selection method is that genetic differences in the biomechanical processes that maintain stem straightness in young plants will continue to control stem form throughout the life of the tree. We analyzed the components contributing most to genetic differences among provenances in stem straightening processes by kinetic analysis and with a biomechanical model defining the interactions between the variables involved (Fournier's model). This framework was tested on three P. pinaster provenances differing in adult stem straightness and growth. One-year-old plants were tilted at 45 degrees, and individual stem positions and sizes were recorded weekly for 5 months. We measured the radial extension of reaction wood and the anatomical features of wood cells in serial stem cross sections. The integral effect of reaction wood on stem leaning was computed with Fournier's model. Responses driven by both primary and secondary growth were involved in the stem straightening process, but secondary-growth-driven responses accounted for most differences among provenances. Plants from the straight-stemmed provenance showed a greater capacity for stem straightening than plants from the sinuous provenances mainly because of (1) more efficient reaction wood (higher maturation strains) and (2) more pronounced secondary-growth-driven autotropic decurving. These two process-based traits are thus good candidates for early selection of stem straightness, but additional tests on a greater number of genotypes over a longer period are required.

BREEDING AND GENETICS SYMPOSIUM: Climate change and selective breeding in aquaculture.

PubMed

Sae-Lim, P; Kause, A; Mulder, H A; Olesen, I

2017-04-01

Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from breeding programs would be more heavily used. Aquaculture should use genetically improved and robust organisms not suffering from inbreeding depression. This will require using fish from well-managed selective breeding programs with proper inbreeding control and breeding goals. Policymakers and breeding organizations should provide incentives to boost selective breeding programs in aquaculture for more robust fish tolerating climatic change.

The development of genomics applied to dairy breeding

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QT...

Using Economics and Genetics To Produce Leaner Pork.

ERIC Educational Resources Information Center

Welch, Mary A., Ed.

1994-01-01

The booklet describes the STAGES (Swine Testing and Genetic Evaluation System) program developed at Purdue University (Indiana), along with the USDA, National Pork Producers Council and swine breed associations. By selecting breeding stock from a coded catalogue developed by STAGES, producers are able to select the best breeding stock for more…

Breeding Perspectives and Programs at East Lansing

USDA-ARS?s Scientific Manuscript database

USDA-ARS sugar beet breeding activities for both Aphanomyces resistance and CMS/O-type conversion at East Lansing reach back to the 1940’s, with variety testing activities at Michigan State University reaching back to circa 1911. Many of those contributions are well known in the sugar beet breeding ...

75 FR 25103 - Tree Assistance Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... 1416 RIN 0560-AH96 Tree Assistance Program AGENCY: Farm Service Agency and Commodity Credit Corporation, USDA. ACTION: Final rule. SUMMARY: This rule implements specific requirements for the Tree Assistance... provides disaster assistance to eligible orchardists and nursery tree growers to replant or rehabilitate...

Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.

USDA-ARS?s Scientific Manuscript database

Unfortunately, 80% of the genotypes from the "hybrid seeds" are unproductive in farmers' fields. In 1999 the USDA and Mars Inc. initiated a Marker Assisted Selection (MAS) program for cacao that has reduces many of the problems in traditional breeding. One limitation of the MAS program is the distan...

Phenotypic evidence suggests a possible major-gene element to weevil resistance in Sitka spruce

Treesearch

John N. King; René I. Alfaro; Peter Ott; Lara vanAkker

2012-01-01

The weevil resistance breeding program against the white pine weevil, Pissodes strobi Peck (Coleoptera: Curculionidae), particularly for Sitka spruce (Picea sitchensis (Bong.) Carr), is arguably one of the most successful pest resistance breeding programs for plantation forest species, and it has done a lot to rehabilitate...

Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana

USDA-ARS?s Scientific Manuscript database

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation wa...

Varieties from the USDA are the foundation of the Florida specialty citrus industry

USDA-ARS?s Scientific Manuscript database

The Florida citrus industry is poised to grow diverse new cultivars from the USDA breeding program, the University of Florida breeding program, and from importation of budwood from new selections from around the world. The top six cultivars of specialty citrus from the USDA (‘Murcott’, ‘Sunburst’, ‘...

Climate correlates of 20 years of trophic changes in a high-elevation riparian system

USGS Publications Warehouse

Martin, T.E.

2007-01-01

The consequences of climate change for ecosystem structure and function remain largely unknown. Here, I examine the ability of climate variation to explain long-term changes in bird and plant populations, as well as trophic interactions in a high-elevation riparian system in central Arizona, USA, based on 20 years of study. Abundances of dominant deciduous trees have declined dramatically over the 20 years, correlated with a decline in overwinter snowfall. Snowfall can affect overwinter presence of elk, whose browsing can significantly impact deciduous tree abundance. Thus, climate may affect the plant community indirectly through effects on herbivores, but may also act directly by influencing water availability for plants. Seven species of birds were found to initiate earlier breeding associated with an increase in spring temperature across years. The advance in breeding time did not affect starvation of young or clutch size. Earlier breeding also did not increase the length of the breeding season for single-brooded species, but did for multi-brooded species. Yet, none of these phenology-related changes was associated with bird population trends. Climate had much larger consequences for these seven bird species by affecting trophic levels below (plants) and above (predators) the birds. In particular, the climate-related declines in deciduous vegetation led to decreased abundance of preferred bird habitat and increased nest predation rates. In addition, summer precipitation declined over time, and drier summers also were further associated with greater nest predation in all species. The net result was local extinction and severe population declines in some previously common bird species, whereas one species increased strongly in abundance, and two species did not show clear population changes. These data indicate that climate can alter ecosystem structure and function through complex pathways that include direct and indirect effects on abundances and interactions of multiple trophic components. ?? 2007 by the Ecological Society of America.

Climate correlates of 20 years of trophic changes in a high-elevation riparian system.

PubMed

Martin, Thomas E

2007-02-01

The consequences of climate change for ecosystem structure and function remain largely unknown. Here, I examine the ability of climate variation to explain long-term changes in bird and plant populations, as well as trophic interactions in a high-elevation riparian system in central Arizona, USA, based on 20 years of study. Abundances of dominant deciduous trees have declined dramatically over the 20 years, correlated with a decline in overwinter snowfall. Snowfall can affect overwinter presence of elk, whose browsing can significantly impact deciduous tree abundance. Thus, climate may affect the plant community indirectly through effects on herbivores, but may also act directly by influencing water availability for plants. Seven species of birds were found to initiate earlier breeding associated with an increase in spring temperature across years. The advance in breeding time did not affect starvation of young or clutch size. Earlier breeding also did not increase the length of the breeding season for single-brooded species, but did for multi-brooded species. Yet, none of these phenology-related changes was associated with bird population trends. Climate had much larger consequences for these seven bird species by affecting trophic levels below (plants) and above (predators) the birds. In particular, the climate-related declines in deciduous vegetation led to decreased abundance of preferred bird habitat and increased nest predation rates. In addition, summer precipitation declined over time, and drier summers also were further associated with greater nest predation in all species. The net result was local extinction and severe population declines in some previously common bird species, whereas one species increased strongly in abundance, and two species did not show clear population changes. These data indicate that climate can alter ecosystem structure and function through complex pathways that include direct and indirect effects on abundances and interactions of multiple trophic components.

Developments in amphibian captive breeding and reintroduction programs.

PubMed

Harding, Gemma; Griffiths, Richard A; Pavajeau, Lissette

2016-04-01

Captive breeding and reintroduction remain high profile but controversial conservation interventions. It is important to understand how such programs develop and respond to strategic conservation initiatives. We analyzed the contribution to conservation made by amphibian captive breeding and reintroduction since the launch of the International Union for Conservation of Nature (IUCN) Amphibian Conservation Action Plan (ACAP) in 2007. We assembled data on amphibian captive breeding and reintroduction from a variety of sources including the Amphibian Ark database and the IUCN Red List. We also carried out systematic searches of Web of Science, JSTOR, and Google Scholar for relevant literature. Relative to data collected from 1966 to 2006, the number of species involved in captive breeding and reintroduction projects increased by 57% in the 7 years since release of the ACAP. However, there have been relatively few new reintroductions over this period; most programs have focused on securing captive-assurance populations (i.e., species taken into captivity as a precaution against extinctions in the wild) and conservation-related research. There has been a shift to a broader representation of frogs, salamanders, and caecilians within programs and an increasing emphasis on threatened species. There has been a relative increase of species in programs from Central and South America and the Caribbean, where amphibian biodiversity is high. About half of the programs involve zoos and aquaria with a similar proportion represented in specialist facilities run by governmental or nongovernmental agencies. Despite successful reintroduction often being regarded as the ultimate milestone for such programs, the irreversibility of many current threats to amphibians may make this an impractical goal. Instead, research on captive assurance populations may be needed to develop imaginative solutions to enable amphibians to survive alongside current, emerging, and future threats. © 2015 Society for Conservation Biology.

The use of integer programming to select bulls across breeding companies with volume price discounts.

PubMed

McConnel, M B; Galligan, D T

2004-10-01

Optimization programs are currently used to aid in the selection of bulls to be used in herd breeding programs. While these programs offer a systematic approach to the problem of semen selection, they ignore the impact of volume discounts. Volume discounts are discounts that vary depending on the number of straws purchased. The dynamic nature of volume discounts means that, in order to be adequately accounted for, they must be considered in the optimization routine. Failing to do this creates a missed economic opportunity because the potential benefits of optimally selecting and combining breeding company discount opportunities are not captured. To address these issues, an integer program was created which used binary decision variables to incorporate the effects of quantity discounts into the optimization program. A consistent set of trait criteria was used to select a group of bulls from 3 sample breeding companies. Three different selection programs were used to select the bulls, 2 traditional methods and the integer method. After the discounts were applied using each method, the integer program resulted in the lowest cost portfolio of bulls. A sensitivity analysis showed that the integer program also resulted in a low cost portfolio when the genetic trait goals were changed to be more or less stringent. In the sample application, a net benefit of the new approach over the traditional approaches was a 12.3 to 20.0% savings in semen cost.

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

Treesearch

S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

2004-01-01

Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

Mountain pine beetle host selection between lodgepole and ponderosa pines in the southern Rocky Mountains

Treesearch

Daniel R. West; Jennifer S. Briggs; William R. Jacobi; Jose F. Negron

2016-01-01

Recent evidence of range expansion and host transition by mountain pine beetle (Dendroctonus ponderosae Hopkins; MPB) has suggested that MPB may not primarily breed in their natal host, but will switch hosts to an alternate tree species. As MPB populations expanded in lodgepole pine forests in the southern Rocky Mountains, we investigated the potential for...

HOW to Identify and Control Sapsucker Injury on Trees

Treesearch

Michael E. Ostry; Thomas H. Nicholls

1976-01-01

The yellow-bellied sapsucker (Sphyrapicus varius), a member of the woodpecker family, is a migratory bird whose summer breeding range includes the Lakes States region. The identifying field markings of adult birds are a black crescent on the breast, pale yellow belly, white wing stripe, and a crimson crown. The male also has a crimson chin and throat, distinguishing...

Breeding bird communities in regenerating and mature broadleaf forests in the USA Lake States

Treesearch

John R. Probst; Don R. Rakstad; David J. Rugg

1992-01-01

When Lake States aspen tree canopy is removed by clearcut harvest, bird species turnover is almost complete. Bird species richness and total populations were highest in mature stands with well-developed understories and in regenerating stands about 4 years after clearcutting. However, species composition in regenerating stands was different to that in mature stands....

Covariance patterns among birds and vegetation in a California oak woodland

Treesearch

Randolph A. Wilson; Patricia Manley; Barry R. Noon

1991-01-01

We sampled characteristics of vegetation and estimated abundances of bird species on 23 plots representing a continuum of tree densities of the blue oak phase of the Coast Range foothill woodland near Hopland, California. Fifty-one bird species were found breeding. Cavity-nesters dominated the bird community in number of species and individuals. Cavity nesters used a...

Relationships among red-cockaded woodpecker group density, nestling provisioning rates, and habitat

Treesearch

Richard N. Conner; D. Craig Rudolph; Richard R. Schaefer; Daniel Saenz; Clifford E. Shackelford

1999-01-01

We examined Red-cockaded Woodpecker (Picoides borealis) food provisioning rates of nestlings during the 1992 and 1993 breeding seasons on the Vernon Ranger District of the Kisatchie National Forest in Louisiana. Provisioning rates were monitored at nest trees in moderate (9.8 groups/2 km radius, n=10) and low (5.9 groups/2 km radius, n=10) density...

7 CFR 760.502 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.502 Definitions. The following...) Service Center that is responsible for servicing the farm on which the trees, bushes, or vines are located... tree grower means a person or legal entity that produces nursery, ornamental, fruit, nut, or Christmas...

7 CFR 760.502 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.502 Definitions. The following...) Service Center that is responsible for servicing the farm on which the trees, bushes, or vines are located... tree grower means a person or legal entity that produces nursery, ornamental, fruit, nut, or Christmas...

7 CFR 760.502 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.502 Definitions. The following...) Service Center that is responsible for servicing the farm on which the trees, bushes, or vines are located... tree grower means a person or legal entity that produces nursery, ornamental, fruit, nut, or Christmas...

7 CFR 1214.60 - Programs, plans, and projects.

Code of Federal Regulations, 2014 CFR

2014-01-01

... the image, desirability, or quality of Christmas trees. (b) A program, plan, or project may not be... TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information... Christmas trees; (2) The establishment and conduct of research with respect to the image, desirability, use...

7 CFR 1214.60 - Programs, plans, and projects.

Code of Federal Regulations, 2013 CFR

2013-01-01

... the image, desirability, or quality of Christmas trees. (b) A program, plan, or project may not be... TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information... Christmas trees; (2) The establishment and conduct of research with respect to the image, desirability, use...

7 CFR 1214.60 - Programs, plans, and projects.

Code of Federal Regulations, 2012 CFR

2012-01-01

... the image, desirability, or quality of Christmas trees. (b) A program, plan, or project may not be... TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information... Christmas trees; (2) The establishment and conduct of research with respect to the image, desirability, use...

The fault-tree compiler

NASA Technical Reports Server (NTRS)

Martensen, Anna L.; Butler, Ricky W.

1987-01-01

The Fault Tree Compiler Program is a new reliability tool used to predict the top event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N gates. The high level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Corporation VAX with the VMS operation system.

7 CFR 783.1 - Applicability.

Code of Federal Regulations, 2010 CFR

2010-01-01

... SPECIAL PROGRAMS TREE ASSISTANCE PROGRAM § 783.1 Applicability. This part governs and provides the requirements and authorities for administration of the Tree Assistance Program (TAP) of the Farm Service Agency... limited to lost eligible trees, bushes or vines, and all claims are subject to the availability of funds. ...

7 CFR 760.505 - Application.

Code of Federal Regulations, 2012 CFR

2012-01-01

... date when the loss of trees, bushes, or vines is apparent to the producer. (b) The producer must submit... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.505 Application. (a) To apply for TAP, a producer that suffered eligible tree, bush, or vine losses that occurred: (1) During...

7 CFR 760.505 - Application.

Code of Federal Regulations, 2014 CFR

2014-01-01

... date when the loss of trees, bushes, or vines is apparent to the producer. (b) The producer must submit... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.505 Application. (a) To apply for TAP, a producer that suffered eligible tree, bush, or vine losses that occurred: (1) During...

7 CFR 760.505 - Application.

Code of Federal Regulations, 2011 CFR

2011-01-01

... date when the loss of trees, bushes, or vines is apparent to the producer. (b) The producer must submit... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.505 Application. (a) To apply for TAP, a producer that suffered eligible tree, bush, or vine losses that occurred: (1) During...

7 CFR 760.505 - Application.

Code of Federal Regulations, 2013 CFR

2013-01-01

... date when the loss of trees, bushes, or vines is apparent to the producer. (b) The producer must submit... SPECIAL PROGRAMS INDEMNITY PAYMENT PROGRAMS Tree Assistance Program § 760.505 Application. (a) To apply for TAP, a producer that suffered eligible tree, bush, or vine losses that occurred: (1) During...

Molecular genetic analysis of ancient cattle bones excavated from archaeological sites in Jeju, Korea.

PubMed

Kim, Jae-Hwan; Oh, Ju-Hyung; Song, Ji-Hoon; Jeon, Jin-Tae; Han, Sang-Hyun; Jung, Yong-Hwan; Oh, Moon-You

2005-12-31

Ancient cattle bones were excavated from archaeological sites in Jeju, Korea. We used molecular genetic techniques to identify the species and establish its relationship to extant cattle breeds. Ancient DNA was extracted from four sources: a humerus (Gonae site, A.D. 700-800), two fragments of radius, and a tooth (Kwakji site, A.D. 0-900). The mitochondrial DNA (mtDNA) D-loop regions were cloned, sequenced, and compared with previously reported sequences of various cattle breeds (9 Asian, 8 European, and 3 African). The results revealed that these bones were of the breed, Bos taurus, and a phylogenetic tree indicated that the four cattle bones formed a monophyletic group with Jeju native black cattle. However, the patterns of sequence variation and reports from archaeological sites suggest that a few wild cattle, with a different maternal lineage, may have existed on Jeju Island. Our results will contribute to further studies of the origin of Jeju native cattle and the possible existence of local wild cattle.

Automatic translation of digraph to fault-tree models

NASA Technical Reports Server (NTRS)

Iverson, David L.

1992-01-01

The author presents a technique for converting digraph models, including those models containing cycles, to a fault-tree format. A computer program which automatically performs this translation using an object-oriented representation of the models has been developed. The fault-trees resulting from translations can be used for fault-tree analysis and diagnosis. Programs to calculate fault-tree and digraph cut sets and perform diagnosis with fault-tree models have also been developed. The digraph to fault-tree translation system has been successfully tested on several digraphs of varying size and complexity. Details of some representative translation problems are presented. Most of the computation performed by the program is dedicated to finding minimal cut sets for digraph nodes in order to break cycles in the digraph. Fault-trees produced by the translator have been successfully used with NASA's Fault-Tree Diagnosis System (FTDS) to produce automated diagnostic systems.

Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

PubMed Central

Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

2015-01-01

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

TILLING for plant breeding.

PubMed

Sharp, Peter; Dong, Chongmei

2014-01-01

TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure.