National Center for Genetic Resources Preservation

Fort Collins, CO, United States

National Center for Genetic Resources Preservation

Fort Collins, CO, United States

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Richards C.M.,National Center for Genetic Resources Preservation | Reeves P.A.,National Center for Genetic Resources Preservation | Fenwick A.L.,1701 Center Ave | Panella L.,Sugarbeet Research Unit
Genetic Resources and Crop Evolution | Year: 2013

Locating and quantifying genetic variation within crop wild relatives is an ongoing activity of gene banks tasked with ex situ conservation. Without detailed information about the population genetics of a species, geography often serves as a reasonable proxy for differentiation. With this in mind, this paper examines the genetic diversity and differentiation of Beta vulgaris subsp. maritima accessions collected along a well-studied latitudinal gradient along the French Atlantic coast of France as well as Corsica, for use as representative genotypes from the Mediterranean basin. The aim of this work is to identify the scale and magnitude of differentiation and diversity in this set of accessions, using both molecular and quantitative traits. We assessed clinal variation and admixture in genetic and morphometric data along this latitudinal gradient. Results from this study revealed a complex pattern of recent gene flow and immigration on a historical biogeographic structure. Our data suggest that a presumed latitudinal cline is in reality an admixed mosaic of genotypes. © 2013 Springer Science+Business Media Dordrecht (outside the USA).


Richards C.M.,National Center for Genetic Resources Preservation | Reeves P.A.,National Center for Genetic Resources Preservation | Fenwick A.L.,701 Center Ave | Panella L.,Sugarbeet Research Unit
Genetic Resources and Crop Evolution | Year: 2014

Locating and quantifying genetic variation within crop wild relatives is an ongoing activity of gene banks tasked with ex situ conservation. Without detailed information about the population genetics of a species, geography often serves as a reasonable proxy for differentiation. With this in mind, this paper examines the genetic diversity and differentiation of Beta vulgaris subsp. maritima accessions collected along a well-studied latitudinal gradient along the French Atlantic coast of France as well as Corsica, for use as representative genotypes from the Mediterranean basin. The aim of this work is to identify the scale and magnitude of differentiation and diversity in this set of accessions, using both molecular and quantitative traits. We assessed clinal variation and admixture in genetic and morphometric data along this latitudinal gradient. Results from this study revealed a complex pattern of recent gene flow and immigration on a historical biogeographic structure. Our data suggest that a presumed latitudinal cline is in reality an admixed mosaic of genotypes. © 2013, Springer Science+Business Media Dordrecht (outside the USA).


Thormann I.,Bioversity International | Reeves P.,National Center for Genetic Resources Preservation | Reilley A.,National Center for Genetic Resources Preservation | Engels J.M.M.,Bioversity International | And 4 more authors.
PLoS ONE | Year: 2016

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum. © This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.


PubMed | Martin Luther University of Halle Wittenberg, Bioversity International, Leibniz Institute of Plant Genetics and Crop Plant Research and National Center for Genetic Resources Preservation
Type: Journal Article | Journal: PloS one | Year: 2016

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.


Perez H.E.,University of Hawaii at Manoa | Perez H.E.,University of Florida | Hill L.M.,National Center for Genetic Resources Preservation | Walters C.,National Center for Genetic Resources Preservation
Seed Science Research | Year: 2012

Assessments of seed storage physiology among Arecaceae (palm) species are often inconclusive because seeds exhibit diverse responses to low temperature and moisture conditions. Interrelationships between dry matter accumulation, cell structure and water relations during seed development of the endangered Hawaiian endemic palm, Pritchardia remota, suggest that damage from drying results from mechanical strain. Endosperm and fruits accumulate dry mass through most of the 400d gestation period, but embryos reached maximum dry mass about 250d post-anthesis (DPA). Mostly sucrose and some triacylglycerols accumulated in the cytoplasm and vacuoles of embryo cells, and organelles in mature embryo cells de-differentiated. Water content and water potential decreased as embryos matured and embryos contained about 0.45 gH2O(g dry mass) -1 (-26MPa) at shedding. Mature embryos survived drying to 0.16 g g-1 (-49MPa), but further drying was lethal. A model of allowable cell shrinkage is consistent with the substantial, but incomplete, desiccation tolerance acquired in P. remota embryos, and provides a new framework to explain variation in critical water contents as embryos develop. We suggest that desiccation tolerance, which distinguishes recalcitrant and orthodox physiologies among seeds, can be quantified by mechanical strain when embryo cells shrink during drying. © 2012 Cambridge University Press.


White J.W.,Us Arid Land Agricultural Research Center | Dierig D.A.,National Center for Genetic Resources Preservation
Journal of Plant Registrations | Year: 2011

Descriptions of new germplasm published in the Journal of Plant Registrations (JPR), and previously in Crop Science, are important vehicles for informing researchers about advances in plant breeding. Launched in 2007, JPR introduced a format that allowed more detailed descriptions of registrations; however, an informal review suggests that further improvements are possible. This paper explores these suggestions. To support our arguments, we assessed the new format by reviewing 234 papers from JPR, focusing on 106 papers (53 each in the old-Crop Science-and new-JPR-formats) for cultivar releases in 14 self-pollinated crops. We examined genealogies (pedigrees), breeding processes, experimental techniques, phenotypes, and genotypes. In the new format, there was more extensive information on the chronology of the breeding process, the expected area of adaptation, experimental techniques, the quantification of phenotypes, and citation of web-based reports. Nonetheless, improvement appeared possible, including by (i) documenting genealogies in databases structured for breeding records; (ii) quantifying the degree of relatedness to other germplasm; (iii) describing the breeding process in tables that include key dates, population types and sizes, and numbers of test environments; (iv) describing adaptation through standardized scales, environmental classifications, or quantitative responses; (v) providing genotypic data; and (vi) providing access to supplementary materials from databases or Internet resources. © Crop Science Society of America.


Comas L.H.,Water Management Research | Becker S.R.,Colorado State University | Cruz V.M.V.,National Center for Genetic Resources Preservation | Cruz V.M.V.,Colorado State University | And 2 more authors.
Frontiers in Plant Science | Year: 2013

Geneticists and breeders are positioned to breed plants with root traits that improve productivity under drought. However, a better understanding of root functional traits and how traits are related to whole plant strategies to increase crop productivity under different drought conditions is needed. Root traits associated with maintaining plant productivity under drought include small fine root diameters, long specific root length, and considerable root length density, especially at depths in soil with available water. In environments with late season water deficits, small xylem diameters in targeted seminal roots save soil water deep in the soil profile for use during crop maturation and result in improved yields. Capacity for deep root growth and large xylem diameters in deep roots may also improve root acquisition of water when ample water at depth is available. Xylem pit anatomy that makes xylem less "leaky" and prone to cavitation warrants further exploration holding promise that such traits may improve plant productivity in water-limited environments without negatively impacting yield under adequate water conditions. Rapid resumption of root growth following soil rewetting may improve plant productivity under episodic drought. Genetic control of many of these traits through breeding appears feasible. Several recent reviews have covered methods for screening root traits but an appreciation for the complexity of root systems (e.g., functional differences between fine and coarse roots) needs to be paired with these methods to successfully identify relevant traits for crop improvement. Screening of root traits at early stages in plant development can proxy traits at mature stages but verification is needed on a case by case basis that traits are linked to increased crop productivity under drought. Examples in lesquerella (Physaria) and rice (Oryza) show approaches to phenotyping of root traits and current understanding of root trait genetics for breeding. © 2013 Comas, Becker, Cruz, Byrne and Dierig.


Reeves P.A.,National Center for Genetic Resources Preservation | Panella L.W.,Northern Plains Area Sugarbeet Research Unit | Richards C.M.,National Center for Genetic Resources Preservation
Theoretical and Applied Genetics | Year: 2012

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. We show that the popular core collection assembly procedure "M" (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Betavulgaris L. subsp. vulgaris) that is under selection. We present a corrected procedure ("M+") that outperforms M. An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled with M+. A negative correlation in level of allelic diversity between neutral and selected loci was observed in 42% of simulated data sets. When core collection assembly is guided by neutral marker loci, as is the current common practice, enhanced allelic variation at agronomically important loci should not necessarily be expected. © 2012 Springer-Verlag (outside the USA).


Paiva S.R.,EMBRAPA - Empresa Brasileira de Pesquisa Agropecuária | Mariante A.D.S.,EMBRAPA - Empresa Brasileira de Pesquisa Agropecuária | Blackburn H.D.,National Center for Genetic Resources Preservation
Journal of Heredity | Year: 2011

Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs. © 2011 The American Genetic Association. All rights reserved.


PubMed | National Center for Genetic Resources Preservation
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2012

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. We show that the popular core collection assembly procedure M (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Beta vulgaris L. subsp. vulgaris) that is under selection. We present a corrected procedure (M+) that outperforms M. An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled with M+. A negative correlation in level of allelic diversity between neutral and selected loci was observed in 42% of simulated data sets. When core collection assembly is guided by neutral marker loci, as is the current common practice, enhanced allelic variation at agronomically important loci should not necessarily be expected.

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