scholarly journals Genotypic characterization of the U.S. peanut core collection

2020 ◽  
Author(s):  
Paul I. Otyama ◽  
Roshan Kulkarni ◽  
Kelly Chamberlin ◽  
Peggy Ozias-Akins ◽  
Ye Chu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Regional Distribution ◽  
Country Of Origin ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genotypic Diversity ◽  
Link Type ◽  
Food And Feed ◽  
Genetic Clustering

AbstractCultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. the genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.All data is available at the National Ag Library: https://doi.org/10.15482/USDA.ADC/1518508 and at PeanutBase: https://peanutbase.org/data/public/Arachis_hypogaea/mixed.esm.KNWV

scholarly journals Genotypic Characterization of the U.S. Peanut Core Collection

2020 ◽  
Vol 10 (11) ◽  
pp. 4013-4026
Author(s):  
Paul I. Otyama ◽  
Roshan Kulkarni ◽  
Kelly Chamberlin ◽  
Peggy Ozias-Akins ◽  
Ye Chu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Regional Distribution ◽  
Country Of Origin ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genotypic Diversity ◽  
Cultivated Peanut ◽  
Food And Feed ◽  
Genetic Clustering

Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

scholarly journals A CORE SUBSET ESTABLISHED FOR THE USDA COWPEA [VIGNA UNGUICULATA (L.) WALP.] GERMPLASM COLLECTION

HortScience ◽  
1996 ◽  
Vol 31 (5) ◽  
pp. 762c-762
Author(s):  
A.G. Gillaspie ◽  
O.L. Chambliss ◽  
R.L. Fery ◽  
A.E. Hall ◽  
J.C. Miller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Vigna Unguiculata ◽  
Country Of Origin ◽  
Germplasm Collection ◽  
Pest Resistance ◽  
Information Network ◽  
Germplasm Resources ◽  
Core Subset ◽  
Entire Collection ◽  
Crop Germplasm

The Vigna Crop Germplasm Committee has established a core subset for the USDA cowpea germplasm collection. The subset consists of 9.3% (700 accessions) of the 7525 accessions currently contained in the collection. The subset was selected on the basis of country of origin, taxonomic characteristics, and known disease and pest resistance characteristics. Theoretically, the lines in the subset represent the genetic diversity present in the entire collection. A listing of the accessions in the subset is available from the Vigna germplasm curator (A.G. Gillaspie). The listing can also be accessed through the USDA's Germplasm Resources Information Network (GRIN).

scholarly journals Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pablo Federico Roncallo ◽  
Adelina Olga Larsen ◽  
Ana Laura Achilli ◽  
Carolina Saint Pierre ◽  
Cristian Andrés Gallo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Durum Wheat ◽  
Triticum Turgidum ◽  
Snp Array ◽  
Low Frequency ◽  
Germplasm Collection ◽  
Climate Change Scenarios ◽  
Allelic Variants

Abstract Background Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

scholarly journals Evaluation of the USDA National Clonal Pyrus Germplasm Collection for Resistance to Podosphaera leucotricha

HortScience ◽  
2006 ◽  
Vol 41 (3) ◽  
pp. 717-720 ◽  
Author(s):  
Maryna Serdani ◽  
Robert A. Spotts ◽  
Jill M. Calabro ◽  
Joseph D. Postman ◽  
Annie P. Qu
Keyword(s):  
Genetic Diversity ◽  
Powdery Mildew ◽  
Core Collection ◽  
Germplasm Collection ◽  
Economic Losses ◽  
Podosphaera Leucotricha ◽  
Breeding Programs ◽  
Natural Field ◽  
Resistant Cultivars ◽  
The Core

Powdery mildew (PM) occurs worldwide and is prevalent on susceptible cultivars wherever pears are grown, causing economic losses due to russeted fruit and an increased need for fungicides. A core subset of the Pyrus germplasm collection at the USDA National Clonal Germplasm Repository in Corvallis, Ore., was evaluated for resistance to Podosphaera leucotricha, the causal agent of PM, using greenhouse and field inoculations of potted trees. The core collection consists of about 200 cultivars and species selections, representing most of the genetic diversity of pears and includes 31 Asian cultivars (ASN), 122 European cultivars (EUR), 9 EUR × ASN hybrids and 46 pear species selections. Three trees of each core accession were grafted on seedling rootstocks. In 2001–02, trees were artificially inoculated in a greenhouse, grown under conditions conducive for PM, and evaluated for symptoms. The same trees were subsequently evaluated for PM symptoms from natural field infections during 2003 and 2004. In the greenhouse, 95% of EUR and 38% of ASN were infected with PM. Average PM incidence (percent of leaves infected) in the greenhouse (8% for ASN and 30% for EUR) was much higher than incidence in the field (2% for ASN and 5% for EUR) during 2003. Symptoms were also more severe in the greenhouse, with 46% of ASN and 83% of EUR with PM symptoms having a mean PM incidence of >10%. In the field, 42% and 22% of EUR and 23% and 13% of ASN were infected with P. leucotricha in 2003 and 2004, respectively. Field infection was very low during both years, with percentage leaves infected in ASN and species selections significantly different from EUR. In the field, 6% of ASN with PM symptoms had a mean PM incidence >10% during both years, while 15% and 2% of EUR accessions with PM symptoms had a mean PM incidence >10% in 2003 and 2004 respectively. These results should be very useful to pear breeding programs to develop improved PM resistant cultivars in the future, by using accessions with consistent low PM ratings.

scholarly journals Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 56
Author(s):  
Hea-Young Lee ◽  
Siyoung Jang ◽  
Chea-Rin Yu ◽  
Byoung-Cheorl Kang ◽  
Joong-Hyoun Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
East Asia ◽  
Core Collection ◽  
Food Resource ◽  
Germplasm Collection ◽  
Gene Pools ◽  
Cucurbita Moschata ◽  
High Quality ◽  
High Quality Snps

Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.

Study of genetic diversity in wild raspberry (Rubus idaeus L.) germplasm collection using morphological characters and RAPD markers

Biologija ◽  
2008 ◽  
Vol 54 (2) ◽  
pp. 66-74 ◽  
Author(s):  
Jolanta Patamsytė ◽  
Donatas Žvingila ◽  
Juozas Labokas ◽  
Virgilijus Baliuckas ◽  
Laimutė Balčiūnienė ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Morphological Characters ◽  
Rubus Idaeus

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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