Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide 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.

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Genetic diversity and population structure of sheep (Ovis aries) in Sichuan, China

PLoS ONE ◽

10.1371/journal.pone.0257974 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257974

Author(s):

Mingliang Zhou ◽

Gaofu Wang ◽

Minghua Chen ◽

Qian Pang ◽

Shihai Jiang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ovis Aries ◽

Fixation Index ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genome Wide ◽

High Quality Snps ◽

Exotic Breed ◽

Population Structures

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

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On genetic diversity in caraway: Genotyping of a large germplasm collection

PLoS ONE ◽

10.1371/journal.pone.0244666 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244666

Author(s):

Daniel von Maydell ◽

Heike Lehnert ◽

Thomas Berner ◽

Evelyn Klocke ◽

Wolfram Junghanns ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genome Size ◽

Phylogenetic Trees ◽

Germplasm Collection ◽

Genotyping By Sequencing ◽

Gene Pools ◽

History Of ◽

Winter Annual ◽

Neighbor Network

Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted material are necessary. Analysis of genetic diversity can accompany this process, for instance, by revealing untapped gene pools. Here, we analyzed 137 accessions using genotyping by sequencing (GBS). Hence, we can report a broad overview of population structure and genetic diversity of caraway. Population structure was determined using a principal coordinate analysis, a Bayesian clustering analysis, phylogenetic trees and a neighbor network based on 13,155 SNPs. Genotypic data indicate a clear separation of accessions into two subpopulations, which correlates with the flowering type (annual vs. biennial). Four winter-annual accessions were closer related to biennial accessions. In an analysis of molecular variance, genetic variation between the two subpopulations was 7.84%. In addition, we estimated the genome size for 35 accessions by flow cytometry. An average genome size of 4.282 pg/2C (± 0.0096 S.E.) was estimated. Therefore, we suggest a significantly smaller genome size than stated in literature.

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

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

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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Assessing the Genetic Diversity and Population Structure of World Germplasm Collection of Erianthus arundinaceus (Retz.) Jeswiet Using Sequence-Related Amplified Polymorphic Markers

Sugar Tech ◽

10.1007/s12355-021-01037-8 ◽

2021 ◽

Author(s):

R. Valarmathi ◽

H. K. Mahadevaswamy ◽

V. Ulaganathan ◽

C. Appunu ◽

S. Karthigeyan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Polymorphic Markers ◽

Erianthus Arundinaceus

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Genetic diversity and population structure in cultivated and weedy types of Perilla in East Asia and other countries as revealed by SSR markers

Horticulture Environment and Biotechnology ◽

10.1007/s13580-015-0039-8 ◽

2015 ◽

Vol 56 (4) ◽

pp. 524-534 ◽

Cited By ~ 7

Author(s):

Kyu Jin Sa ◽

Seung Hun Choi ◽

Mariko Ueno ◽

Ju Kyong Lee

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

East Asia ◽

Ssr Markers ◽

Cultivated And Weedy Types

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Genetic diversity and population structure of a mini-core subset from the world cowpea (Vigna unguiculata (L.) Walp.) germplasm collection

Scientific Reports ◽

10.1038/s41598-018-34555-9 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 12

Author(s):

Christian Fatokun ◽

Gezahegn Girma ◽

Michael Abberton ◽

Melaku Gedil ◽

Nnanna Unachukwu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Vigna Unguiculata ◽

Germplasm Collection ◽

Core Subset ◽

The World

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Genotypic Characterization of the U.S. Peanut Core Collection

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401306 ◽

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.

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