Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Yang, Xin; Tan, Binwen; Liu, Haijiao; Zhu, Wei; Xu, Lili; Wang, Yi; Fan, Xing; Li, Sha; Zhang, Haiqin; Zeng, Jian; Wu, Dandan; Hu, Xigui; Chen, Guoyue; Zhou, Yonghong; Kang, Houyang

doi:10.3389/fgene.2020.580782

Cited by 36 publications

(27 citation statements)

References 79 publications

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“…GBS has been used to analyze the population structure of maize [ 48 ], common bean ( Phaseolus vulgaris L. ) [ 44 ], wheat [ 49 ], and tea [ 15 , 50 ]. A previous study reported that 390.3 Gb clean data was obtained from 415 tea accessions and there was an average of 0.94 Gb clean data per accession.…”

Section: Discussionmentioning

confidence: 99%

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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Background Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. Results We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. Conclusions The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

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Section: Discussionmentioning

confidence: 99%

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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“…To date, molecular markers have been used to study population structure and genetic relationships of L. siceraria, such as inter-sequence simple repeats [20], SSRs [15,17], and SNPs [19,21]. Next-generation sequencing (NGS)-based SNPs are the most widely used molecular markers to study genome-wide association, population structure, genomic selection, and genetic diversity due to their genome-wide abundance, particularly when many markers are required [22,23]. Genotyping-by-sequencing (GBS) has emerged as one NGS-based genotyping platform for marker design and development [22,23]; in fact, the NGS technology provide large amounts of sequence data to develop numerous SNP and microsatellite markers at the whole-genome scale [24].…”

Section: Introductionmentioning

confidence: 99%

“…Next-generation sequencing (NGS)-based SNPs are the most widely used molecular markers to study genome-wide association, population structure, genomic selection, and genetic diversity due to their genome-wide abundance, particularly when many markers are required [22,23]. Genotyping-by-sequencing (GBS) has emerged as one NGS-based genotyping platform for marker design and development [22,23]; in fact, the NGS technology provide large amounts of sequence data to develop numerous SNP and microsatellite markers at the whole-genome scale [24]. Furthermore, this approach provides accurate results independently of the population or target species.…”

Section: Introductionmentioning

confidence: 99%

The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Contreras‐Soto

Salvatierra²,

Maldonado

et al. 2021

Agronomy

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Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

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“…The results can not only help breeders understand the genetic diversity of wheat germplasm resources but also provide valuable information for wheat genetic improvement through the exploitation of new genetic variations in this region [21].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

Ming

Song

Ren

et al. 2022

Preprint

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Bupleurum (named “Chai-hu”) is an important traditional Chinese medicine resource in China. It has been widely used since ancient times and has antipyretic, analgesic and cholagogic functions, but there is little research on its genetic diversity. In this study, genotyping-by-sequencing (GBS) was used to detect SNP loci in 39 Bupleurum germplasm resources from different regions in China and analyse their genetic diversity. A total of 25.1 Gb of data was obtained by sequencing, with an average of 0.64 Gb per sample. After screening, 83898 high-quality SNPs were obtained. The results of genetic research were obtained by phylogenetic tree, principal component analysis and population structure analysis, and the 39 experimental materials were divided into three groups. The average observed heterozygosity and expected heterozygosity of Bupleurum populations were 0.24 and 0.17, respectively, indicating that Bupleurum populations from five different provinces had a low level of genetic diversity. Population nucleotide diversity analysis and analysis of molecular variance showed that the percentage of intrapopulation variation was 120.88%, while the percentage of interpopulation variation was only 2.46%. There was relative aggregation of Bupleurum samples with the same geographical origin, but the division of population structure was not completely correlated with sample origin. The results showed that the genetic diversity of the materials was low and that the genetic variation was narrow. This provides a good basis for the genetic breeding and protection of species diversity of Bupleurum.

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Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Cited by 36 publications

References 79 publications

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

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