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

2022 ◽  
Author(s):  
Ming Jiang ◽  
Song Yan ◽  
Weichao Ren ◽  
Nannan Xing ◽  
Hongyuan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Chinese Herb ◽  
Genetic Research ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Intrapopulation Variation ◽  
Traditional Chinese Herb ◽  
High Quality Snps ◽  
Population Structure Analysis

Abstract 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.

scholarly journals Genetic Diversity and Population Structure Analysis of Bigleaf Hydrangea Using Genotyping-by-sequencing

2019 ◽  
Vol 144 (4) ◽  
pp. 257-263 ◽  
Author(s):  
Xingbo Wu ◽  
Lisa W. Alexander
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Breeding Cycle ◽  
Nucleotide Polymorphisms ◽  
Hydrangea Macrophylla ◽  
High Quality Snps ◽  
Population Structure Analysis

Hydrangea macrophylla (bigleaf hydrangea) is one of the most important floral and nursery crops worldwide. However, breeding of new bigleaf hydrangea cultivars has been hampered by a long breeding cycle and lack of genetic resources. This study investigated the genetic diversity and population structure of 82 bigleaf hydrangea cultivars using single-nucleotide polymorphisms (SNPs) originated from genotyping-by-sequencing. A total of 5803 high-quality SNPs were discovered in a bigleaf hydrangea cultivar panel. A phylogenetic analysis and analysis of molecular variance based on discovered SNPs concluded the taxonomic classification of H. macrophylla ssp. serrata as a subspecies of H. macrophylla. Principal component analysis confirmed ‘Preziosa’ as a hybrid between H. macrophylla ssp. macrophylla and H. macrophylla ssp. serrata. In addition, the cultivar Lady in Red was also found to be a hybrid between the two subspecies. The population structure analysis identified three groups among the 82 cultivars. All H. macrophylla ssp. serrata cultivars belonged to one group, and two groups were revealed within H. macrophylla ssp. macrophylla. The separation within H. macrophylla ssp. macrophylla indicated a second gene pool due to breeding efforts that have targeted similar breeding goals for bigleaf hydrangea. The discovered SNPs and the phylogenetic results will facilitate further exploitation and understanding of phylogenetic relationships of bigleaf hydrangea and will serve as a reference for hydrangea breeding improvements.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

scholarly journals Population Structure Analysis Revealed Water or Ancient Hub-induced Genetic Diversity of Cultivated-type Tea Plants in Guizhou Plateau

2021 ◽  
Author(s):  
Zhifei Zhao ◽  
Qinfei Song ◽  
Dingchen Bai ◽  
Suzhen Niu ◽  
Yingqin He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Core Collection ◽  
Genotyping By Sequencing ◽  
Tea Plant ◽  
Transmission Model ◽  
Population Structure Analysis ◽  
Tea Plants ◽  
Guizhou Plateau

Abstract Background Tea plants originated from the southwest of China. Guizhou is one of the origin center of tea plants, which is rich in tea plant germplasm resources. However, the distribution characteristics and transmission model of tea plant were still unclear. Results We collected 253 cultivated-type tea plant accessions from Guizhou plateau and analyzed the genetic diversity, PCA, phylogenetic, population structure, LD, and development of core collection using the genotyping-by-sequencing (GBS) approach. A total of 112,072 high-quality SNPs were identified, which was further used to analyze the genetic diversity and population structure. In this study, we found that the genetic diversity in cultivated-type tea accessions of PR Basin were significantly higher than that in cultivated-type tea accessions of YR Basin. Moreover, four groups, including three pure groups (CG-1, CG-2 and CG-3) and one admixture group (CG-4), were identified based on population structure analysis, which was verified by PAC and phylogenetic analysis. Our results showed that the highest GD and Fst values were found in CG-2 vs CG-3, followed by CG-1 vs CG-2 and CG-1 vs CG-3. The lowest GD and Fst values were detected in CG-4 vs CG-1, CG-4 vs CG-2, and CG-4 vs CG-3. Conclusions This study provided the evidence to confirm the contribution of PR and YR Basins and ancient hub road section to the transmission of cultivated-type tea accessions in Guizhou plateau. The genetic diversity, population structure and core collection revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

scholarly journals Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 676 ◽  
Author(s):  
Farahani ◽  
Maleki ◽  
Mehrabi ◽  
Kanouni ◽  
Scheben ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Large Scale ◽  
Principal Component ◽  
Snp Markers ◽  
Genome Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Population Structure Analysis

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

scholarly journals Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Kamal Khadka ◽  
Davoud Torkamaneh ◽  
Mina Kaviani ◽  
Francois Belzile ◽  
Manish N. Raizada ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Population Structure ◽  
Food Security ◽  
Spring Wheat ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Exotic Germplasm

Abstract Background Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security. Results We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s–1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s. Conclusion We suggest that only a subset of wheat “landraces” in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives.

scholarly journals Genome-wide diversity of coconut from northern South America uncovers genotypes present in Colombia and strong population structure

2019 ◽  
Author(s):  
Jorge Mario Muñoz-Pérez ◽  
Gloria Patricia Cañas ◽  
Lorena López ◽  
Tatiana Arias
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South America ◽  
Genetic Relationships ◽  
Cocos Nucifera ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
The Pacific ◽  
Population Structure Analysis ◽  
Northern South America

SummaryCoconut palms (Cocos nucifera) are a combination of wild admixed populations and perennial crops with a worldwide distribution. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) for at least four different commercially important and widely cultivated coconut varieties and hybrids growing in northern South America. We present a comprehensive catalog of approximately 27K SNPs to conduct genetic diversity, population structure and linkage disequilibrium analysis. A relatively fast LD decay for the Atlantic accessions within ~250Kb was observed in comparison to the Pacific accessions ~ 1500 Kb.The complete SNPs sampling showed a strong population structure at K = 2, separating accessions from the Pacific and Atlantic coasts as it has been found in previous studies. At higher K values, one non-admixed group was observed for the Atlantic while further substructures emerged for the Pacific accessions, where three non-admixed groups were found. Population structure analysis also showed a great degree of admixture between the Atlantic and Pacific populations, and SNPs of the Pacific non-admixed genetic groups were mostly introgressed into the Atlantic individuals but the contrary was rarely observed. The results of principal component analysis and Neighbor-Joining Hierarchical Clustering were consistent with the results from Structure and provided a measure of genetic relationships among individual genotypes. The Pacific group has a lower genetic diversity and a higher rate of inbreeding than the Atlantic group. These results suggest that the Pacific coconuts of Colombia belong to the pre-Columbian population found on the Pacific coast of Panama and Peru. If it had been introduced after Columbus (as in Mexico), genetic diversity would have been higher than on the Atlantic coast.

scholarly journals Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

2019 ◽  
Author(s):  
Somayeh Farahani ◽  
Mojdeh Maleki ◽  
Rahim Mehrabi ◽  
Homayoun Kanouni ◽  
Reza Talebi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Large Scale ◽  
Principal Component ◽  
Snp Markers ◽  
Genome Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Population Structure Analysis

Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2≥0.8, while 2961 pairs of markers showed complete LD (r2=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

scholarly journals Population structure and genetic diversity in common bean accessions from Northeast Brazil

2021 ◽  
Vol 12 (1) ◽  
pp. 287-297
Author(s):  
Maria da Conceição Martiniano-Souza ◽  
Maria Celeste Gonçalves-Vidigal ◽  
Giseli Valentini ◽  
Julio Cesar Ferreira Elias ◽  
Larissa Fernanda Sega Xavier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Pool ◽  
Northeast Brazil ◽  
Tropical Regions ◽  
High Quality Snps ◽  
Population Structure Analysis ◽  
Great Relevance ◽  
Bioclimatic Conditions

Common bean is of great relevance for several countries, especially those located in tropical regions. Common bean in Brazil has a wide genetic diversity, which is used by breeders to improve this crop. In this study, we used GBS methodology to genotype common bean accessions from Northeast Brazil, and to study its population structure and genetic diversity. After a filtering process, we identified 30,529 high-quality SNPs distributed in 11 linkage groups. The number of SNPs per chromosome ranged from 1,731 to 3,853. The population structure analysis separated the accessions into two subpopulations, according to K=2, one subpopulation with 26 Andean and the other with 60 Middle American accessions. Considering K=3, Middle American accessions were divided into two subpopulations with presence of allele mixture between these two groups. Based on the PCA, we were able to verify a narrow genetic base of accessions belonging to the Andean gene pool, as well as a vast genetic diversity among the accessions from the Middle American gene pool. The knowledge on the genetic diversity among the accessions is of extreme importance to subsidize the common bean breeding programs in Northeast Brazil, and to explore the variability existing in cultivars adapted to the specific bioclimatic conditions.

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