scholarly journals Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11593
Author(s):  
Vipin Tomar ◽  
Guriqbal Singh Dhillon ◽  
Daljit Singh ◽  
Ravi Prakash Singh ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Genome Wide Association Studies ◽  
Breeding Lines ◽  
Structure Information

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

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 Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 518 ◽  
Author(s):  
Ana Campa ◽  
Ester Murube ◽  
Juan José Ferreira
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Snap Bean ◽  
Diversity Panel ◽  
Main Gene

A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker–trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

scholarly journals Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jessica Delfini ◽  
Vânia Moda-Cirino ◽  
José dos Santos Neto ◽  
Paulo Maurício Ruas ◽  
Gustavo César Sant’Ana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Pool ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Mesoamerican Gene Pool ◽  
Diversity Panel

AbstractBrazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

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, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

2020 ◽  
Vol 61 (5) ◽  
pp. 922-932 ◽  
Author(s):  
N Tanaka ◽  
M Shenton ◽  
Y Kawahara ◽  
M Kumagai ◽  
H Sakai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Sequence Data ◽  
Association Studies ◽  
Crop Improvement ◽  
Heading Date ◽  
Principal Component ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Population Structure Analysis

Abstract Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion–deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

scholarly journals Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1437
Author(s):  
Ranjana Bhattacharjee ◽  
Paterne Agre ◽  
Guillaume Bauchet ◽  
David De Koeyer ◽  
Antonio Lopez-Montes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Optimum Number ◽  
Admixture Analysis ◽  
Clustering Methods ◽  
Breeding Lines ◽  
White Yam

White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam.

scholarly journals A New Strategy for Using Historical Imbalanced Yield Data to Conduct Genome-Wide Association Studies and Develop Genomic Prediction Models for Wheat Breeding

2021 ◽  
Author(s):  
Chenggen Chu ◽  
Shichen Wang ◽  
Jackie C. Rudd ◽  
Amir M.H. Ibrahim ◽  
Qingwu Xue ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Prediction Models ◽  
Association Studies ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Yield Data ◽  
Breeding Lines ◽  
Genome Wide ◽  
Genomic Regions

Abstract Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments (year-by-location) over ten years, through testing yield in 40–66 lines each year at 6–14 locations with 38–41 lines repeated in the test in any two consecutive years, was used. Based on correlations among data from different environments within two adjacent years and heritability estimated in each environment, yield data from 87 environments were selected and assigned to two correlation-based groups. The yield best linear unbiased estimation (BLUE) from each group, along with reaction to greenbug and Hessian fly in each line, were used for GWAS to reveal genomic regions associated with yield and insect resistance. A total of 74 genomic regions were associated with grain yield and two of them were commonly detected in both correlation-based groups. Greenbug resistance in TXE lines was mainly controlled by Gb3 on chromosome 7DL in addition to two novel regions on 3DL and 6DS, and Hessian fly resistance was conferred by the region on 1AS. Genomic prediction models developed in two correlation-based groups were validated using a set of 105 new advanced breeding lines and the model from correlation-based group G2 was more reliable for prediction. This research not only identified genomic regions associated with yield and insect resistance but also established the method of using historical imbalanced breeding data to develop a genomic prediction model for crop improvement.

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