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

Abstract Background Availability of information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N.Results In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content ranged from 0.1 to 0.4, with an average of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was higher as indicated by the Shannon’s information index ( I ) = 0.512, diversity index ( h ) = 0.334, observed heterozygosity ( H o ) = 0.226, and unbiased diversity index (uh) = 0.338.Conclusion The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

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Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

10.21203/rs.3.rs-516783/v1 ◽

2021 ◽

Author(s):

Maya Peringottillam ◽

Smitha Kunhiraman Vasumathy ◽

Hari Krishna Kumar ◽

Manickavelu Alagu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Genetic Purity ◽

Next Generation Sequencing Technology ◽

Distance Analysis ◽

Rice Landraces ◽

Genetic Diversity And Structure ◽

Rice Landrace

Abstract Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

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Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽

10.1371/journal.pone.0243238 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243238

Author(s):

Wilson Nkhata ◽

Hussein Shimelis ◽

Rob Melis ◽

Rowland Chirwa ◽

Tenyson Mzengeza ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Bean ◽

Southern Africa ◽

Crop Improvement ◽

Phenotypic Expression ◽

Snp Markers ◽

High Yield ◽

Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

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

BMC Plant Biology ◽

10.1186/s12870-020-02722-8 ◽

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.

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

Frontiers in Genetics ◽

10.3389/fgene.2020.580782 ◽

2020 ◽

Vol 11 ◽

Author(s):

Xiu Yang ◽

Binwen Tan ◽

Haijiao Liu ◽

Wei Zhu ◽

Lili Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Common Wheat ◽

Genotyping By Sequencing

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Genetic variation and population structure in China summer maize germplasm

Scientific Reports ◽

10.1038/s41598-021-84732-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Guoping Shu ◽

Gangqiang Cao ◽

Niannian Li ◽

Aifang Wang ◽

Fang Wei ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Linkage Disequilibrium ◽

Germplasm Collection ◽

Genotyping By Sequencing ◽

Inbred Lines ◽

Summer Maize ◽

Heterotic Groups ◽

Breeding Germplasm

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

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Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China by 3 Types of Genetic Markers

10.21203/rs.3.rs-1050153/v1 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Yewen Wang ◽

Peijiang Li ◽

Yuexing Wang ◽

Shimao Zheng ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Markers ◽

Ssr Markers ◽

Diversity Index ◽

Indica Rice ◽

Mantel Test ◽

Phenotypic Traits ◽

Phenotypic Analysis

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

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Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China By 3 Types of Genetic Markers

10.21203/rs.3.rs-1050153/v2 ◽

2022 ◽

Author(s):

Yu Zhang ◽

Qiaoqiao He ◽

Xixi Zhou ◽

Yewen Wang ◽

Peijiang Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Markers ◽

Ssr Markers ◽

Diversity Index ◽

Indica Rice ◽

Mantel Test ◽

Phenotypic Traits ◽

Phenotypic Analysis

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Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)

Genes ◽

10.3390/genes12122007 ◽

2021 ◽

Vol 12 (12) ◽

pp. 2007

Author(s):

A. S. M. Faridul Islam ◽

Dean Sanders ◽

Amit Kumar Mishra ◽

Vijay Joshi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Structure Analysis ◽

Genotyping By Sequencing ◽

The United States ◽

Snp Markers ◽

Breeding Programs ◽

The Us ◽

The Mediterranean ◽

Olive Breeding

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

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Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Diversity ◽

10.3390/d12030088 ◽

2020 ◽

Vol 12 (3) ◽

pp. 88

Author(s):

Alemayehu Teressa Negawo ◽

Yilikal Assefa ◽

Jean Hanson ◽

Asebe Abdena ◽

Meki S. Muktar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Reference Genome ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Soil Conditions ◽

Cenchrus Ciliaris ◽

Population Structure Analysis ◽

Wide Range

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.

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

PeerJ ◽

10.7717/peerj.11593 ◽

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.

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