scholarly journals Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259883
Author(s):  
Seltene Abady ◽  
Hussein Shimelis ◽  
Pasupuleti Janila ◽  
Shasidhar Yaduru ◽  
Admire I. T. Shayanowako ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Drought Tolerance ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Optimum Conditions ◽  
Pod Yield ◽  
Germplasm Collections

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.

scholarly journals Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1116
Author(s):  
Vladimir Aleksandrov ◽  
Tania Kartseva ◽  
Ahmad M. Alqudah ◽  
Konstantina Kocheva ◽  
Krasimira Tasheva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Bread Wheat ◽  
Clustering Algorithm ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Geographic Region ◽  
Snp Markers ◽  
Genetic Diversity And Structure

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r2), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

scholarly journals Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Nelia Nkhoma ◽  
Hussein Shimelis ◽  
Mark D. Laing ◽  
Admire Shayanowako ◽  
Isack Mathew
Keyword(s):  
Genetic Diversity ◽  
Grain Yield ◽  
Vigna Unguiculata ◽  
Polymorphic Information Content ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Lattice Design ◽  
Cultivar Development ◽  
Parental Lines

Abstract Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1–8–1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1–8–1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

scholarly journals Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

2020 ◽  
Author(s):  
Nelia Nkhoma ◽  
Hussein Shimelis ◽  
Mark Laing ◽  
Admire Shayanowako ◽  
Isack Mathew
Keyword(s):  
Genetic Diversity ◽  
Grain Yield ◽  
Vigna Unguiculata ◽  
Polymorphic Information Content ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Lattice Design ◽  
Cultivar Development ◽  
Parental Lines

Abstract Background: Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10×10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results: Number of pods plant-1 (NPP), pod length (PDL), and number of seeds pod-1 (NSP), were significantly (p<0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1-8-1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p<0.05) associations with NPP (r=0.50), NSP (r=0.46) and PDL (r=0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions: Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1-8-1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

scholarly journals Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

2020 ◽  
Author(s):  
Nelia Nkhoma ◽  
Hussein Shimelis ◽  
Mark Laing ◽  
Admire Shayanowako ◽  
Isack Mathew
Keyword(s):  
Genetic Diversity ◽  
Grain Yield ◽  
Vigna Unguiculata ◽  
Polymorphic Information Content ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Lattice Design ◽  
Cultivar Development ◽  
Parental Lines

Abstract Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1-8-1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1-8-1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

scholarly journals Phenotypic diversity and population structure of Ethiopian barley (Hordeum vulgare L.) landrace collections

2020 ◽  
Vol 7 (12) ◽  
pp. 144-161
Author(s):  
Allo A. Dido ◽  
◽  
Kassahun Tesfaye ◽  
M.S.R. Krishna ◽  
Dawit T. Degefu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Hordeum Vulgare ◽  
Agronomic Traits ◽  
Phenotypic Diversity ◽  
Geographic Origin ◽  
Principal Component ◽  
Environment Interaction ◽  
Hordeum Vulgare L ◽  
Shoot Fly

Landraces play a key role in crop breeding by providing beneficial trait for improvement of related crops and their genetic diversity studies are very important for breeding program and identification of parental lines. In this study, 585 barley (Hordeum vulgare L.) landraces collected from 13 agro-ecological zones of Ethiopia were evaluated along with 10 cultivars for their phenotypic diversity and population structure in relation to agronomic traits, resistance to major diseases and barley shoot fly. Data on 22 agronomic traits, three major diseases and barley shoot fly resistance-related traits were recorded. Univariate and multivariate approaches such as principal component and cluster analyses were applied to assess the genetic diversity and population structure. The analysis of variance indicated significant genotypic main, accessions x year and accession x environment interaction effects for almost all the traits evaluated. However, the accessions x environment interactions were mainly due to changes in magnitude rather than crossover types of interactions. The diversity analysis indicated that the population was highly structured according to kernel row-type, region (geographic) origin and altitude classes. Since the population is highly structured, appropriate statistical models will be needed when this population is used for association mapping studies. Eight principal components (PCs) in principal component analysis (PCA) accounted for the variation of 83.01%. The most related traits were included in the same PC, implying that results from PCA could give clues as to the relationship among traits. Though variability existed within and among clusters, useful germplasm clustered together. These materials are important sources of germplasm for the improvement of agronomic, disease and insect pest resistance traits. Keywords: Barley, diseases, genetic diversity, landraces, multivariate, shoot fly

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

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.

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 Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to WaterStressed Environments

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 487 ◽  
Author(s):  
Acuña ◽  
Rivas ◽  
Brambilla ◽  
Cerrillo ◽  
Frusso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Stress Resistance ◽  
Prunus Persica ◽  
Agronomic Traits ◽  
Phenotypic Traits ◽  
Flesh Color ◽  
Japanese Plum ◽  
Prunus Salicina

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

Genetic diversity of safflower (Carthamus tinctorius L.) germplasm as revealed by SSR markers

2015 ◽  
Vol 15 (1) ◽  
pp. 1-11 ◽  
Author(s):  
B. Usha Kiran ◽  
N. Mukta ◽  
P. Kadirvel ◽  
K. Alivelu ◽  
S. Senthilvel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Seed Yield ◽  
Edible Oils ◽  
Agronomic Traits ◽  
Allelic Variation ◽  
Fatty Acid Content ◽  
Bootstrap Support ◽  
Oilseed Crop ◽  
Core Subset

Safflower is a multi-purpose oilseed crop, primarily known for good quality oil containing highest polyunsaturated fatty acid content (>80%) among edible oils. In this study, a core subset of 148 safflower accessions representing 15 countries, predominantly of Indian origin, was evaluated for agronomic traits and characterized for genetic diversity, population structure and linkage disequilibrium (LD) using 44 simple sequence repeat (SSR) loci across 11 linkage groups to enable its utilization in breeding and genetic mapping purposes. The collection had substantial variation for seed yield-related traits. SSR allelic variation was low as indicated by average number of alleles (3.6) per locus, gene diversity (0.314) and polymorphism information content (0.284). Cluster analysis (neighbour-joining tree) revealed five major genotypic groups with very low bootstrap support. STRUCTURE analysis showed recognizable population structure; based on membership coefficients ( ≥ 0.75), 52% accessions were classified into four populations (K= 4) and the remaining 48% accessions into admixture group. High Fst values (0.30–0.48) suggested that the populations were substantially differentiated. Analysis of molecular variance results showed that maximum of genetic variation (85%) was explained between individuals within the population suggesting that the population structure was only weak. About 1.9% of SSR locus pairs were in LD, which appeared to be low. High phenotypic variation, mild population structure and low level of LD among unlinked loci suggested that the core subset can be explored for association mapping of seed yield components in safflower.

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