AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set

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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Genetic Diversity, Population Structure and Screening of Molecular Markers Associated to Agronomic Traits in Safflower (Carthamus tinctorius L.)

Iranian Journal of Science and Technology Transactions A Science ◽

10.1007/s40995-021-01161-w ◽

2021 ◽

Author(s):

Mehdi Rahimi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Agronomic Traits ◽

Carthamus Tinctorius

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Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines

Genetics and Molecular Research ◽

10.4238/2015.july.3.26 ◽

2015 ◽

Vol 14 (3) ◽

pp. 7502-7518 ◽

Cited By ~ 5

Author(s):

K.J. Sa ◽

J.Y. Park ◽

S.H. Choi ◽

B.W. Kim ◽

K.J. Park ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Association Mapping ◽

Agronomic Traits ◽

Inbred Lines ◽

Maize Inbred Lines ◽

Normal Maize

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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 ◽

10.3390/plants10061116 ◽

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.

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Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

BioMed Research International ◽

10.1155/2021/7588652 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Guofeng Yang ◽

Yong Yang ◽

Yali Guan ◽

Zhixia Xu ◽

Junyu Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Height ◽

Ssr Markers ◽

Agronomic Traits ◽

Upland Rice ◽

Diversity Index ◽

Oryza Sativa L ◽

Grain Number ◽

Rice Germplasm ◽

Panicle Number

Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2-19. The observed heterozygosity was 0.0655-0.3115. The Shannon diversity index was 0.1352-0.4827. The genetic similarity coefficient was 0.6736-0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000-grain weight were obtained ( P < 0.01 ), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.

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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 ◽

10.1371/journal.pone.0259883 ◽

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.

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