scholarly journals Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

2016 ◽  
Author(s):  
Jun Qin ◽  
Ainong Shi ◽  
Haizheng Xiong ◽  
Bei-quan Mou ◽  
Dennis R. Motes ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Structure Analysis ◽  
Vigna Unguiculata ◽  
Core Collection ◽  
Antioxidant Content ◽  
Population Structure Analysis

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 Association Mapping, Trait Variation, Interaction and Population Structure Analysis in Cucumber (Cucumis Sativus L.)

2021 ◽  
Author(s):  
Rahul Kumar ◽  
Anilabh Das Munshi ◽  
Tusar Kanti Behera ◽  
GOGRAJ SINGH JAT ◽  
Harshwardhan Choudhary ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Open Field ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Fruit Quality ◽  
Field Condition ◽  
Trait Variation ◽  
Population Structure Analysis ◽  
Open Field Condition

Abstract In several regions of the world, low productivity in this crop is attributed to several factors including poor understanding of the genomic complexity of important traits associated with fruit quality and yield. Therefore, genome wide association analysis was performed for important traits using simple sequence repeats (SSR) markers. Significant variation was recorded for all the studied traits in 78 cucumber genotypes under two environments (open field and net house) which indicated that the constituted association panel was suitable for association mapping. Genotyping was done using 60 highly polymorphic SSRs. By performing genome scanning out of 60 SSR markers, using mixed linear model (MLM) approach 4 and 6 markers explained an average of 23.93% and 17.37 % of the trait variation under net house and open field condition, respectively. Based on MLM approach two markers on 3rd chromosome (UW084942) and 4th chromosome (UW062953) found to be associated with the average fruit weight (g) under both net house and open field condition. Population structure analysis revealed four distinct sub-populations that corroborated with the geographical origin as well as fruit quality and quantitative traits. The four sub-populations (A–D) had fixation index percentage (Fst) equal to 24.35 29.48, 37.17 and 8.97 respectively, supporting the existence of moderate population structures. Therefore, the extensive phenotypic and genotypic characterization, population structure, and markers associated with critical traits provided in this study will facilitate marker assisted improvement programs in cucumber.

Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping

2014 ◽  
Vol 289 (4) ◽  
pp. 513-521 ◽  
Author(s):  
Padma Nimmakayala ◽  
Venkata L. Abburi ◽  
Lavanya Abburi ◽  
Suresh Babu Alaparthi ◽  
Robert Cantrell ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Association Mapping ◽  
Capsicum Annuum ◽  
Structure Analysis ◽  
Capsicum Annuum L ◽  
Population Structure Analysis

scholarly journals Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

BMC Genetics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Hea-Young Lee ◽  
Na-Young Ro ◽  
Hee-Jin Jeong ◽  
Jin-Kyung Kwon ◽  
Jinkwan Jo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Core Collection ◽  
Population Structure Analysis
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