scholarly journals Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations

2017 ◽  
Vol 53 (No. 4) ◽  
pp. 159-167 ◽  
Author(s):  
K. Sethi ◽  
P. Siwach ◽  
S.K. Verma
Keyword(s):  
Linkage Disequilibrium ◽  
Association Mapping ◽  
Linear Model ◽  
Ssr Markers ◽  
Mixed Linear Model ◽  
Quality Traits ◽  
Fibre Quality ◽  
Gossypium Arboreum ◽  
Mixed Ancestry ◽  
Ssr Loci

Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre quality traits in genotypes belonging to six races of Gossypium arboreum were assessed. Out of 300 simple sequence repeat (SSR) markers, 100 were found polymorphic, yielding a total of 240 alleles (all polymorphic). Structure analysis revealed allelic admixtures between genotypes. A Q-matrix exhibited mixed ancestry for the majority of genotypes, the race indicum forming a significant percent ancestry for almost all genotypes. At significant threshold values of r<sup>2</sup> ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r<sup>2</sup> ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9–10 cM, with r<sup>2</sup> ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model.

Association mapping and favourable QTL alleles for fibre quality traits in Upland cotton (Gossypium hirsutum L.)

2018 ◽  
Vol 97 (S1) ◽  
pp. 1-12 ◽  
Author(s):  
Cheng-Guang Dong ◽  
Juan Wang ◽  
Yu Yu ◽  
Bao-Cheng Li ◽  
Quan-Jia Chen
Keyword(s):  
Gossypium Hirsutum ◽  
Association Mapping ◽  
Upland Cotton ◽  
Quality Traits ◽  
Fibre Quality ◽  
Gossypium Hirsutum L

scholarly journals Mixed Linear Model Approaches of Association Mapping for Complex Traits Based on Omics Variants

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Fu-Tao Zhang ◽  
Zhi-Hong Zhu ◽  
Xiao-Ran Tong ◽  
Zhi-Xiang Zhu ◽  
Ting Qi ◽  
...  
Keyword(s):  
Association Mapping ◽  
Linear Model ◽  
Complex Traits ◽  
Mixed Linear Model

Association mapping for seed cotton yield, yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

2017 ◽  
Vol 136 (6) ◽  
pp. 958-968 ◽  
Author(s):  
Suresh S. Handi ◽  
Ishwarappa S. Katageri ◽  
Sateesh Adiger ◽  
Mangesh P. Jadhav ◽  
Sivarama P. Lekkala ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Association Mapping ◽  
Yield Components ◽  
Upland Cotton ◽  
Quality Traits ◽  
Fibre Quality ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Gossypium Hirsutum L ◽  
Seed Cotton Yield

Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection

2016 ◽  
Vol 15 (6) ◽  
pp. 515-526 ◽  
Author(s):  
Sofía E. Olmos ◽  
Verónica V. Lia ◽  
Guillermo H. Eyhérabide
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Association Mapping ◽  
High Ratio ◽  
Joint Analysis ◽  
Phenotypic Variance ◽  
Entire Collection ◽  
Ssr Loci ◽  
Core Sets

AbstractKnowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.

scholarly journals Population genetic structure and association mapping for iron toxicity tolerance in rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0246232
Author(s):  
S. Pawar ◽  
E. Pandit ◽  
I. C. Mohanty ◽  
D. Saha ◽  
S. K. Pradhan
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Association Mapping ◽  
Stress Tolerance ◽  
Linear Model ◽  
Generalized Linear Model ◽  
Mixed Linear Model ◽  
Iron Toxicity ◽  
Rice Grain ◽  
Fe Toxicity

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

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