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

Sethi K., Siwach P., Verma S.K. (2017): Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations. Czech J. Genet. Plant Breed., 53: 159−167. Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibriumbased 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 r2 ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r2 ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9–10 cM, with r2 ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model.

• Publication year

  2017

• Venue

  Czech Journal of Genetics and Plant Breeding

• Publication date

  2017-11-10

• Fields of study

  Agricultural and Food Sciences, Biology

• Identifiers
  DOI 10.17221/142/2016-CJGPB
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Additional file 10: Table S6. of Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China

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  2014influential reference
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  2013influential reference
• A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome

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  2009cited by this paper
• Documentation for structure software : Version 2 . 3

  2009cited by this paper
• QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium.

  2008cited by this paper
• Association analysis of fibre traits in Gossypium arboreum accessions

  2008cited by this paper
• Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

  2008influential reference
• CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

  2007cited by this paper
• TASSEL: software for association mapping of complex traits in diverse samples

  2007cited by this paper
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• A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

  2006cited by this paper
• Detecting the number of clusters of individuals using the software structure: a simulation study

  2005cited by this paper
• Logistic regression protects against population structure in genetic association studies.

  2005cited by this paper
• Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population

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• To clone or not to clone plant QTLs: present and future challenges.

  2005cited by this paper
• Use of SSR Marker Data to Study Linkage Disequilibrium and Population Structure in Hordeum vulgare: Prospects for Association Mapping in Barley

  2004cited by this paper
• distruct: a program for the graphical display of population structure

  2003influential reference
• Dwarf8 polymorphisms associate with variation in flowering time

  2001influential reference
• Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP

  2001cited by this paper
• Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds.

  2001cited by this paper
• Association mapping in structured populations.

  2000influential reference
• Genetic Data Analysis II.

  1997influential reference
• Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.

  1984cited by this paper

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