Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach.

BMC Plant Biology
Corina M FusariNorma B Paniego

Abstract

Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred mate...Continue Reading

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Citations

Sep 17, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Peter WestermeierVolker Mohler
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Dec 21, 2017·PloS One·Jeremías Enrique ZubrzyckiNorma Beatriz Paniego
Jul 10, 2020·BMC Plant Biology·C V FilippiV V Lia

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Methods Mentioned

BETA
PCR
environmental stresses
electrophoresis

Software Mentioned

DnaSP
Primer3
BLASTx
SNP Discovery
Origin
SeqScape
ABI Prism SeqScape
STRUCTURE

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