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PubMed | Genetic Resources and Seed Unit, West Virginia State University and Seoul National University
Type: | Journal: Frontiers in plant science | Year: 2016

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for

Rao E.S.,Indian Institute of Horticultural Research | Rao E.S.,Genetic Resources and Seed Unit | Kadirvel P.,ICAR Indian Institute of Oilseeds Research | Kadirvel P.,Genetic Resources and Seed Unit | And 6 more authors.
PLoS ONE | Year: 2015

Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0%to 25.8%phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A-297-6 and SpDREB1A-297-12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten markerassisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato. © 2015 Rao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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