Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium) | Zendy

Eguru Sreenivasa Rao | Zendy; P. Kadirvel | Zendy; Rachael C. Symonds | Zendy; S. Geethanjali | Zendy; Ramadihalli N. Thontadarya | Zendy; Andreas W. Ebert | Zendy

Open Access

Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium)

Author(s) -

Eguru Sreenivasa Rao,

P. Kadirvel,

Rachael C. Symonds,

S. Geethanjali,

Ramadihalli N. Thontadarya,

Andreas W. Ebert

Publication year - 2015

Publication title -

plos one

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.99

H-Index - 332

ISSN - 1932-6203

DOI - 10.1371/journal.pone.0132535

Subject(s) - introgression , biology , genetics , allele , candidate gene , haplotype , indel , quantitative trait locus , phenotypic trait , gene , phenotype , genotype , single nucleotide polymorphism

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 marker-assisted introgression of salt tolerance from S . pimpinellifolium into cultivated tomato.

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