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

Rao ES 1 , Kadirvel P 2 , Symonds RC 3 , Geethanjali S 4 , Thontadarya RN 5 , Ebert AW 6

Affiliations 

  • 1 Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India; Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan
  • 2 Crop Improvement Section, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, India; Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan
  • 3 School of Biosciences, The University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor, Darul Ehsan, Malaysia; Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan
  • 4 Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India; Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan
  • 5 Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
  • 6 Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan
PLoS One, 2015;10(7):e0132535.
PMID: 26161546 DOI: 10.1371/journal.pone.0132535

Abstract

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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