title: Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium).
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.
authors.affiliation: 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.
authors.forename: Eguru Sreenivasa
authors.initials: ES
authors.lastname: Rao
authors.affiliation: 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.
authors.forename: Palchamy
authors.initials: P
authors.lastname: Kadirvel
authors.affiliation: 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.
authors.forename: Rachael C
authors.initials: RC
authors.lastname: Symonds
authors.affiliation: 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.
authors.forename: Subramaniam
authors.initials: S
authors.lastname: Geethanjali
authors.affiliation: Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India.
authors.forename: Ramadihalli N
authors.initials: RN
authors.lastname: Thontadarya
authors.affiliation: Genetic Resources and Seed Unit, AVRDC-The World Vegetable Center, Shanhua, Tainan, Taiwan.
authors.forename: Andreas W
authors.initials: AW
authors.lastname: Ebert
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001483:Base Sequence; D017343:Genes, Plant; D056726:Genetic Association Studies; D005819:Genetic Markers; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D055049:Salt Tolerance; D017386:Sequence Homology, Amino Acid; D032322:Solanum / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D025262:Vacuolar Proton-Translocating ATPases / Q000235:genetics* / Q000378:metabolism
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins; D014157:Transcription Factors; D025262:Vacuolar Proton-Translocating ATPases