Predicted protein sequence alignment for alleles corresponding to 297 bp position in DREB1A gene identified in a panel of 94 accessions of <i>S</i>. <i>pimpinellifolium</i> along with a reference sequence of DREB1A in <i>S</i>. <i>lycopersicum</i> (AF 500011.1).

<p>The amino acid sequence variation corresponding to 297 bp is highlighted.</p

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

<div><p>Association analysis was conducted in a core collection of 94 genotypes of <i>Solanum pimpinellifolium</i> 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., <i>SpDREB1A_297_6</i> and <i>SpDREB1A_297_12</i>. 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 <i>S</i>. <i>pimpinellifolium</i> into cultivated tomato.</p></div

Distribution of survival score ratings among 94 accessions of <i>S</i>. <i>pimpinellifolium</i> under salt stress along with <i>S</i>. <i>lycopersicum</i> checks ‘CA4’ and ‘Arka Meghali’.

<p>Distribution of survival score ratings among 94 accessions of <i>S</i>. <i>pimpinellifolium</i> under salt stress along with <i>S</i>. <i>lycopersicum</i> checks ‘CA4’ and ‘Arka Meghali’.</p

LD analysis of the four candidate genes DREB1A, VP1.1, NHX1, and TIP for salt tolerance.

<p>LD analysis of the four candidate genes DREB1A, VP1.1, NHX1, and TIP for salt tolerance.</p

Trait correlation (R²) with population structure (Q) under control conditions, salt stress and percent reduction due to stress.

<p>** significant at P = 0.01</p><p>Trait correlation (R²) with population structure (Q) under control conditions, salt stress and percent reduction due to stress.</p

Summary of parameters of nucleotide variability in the four candidate genes DREB1A, VP1.1, NHX1, and TIP for salt tolerance.

<p>*MAF: Minimum Allele Frequency</p><p>Summary of parameters of nucleotide variability in the four candidate genes DREB1A, VP1.1, NHX1, and TIP for salt tolerance.</p