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Background  Rice is one of the most important crops for global food security but its productivity is adversely affected by salt stress prevalent in about 30 % of the cultivated land. For developing salt-tolerant rice varieties through conventional breeding or biotechnological interventions, there is an urgent need to identify natural allelic variants that may confer salt tolerance. Here, 299 wild rice accessions collected from different agro-climatic regions of India were evaluated during growth under salt stress. Of these 95 representative accessions were sequenced for members of  HKT  ion transporter family genes by employing Ion Torrent PGM sequencing platform.    Results  Haplotype analysis revealed haplotypes H5 and H1 of  HKT1 ; 5  and  HKT2 ; 3 , respectively associated with high salinity tolerance. This is the first study of allele mining of eight members of  HKT  gene family from Indian wild rice reporting a salt tolerant allele of HKT2;3. HKT1;5 also showed a salt tolerant allele from wild rice. Phylogenetic analysis based on the nucleotide sequences showed different grouping of the  HKT  family genes as compared to the prevailing protein sequence based classification.    Conclusions  The salt tolerant alleles of the HKT genes from wild rice may be introgressed into modern high yielding cultivars to widen the existing gene pool and enhance rice production in the salt affected areas.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0083-8) contains supplementary material, which is available to authorized users.

Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm