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Whole Genome Sequencing and Analysis of Godawee, a Salt Tolerant Indica Rice Variety

Sanjeewa Singhabahu, Chathura Wijesinghe, Dilini Gunawardana, Muditha D. Senarath-Yapa, Madushani Kannangara, Roshani Edirisinghe and Vajira H.W. Dissanayake

Godawee is a cultivated salt tolerant Oryza sativa rice variety indigenous to Sri Lanka, but its genetic basis is unknown. The whole genome of Godawee was sequenced using Illumina paired-end technology. The reads were mapped to Oryza sativa Nipponbare reference genome. Investigation of genome wide variation patterns resulted in the identification of 2,231,717 SNPs and 480,460 InDels. In silico analysis identified 192,249 non-synonymous SNPs in 31,287 genes. Variants in 28 Salt Tolerance Related Genes (STRGs) were examined. The OsHKT 2;1 gene had the largest number of SNPs in comparison to the reference genome. 16 non-synonymous SNPs that were predicted to have functional effects either by SIFT, Provean or SNAP algorithms were detected in the STRGs. The upstream regions of the STRGs were examined for cis-regulatory elements found in STIFDB, Plant CARE and PLACE databases. The most striking of this was the WRKY cis-acting family of elements which were found in abundance in the upstream regions of OsAPx8, OsMSR2, OsTIR1, OsHKT2;3, OsHKT14 and OsSOS1 genes. Sequencing and whole genome analysis of Godawee helped to understand the genetic basis of its salinity tolerance which is a complex trait involving multiple factors.