Novel InDel variation in GS3 locus and development of InDel based marker for marker assisted breeding of short grain aromatic rices

Abstract

A single nucleotide C/A polymorphism in the exon-2 of GS3 (Grain Size 3) locus is associated with long grain in rice. We sequenced the GS3 gene from Sonasal, a short grain aromatic landrace and Pusa Basmati 1121 (PB1121), an extra long slender grain variety with grain length of 5.60 mm and 12.05 mm, respectively. Sequence comparison revealed four SNPs and three InDels involving promoter, exon-2, intron-1, intron-4 and 3′ UTR regions of the gene. Genomic rearrangements including an insertion of 22 bp and a deletion of 342 bp in exon-5 and 3′ UTR, respectively were identified in Sonasal in comparison to the sequence from GS3 reference genotype and PB1121. The InDel affected the tumour necrosis factor receptor domain and a von Willebrand factor type C domain of GS3 protein. However, protein modelling showed formation of stable structures in both Sonasal and PB1121. An InDel marker, aksGS3-12 involving 342 bp deletion specific to Sonasal was developed and validated in a set of diverse rice germplasm varying for grain length. The deletion was present predominantly in the landraces, while it was absent in long grain genotypes and also in the accessions of O. rufipogon and O. nivara, the immediate progenitors of cultivated rice. Hence, the deletion associated with the short grain length might have occurred during the course of domestication of short grain aromatic rice varieties from the progenitor species. The gene based InDel marker, aksGS3-12 can help in marker assisted breeding of short grain aromatic rice varieties.