Haplotype diversity analysis of bacterial leaf blight resistance gene Xa21 in rice

Bacterial leaf blight (BLB) caused by Xanthomonasoryzaepv. oryzae (Xoo) is a devastative rice disease. Resistance gene Xa21 is known to convey a stable resistance against a broad spectrum of Xoo races. Assessment of Xa21 genetic diversity and defining haplotypes is the initial step towards identification of haplotypes that associate with desired phenotypes. In this study, an alignment of a 2,778 bp coding sequence (CDS) from 1,618 rice accessions revealed 18 single nucleotide polymorphisms and six insertion/deletions (InDel), each with ≥ 5% occurrence among the accessions. A total of 13 confirmed-haplotypes (≥ 1% occurrence) and 113 putative haplotypes (≤ 1 % occurrence) were identified. The 13 confirmed haplotypes were represented by 1,341 rice accessions that deferred at 22 sites belonging to 12 rice subpopulations from 70 countries. The Xa21 CDS has a haplotype diversity of 0.8203, and a nucleotide diversity of 0.15448. Further, the haplotype network shows a high substitution rate between the haplotype pairs of Xa21, with two distinctive clusters created as a result of a 19-bp InDel in CDS. Based on 14 non-synonymous sites identified within the CDS, nine protein-types were identified. Of these three protein-types are truncated owing to a premature stop codon at 180th position of the polypeptide chain due to the said 19-bp InDel in the ectodomain, and represents 45% of the accessions. The ectodomain of XA21 protein is crucial for immune responses, and hence, these haplotypes with truncated proteins could be important in eliciting the function of XA21.