Mining resistance alleles of gene Xa38 for bacterial blight resistance in Sri Lankan rice accessions

Abstract

Bacterial Blight (BB) caused by Xanthomonas oryzae pv. oryzae is one of the devastating rice diseases in Sri Lanka. Currently, 42 genes have been identified as important for conveying BB resistance, out of which Xa38 (Os04g53030) is considered as a gene with major importance. For marker-assisted selection of Xa38 resistance allele, a co-dominant linked-marker (Os04g53050-1) designed based on an adjacent gene (Os04g53050), co-segregating with Os04g53030 is recommended. Among Sri Lankan germplasm, the Xa38 resistance allele carrying rice accessions have not been identified to-date. In the current study, a panel of 48 rice accessions was genotyped using the marker Os04g53050-1 and 12 traditional Sri Lankan rice accessions (Batapola el, Dik wee, Halsuduwee, Herath banda, Sudu goda wee, Kuru wee, Suwadel, Katteyaran, Mada el, Pachchaperumal, Gonabaru and Mahakuru wee) and 21 newly improved Sri Lankan varieties were identified as resistance allele carriers for Xa38. These accessions can be used as Xa38-mediated resistance donors in future rice breeding programs. Further, the present study focused on the development of an intragenic marker for the Xa38 gene as an alternative to the currently used linked-marker. Haplotypes were defined to identify a potential site for designing an intragenic molecular marker. Haplotyping was carried out using the coding sequence of Os04g53030 from 2,395 rice accessions sequenced in the 3K Rice Genomes Project. Based on the multiple sequence alignment, haplotype- defining polymorphisms with ≥5% occurrence in the panel of accessions (64 single nucleotide polymorphisms and 13 insertion/deletion sites) were identified and was used to define 20 confirmed haplotypes (H1 to H20; ≥1% occurrence frequency in the panel of accessions). Further investigation is underway to develop an intragenic molecular marker based on the identified polymorphic target sites.