Identification and Fine-Mapping of Xa33, a Novel Gene for Resistance to Xanthomonas oryzae pv. oryzae

Abstract

Broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding programs across the world. An accession of Oryza nivara, International Rice Germplasm Collection (IRGC) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to Xanthomonas oryzae pv. oryzae. In order to study the genetics of resistance and to tag and map the resistance gene or genes present in IRGC 105710, it was crossed with the bacterial blight (BB)-susceptible varieties 'TN1' and 'Samba Mahsuri' (SM) and then backcrossed to generate backcross mapping populations. Analysis of these populations and their progeny testing revealed that a single dominant gene controls resistance in IRGC 105710. The BC(1)F(2) population derived from the cross IRGC 105710/TN1//TN1 was screened with a set of 72 polymorphic simple-sequence repeat (SSR) markers distributed across the rice genome and the resistance gene was coarse mapped on chromosome 7 between the SSR markers RM5711 and RM6728 at a genetic distance of 17.0 and 19.3 centimorgans (cM), respectively. After analysis involving 49 SSR markers located between the genomic interval spanned by RM5711 and RM6728, and BC(2)F(2) population consisting of 2,011 individuals derived from the cross IRGC 105710/TN1//TN1, the gene was fine mapped between two SSR markers (RMWR7.1 and RMWR7.6) located at a genetic distance of 0.9 and 1.2 cM, respectively, from the gene and flanking it. The linkage distances were validated in a BC(1)F(2) mapping population derived from the cross IRGC 105710/SM//2 × SM. The BB resistance gene present in the O. nivara accession was identified to be novel based on its unique map location on chromosome 7 and wider spectrum of BB resistance; this gene has been named Xa33. The genomic region between the two closely flanking SSR markers was in silico analyzed for putatively expressed candidate genes. In total, eight genes were identified in the region and a putative gene encoding serinethreonine kinase appears to be a candidate for the Xa33 gene.

Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.)

“…Among the biotic stresses, blast and BB are the most devastating diseases that lead to severe yield and economic losses (Ou 1985;Mew et al 1993;Lin et al 2007;Kumar et al 2012). Enhancement of host plant resistance by means of incorporating resistance genes is the best strategy to control biotic stresses.…”

“…BB disease caused by Xanthomonas oryzae pv. oryzae (Xoo) limits rice production up to 81 % (Kumar et al 2012). Thirty-eight different resistance genes have been identified to combat this serious disease of rice (Suh et al 2013).…”

Exploring Key Blast and Bacterial Blight Resistance Genes in Genetically Diverse Rice Accessions through Molecular and Phenotypic Evaluation

“…However, in the recent past, the rate of increase in rice production (~1.0% yr −1 ) has been lower than the population growth rate (1.5% yr −1 ). oryzae (Xoo), and it limits rice production up to 81% annually (Kumar et al, 2012). Among the biotic stresses, blast and bacterial blight (BB) are the major diseases that severely affect rice production.…”

Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.)

“…Enhancing genetic resistance of rice has proven to be the most effective method of controlling BLB disease (Khan et al 2014a). To date, at least 38 BLB resistance genes (R genes) (both dominant and recessive) have been identified (Bhasin et al 2012;Kumar et al 2012) and designated in a series from Xa1 to Xa38 (given the prefix Xa for Xanthomonas) (Khan et al 2014a). There are various DNA markers that have been already developed for many Xa genes.…”