Pyramiding of two rice bacterial blight resistance genes, Xa3 and Xa4, and a closely linked cold-tolerance QTL on chromosome 11

Abstract

We fine mapped the Xa4 locus and developed a pyramided rice line containing Xa3 and Xa4 R - alleles and a cold-tolerance QTL. This line will be valuable in rice breeding. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of cultivated rice. Pyramiding BB resistance genes is an essential approach for increasing the resistance level of rice varieties. We selected an advanced backcross recombinant inbred line 132 (ABL132) from the BC3F7 population derived from a cross between cultivars Junam and IR72 by K3a inoculation and constructed the mapping population (BC4F6) to locate the Xa4 locus. The Xa4 locus was found to be delimited within a 60-kb interval between InDel markers InDel1 and InDel2 and tightly linked with the Xa3 gene on chromosome 11. After cold (4 °C) treatment, ABL132 with introgressions of IR72 in chromosome 11 showed lower survival rate, chlorophyll content, and relative water content compared to Junam. Genetic analysis showed that the cold stress-related quantitative trait locus (QTL) qCT11 was located in a 1.3-Mb interval close to the Xa4 locus. One line, ABL132-36, containing the Xa3 resistance allele from Junam, the Xa4 resistance allele from IR72, and the cold-tolerance QTL from Junam (qCT11), was developed from a BC4F6 population of 250 plants. This is the first report on the pyramiding of Xa3 and Xa4 genes with a cold-tolerance QTL. This region could provide a potential tool for improving resistance against BB and low-temperature stress in rice-breeding programs.

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm

“…Among them, S11_27603799 accounted for 29% of phenotypic variance and was a cofactor for resistance to PXO61, PXO71, PXO112 and PXO341 based on MLMM ( p -value of 4.66 −25 ). The three most downstream SNPs (S11_27672709, S11_27677853 and S11_27831021) overlapped with the recently fine-mapped Xa4 region containing NBS-LRR and WRKY gene family members (Hur et al 2016). The resistance reactions associated with these SNPs including 2 additional upstream SNPs (S11_27007623 and S11_27007628) agreed with earlier reports for Xa4 (Nino-Liu et al 2006).…”

“…3). However, Hur et al (2016) recently fine mapped Xa4 to a 60 kb region suggesting LOC_Os11g45930, a NBS–LRR-type disease-resistance protein or LOC_Os11g45930, a hypothetical protein as candidates, which lie between SNPs S11_27677853 and S11_27831021, the most downstream of a cluster of 8 significant SNPs overlapping with Xa4. Seven significant SNPs were flanking the region of Xa7 described by Zhang et al (2009a).…”

A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population

“…The locus narrowed down by fine mapping was located nearby a region known to harbor three BB R-genes, Xa3 , Xa4 and Xa40 . However the positions covering R -genes were not physically identical each other [19,35,36]. In addition, Xa3 has a susceptible reaction to K3a (data not shown) and Xa43 also has a different haplotype to Xa40 and Xa4 based on testing with a primer specific to Xa43 (S3 Fig).…”

Identification of Bacterial Blight Resistance Loci in Rice (Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study

“…Rice accessions carrying the closely linked Xa4 [ 60 ] and Xa3/Xa26 genes on chromosome 11 exhibit broad resistance to numerous Xoo strains (NB these are also close to the more strain specific gene, Xa43 ). We did not find significant SNPs present within these gene regions although we identified significant SNPs within calculated linkage disequilibrium distance including within a nearby stress response gene (LOC_Os11g45620; Figure 6 ).…”