Genetic Mapping of a Bacterial Blight Resistance Gene <I>Xa14</I> in Rice

Abstract

Bacterial blight of rice, which is a vascular bundle disease caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases of rice worldwide, and leads to the yield of rice reduced greatly. The dominant gene Xa14 is highly resistant to Philippine race 5 of bacterial blight. The gene was located at the distal end on the long arm of chromosome 4 by Taura et al. Near-isogenic line in the background of IR24, namely IRBB14 carrying the gene Xa14 has been developed at International Rice Research Institute (IRRI). In order to construct the high-resolution likage maps for the Xa14 region on chromosome 4 for finally clone by positional cloning, two F 2 populations were used to estimate linkage based on marker genotype and reaction to disease inoculation with Xanthomonas oryzae pv. oryzae. Using 145 highly susceptible individuals from a total of 775 plants of F 2 population of the cross between IRBB14 and IR24, the gene Xa14 was located in a 0.68 cM region on the nearby end of chromosome 4, which was flanked by the molecular markers HZR970-8 and HZR988-1, with the distance of 0.34 cM between the flanked markers and Xa14, respectively, and completely cosegregated with the SSR markers HZR645-4, HZR669-2, HZR669-5, and HZR669-7 in this population. Using 158 highly susceptible individuals from a total of 763 plants of F 2 population of the cross between IRBB14 and ZZA, the gene Xa14 locus was mapped to the interval between HZR648-5 and RM280, and was 1.90 cM away from HZR648-5 which was the closest marker flanking the Xa14 locus. Combining recombination frequencies for the two populations together, the gene Xa14 was mapped to 3 BAC clones spanned approximately 300 kb in length between SSR markers HZR970-8 and HZR988-1.

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

“…Known genes and loci ( Xa ) conferring resistance to specific Xoo races (Table 1 ) were overlaid with the Manhattan plots (Additional file 3 : Figure S2 and Additional file 4 : Figure S3). Among the known Xa loci, the regions of Xa4, xa5, Xa7, xa13, Xa14 , Xa21, and xa25 (Wang et al 2001 ; Blair et al 2003 ; Chen et al 2008 ; Chu et al 2006a , b ; Bao et al 2010 ; Song et al 1995 ; Chen et al 2002 ) were identified as overlapping with significant SNPs in this study (Additional file 3 : Figure S2, Additional file 4 : Figure S3 and Additional file 5 : Table S2).…”

“…Significant SNP loci exclusively associated with resistance to PXO112 in the indica panel (Additional file 5 : Table S2) clustered in the flanking region of Xa14 (Bao et al 2010 ) that ranges from 30,063,575 bp-32,807,203 bp in the long arm of chromosome 4 (Additional file 4 : Figure S3e). On the other hand, SNP loci located in the short arm of chromosome 5 namely, S5_440644 and S5_453169 were highly associated with resistance to all seven strains of Xoo (Additional file 3 : Figure S2, Additional file 4 : Figure S3 and Additional file 5 : Table S2).…”

“…Bao et al ( 2010 ) have mapped the Xa14 locus between two SSRs having a 300 kb interval. SNPs flanking this mapped region were linked to ATBAG1 (LOC_Os04g52890), OsFBW1-F-box family protein/WD-40 repeat family protein (LOC_Os04g52870) and an ABC transporter (LOC_Os04g52900).…”

Xa1 Allelic R Genes Activate Rice Blight Resistance Suppressed by Interfering TAL Effectors

“…Previous studies have mapped Xa2 in IRBB2 ( He et al., 2006 ) , Xa14 in IRBB14 ( Bao et al., 2010 ) , Xa31(t) in Zhachanglong (ZCL) ( Wang et al., 2009 ), and Xo1 in CGS ( Triplett et al., 2016 ) within the regions corresponding to the Xa1 locus in IRBB1. We asked whether these loci, in which all four respective R genes have not yet been cloned, could confer disease responses similar or different from that of Xa1 , i.e., susceptible to PXO99 A and resistant to its mutant strain ΔTal3.…”

“…The cloning of a gene usually involves mapping of the gene and functional complementation of the lines otherwise lacking the gene or the functional allele. For Xa2 , Xa31(t) , and Xa14 , all three R genes were mapped in their respective donors within the regions, wherein Xa1 in IRBB1 was cloned ( He et al., 2006 ; Wang et al., 2009 ; Bao et al., 2010 ). The transgenic Kitaake plants containing putative Xa2 , Xa31(t) , and Xa14 genomic clones were resistant to Xoo strains lacking iTALEs and were susceptible to Xoo strains carrying iTALE genes.…”