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

Abstract

Background: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding.

Results: A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes.

Conclusions: The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.

Keywords: Genome-wide association; Oryza sativa; SNPs; Xanthomonas oryzae; bacterial blight (BB); disease resistance; genotyping-by-sequencing (GBS).

Fig. 1

Sub-population resistance of the 285 diverse germplasm to nine representative strains of Xanthomonas oryzae pv. oryzae

Fig. 2

Highly associated SNPs with resistance to Xoo Race 3b (PXO79) and overlapping the xa5 gene. a Manhattan plot based on Efficient Mixed-Model Association eXpedited Model (EMMAX) where x-axis shows the SNPs along each chromosome and y-axis is the − log10 (P-value) for the association. Significant SNPs are those beyond the red line having P-value < 1 × 10⁻⁵. b LD (r²) and haplotype blocks based Expectation Maximization (EM) algorithm. c Significant SNP S5_440644 overlapping the region of LOC_Os05g01710, a transcription initiation factor IIA gamma chain

Fig. 3

Highly associated SNPs with resistance to Xoo Race 4 (PXO71) and flanking Xa4 gene. a Manhattan plot based on Efficient Mixed-Model Association eXpedited Model (EMMAX) where x-axis shows the SNPs along each chromosome and y-axis is the − log₁₀ (P-value) for the association. Significant SNPs are those beyond the red line having P-value < 1 × 10⁻⁵. b LD matrix (r²) and haplotype blocks based on Expectation Maximization (EM) algorithm. c Significant SNPs (S11_27603791 and S11_27603799) overlapping the exon region of LOC_Os11g45620 (rust-resistance protein Lr21), flanking the Xa4 locus

Fig. 4

Haplotype blocks overlapping or flanking Xa genes. Values below the x-axis indicates the CHM probabilities of the haplotypes (a) Haplotype allele frequency of HB1736 overlapping the xa5 gene in terms of average disease reaction to PXO86, PXO79, and PXO99. b Haplotype allele frequency of HB3693 flanking the Xa4 gene in terms of average disease reaction to PXO61, PXO71, PXO112, PXO99, and PXO341