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

Abstract

Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1–6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.

Superior haplotypes towards the development of blast and bacterial blight-resistant rice

“…Scores 0–2 were considered resistant (R), 3 as moderately resistant (MR), and 4-5 as susceptible (S). # Average lesion length <5 cm is resistant, >5-10 cm is moderately resistant, >10-15 cm is moderately susceptible, and >15 cm susceptible ( Korinsak et al., 2021 ); Chr, Chromosome. Different alphabet of small letters denoted in superscript is defined as significantly different groups which authors have got from duncan's test to perform haplo-pheno test.…”

“…The mean of two fully expanded leaf from three replicate plants for each accession were taken for determining the reaction type. A plant was classified as resistant if the average lesion length was shorter than 5 cm, moderately resistant if the lesion was >5-10 cm, moderately susceptible if the lesion was >10-15 cm, and susceptible if the lesion was >15 cm ( Korinsak et al., 2021 )…”

Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

“…Our results showed that the LD levelness was the highest at r 2 = 0.24, gradually beginning to decrease at r 2 = 0.12 when the physical distance increased to 7 kb, and low ( r 2 = 0.035) when the physical distance increased to 50 kb. The result was lower than self-pollination plants Prunus avium [ 44 ] and rice [ 20 ]. This may be due to the self-incompatibility of tea plants [ 45 ].…”

Recent Progress in Rice Broad-Spectrum Disease Resistance

“…A GWAS analysis of 236 diverse rice accessions revealed 12 QTLs, of which two QTLs showed broad-spectrum resistance to Xoc [ 91 ]. Recently, 147 SNP associated with Xoo resistance were identified in 222 predominantly Thai rice accessions; however, the significantly associated SNP only occurred across a maximum of five Xoo isolates [ 92 ]. In rice, most resistance QTLs are conditioned to different populations and different QTL mapping analyses, which makes it difficult to handpick suitable QTL candidates for breeding programs with multiple resistances.…”