Abstract
BackgroundBacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL).ResultsBB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5–11.1 was validated as positively regulating resistance against strain C5.ConclusionsOur findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.
Highlights
Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions
Most BB resistance genes were detected through bi-parental population (F2 or recombinant inbred line populations) studies except for Xa43(t), which was discovered in a multi-parent advanced generation inter-cross (MAGIC) population through genome-wide association study (GWAS) (Kim and Reinke 2019)
Population Structure of Rice Accessions Based on 527,165 independent single nucleotide polymorphisms (SNPs) with genotype missing rate ≤ 5% and minor allele frequency ≥ 1%, a phylogenetic tree was developed using the neighborjoining method, dividing 340 accessions into four distinct major clusters, namely XI, GJ, cA and cB subgroups (Fig. 1a)
Summary
Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Among the 45 major resistance genes, 11 genes (Xa1, Xa3/Xa26, Xa4, xa, Xa10, xa, Xa21, Xa23, xa, Xa27 and xa41(t)) have been cloned and characterized (https://shigen.nig.ac.jp/rice/oryzabase/) Because of either their lower level of resistance or their narrow spectrum of resistance, only a few genes (such as Xa4, Xa21, Xa23 and Xa39) with broad-spectrum resistance have been widely deployed in breeding programs so far (Hu et al 2017; Song et al 1997; Wang et al 2015; Zhang et al 2015). In order to manage this disease effectively, it is necessary to identify QTL associated with BB resistance using new strategies, and to pyramid multiple genes/ QTL or introduce genes conferring broad-spectrum resistance and so breed durable resistance cultivars through advanced breeding programs
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