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

Abstract

BackgroundA 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.ResultsA 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0147-4) contains supplementary material, which is available to authorized users.

Dissection of the genetic architecture of rice resistance to Xanthomonas oryzae pv. oryzae using a genomewide association study

“…In addition, in the analysis of the resistance levels of 267 RDP1 to Xoo C1, the AUS subgroup displayed more resistance than other subgroup, which is in line with the results reported by Dillaermita et al. (). The identified diverse rice accessions with strong resistance to Xoo C1 are valuable donors for bacterial blight breeding programs.…”

“…Using traditional QTL mapping, many QTLs involving in BB resistance have been identified in rice. With available high‐resolution DNA markers and updating algorithm for GWAS, researchers tend to use GWAS to map QTLs for BB to overcome the limitations of traditional QTL mapping (Dillaermita et al., ; Zhang et al., ). To investigate the genetic architecture of rice resistance to Xoo , we performed a GWAS to identify qBBRs for resistance to Xoo race C1 in rice.…”

“…Xa25 (Gao et al., ) and xa32(t) (Ruan, Yan, AN, Liu, & Chen,) locate in the Chromosome 12, xa5 (Petpisit, Khush Gurdev, & Kauffman,) locates in the Chromosome 5, xa8 (Singh et al.,) locates in the Chromosome 7, xa13 (Ogawa, Luo, Tabien, & Khush, ) locates in the Chromosome 8. According to the qBBR donor rice subgroup: five loci ( xa5 , Xa7 , xa13 , xa24 and xa34(t) ) were from AUS, ten loci ( Xa2 , Xa4 , Xa11 , Xa14 , Xa16 , Xa18 , xa25 , Xa26 , xa28 and Xa39 ) originated from indica , and nine loci ( Xa21 , Xa23 , Xa27 , Xa29(t) , Xa30(t) , Xa32(t) , Xa35(t) , Xa38 and Xa40(t) ) were derived from wild relatives of rice (Dillaermita et al., ). Based on qBBR, nine major Xa genes have been cloned and characterized, including Xa21 , Xa1 , Xa3/Xa26 , xa5 , Xa27 , xa13 , Xa25 , Xa10 and Xa23 (Liu, Liu, Triplett, Leach, & Wang, ; Wang et al.,).…”

Identification of the blast resistance gene Picl(t) from Chaling common wild rice (Oryza rufipogon Griff.)

“…A series of valuable genes have been identified from wild rice, which are expected to improve agronomic traits of modern rice cultivars, including disease resistance. Except the four rice blast resistance genes isolated from wild rice species, the bacterial blight resistance genes Xa21 , Xa23 , Xa27 , Xa29(t) , Xa30(t) , Xa32(t) , Xa35(t) , Xa38(t) and Xa40(t) are originated from the wild rice species as well (Dilla‐Ermita et al, 2017). Oryza rufipogon Griff., commonly found in marsh or aquatic habitats of eastern and southern Asia, is considered as the ancestor of the Asian cultivated rice, O. sativa L. (Huang, Molina, et al, 2012; Oka, 2012).…”

“…A series of valuable genes have been identified from wild rice, which are expected to improve agronomic traits of modern rice cultivars, including disease resistance. Except the four rice blast resistance genes isolated from wild rice species, the bacterial blight resistance genes Xa21, Xa23, Xa27, Xa29(t), Xa30(t), Xa32(t), Xa35(t), Xa38(t) and Xa40(t) are originated from the wild rice species as well (Dilla-Ermita et al, 2017).…”