Abstract
SummaryQuantitative trait loci (QTL) that confer broad‐spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub‐Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar‐specific QTL. The most promising BSR QTL (qXO‐2‐1, qXO‐4‐1 and qXO‐11‐2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes.
Highlights
Disease resistance in rice (Oryza sativa L.) is classified into two main categories, qualitative and quantitative
multiparent advanced generation intercross (MAGIC) indica population reveals sources of resistance to Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and Xanthomonas oryzae pv. oryzae (Xoo) strains Two subsets of the MAGIC population were chosen at early and advanced selfed generations, consisting of 200 and 340 advanced intercross lines (AILs), respectively. Both subsets were used to map quantitative trait loci (QTL)/genes associated with resistance and susceptibility, and to evaluate the suitability of MAGIC populations for the discovery of disease resistance-associated regions
The MAGIC S4 subset was screened with two Xoc and two Xoo African strains (Table S2)
Summary
Disease resistance in rice (Oryza sativa L.) is classified into two main categories, qualitative and quantitative. Qualitative resistance is controlled by a single resistance (R) gene and is usually effective against only certain strains of a pathogen species. As it imposes a greater selection pressure on pathogen evolution, this type of resistance can be more readily overcome. Quantitative resistance is conferred by quantitative trait loci (QTL), encompassing multiple genes, and is frequently associated with partial but durable resistance to an entire pathogen species or even different pathogen genera (Boyd et al, 2013; Wisser et al, 2005). Benefits of MAGIC populations to QTL mapping are increased recombination, transgressive segregation events revealing novel phenotypes and capacity for fine mapping, which expedite the discovery of new resistance sources against pathogens (Bandillo et al, 2013; Raghavan et al, 2017)
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