High‐resolution bulked segregant analysis enables candidate gene identification for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.).

SUMMARY: Bacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole‐genome deep sequencing of pools of the most resistant and most susceptible individuals of a large (n = 7484) biparental F2 population segregating for resistance to Xtg. Using chromosome‐level genome assemblies as references, we were able to define a ~300 kb region highly associated with resistance on pseudo‐chromosome 4. Further investigation of this region revealed multiple genes with a known role in disease resistance, including genes encoding for Pik2‐like disease resistance proteins, cysteine‐rich kinases, and RGA4‐ and RGA5‐like disease resistance proteins. Investigation of allele frequencies in the pools and comparative genome analysis in the grandparents of the F2 population revealed that some of these genes contain variants with allele frequencies that correspond to the expected heterozygosity in the resistant grandparent. This study emphasizes the efficacy of combining BSA studies in very large populations with whole genome deep sequencing and high‐quality genome assemblies to pinpoint regions associated with a binary trait of interest and accurately define a small set of candidate genes. Furthermore, markers identified in this region hold significant potential for marker‐assisted breeding strategies to breed resistance to Xtg in Italian ryegrass cultivars more efficiently. Significance Statement: Elucidating the genetic control of phenotypic traits in highly heterozygous, outbreeding plant species is laborious as it requires phenotyping and genotyping of a large number of individuals. Using 7484 individuals of an Italian ryegrass population, bulked segregant analysis, and whole genome deep sequencing of pools, we identified a 300 kb genomic region harboring promising candidate genes for resistance to bacterial wilt, an important target trait in forage grass breeding. [ABSTRACT FROM AUTHOR]