Fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley by exploiting near isogenic lines, transcriptome profiling and a large near isogenic line-derived population

Abstract

Abstract Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a chronic and serious disease affecting semi-arid regions globally. The increasing prevalence of this disease in recent years is attributed to the widespread adoption of minimum tillage and stubble retention practices. In the study reported here, we generated eight pairs of near isogenic lines (NILs) targeting a putative QTL (Qcrs.caf-6H) conferring FCR resistance in barley. Assessing the NILs confirmed the large effect of this locus. Aimed to develop markers that can be reliably used in incorporating this resistant locus into breeding programs and identify candidate genes, transcriptomic analyses were conducted against three of the NIL pairs and a large NIL-derived population consisting of 1,085 F7 recombinant inbred lines (RILs) was generated. By analysing the transcriptomic data and the fine mapping population, Qcrs.caf-6Hwas delineated into an interval of 0.9 cM covering a physical distance of ~547 kb. Six markers co-segregating with this locus were developed. Based on differential gene expression and SNP variations between the two isolines among the three NIL pairs, candidate genes underlying the resistance at this locus were detected. These results would improve the efficiency of incorporating the targeted locus into barley breeding programs and facilitate the cloning of causal gene(s) responsible for the resistance.