Validation and delineation of a locus conferring <i>Fusarium</i> crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines

<div>Background<p><i>Fusarium</i> crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, <i>Qcrs.cpi-1H,</i> had previously been mapped on the long arm of chromosome 1H in barley.</p>Results<p>In this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at <i>Qcrs.cpi-1H</i> significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the <i>Qcrs.cpi-1H</i> locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing single nucleotide polymorphisms (SNPs) were detected in this interval. Five of them contain non-synonymous SNPs<i>.</i> These results would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus.</p>Conclusion<p>NILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus <i>Qcrs.cpi-1H</i> and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.</p></div>