Fine-mapping the low number of tillers (lnt2) locus in barley

Tiller number is an essential agronomic characteristic that influences barley morphology and yield. A barley low number of tillers mutant CIHO 11,530 exhibits few tillers and in this study, we conducted a genetic analysis of the barley low number of tillers 2 (lnt2) locus. Linkage analysis showed that lnt2 was mapped in an interval of 3.39 cM on chromosome 6HS between the flanking markers SNP1765 and SNP526, explaining 53.06% of the phenotypic variance. The genetic effect of lnt2 was further verified in two other genetic backgrounds, explaining variances of 86.43% and 91.01% in tiller numbers between lines carrying the lnt2 mutant and wild-type alleles, respectively. Furthermore, we constructed a large F₂ population and fine-mapped lnt2. Finally, lnt2 was mapped within a 0.19 cM genetic interval delimited by the tightly linked KASP markers KASP6359 and KASP365, and the physical interval was located at 40.57-42.35 Mb. In this interval, three genes were highly likely lnt2 based on gene annotations, sequence and gene expression analyses. Our research provides valuable information for the map-based cloning of lnt2.

The online version contains supplementary material available at 10.1007/s11032-025-01589-7.