Fine mapping and characterization of a major QTL QGl.cau-2D.1 for grain length with pleiotropic effects in synthetic allohexaploid wheat

Grain size is one of the determinants of grain yield, and identification of the genetic loci controlling grain size will be helpful to increase grain yield. In our previous study, a quantitative trait locus (QTL) for grain length (GL), QGl.cau-2D.1, was identified from a F2 population developed from the cross between the natural (TAA10) and resynthetic (XX329) allohexaploid wheat. In the present study, we mainly aimed to fine map and validate its genetic effects. To this end, multiple near-isogenic lines (NILs) were obtained through marker-assisted selection with TAA10 as the recurrent parent. The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1, and the allele from XX329 significantly increased GL, thousand grain weight (TGW), total spikelet number per spike (TSN) and spike compactness (SC). Using NILs for XX329 (2D+) and TAA10 (2D−), we determined the genetic and pleiotropic effects of QGl.cau-2D.1. The target sequences were employed to align the wheat reference genome RefSeq v2.1 and hit an ~0.9 Mb genomic region. TraesCS2D03G0114900 (ortholog of Os03g0594700) was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses. In summary, the map-based cloning of QGl.cau-2D.1 will be beneficial to improve grain weight with enhanced GL and TSN.