Fine mapping and validation of a stable QTL for thousand-kernel weight in wheat (Triticum aestivum L.)

Thousand-kernel weight (TKW) is a measure of grain weight, a target of wheat breeding. The object of this study was to fine-map a stable quantitative trait loci (QTL) for TKW and identify its candidate gene in a recombinant inbred line (RIL) population derived from the cross of Kenong 9204 (KN9204) and Jing 411 (J411). On a high-density genetic linkage map, 24, 26 and 25 QTL were associated with TKW, kernel length (KL), and kernel width (KW), respectively. A major and stable QTL, QTkw-2D, was mapped to an 8.3 cM interval on chromosome arm 2DL. By saturation of polymorphic markers in its target region, QTkw-2D was confined to a 9.13 Mb physical interval using a secondary mapping population derived from a residually heterozygous line (F_6:7). This interval was further narrowed to 2.52 Mb using QTkw-2D near-isogenic lines (NILs). NILs^KN9204 had higher fresh and dry weights than NILs^J411 at various grain-filling stages. The TKW and KW of NILs^KN9204 were much higher than those of NILs^J411 in field trials. By comparison of both DNA sequence and expression between KN9204 and J411, TraesCS2D02G460300.1 (TraesKN2D01HG49350) was assigned as a candidate gene for QTkw-2D. This was confirmed by RNA sequencing (RNA-seq) of QTkw-2D NILs. These results provide the basis of map-based cloning of QTkw-2D, and DNA markers linked to the candidate gene may be used in marker-assisted selection.