Identification, validation and candidate gene analysis of major QTL for Supernumerary Spikelets in wheat

Abstract The number of spikelets per spike is a key trait that affects The number of spikelets per spike is a key trait that affects grain yield in bread wheat ( Triticum aestivum L.) In this study, four recombinant inbred lines (RILs) populations were generated and used, having YuPi branching wheat (YP), with Supernumerary Spikelets (SS) phenotype, as a common parent. QTL ( QSS.sicau-2A and QSS.sicau-2D ) related to SS trait were mapped on chromosomes 2A and 2D (Chr.2A and Chr.2D) through bulked segregant exome sequencing (BSE-Seq) analysis. 14 molecular markers were further developed within the localization interval, QSS.sicau-2A was narrowed to 7.3 cM covering 11.3 Mb physical region of the reference genome, explained 6.3%~15.6% the phenotypic variance, and QSS.sicau-2D was narrowed to 0.9 cM covering 6.9 Mb physical region of the reference genome, explained 23.4%~34.8% the phenotypic variance, respectively. These two QTL were validated in three different genetic backgrounds by the linked markers. QSS.sicau-2A was identified as WFZP-A , and QSS.sicau-2D was a novel locus that was different from WFZP-D . TraesCS2D03G0260700 was predicted to be a potential candidate gene for QSS.sicau-2D based on the gene expression patterns, gene annotation and sequence analysis. Overall, This study will be useful for cloning QSS.sicau-2D in wheat.