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

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10540-7

BMC Genomics,volume25, Article number:675(2024)

Zhiqiang Wang,Haojie Li,Xinjian Zhou,Yuzhou Mou,Ying Zhang,Lang Yu,Xudong Chen,Fangkun Wu,Hong Zhou,Yu Lin,Caixia Li&Yaxi Liu

Abstart

Background

The number of spikelets per spike is a key trait that affects the yield of bread wheat (Triticum aestivumL.). Identification of the QTL for spikelets per spike and its genetic effects that could be used in molecular assistant breeding in the future.

Results

In this study, four recombinant inbred line (RIL) populations were generated and used, having YuPi branching wheat (YP), with Supernumerary Spikelets (SS) phenotype, as a common parent. QTL (QSS.sicau-2 AandQSS.sicau-2D) related to SS trait were mapped on chromosomes 2 A and 2D through bulked segregant exome sequencing (BSE-Seq). Fourteen molecular markers were further developed within the localization interval, andQSS.sicau-2 Awas narrowed to 3.0 cM covering 7.6 Mb physical region of the reference genome, explaining 13.7 − 15.9% the phenotypic variance. Similarly, theQSS.sicau-2Dwas narrowed to 1.8 cM covering 2.4 Mb physical region of the reference genome, and it explained 27.4 − 32.9% the phenotypic variance. These two QTL were validated in three different genetic backgrounds using the linked markers.QSS.sicau-2 Awas identified asWFZP-A, andQSS.sicau-2Dwas identified a novel locus, different to the previously identifiedWFZP-D. Based on the gene expression patterns, gene annotation and sequence analysis,TraesCS2D03G0260700was predicted to be a potential candidate gene forQSS.sicau-2D.

Conclusion

Two significant QTL for SS, namelyQSS.sicau-2 AandQSS.sicau-2Dwere identified in multiple environments were identified and their effect in diverse genetic populations was assessed.QSS.sicau-2Dis a novel QTL associated with the SS trait, withTraesCS2D03G0260700predicted as its candidate gene.