Construction of a Genetic Linkage Map and QTL Mapping of the Agronomic Traits in Foxtail Millet (Setaria Italica)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2025 Feb 18

PMID 39962405

Authors

Lulu Gao

Qianxue Zhu

Huan Li

Shiyuan Wang

Jiahui Fan

Tianguo Wang

Lejie Yang

Yuqin Zhao

Yixuan Ma

Lu Chen

Xiaorui Li

Shuqi Dong

Xiaoqian Chu

Xianmin Diao

Xiangyang Yuan

Jiagang Wang

Guanghui Yang

Affiliations

Soon will be listed here.

Abstract

Foxtail millet (Setaria italica) is one of the most ancient cultivated cereal crops and is ideal for the functional genomics of the Panicoideae crops. In the present study, we generated an F population consisting of 300 individuals by crossing an elite foxtail millet variety Jingu28 with a backbone line Ai88, and constructed a genetic linkage map with 213 published SSR markers and two InDel markers. Quantitative trait locus (QTL) mapping identified 46 QTL for 12 agronomic traits, including 13 major effect QTL. Meanwhile, 40 QTL controlling different traits formed 13 co-located QTL clusters. Moreover, one putative candidate gene Seita.9G020100 for qHD9-1 with conserved CCT motif and a gibberellin biosynthesis related GA20 oxidase gene Seita.5G404900 for qPH5-1 were identified based on homologous gene comparison. The 277 bp insertion/deletion on the promoter of Seita.9G020100 and the one-base (G) insertion/deletion in the third exon of Seita.5G404900 might be candidate functional sites. Furthermore, two markers (Ghd7InDel and GA20oxSTARP-1) were developed based on these two variation sites, respectively. These results will help to elucidate the genetic basis of important agronomic traits in foxtail millet and be useful for marker-assisted selection of varieties with ideal plant architecture and high yield potential.

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