QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome

Wei Wei; Shuangdong Li; Peiyu Li; Kuohai Yu; Guangyu Fan; Yixiang Wang; Fang Zhao; Xiaolei Zhang; Xiaolei Feng; Gaolei Shi; Weiqin Zhang; Guoliang Song; Wenhan Dan; Feng Wang; Yali Zhang; Xinru Li; Dequan Wang; Wenying Zhang; Jingjing Pei; Xiaoming Wang; Zhihai Zhao

doi:10.3389/fpls.2022.1035906

QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome

Front Plant Sci. 2023 Jan 10:13:1035906. doi: 10.3389/fpls.2022.1035906. eCollection 2022.

Authors

Wei Wei¹, Shuangdong Li¹, Peiyu Li², Kuohai Yu², Guangyu Fan¹, Yixiang Wang², Fang Zhao¹, Xiaolei Zhang¹, Xiaolei Feng¹, Gaolei Shi¹, Weiqin Zhang², Guoliang Song¹, Wenhan Dan², Feng Wang¹, Yali Zhang¹, Xinru Li¹, Dequan Wang¹, Wenying Zhang¹, Jingjing Pei¹, Xiaoming Wang¹, Zhihai Zhao¹

Affiliations

¹ Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China.
² Wuhan Metware Biotechnology Co., Ltd., Wuhan, China.

Abstract

As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.

Keywords: RIL population; foxtail millet; metabolic QTL; phenotypic QTL; widely targeted metabolomics.

Grants and funding

This research was supported by the following funding sources: the key research and development plan “Technology Innovation Team of Hybrid and High Quality Millet Modern Seed Industry” of Hebei Province (21326302d); Science and technology research and development plan “hybrid millet industry chain innovation” of Hebei Province (16226310d); National millet Sorghum Industry Technology System heterosis utilization post (cars-06-14.5-a5); Hebei Province miscellaneous grain and soybean industry technology system high quality spring valley post.