Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet
Mengyuan Zhu,
Qiang He,
Mingjie Lyu,
Tiantian Shi,
Qian Gao,
Hui Zhi,
Huan Wang,
Guanqing Jia,
Sha Tang,
Xiliu Cheng,
Rui Wang,
Andi Xu,
Haigang Wang,
Zhijun Qiao,
Jun Liu,
Xianmin Diao,
Ying Gao
Affiliations
Mengyuan Zhu
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Qiang He
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Mingjie Lyu
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300112, China
Tiantian Shi
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Qian Gao
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Hui Zhi
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Huan Wang
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610213, Sichuan, China
Guanqing Jia
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Sha Tang
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Xiliu Cheng
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Rui Wang
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Andi Xu
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
Haigang Wang
Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
Zhijun Qiao
Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
Jun Liu
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Corresponding authors.
Xianmin Diao
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Corresponding authors.
Ying Gao
National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Corresponding authors.
Foxtail millet (Setaria italica) is an important C4 model crop; however, due to its high-density planting and high stature, lodging at the filling stage resulted in a serious reduction in yield and quality. Therefore, it is imperative to identify and deploy the genes controlling foxtail millet plant height. In this study, we used a semi-dwarf line 263A and an elite high-stalk breeding variety, Chuang 29 to construct an F2 population to identify dwarf genes. We performed transcriptome analysis (RNA-seq) using internode tissues sampled at three jointing stages of 263A and Chuang 29, as well as bulk segregant analysis (BSA) on their F2 population. A total of 8918 differentially expressed genes (DEGs) were obtained from RNA-seq analysis, and GO analysis showed that DEGs were enriched in functions such as “gibberellin metabolic process” and “oxidoreductase activity”, which have previously been shown to be associated with plant height. A total 593 mutated genes were screened by BSA-seq method. One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines, and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions, which indicated they play a crucial role in plant height determination. Among them, we found a gibberellin biosynthesis related GA20 oxidase gene (Seita.5G404900), which had a single-base deletion at the third exon, leading to the frameshift mutation at 263A. Cleaved amplified polymorphic sequence assay and association analysis proved the single-base deletion in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments. Taken together, the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the molecular marker will be useful for marker-assisted dwarf breeding.
