Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet

文献类型： 外文期刊

第一作者： Zhu, Mengyuan

作者： Zhu, Mengyuan;He, Qiang;Lyu, Mingjie;Shi, Tiantian;Gao, Qian;Zhi, Hui;Jia, Guanqing;Tang, Sha;Cheng, Xiliu;Wang, Rui;Xu, Andi;Liu, Jun;Diao, Xianmin;Gao, Ying;Wang, Huan;Wang, Huan;Wang, Haigang;Qiao, Zhijun;Lyu, Mingjie

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关键词： Foxtail millet; Plant height; Transcriptome analysis; Bulk segregant analysis; Functional markers; Association analysis

期刊名称：CROP JOURNAL （ 影响因子：6.6； 五年影响因子：6.5 ）

ISSN： 2095-5421

年卷期： 2023 年 11 卷 2 期

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收录情况： SCI

摘要： 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 intern -ode 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 at the third exon, leading to the frameshift mutation at 263A. Cleaved amplified polymorphic sequence assay and association analysis proved the single-base 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. (c) 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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