Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks

Luchang Ming, Debao Fu, Zhaona Wu, Hu Zhao, Xingbing Xu, Tingting Xu, Xiaohu Xiong, Mu Li, Yi Zheng, Ge Li, Ling Yang, Chunjiao Xia, Rongfang Zhou, Keyan Liao, Qian Yu, Wenqi Chai, Sijia Li, Yinmeng Liu, Xiaokun Wu, Jianquan Mao, Julong Wei, Xu Li, Lei Wang, Changyin Wu () and Weibo Xie ()
Additional contact information
Luchang Ming: Huazhong Agricultural University
Debao Fu: Huazhong Agricultural University
Zhaona Wu: Huazhong Agricultural University
Hu Zhao: Huazhong Agricultural University
Xingbing Xu: Huazhong Agricultural University
Tingting Xu: Huazhong Agricultural University
Xiaohu Xiong: Huazhong Agricultural University
Mu Li: Huazhong Agricultural University
Yi Zheng: Huazhong Agricultural University
Ge Li: Huazhong Agricultural University
Ling Yang: Huazhong Agricultural University
Chunjiao Xia: Huazhong Agricultural University
Rongfang Zhou: Huazhong Agricultural University
Keyan Liao: Huazhong Agricultural University
Qian Yu: Huazhong Agricultural University
Wenqi Chai: Huazhong Agricultural University
Sijia Li: Huazhong Agricultural University
Yinmeng Liu: Huazhong Agricultural University
Xiaokun Wu: Huazhong Agricultural University
Jianquan Mao: Huazhong Agricultural University
Julong Wei: Wayne State University School of Medicine
Xu Li: Huazhong Agricultural University
Lei Wang: Huazhong Agricultural University
Changyin Wu: Huazhong Agricultural University
Weibo Xie: Huazhong Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.

Date: 2023
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DOI: 10.1038/s41467-023-43077-6

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