J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (7): 1753-1766.DOI: 10.1111/jipb.13484

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice

Fuying Ma1†, Fan Zhang2,3†*, Yu Zhu1†, Dengyong Lan1, Peiwen Yan1, Ying Wang1, Zejun Hu4, Xinwei Zhang1, Jian Hu1, Fuan Niu1,4, Mingyu Liu1, Shicong He1, Jinhao Cui1, Xinyu Yuan1, Ying Yan4, Shujun Wu4, Liming Cao4, Hongwu Bian5, Jinshui Yang1, Zhikang Li2,3,6* and Xiaojin Luo1*   

  1. 1. State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China;
    2. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
    3. College of Agronomy, Anhui Agricultural University, Hefei 230036, China;
    4. Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
    5. Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
    6. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
    These authors contributed equally to this work.
    *Correspondences: Xiaojin Luo (luoxj@fudan.edu.cn, Dr. Luo is fully responsible for the distributions of the materials associated with this article); Zhikang Li (lizhikang@caas.cn); Fan Zhang (zhangfan03@caas.cn)
  • Received:2023-01-30 Accepted:2023-03-20 Online:2023-03-20 Published:2023-07-01

Abstract: Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the ‘best’ gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.

Key words: allele evolution, auxin signaling pathways, OsARFs, OsIAA10, yield traits

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