Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping

文献类型： 外文期刊

第一作者： Yin, Ming

作者： Yin, Ming;Zhang, Yue;Zuo, Liying;Lei, Yuxin;Zhao, Yaqiong;Zhao, Xiuqin;Fu, Binying;Xu, Jianlong;Wang, Wensheng;Zheng, Zhenzhen;Shi, Yingyao;Wang, Wensheng;Yin, Ming;Zhang, Yue;Wang, Wensheng;Wang, Shanwen;Wang, Wensheng

作者机构：

关键词： WGCNA; QTL; RNA-seq; Tolerance to anaerobic germination; Haplotype analysis

期刊名称：RICE （ 影响因子：5.5； 五年影响因子：5.8 ）

ISSN： 1939-8425

年卷期： 2024 年 17 卷 1 期

页码：

收录情况： SCI

摘要： Background Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.Results In this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes.Conclusion The results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.

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