Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement

Jinguo Zhang; Xinchen Wang; Guohui Dou; Dezhuang Meng; Chenghang Tang; Jiaqi Lv; Nansheng Wang; Xingmeng Wang; Jianfeng Li; Yaling Bao; Guogeng Zhang; Tao Huang; Yingyao Shi

doi:10.3389/fpls.2024.1435420

Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement

Front Plant Sci. 2024 Oct 17:15:1435420. doi: 10.3389/fpls.2024.1435420. eCollection 2024.

Authors

Jinguo Zhang¹, Xinchen Wang¹, Guohui Dou¹, Dezhuang Meng¹, Chenghang Tang¹, Jiaqi Lv¹, Nansheng Wang¹, Xingmeng Wang¹, Jianfeng Li¹, Yaling Bao¹, Guogeng Zhang^{1

2}, Tao Huang¹, Yingyao Shi¹

Affiliations

¹ School of Agronomy, Anhui Agricultural University, Hefei, China.
² Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Abstract

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an α/β folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity.

Keywords: biological stress; carboxylesterase; gene-CDS-haplotype (gcHap) diversity; rice; yield traits.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the National Key Research and Development Program of China “Creation and Application of Novel Japonica Rice Germplasm with High Quality and Yeild in the Middle and Lower Reaches of Yangtze River” (grant number 2023YFD1200900), the Key Research and Development Program of Anhui Province (grant number 2023n06020013), the Scientific Research Plan Major Projects of Anhui Province (grant number 2022AH040126), the Improved Varieties Joint Research (Rice) Project of Anhui Province (the 14th five-year plan), the Science and Technology Major Project of Anhui Province (grant number 2021d06050002), and the National Natural Science Foundation of China (grant number U21A20214).