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

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 <i>CXE</i> genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (<i>Xian</i>-1B1 var.IR64), and Oryza sativa Japonica (<i>Geng</i>-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of <i>CXE</i> 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 <i>OsCXE</i> genes. Our results indicated that fragment replication is the main reason for amplification of the <i>CXE</i> gene family in rice, and the gene family has undergone strong purification selection. <i>OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1</i>, and <i>OsCXE7.3</i> may be used to improve the tolerance of rice to abiotic stress. <i>OsCXE</i> play important roles in rice population differentiation and improvement, and the major gcHaps at most <i>OsCXE</i> locus are significantly associated with yield traits. Therefore, natural variations of most <i>OsCXE</i> locus have great potential value for improvement of rice productivity.