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