Functional differentiation and genetic diversity of rice cation exchanger (CAX) genes and their potential use in rice improvement

Abstract

Cation exchanger (CAX) genes play an important role in plant growth/development and response to biotic and abiotic stresses. Here, we tried to obtain important information on the functionalities and phenotypic effects of CAX gene family by systematic analyses of their expression patterns, genetic diversity (gene CDS haplotypes, structural variations, gene presence/absence variations) in 3010 rice genomes and nine parents of 496 Huanghuazhan introgression lines, the frequency shifts of the predominant gcHaps at these loci to artificial selection during modern breeding, and their association with tolerances to several abiotic stresses. Significant amounts of variation also exist in the cis-regulatory elements (CREs) of the OsCAX gene promoters in 50 high-quality rice genomes. The functional differentiation of OsCAX gene family were reflected primarily by their tissue and development specific expression patterns and in varied responses to different treatments, by unique sets of CREs in their promoters and their associations with specific agronomic traits/abiotic stress tolerances. Our results indicated that OsCAX1a and OsCAX2 as general signal transporters were in many processes of rice growth/development and responses to diverse environments, but they might be of less value in rice improvement. OsCAX1b, OsCAX1c, OsCAX3 and OsCAX4 was expected to be of potential value in rice improvement because of their associations with specific traits, responsiveness to specific abiotic stresses or phytohormones, and relatively high gcHap and CRE diversity. Our strategy was demonstrated to be highly efficient to obtain important genetic information on genes/alleles of specific gene family and can be used to systematically characterize the other rice gene families.

Figure 1

The phylogenetic relations of the CAX gene family in different species. The phylogenetic relations of CAX from Oryza sativa based on the Os-Nipponbare-Reference-IRGSP-1.0 reference genome and other species, including Arabidopsis thaliana (At), Triticum aestivum (Ta), Zea mays (Zm), Glycine max (Glyma), Hordeum vulgare (Hv), Solanum tuberosum (St), Solanum lycopersicum (Sl), Saccharomyces cerevisiae (Sc), Synechococcus sp (Ssp), and Escherichia coli (Ec). The 11 species are depicted by different colored shapes.

Figure 2

Haplotype networks of OsCAX gene family and their associations with six traits in 3KRG. (a) OsCAX1a, (b) OsCAX1b, (c) OsCAX1c, (d) OsCAX2, (e) OsCAX3, (f) OsCAX4. Within each haplotype network, two adjacent gcHaps are separated by mutational changes with hatches indicating differences between the two most related haplotypes. The right side of each gene haplotype network corresponds to the phenotypic variation among the haplotypes. Boxplots are shown for the following traits: culm length (CL, cm); culm number (CN, count); grain length (GL, mm); 1000 grain weight (TGW, g); grain width (GW, mm); and days to heading (HD, day). The P values under trait names indicate differences between the haplotypes assessed by two-way ANOVA, with different letters on the boxplots indicating statistically significant differences at P < 0.05 based on Duncan’s multiple range test. The bar charts on the right show the differences in frequency of the predominant gcHaps between landraces (LANs) and modern varieties (MVs) in Xian and Geng. Chi-square tests were used to determine significant differences in the proportions of the same gcHap between the different populations with ****P < 0.0001, **P < 0.01, *P < 0.05, and n.s., not significant.

Figure 3

Expression profiles of the OsCAX genes in different tissues and developmental stages. (a) Different tissues and developmental stages expression patterns of the OsCAX gene family in Nipponbare (Geng) and R498 (Xian). (b) Different tissues and developmental stages expression patterns of the OsCAX gene family in IR64 (Xian).

Figure 4

Expression profiles of the OsCAX genes under different abiotic stresses. (a) Expression profiles of OsCAX genes in Nipponbare (Geng) under salt, drought, Pi, Cd, Submergence and cold treatment in shoot and root. (b) Expression profiles of OsCAX genes in Nipponbare (Geng) under ABA and JA treatment in shoot and root. (c) Expression profiles of OsCAX genes in IR64 (Xian) under salt, drought, nitrogen, Submergence, cold and GA treatment in Shoot. (d) Expression profiles of OsCAX genes in IR64 (Xian) under drought, Al and nitrogen treatment in root.