Genome-wide analysis of KIX gene family for organ size regulation in soybean (Glycine max L.)

Abstract

The KIX domain, conserved among various nuclear and co-activator factors, acts as a binding site that interacts with other transcriptional activators and co-activators, playing a crucial role in gene expression regulation. In plants, the KIX domain is involved in plant hormone signaling, stress response regulation, cell cycle control, and differentiation, indicating its potential relevance to crop productivity. This study aims to identify and characterize KIX domains within the soybean (Glycine max L.) genome to predict their potential role in improving crop productivity. The conservation and evolutionary history of the KIX domains were explored in 59 plant species, confirming the presence of the KIX domains in diverse plants. Specifically, 13 KIX domains were identified within the soybean genome and classified into four main groups, namely GmKIX8/9, GmMED15, GmHAC, and GmRECQL, through sequence alignment, structural analysis, and phylogenetic tree construction. Association analysis was performed between KIX domain haplotypes and soybean seed-related agronomic traits using re-sequencing data from a core collection of 422 accessions. The results revealed correlations between SNP variations observed in GmKIX8-3 and GmMED15-4 and soybean seed phenotypic traits. Additionally, transcriptome analysis confirmed significant expression of the KIX domains during the early stages of soybean seed development. This study provides the first characterization of the structural, expression, genomic haplotype, and molecular features of the KIX domain in soybean, offering a foundation for functional analysis of the KIX domain in soybean and other plants.

Keywords: glycine max; haplotype; kix domain; soybean core collection; yield.

Figure 1

Distribution of KIX domains and phylogenetic relationship among 59 plant species. (A) Distribution of KIX domains based on plant classification. The pink bars represent the number of KIX domains present in each plant species. The green bars indicate the average number of KIX domains for each plant group. (B) Phylogenetic tree illustrating the protein sequence relationships of 591 identified KIX domains from 59 plant species. The phylogenetic tree was constructed using the neighbor-joining (NJ) method implemented in MEGA-X. The black triangle represents the KIX domain of soybean, while the red triangle represents the KIX domain of Arabidopsis. *NOD, Number of KIX domain.

Figure 2

Phylogenetic relationships and structure of KIX proteins from Fabaceae and Arabidopsis. (A) Phylogenetic tree of KIX protein amino acid sequences from Arabidopsis, soybean, and three species of Fabaceae. Protein sequences include AtKIX (Arabidopsis), GmKIX (Glycine max), Ca (Cicer arietinum), Phvul (Phaseolus vulgaris), and Medtr (Medicago truncatula). The phylogenetic tree was generated using MEGA-X with the neighbor-joining (NJ) method. (B). A schematic diagram of the motifs present in proteins that include the KIX domain. The Red box indicates KIX domain region. Other major domains are described at the bottom of the figure.

Figure 3

Haplotype analysis for GmKIX genes and distribution of haplotype variations across each gene. The bar chart represents the number of haplotypes for each GmKIX gene, and the pie chart illustrates the distribution of each haplotype. The box on the right represents the information of the pie chart.

Figure 4

Association between haplotype in GmKIX8-1 and seed agronomic traits. (A) Haplotype analysis of GmKIX8-1 based on re-sequencing data from the soybean core collection. Four haplotypes of the GmKIX8-1 gene were determined based on the polymorphisms detected in the coding region. (B-G) boxplot displays the distribution of various agronomic traits (100-SW, area, thickness, and minor and major axes) values for the four haplotype types of GmKIX8-1. NS, not significant, *p < 0.05, **p < 0.01, ***p < 0.001. 100-SW, 100 seed weight.

Figure 5

Association between haplotype in GmMED15-4 and seed agronomic traits. (A) Haplotype analysis of GmMED15-4 based on re-sequencing data from the soybean core collection. Two haplotypes of the GmMED15-4 gene were determined based on the polymorphisms detected in the coding region. (B-G) boxplot displays the distribution of various agronomic traits (100-SW, area, thickness, and minor and major axes) values for the two haplotype types of GmKIX8-1. NS, not significant, **p < 0.01, ***p < 0.001. 100-SW, 100 seed weight.

Figure 6

Analysis of population structure in the soybean core collection and haplotype network of GmKIX8-1 and GmMED15-4. (A) Population structure of the 422 soybean core collection with 542,422 SNPs. (B) Boxplot of 100-seed weights of resources distributed among four subpopulations. (C) The haplotype network of GmKIX8-1. (D) The haplotype network of GmMED15-4. * 100-SW (mean ± standard deviation). ***p < 0.001, NS, not significant. 100-SW, 100 seed weight.

Figure 7

Heatmap of GmKIX genes expression in three stage of seed development. Expression analysis of GmKIX genes was conducted based on the developmental stages of seeds in four variations: Hoseo, PI86490, KLS88035, and Soheung-2. The RPKM values of each gene were normalized to Z-scores. Detailed information regarding the developmental stages and resources can be found in Supplementary Figure 2 .