水稻粒形调控相关基因进化的全基因组尺度分析

Whole-genome Scale Analysis of Grain Shape Regulation Related Gene Evolution in Rice

水稻粒形相关基因,对于调控作物产量和品质都具有十分重要的作用,但关于其进化缺少一个系统的、全基因组尺度的比较基因组学分析。研究以已鉴定的水稻粒形相关基因为目标序列,在8个禾本科植物中进行比较基因组学分析,旨在全基因组范围揭示不同粒形基因在多个禾本科作物种系中的进化规律。基于同源比对分析发现,不同基因组中粒形相关基因数量不具有明显差异,平均每个基因组中粒长和粒宽相关的基因分别有364和75,其中较多的是谷子,有423粒长、71粒宽调控基因。基因组同源共线分析,发现全基因组加倍和串联重复对于家族基因拷贝数增加具有重要贡献,但是重复基因丢失可能维持了基因数量的稳定。通过粒形基因中旁系同源基因对间的同义核苷酸置换率(Ks)比较,揭示不同的粒形基因具有不同的进化速率,进化最快的是粒长调控相关基因An-1。本研究为认识水稻粒形调控相关基因进化提供了重要的理论基础,对于禾本科粒形相关基因从全局尺度到单基因的进化具有极为重要的意义。

Rice grain shape genes have an important role in regulating crop yield and quality, but there is a lack of systematic and genome-wide analysis of comparative genomics about their evolution. In this study, we used the rice grain shape genes that had been identified as the target sequence, conducted comparative genomic analysis in 8 genomes of Gramineae, aiming to reveal the evolution of different grain shape genes in in various species of Gramineae in whole genome scale. According to the homology comparison analysis, there was no significant difference in the number of grain shape genes in different genomes. Each genome had 364 grain length genes and 75 grain width genes on average, of which the most was millet who had 423 grain length genes and 71 grain width genes. Genome homologous collinear analysis found that the whole genome doubling and tandem repeats had important contributions to the increase in family gene copy number, but the loss of repeat genes might maintain the stability of gene number. Compared with synonymous mutation rate（Ks） between paralog gene pairs in grain shape genes, it was revealed that different grain genes had different evolutionary rates, and the fastest evolution was the grain-related genes An-1. This study provided an important theoretical basis for understanding the evolution of rice grain shape genes, and it was of great significance for the evolution of grain shape genes in Gramineae plants from the global scale to the single gene.