The rice nucleotide-binding site–leucine-rich repeat (NBS-LRR)-encoding resistance (R) gene Pi9 confers broad-spectrum resistance to the fungal pathogen Magnaporthe oryzae. The Pi9 locus comprises many NBS-LRR-like genes and is an ancient locus that is highly conserved in cultivated and wild rice species. To understand the genetic variation and molecular evolutionary mechanism of the Pi9 alleles in different rice species, we studied five AA genome Oryza species including two cultivated rice species (Oryza sativa and Oryza glaberrima) and three wild rice species (Oryza nivara, Oryza rufipogon, and Oryza barthii). A 2.9-kb fragment spanning the NBS-LRR core region of the Pi9 gene was amplified and sequenced from 40 accessions. Sequence comparison revealed that the Pi9 alleles had an intermediate-diversified nucleotide polymorphism among the AA genome Oryza species. Sequence variations were more abundant in the LRR region than in the NBS region, indicating that the LRR region has played a more important role for the evolution of the Pi9 alleles. Furthermore, positive selection was found to be the main force promoting the divergence of the Pi9 alleles, especially in the LRR region. Our results reveal the characteristics and evolutionary dynamics of the Pi9 alleles among the two cultivated and three wild rice species.
水稻广谱抗稻瘟病基因（R）Pi9是一个核苷酸结合位点富含亮氨酸重复序列（ NBS-LRR ）基因。Pi9的位点包括许多NBS-LRR类基因，是一个在栽培品种和野生稻中高度保守的古老的基因位点。为了了解Pi9的等位基因在不同水稻品种中的遗传变异和分子进化机制，我们研究了五个AA基因组稻种，包括两个栽培稻（亚洲栽培稻和非洲栽培稻）和三个野生稻（一年生野生稻，普通野生稻和巴蒂野生稻）。我们从40份材料中扩增了一个跨越Pi9的NBS-LRR核心区域约2.9 kb的片段并测序。序列比对结果显示含AA基因组稻种中Pi9的等位基因具有中间多元化的核苷酸多态性，LRR区域的序列变异明显高于NBS区，表明LRR区对Pi9等位基因的进化起到更加重要的作用。此外，正向选择被认为是推动Pi9进化的主要动力，特别在LRR结构域。我们的研究结果阐述了Pi9等位基因在两个栽培稻和三个野生稻物种间的进化动力学特征。