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.
水稻廣譜抗稻瘟病基因（R）Pi9是一個核苷酸結(jié)合位點富含亮氨酸重復(fù)序列（ NBS-LRR ）基因。Pi9的位點包括許多NBS-LRR類基因，是一個在栽培品種和野生稻中高度保守的古老的基因位點。為了了解Pi9的等位基因在不同水稻品種中的遺傳變異和分子進(jìn)化機(jī)制，我們研究了五個AA基因組稻種，包括兩個栽培稻（亞洲栽培稻和非洲栽培稻）和三個野生稻（一年生野生稻，普通野生稻和巴蒂野生稻）。我們從40份材料中擴(kuò)增了一個跨越Pi9的NBS-LRR核心區(qū)域約2.9 kb的片段并測序。序列比對結(jié)果顯示含AA基因組稻種中Pi9的等位基因具有中間多元化的核苷酸多態(tài)性，LRR區(qū)域的序列變異明顯高于NBS區(qū)，表明LRR區(qū)對Pi9等位基因的進(jìn)化起到更加重要的作用。此外，正向選擇被認(rèn)為是推動Pi9進(jìn)化的主要動力，特別在LRR結(jié)構(gòu)域。我們的研究結(jié)果闡述了Pi9等位基因在兩個栽培稻和三個野生稻物種間的進(jìn)化動力學(xué)特征。