Rice Genetics IV - IRRI books - International Rice Research Institute

612-amino acid protein, including the signal peptide, and GC-rich and LRR domain.Up to Retrofit insertion, Xa21D is 99.1% identical to Xa21 in nucleotide sequence.This result supported the hypothesis that the Xa21D LRR domain is involved in pathogenrecognition.To gain insight into the function and evolution of particular coding domains, analysisof the rates of synonymous (no amino acid alteration) and nonsynonymous(altered amino acids) nucleotide substitutions has been used to investigate the nucleotidesubstitution patterns in members of the Xa21 gene family. The type of selectionacting on a gene family can be inferred by comparing synonymous and nonsynonymoussubstitution rates per synonymous/nonsynonymous site (Hughes and Nei 1988). Inthe absence of selection pressure, the nonsynonymous/synonymous ratio is predictedto be 1. The nonsynonymous/synonymous ratio in the Cf4 and Cf9 LRR region wasgreater than 1, indicating positive selection for diversification of the gene family (Thomaset al 1997). Comparison of nucleotide substitutions in the LRR coding regions ofXa21 and Xa21D revealed that, although Xa21 and Xa21D share 99.1% sequenceidentity, nonsynonymous substitutions occur significantly more frequently than synonymoussubstitutions in the LRR. Thus, the results further support the hypothesisthat LRRs play a role in ligand binding and that the LRR domain is subject to adaptiveevolution (Wang et al 1998).Evolution of the Xa21 gene familyIt has long been speculated that DNA alterations play a key role in the evolution ofdisease resistance loci. These changes will allow plants to generate new resistances tomatch the changing pattern of pathogen virulence. To investigate the evolution of theXa21 gene family, seven Xa21 gene family members, designated A1, A2, B, C, D, E,and F, were cloned and sequenced (Song et al 1997). They are grouped into twoclasses based on sequence similarity. The Xa21 class contains Xa21, as well as membersD and F. The A2 class contains members A1, A2, C, and E. Although the nucleotidesequences within each class are nearly identical (98.0% average identity for themembers of the Xa21 class, 95.2% average identity for the members of the A2 class),sequence identity between members of the two classes is low (63.5% identity betweenXa21 and A2) (Song et al 1997). A highly conserved (HC) 233-bp sequencewas identified among the seven family members such that recombination at the HCregion between family members resulted in a precise swapping of the promoter regions.Large sequence duplications were generated by a presumed unequal crossoverevent in the intergenic regions.Furthermore, sequence analysis of the seven members revealed that 17 transposonlikeelements were identified in the 5’ and 3’ flanking regions and introns of thesemembers (Song et al 1995). Recently, He et al (2000) found another transposon-likeelement (Rim2) in the Xa21 locus. Its transcript accumulates in response toMagnaporthe grisea and its predicted protein shares similarity with TNP2-like proteinsencoded by CACTA transposons. These elements are diverse, showing similarityto maize Ds, CACTA, and miniature inverted repeat-like elements, as well as novel338 Guo-Liang Wang et al