Pattern of LRR nucleotide variation in plant resistance genes

• Published in: Plant science (Limerick) 2007-08, Vol.173 (2), p.253-261
• Main Authors: Jiang, Haiyang, Wang, Cuicui, Ping, Ling, Tian, Dacheng, Yang, Sihai
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Arabidopsis thaliana; Biological and medical sciences; corn; disease resistance; Fulvia fulva; Fundamental and applied biological sciences. Psychology; Genetic variation; Genetics and breeding of economic plants; host-pathogen relationships; Linum usitatissimum; LRR domain; Magnaporthe grisea; Melampsora lini; Oryza sativa; Pernonspora parasiotica; Pest resistance; plant pathogenic fungi; Plant pathogens; Plant R genes; plant viruses; Puccinia sorghi; rice; Solanum habrochaites; Solanum lycopersicum var. lycopersicum; tomatoes; Tospovirus; Varietal selection. Specialized plant breeding, plant breeding aims; Zea mays
• ISSN: 0168-9452; 1873-2259
• DOI: 10.1016/j.plantsci.2007.05.010

LRR domain of plant R genes, consisting of individual LRRs with a parallel β-sheets (xxLxLxx) structure each, plays a major role in recognition specificity for pathogen effector molecules. However, little is known about variation pattern of individual LRRs. Here, we investigated nucleotide diversity, synonymous and nonsynonymous substitution for each of the LRRs in 12 functional R genes. We found that the level of nucleotide diversity and the ratio of Ka to Ks were significantly different among individual LRR units. A significant Ka > Ks was detected in 50.2% individual LRR units, ∼70% xxLxLxx motifs and ∼43% C-terminal flanking of the xxLxLxx motif, respectively, suggesting a role in these units or motifs in recognition specificity. Contrastingly, the sequences N-terminal to the xxLxLxx motif showed a very conservative evolution, similar to the non-LRR or NBS domain. Moreover, most of the xxLxLxx motifs with significant Ka > Ks values were linked, mainly locating in the C-terminal half of the LRR repeats in most of the NBS-LRR genes, which was consistent with that of the region of the recognition specificity. Uneven distribution of the LRR units with significant Ka > Ks values indicates that only some linked LRRs account for plant recognition specificity, and that diversifying selection have acted on them for profiling their functions.