Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patternsReportar como inadecuado

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BMC Genomics

, 13:502

First Online: 21 September 2012Received: 12 April 2012Accepted: 12 September 2012DOI: 10.1186-1471-2164-13-502

Cite this article as: Wan, H., Yuan, W., Ye, Q. et al. BMC Genomics 2012 13: 502. doi:10.1186-1471-2164-13-502


BackgroundPepper Capsicum annuum L. is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site NBS-leucine-rich repeat LRR gene family is the largest class of known disease resistance genes R genes effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs.

ResultsA total of 78 R gene analogues CaRGAs were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs P-loop, kinase-2 and GLPL along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor TIR-NBS-LRR CaRGAs I to IV and TIR-NBS-LRR CaRGAs V to VII subfamilies. The presence of consensus motifs i.e. P-loop, kinase-2 and hydrophobic domain is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in defence responses by activating signaling pathways.

ConclusionThe identified CaRGAs are a valuable resource for discovering R genes and developing RGA molecular markers for genetic map construction. They will also be useful for improving disease resistance in pepper. The findings of this study provide a better understanding of the evolutionary mechanisms that drive the functional diversification of non-TIR- and TIR-NBS-LRR R genes in pepper.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-13-502 contains supplementary material, which is available to authorized users.

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Autor: HongjianWan - WeiYuan - QingjingYe - RongqingWang - MeiyingRuan - ZhimiaoLi - GuozhiZhou - ZhupingYao - JingZhao - ShujunLiu - Yue


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