Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns
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- 作者：Hongjian Wan (1)
Wei Yuan (1)
Qingjing Ye (1)
Rongqing Wang (1)
Meiying Ruan (1)
Zhimiao Li (1)
Guozhi Zhou (1)
Zhuping Yao (1)
Jing Zhao (1)
Shujun Liu (1)
Yuejian Yang (1) - 刊名：BMC Genomics
- 出版年：2012
- 出版时间：December 2012
- 年：2012
- 卷：13
- 期：1
- 全文大小：1564KB
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66. Wan HJ, Yuan W, Ruan MY, Ye QJ, Wang RQ, Li ZM, Zhou GZ, Yao ZP, Zhao J, Liu SJ, Yang YJ: Identification of reference genes for reverse transcription quantitative real-time PCR normalization in pepper ( Capsicum annuum L.). / Biochem Biophys Res Commun 2011, 416:24鈥?0. CrossRef - 作者单位：Hongjian Wan (1)
Wei Yuan (1)
Qingjing Ye (1)
Rongqing Wang (1)
Meiying Ruan (1)
Zhimiao Li (1)
Guozhi Zhou (1)
Zhuping Yao (1)
Jing Zhao (1)
Shujun Liu (1)
Yuejian Yang (1)
1. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People鈥檚 Republic of China
文摘
Background Pepper (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. Results A 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. Conclusion The 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.