Limits...
Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns.

Wan H, Yuan W, Ye Q, Wang R, Ruan M, Li Z, Zhou G, Yao Z, Zhao J, Liu S, Yang Y - BMC Genomics (2012)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.

ABSTRACT

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.

Show MeSH

Related in: MedlinePlus

Sliding window analyses of Ka/Ks ratios for any two groups in the non-TIR- and TIR-NBS subfamilies. The Y-axis shows the Ka/Ks ratio, and the X-axis shows the amino acid numbers of the aligned sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3472223&req=5

Figure 5: Sliding window analyses of Ka/Ks ratios for any two groups in the non-TIR- and TIR-NBS subfamilies. The Y-axis shows the Ka/Ks ratio, and the X-axis shows the amino acid numbers of the aligned sequences.

Mentions: A sliding window analysis of the Ka/Ks ratios was carried out alongside the determination of the nucleotide sequences of the RGAs for pairwise comparison of any two groups using CRANN software to explore important regions that may have contributed to the functional diversification of NBS-LRR RGAs in pepper [48]. Within the non-TIR-NBS-LRR subfamily, we observed two groups of pairwise comparisons that showed similar tendencies. One was CaRGA I/CaRGA IV and CaRGA II/CaRGA IV, the other was CaRGA II/CaRGA III and CaRGA III/CaRGA IV. The remaining two groups showed different patterns. Overall, the sliding window profile revealed at least three regions of high peaks that were under positive selection, given that all Ka/Ks values were >1 (Figure 5A). Within the TIR-NBS-LRR subfamily, we observed 2–3 regions of high peaks with high Ka/Ks values, consistent with positive selection in three pairwise comparisons (Figure 5B). These regions may be exposed to strong functional constraints. Two of these regions may be located in the RNBS-B and RNBS-C domains, respectively. Therefore, we inferred that the observed difference in the regions of functional constraint may reflect the functional specificities of NBS-LRR RGAs in pepper.


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

Wan H, Yuan W, Ye Q, Wang R, Ruan M, Li Z, Zhou G, Yao Z, Zhao J, Liu S, Yang Y - BMC Genomics (2012)

Sliding window analyses of Ka/Ks ratios for any two groups in the non-TIR- and TIR-NBS subfamilies. The Y-axis shows the Ka/Ks ratio, and the X-axis shows the amino acid numbers of the aligned sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472223&req=5

Figure 5: Sliding window analyses of Ka/Ks ratios for any two groups in the non-TIR- and TIR-NBS subfamilies. The Y-axis shows the Ka/Ks ratio, and the X-axis shows the amino acid numbers of the aligned sequences.
Mentions: A sliding window analysis of the Ka/Ks ratios was carried out alongside the determination of the nucleotide sequences of the RGAs for pairwise comparison of any two groups using CRANN software to explore important regions that may have contributed to the functional diversification of NBS-LRR RGAs in pepper [48]. Within the non-TIR-NBS-LRR subfamily, we observed two groups of pairwise comparisons that showed similar tendencies. One was CaRGA I/CaRGA IV and CaRGA II/CaRGA IV, the other was CaRGA II/CaRGA III and CaRGA III/CaRGA IV. The remaining two groups showed different patterns. Overall, the sliding window profile revealed at least three regions of high peaks that were under positive selection, given that all Ka/Ks values were >1 (Figure 5A). Within the TIR-NBS-LRR subfamily, we observed 2–3 regions of high peaks with high Ka/Ks values, consistent with positive selection in three pairwise comparisons (Figure 5B). These regions may be exposed to strong functional constraints. Two of these regions may be located in the RNBS-B and RNBS-C domains, respectively. Therefore, we inferred that the observed difference in the regions of functional constraint may reflect the functional specificities of NBS-LRR RGAs in pepper.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus