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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.

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Functional divergence-related amino acid site candidates (posterior probability, Qk > 0.7). A site-specific profile based on the posterior probability (Qk )was used to identify the critical amino acid sites responsible for the functional divergence between the non-TIR- and TIR-NBS RGA subfamilies. According to the definition, a large Qk value indicates a high possibility that the functional constraint of a site is different between the two subfamilies. A) non-TIR-NBS subfamily, B) TIR-NBS subfamily and C) Qk values of 13 amino acid sites. The threshold (%) for shading was set at 50. Similar amino acid residues are shaded grey, and identical amino acid residues are shaded black.
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Figure 4: Functional divergence-related amino acid site candidates (posterior probability, Qk > 0.7). A site-specific profile based on the posterior probability (Qk )was used to identify the critical amino acid sites responsible for the functional divergence between the non-TIR- and TIR-NBS RGA subfamilies. According to the definition, a large Qk value indicates a high possibility that the functional constraint of a site is different between the two subfamilies. A) non-TIR-NBS subfamily, B) TIR-NBS subfamily and C) Qk values of 13 amino acid sites. The threshold (%) for shading was set at 50. Similar amino acid residues are shaded grey, and identical amino acid residues are shaded black.

Mentions: We also found that the degree of conservation of critical amino acid residues differed between non-TIR- and TIR-NBS-LRR RGAs. For example, the amino acid residue at site 22 was valine (V) and leucine (L) in the non-TIR- and TIR-NBS-LRR RGAs, respectively. Nevertheless, some amino acid residues were highly conserved between the subfamilies, such as those at sites 84 (E), 133 (F) and 155 (W) from the non-TIR-NBS-LRR subfamily and sites 23 (S), 116 (W), 118 (G) and 146 (V) from the TIR-NBS-LRR subfamily (Figure 4). These results suggest that these critical amino acid residue sites are subjected to strong functional constraints within the non-TIR- and TIR-NBS-LRR subfamilies.


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)

Functional divergence-related amino acid site candidates (posterior probability, Qk > 0.7). A site-specific profile based on the posterior probability (Qk )was used to identify the critical amino acid sites responsible for the functional divergence between the non-TIR- and TIR-NBS RGA subfamilies. According to the definition, a large Qk value indicates a high possibility that the functional constraint of a site is different between the two subfamilies. A) non-TIR-NBS subfamily, B) TIR-NBS subfamily and C) Qk values of 13 amino acid sites. The threshold (%) for shading was set at 50. Similar amino acid residues are shaded grey, and identical amino acid residues are shaded black.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Functional divergence-related amino acid site candidates (posterior probability, Qk > 0.7). A site-specific profile based on the posterior probability (Qk )was used to identify the critical amino acid sites responsible for the functional divergence between the non-TIR- and TIR-NBS RGA subfamilies. According to the definition, a large Qk value indicates a high possibility that the functional constraint of a site is different between the two subfamilies. A) non-TIR-NBS subfamily, B) TIR-NBS subfamily and C) Qk values of 13 amino acid sites. The threshold (%) for shading was set at 50. Similar amino acid residues are shaded grey, and identical amino acid residues are shaded black.
Mentions: We also found that the degree of conservation of critical amino acid residues differed between non-TIR- and TIR-NBS-LRR RGAs. For example, the amino acid residue at site 22 was valine (V) and leucine (L) in the non-TIR- and TIR-NBS-LRR RGAs, respectively. Nevertheless, some amino acid residues were highly conserved between the subfamilies, such as those at sites 84 (E), 133 (F) and 155 (W) from the non-TIR-NBS-LRR subfamily and sites 23 (S), 116 (W), 118 (G) and 146 (V) from the TIR-NBS-LRR subfamily (Figure 4). These results suggest that these critical amino acid residue sites are subjected to strong functional constraints within the non-TIR- and TIR-NBS-LRR subfamilies.

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