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Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt.

Chen JY, Huang JQ, Li NY, Ma XF, Wang JL, Liu C, Liu YF, Liang Y, Bao YM, Dai XF - BMC Plant Biol. (2015)

Bottom Line: A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications.In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. chenjieyin@caas.cn.

ABSTRACT

Background: Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs.

Results: The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.

Conclusions: The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.

No MeSH data available.


Related in: MedlinePlus

Analysis of RGA gene expression patterns and the screening of potential VdRLs. The RGA genes were arranged in a series from Chr01 to Chr13. RGA genes belonging to the 26 Rgrcs are shown in red. The fold-change of log2Ratio ≥ /2.0/ is marked in dotted lines. The potential VdRLs were screened from Rgrcs using a log2Ratio ≥ /2.0/, and having more than one infection time point up-regulated. The potential VdRLs were marked with asterisks. The numbers 2, 6, 12, 24, 48, and 72 in the boxes represent the time points (in hours) of the cotton inoculation with V. dahliae
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Fig6: Analysis of RGA gene expression patterns and the screening of potential VdRLs. The RGA genes were arranged in a series from Chr01 to Chr13. RGA genes belonging to the 26 Rgrcs are shown in red. The fold-change of log2Ratio ≥ /2.0/ is marked in dotted lines. The potential VdRLs were screened from Rgrcs using a log2Ratio ≥ /2.0/, and having more than one infection time point up-regulated. The potential VdRLs were marked with asterisks. The numbers 2, 6, 12, 24, 48, and 72 in the boxes represent the time points (in hours) of the cotton inoculation with V. dahliae

Mentions: The expression pattern analysis of DEGs in Rgrcs indicated that the RGA genes were up-regulated more often than other genes in Rgrcs (Additional file 2: Figure S10), which suggested that RGA genes were more sensitive to V. dahliae inoculation than the other genes in Rgrcs. To investigate the potential RGA gene responses to V. dahliae infection, highly rigorous conditions (log2Ratio ≥ /2.0/, with more than one up-regulated post-infection time point) were used for screening in this study. In total, 168 differentially expressed RGA genes were identified as potential Verticillium wilt response genes. Of these genes, the proportion of potential Verticillium wilt resistance genes in R-II, R-III and R-IV families was higher than in other families (Additional file 1: Table S12 and Table S13). Notably, 64 DEGs occurred in 19 Rgrcs, and 63 of them were distributed in the 26 small regions defined VdRL01 to VdRL26 (Fig. 6; Additional file 1: Table S12-S14). The total length of the VdRLs is ~2.4 Mb, and a minimum of 15 VdRLs contain at least two significantly differentially expressed RGA genes (Additional file 1: Table S14). A total of 39 differentially expressed RGA genes in the VdRLs belonged to the R-II, R-VII and R-IX families (Additional file 1: Table S12), indicating that these RGA genes were important to the cotton response to Verticillium wilt. Moreover, most VdRLs were primarily distributed in the small regions of a few chromosomes, particularly Chr07 and Chr09, which included seven and six VdRLs respectively (Additional file 1: Table S14). A further analysis showed that the RGA genes of nearly half of the VdRLs encoded NB-ARC domain-containing disease resistance proteins, and the RGA genes of the other VdRLs primarily encoded cysteine-rich RLKs, leucine-rich repeat protein kinase family proteins and RLPs (Additional file 1: Table S15). These results indicated that some RGA genes in the Rgrcs were strongly induced and a portion of them formed the VdRLs that participated in Verticillium wilt response in cotton.Fig. 6


Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt.

Chen JY, Huang JQ, Li NY, Ma XF, Wang JL, Liu C, Liu YF, Liang Y, Bao YM, Dai XF - BMC Plant Biol. (2015)

Analysis of RGA gene expression patterns and the screening of potential VdRLs. The RGA genes were arranged in a series from Chr01 to Chr13. RGA genes belonging to the 26 Rgrcs are shown in red. The fold-change of log2Ratio ≥ /2.0/ is marked in dotted lines. The potential VdRLs were screened from Rgrcs using a log2Ratio ≥ /2.0/, and having more than one infection time point up-regulated. The potential VdRLs were marked with asterisks. The numbers 2, 6, 12, 24, 48, and 72 in the boxes represent the time points (in hours) of the cotton inoculation with V. dahliae
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig6: Analysis of RGA gene expression patterns and the screening of potential VdRLs. The RGA genes were arranged in a series from Chr01 to Chr13. RGA genes belonging to the 26 Rgrcs are shown in red. The fold-change of log2Ratio ≥ /2.0/ is marked in dotted lines. The potential VdRLs were screened from Rgrcs using a log2Ratio ≥ /2.0/, and having more than one infection time point up-regulated. The potential VdRLs were marked with asterisks. The numbers 2, 6, 12, 24, 48, and 72 in the boxes represent the time points (in hours) of the cotton inoculation with V. dahliae
Mentions: The expression pattern analysis of DEGs in Rgrcs indicated that the RGA genes were up-regulated more often than other genes in Rgrcs (Additional file 2: Figure S10), which suggested that RGA genes were more sensitive to V. dahliae inoculation than the other genes in Rgrcs. To investigate the potential RGA gene responses to V. dahliae infection, highly rigorous conditions (log2Ratio ≥ /2.0/, with more than one up-regulated post-infection time point) were used for screening in this study. In total, 168 differentially expressed RGA genes were identified as potential Verticillium wilt response genes. Of these genes, the proportion of potential Verticillium wilt resistance genes in R-II, R-III and R-IV families was higher than in other families (Additional file 1: Table S12 and Table S13). Notably, 64 DEGs occurred in 19 Rgrcs, and 63 of them were distributed in the 26 small regions defined VdRL01 to VdRL26 (Fig. 6; Additional file 1: Table S12-S14). The total length of the VdRLs is ~2.4 Mb, and a minimum of 15 VdRLs contain at least two significantly differentially expressed RGA genes (Additional file 1: Table S14). A total of 39 differentially expressed RGA genes in the VdRLs belonged to the R-II, R-VII and R-IX families (Additional file 1: Table S12), indicating that these RGA genes were important to the cotton response to Verticillium wilt. Moreover, most VdRLs were primarily distributed in the small regions of a few chromosomes, particularly Chr07 and Chr09, which included seven and six VdRLs respectively (Additional file 1: Table S14). A further analysis showed that the RGA genes of nearly half of the VdRLs encoded NB-ARC domain-containing disease resistance proteins, and the RGA genes of the other VdRLs primarily encoded cysteine-rich RLKs, leucine-rich repeat protein kinase family proteins and RLPs (Additional file 1: Table S15). These results indicated that some RGA genes in the Rgrcs were strongly induced and a portion of them formed the VdRLs that participated in Verticillium wilt response in cotton.Fig. 6

Bottom Line: A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications.In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. chenjieyin@caas.cn.

ABSTRACT

Background: Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs.

Results: The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.

Conclusions: The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.

No MeSH data available.


Related in: MedlinePlus