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Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

Burt AJ, William HM, Perry G, Khanal R, Pauls KP, Kelly JD, Navabi A - PLoS ONE (2015)

Bottom Line: A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833.There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies.It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

ABSTRACT
Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

No MeSH data available.


Related in: MedlinePlus

Alignment of predicted protein sequence of gene COK–4 with the annotated genes Phvul.008G028300, Phvul.008G028400, Phvul.008G028500 and Phvul.008G028600.
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pone.0139450.g002: Alignment of predicted protein sequence of gene COK–4 with the annotated genes Phvul.008G028300, Phvul.008G028400, Phvul.008G028500 and Phvul.008G028600.

Mentions: In addition to the seven annotated genes that had no sequence similarity to other putative candidate genes in our study, there were 25 annotated genes that showed nucleotide, amino acid and predicted protein sequence similarities to other members of the putative candidate genes. These 25 annotated sequences belonged to three distinct groups (Fig 1 and Table 2). In one group, there were 17 sequences that had high level of similarity at nucleotide and amino acid sequences and all of them contained LRR-RLK predicted protein domains. Table 3 summarizes the nucleotide alignment details of the 17 annotated genes. The coding sequence length among this group of annotated genes ranged from 660–1128 bases (Table 3). Although there was a high degree of nucleotide sequence similarity among the 17 annotated genes, there were a number of single nucleotide polymorphisms (SNP) and insertions/deletions among the members that characterized this group (S2 Fig). Phvul.008G028600 with a coding sequence length of 1128 bp had a unique 123 bp upstream sequence. Phvul.008G029700 had a unique insertion of 63 bp and Phvul.008G026700 had a unique insertion of 9 bp. GeneBank nun-redundant database searches revealed four annotated genes in this group that identified a high level of sequence similarity to the COK–4 candidate gene with a coding sequence length of 1110 nucleotides that is known to be in close association with Co–42 [42]. Similarity statistics of the annotated gene Phvul.008G028300 (AF 153441/GI 9796477; 95% identity, e = 0, 49 mismatches); Phvul.008G028400 (AF 153441/GI 9796477; 95% identity, e = 0, 37 mismatches); Phvul.008G028500 (AF 153441/GI 9796477; 96% identity, e = 0, 39 mismatches); Phvul.008G028600 (AF 153441/GI 9796477; 98% identity, e = 0, 18 mismatches) indicate the high degree of nucleotide sequence similarities in the coding regions between the Co–4 candidate gene and the four genes identified in the study. The complete nucleotide alignment of the coding sequences of the four annotated genes with the COK–4 candidate gene is available in S3 Fig. Phvul.008G028400 had a coding sequence length of 897 bp which is the shortest of the four sequences. It had a deletion of 48 bp region compared to COK–4 and the other two annotated sequences from position 153 bp (S3 Fig). Compared to the COK–4 sequence, the annotated genes Phvul.008G028300, Phvul.008G028400 and Phvul.008G028500 contained more than 30 SNPs whereas the fourth annotated sequence Phvul.008G028600, with a coding sequence length of 1128 nucleotides had 12 SNPs. Phvul.008G028600 also had a 69 nucleotide deletion from position 849 that was unique to this annotated gene in comparison to COK–4 and the other three annotated genes. Phvul.008G028600 had an upstream 123 nucleotide region unique to this annotated gene. All four annotated genes had a 75–80 nucleotide deletion closer to the downstream region compared to COK–4, whereas the COK–4 had a unique deletion of 73 nucleotides compared to the four annotated genes at the downstream end (S3 Fig). The physical distance between Phvul.008G028300 and Phvul.008G028400 is 5.0 kb whereas Phvul.008G028400 and Phvul.008G028500 is separated by 3.7 kb and the distance between Phvul.008G028500 and Phvul.008G028600 is 6.1 kb. Melotto and Kelly [42] established that the gene COK–4 is part of the Co–4 locus and has a similar function as Pto gene in tomato [21]. The alignment with protein sequence similarities between COK–4 and the four annotated sequences is shown in Fig 2. The sequences contained a significant number of residues of leucine and isoleucine, typical of LRR domains. The COK–4 candidate gene AF 153441 had an insertion of 26 amino acid residues (Fig 2). Although Phvul.008G028600 has an amino acid sequence with 41 extra residues at the upstream end and 9 extra residues at the downstream end compared to the start codon of the other three members of this group and COK–4, the four annotated genes had predicted amino acid similarity of over 90% with COK–4. Melotto et al. [37] indicated the presence of multiple copies of COK–4 in the bean genome. A study by Oblessuc et al. [33] identified 18 COK–4 related genes on Pv08. Interestingly, all the members of the group of 17 annotated genes that had high degree of sequence similarity in our study are among the 18 genes reported by Oblessuc et al. [33]. Therefore, in addition to the four annotated genes that we identified to be associated with COK–4 gene reported by Melotto and Kelly [42], the other 13 genes in the cluster are also functionally related to COK–4. Since we used the genomic sequences flanked by the markers that gave high association with anthracnose resistance, it is likely that the region that was identified in our study covers a broader set of potential candidate genes in addition to the COK–4 gene cluster (Table 2). The 17 annotated genes in this group spanned genomic region of 317.6 kb. This region overlapped the second group of five related annotated genes as well as three annotated genes that did not have significant sequence similarities to other members (Table 2).


Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

Burt AJ, William HM, Perry G, Khanal R, Pauls KP, Kelly JD, Navabi A - PLoS ONE (2015)

Alignment of predicted protein sequence of gene COK–4 with the annotated genes Phvul.008G028300, Phvul.008G028400, Phvul.008G028500 and Phvul.008G028600.
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pone.0139450.g002: Alignment of predicted protein sequence of gene COK–4 with the annotated genes Phvul.008G028300, Phvul.008G028400, Phvul.008G028500 and Phvul.008G028600.
Mentions: In addition to the seven annotated genes that had no sequence similarity to other putative candidate genes in our study, there were 25 annotated genes that showed nucleotide, amino acid and predicted protein sequence similarities to other members of the putative candidate genes. These 25 annotated sequences belonged to three distinct groups (Fig 1 and Table 2). In one group, there were 17 sequences that had high level of similarity at nucleotide and amino acid sequences and all of them contained LRR-RLK predicted protein domains. Table 3 summarizes the nucleotide alignment details of the 17 annotated genes. The coding sequence length among this group of annotated genes ranged from 660–1128 bases (Table 3). Although there was a high degree of nucleotide sequence similarity among the 17 annotated genes, there were a number of single nucleotide polymorphisms (SNP) and insertions/deletions among the members that characterized this group (S2 Fig). Phvul.008G028600 with a coding sequence length of 1128 bp had a unique 123 bp upstream sequence. Phvul.008G029700 had a unique insertion of 63 bp and Phvul.008G026700 had a unique insertion of 9 bp. GeneBank nun-redundant database searches revealed four annotated genes in this group that identified a high level of sequence similarity to the COK–4 candidate gene with a coding sequence length of 1110 nucleotides that is known to be in close association with Co–42 [42]. Similarity statistics of the annotated gene Phvul.008G028300 (AF 153441/GI 9796477; 95% identity, e = 0, 49 mismatches); Phvul.008G028400 (AF 153441/GI 9796477; 95% identity, e = 0, 37 mismatches); Phvul.008G028500 (AF 153441/GI 9796477; 96% identity, e = 0, 39 mismatches); Phvul.008G028600 (AF 153441/GI 9796477; 98% identity, e = 0, 18 mismatches) indicate the high degree of nucleotide sequence similarities in the coding regions between the Co–4 candidate gene and the four genes identified in the study. The complete nucleotide alignment of the coding sequences of the four annotated genes with the COK–4 candidate gene is available in S3 Fig. Phvul.008G028400 had a coding sequence length of 897 bp which is the shortest of the four sequences. It had a deletion of 48 bp region compared to COK–4 and the other two annotated sequences from position 153 bp (S3 Fig). Compared to the COK–4 sequence, the annotated genes Phvul.008G028300, Phvul.008G028400 and Phvul.008G028500 contained more than 30 SNPs whereas the fourth annotated sequence Phvul.008G028600, with a coding sequence length of 1128 nucleotides had 12 SNPs. Phvul.008G028600 also had a 69 nucleotide deletion from position 849 that was unique to this annotated gene in comparison to COK–4 and the other three annotated genes. Phvul.008G028600 had an upstream 123 nucleotide region unique to this annotated gene. All four annotated genes had a 75–80 nucleotide deletion closer to the downstream region compared to COK–4, whereas the COK–4 had a unique deletion of 73 nucleotides compared to the four annotated genes at the downstream end (S3 Fig). The physical distance between Phvul.008G028300 and Phvul.008G028400 is 5.0 kb whereas Phvul.008G028400 and Phvul.008G028500 is separated by 3.7 kb and the distance between Phvul.008G028500 and Phvul.008G028600 is 6.1 kb. Melotto and Kelly [42] established that the gene COK–4 is part of the Co–4 locus and has a similar function as Pto gene in tomato [21]. The alignment with protein sequence similarities between COK–4 and the four annotated sequences is shown in Fig 2. The sequences contained a significant number of residues of leucine and isoleucine, typical of LRR domains. The COK–4 candidate gene AF 153441 had an insertion of 26 amino acid residues (Fig 2). Although Phvul.008G028600 has an amino acid sequence with 41 extra residues at the upstream end and 9 extra residues at the downstream end compared to the start codon of the other three members of this group and COK–4, the four annotated genes had predicted amino acid similarity of over 90% with COK–4. Melotto et al. [37] indicated the presence of multiple copies of COK–4 in the bean genome. A study by Oblessuc et al. [33] identified 18 COK–4 related genes on Pv08. Interestingly, all the members of the group of 17 annotated genes that had high degree of sequence similarity in our study are among the 18 genes reported by Oblessuc et al. [33]. Therefore, in addition to the four annotated genes that we identified to be associated with COK–4 gene reported by Melotto and Kelly [42], the other 13 genes in the cluster are also functionally related to COK–4. Since we used the genomic sequences flanked by the markers that gave high association with anthracnose resistance, it is likely that the region that was identified in our study covers a broader set of potential candidate genes in addition to the COK–4 gene cluster (Table 2). The 17 annotated genes in this group spanned genomic region of 317.6 kb. This region overlapped the second group of five related annotated genes as well as three annotated genes that did not have significant sequence similarities to other members (Table 2).

Bottom Line: A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833.There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies.It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

ABSTRACT
Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

No MeSH data available.


Related in: MedlinePlus