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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

Phaseolus vulgaris chromosome Pv08 linkage group associated with the SCAR and SNP markers.The solid lines originating from the linkage map indicate the physical region selected for candidate gene search. The solid bars indicate the annotated genes with no similarity to other members of the annotated genes. The different shaded regions indicate the groups of annotated genes with high degree of nucleotide similarity.
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pone.0139450.g001: Phaseolus vulgaris chromosome Pv08 linkage group associated with the SCAR and SNP markers.The solid lines originating from the linkage map indicate the physical region selected for candidate gene search. The solid bars indicate the annotated genes with no similarity to other members of the annotated genes. The different shaded regions indicate the groups of annotated genes with high degree of nucleotide similarity.

Mentions: Anthracnose disease ratings for C. lindemuthianum Race 73 of the 94 F5 families of Nautica x B09197 showed a distribution pattern with more entries falling in the resistant category. It is possible that the population showed distorted segregation towards resistance or inadvertent selection for resistance has taken place in early generations. The distribution pattern of the anthracnose resistance rating among the entries used is included in S1 Fig. Out of the 5361 markers used for genotyping, only 538 showed polymorphisms and were used for mapping in the 94 F4:5 RIL population. The 10.4% level of polymorphism observed was low. The two parents of the mapping population belonged to navy and black bean market classes, both of which are of Mesoamerican in origin. A recent QTL mapping study by Yuste-Lisbona et al [53] with 3700 AFLP, 1035 SSR and 251 SNP markers revealed 7.5%, 10.2% and 7.2% polymorphisms respectively between the common bean parents used. It is possible that the level of genetic diversity among cultivated beans is relatively low. Single marker analysis and interval mapping using WinQTL cartographer with the mapping population identified a group of SNP and SCAR markers with significant association with anthracnose resistance (Table 1, S1 File). This marker group including the SCAR markers SAS13, SH18 and SBB14, known to be associated with Co–42 allele and the Co–4 locus was assembled in a linkage group according to the physical positions of the SNP markers on Pv08. Some markers that were clustered together were removed in order to increase clarity (Table 1; Fig 1). Since Co–4 is the only known anthracnose resistance gene located on Pv08 and is the only gene with major effects segregating for resistance to race 73 in the Nautica x B09197 population, it is likely that the identified group of SNP markers span the genomic region of the Co–4 gene. Within a 59.1 Mb region, there were several SNP markers and SCAR markers that had highly significant association with anthracnose resistance (Table 1). Within this physical region, markers within a 2.35 Mb region, flanked by the SNP marker sc00089ln640327_372918 (497385 bp) and sc00065ln699804_339284 (2843266 bp) that had the highest association with anthracnose resistance based on the likelihood ratios as well as the larger amount of the phenotypic variation (R2) explained by markers (Table 1). Genomic sequences within this 2.35 Mb region were used as a query in local BLAST searches against the genomic sequences of Pv08 of G19833 (www.phytozome.org; [43]).


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)

Phaseolus vulgaris chromosome Pv08 linkage group associated with the SCAR and SNP markers.The solid lines originating from the linkage map indicate the physical region selected for candidate gene search. The solid bars indicate the annotated genes with no similarity to other members of the annotated genes. The different shaded regions indicate the groups of annotated genes with high degree of nucleotide similarity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4592015&req=5

pone.0139450.g001: Phaseolus vulgaris chromosome Pv08 linkage group associated with the SCAR and SNP markers.The solid lines originating from the linkage map indicate the physical region selected for candidate gene search. The solid bars indicate the annotated genes with no similarity to other members of the annotated genes. The different shaded regions indicate the groups of annotated genes with high degree of nucleotide similarity.
Mentions: Anthracnose disease ratings for C. lindemuthianum Race 73 of the 94 F5 families of Nautica x B09197 showed a distribution pattern with more entries falling in the resistant category. It is possible that the population showed distorted segregation towards resistance or inadvertent selection for resistance has taken place in early generations. The distribution pattern of the anthracnose resistance rating among the entries used is included in S1 Fig. Out of the 5361 markers used for genotyping, only 538 showed polymorphisms and were used for mapping in the 94 F4:5 RIL population. The 10.4% level of polymorphism observed was low. The two parents of the mapping population belonged to navy and black bean market classes, both of which are of Mesoamerican in origin. A recent QTL mapping study by Yuste-Lisbona et al [53] with 3700 AFLP, 1035 SSR and 251 SNP markers revealed 7.5%, 10.2% and 7.2% polymorphisms respectively between the common bean parents used. It is possible that the level of genetic diversity among cultivated beans is relatively low. Single marker analysis and interval mapping using WinQTL cartographer with the mapping population identified a group of SNP and SCAR markers with significant association with anthracnose resistance (Table 1, S1 File). This marker group including the SCAR markers SAS13, SH18 and SBB14, known to be associated with Co–42 allele and the Co–4 locus was assembled in a linkage group according to the physical positions of the SNP markers on Pv08. Some markers that were clustered together were removed in order to increase clarity (Table 1; Fig 1). Since Co–4 is the only known anthracnose resistance gene located on Pv08 and is the only gene with major effects segregating for resistance to race 73 in the Nautica x B09197 population, it is likely that the identified group of SNP markers span the genomic region of the Co–4 gene. Within a 59.1 Mb region, there were several SNP markers and SCAR markers that had highly significant association with anthracnose resistance (Table 1). Within this physical region, markers within a 2.35 Mb region, flanked by the SNP marker sc00089ln640327_372918 (497385 bp) and sc00065ln699804_339284 (2843266 bp) that had the highest association with anthracnose resistance based on the likelihood ratios as well as the larger amount of the phenotypic variation (R2) explained by markers (Table 1). Genomic sequences within this 2.35 Mb region were used as a query in local BLAST searches against the genomic sequences of Pv08 of G19833 (www.phytozome.org; [43]).

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