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A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes.

Perry G, Dinatale C, Xie W, Navabi A, Reinprecht Y, Crosby W, Yu K, Shi C, Pauls KP - Front Plant Sci (2013)

Bottom Line: Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible.In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared.As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Agriculture, University of Guelph, Guelph ON, Canada.

ABSTRACT
Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared. These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). However, fifty-nine genes unique to OAC Rex were identified, with resistance gene homologues making up the largest category (10 genes identified). Two unique genes in OAC-Rex located within the SU91 resistance QTL have homology to P. acutifolius ESTs and may be potential sources of CBB resistance. As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean.

No MeSH data available.


Related in: MedlinePlus

Gene structure comparisons of genes surrounding the Niemann Pick gene locus in M. truncatula, G. max, and P. vulgaris. Two genes from upstream (A) and downstream (B) of the Niemann Pick like genes are compared for their exon/intron structure similarities. Homologies were very high, BLAST e = 0.0.
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Figure 9: Gene structure comparisons of genes surrounding the Niemann Pick gene locus in M. truncatula, G. max, and P. vulgaris. Two genes from upstream (A) and downstream (B) of the Niemann Pick like genes are compared for their exon/intron structure similarities. Homologies were very high, BLAST e = 0.0.

Mentions: A comparison of the exon/intron structures of the P. vulgaris Niemann Pick-like genes to those in other species indicated that, although the exon structure between the OAC-Rex genes and the G19833 gene are highly conserved, the structures are only marginally conserved between G19833 P. vulgaris, G. max, and Medicago. A BLAST analysis indicated that there is only one copy of the Niemann Pick gene in G19833, three in G. max and one in Medicago (data not shown). An analysis of the surrounding genes in G19833 and OAC-Rex (Figure 9) indicates that the exon structure is conserved across species in these genes, and that only the Niemann Pick genes seem to possess this divergent exon/intron structure. Although expression data from P. vulgaris was not available at this time, an examination of the Medicago Gene Atlas (Benedito et al., 2008; http://mtgea.noble.org/v3/) indicated that the Niemann Pick analogues from M. truncatula (Medtr5g099070.1) and G. max (Glyma14g00400.1 and Glyma02g48070.1) appear to be expressed in all indexed tissues (data not shown).


A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes.

Perry G, Dinatale C, Xie W, Navabi A, Reinprecht Y, Crosby W, Yu K, Shi C, Pauls KP - Front Plant Sci (2013)

Gene structure comparisons of genes surrounding the Niemann Pick gene locus in M. truncatula, G. max, and P. vulgaris. Two genes from upstream (A) and downstream (B) of the Niemann Pick like genes are compared for their exon/intron structure similarities. Homologies were very high, BLAST e = 0.0.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3756299&req=5

Figure 9: Gene structure comparisons of genes surrounding the Niemann Pick gene locus in M. truncatula, G. max, and P. vulgaris. Two genes from upstream (A) and downstream (B) of the Niemann Pick like genes are compared for their exon/intron structure similarities. Homologies were very high, BLAST e = 0.0.
Mentions: A comparison of the exon/intron structures of the P. vulgaris Niemann Pick-like genes to those in other species indicated that, although the exon structure between the OAC-Rex genes and the G19833 gene are highly conserved, the structures are only marginally conserved between G19833 P. vulgaris, G. max, and Medicago. A BLAST analysis indicated that there is only one copy of the Niemann Pick gene in G19833, three in G. max and one in Medicago (data not shown). An analysis of the surrounding genes in G19833 and OAC-Rex (Figure 9) indicates that the exon structure is conserved across species in these genes, and that only the Niemann Pick genes seem to possess this divergent exon/intron structure. Although expression data from P. vulgaris was not available at this time, an examination of the Medicago Gene Atlas (Benedito et al., 2008; http://mtgea.noble.org/v3/) indicated that the Niemann Pick analogues from M. truncatula (Medtr5g099070.1) and G. max (Glyma14g00400.1 and Glyma02g48070.1) appear to be expressed in all indexed tissues (data not shown).

Bottom Line: Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible.In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared.As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Agriculture, University of Guelph, Guelph ON, Canada.

ABSTRACT
Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared. These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). However, fifty-nine genes unique to OAC Rex were identified, with resistance gene homologues making up the largest category (10 genes identified). Two unique genes in OAC-Rex located within the SU91 resistance QTL have homology to P. acutifolius ESTs and may be potential sources of CBB resistance. As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean.

No MeSH data available.


Related in: MedlinePlus