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Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.].

Muchero W, Ehlers JD, Close TJ, Roberts PA - BMC Genomics (2011)

Bottom Line: Based on annotated genic SNPs as well as synteny with soybean (Glycine max) and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals.Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively.Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nematology Dep., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA.

ABSTRACT

Background: Macrophomina phaseolina is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [Vigna unguiculata (L) Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance to M. phaseolina and the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs).

Results: Nine quantitative trait loci (QTLs), accounting for between 6.1 and 40.0% of the phenotypic variance (R2), were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (Glycine max) and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals. QTL Mac-2 explained the largest percent R2 and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively. Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions. Only three Macrophomina resistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress and Macrophomina infection.

Conclusion: Effective sources of host resistance were identified in this study. QTL mapping and synteny analysis identified genomic loci harboring resistance factors and revealed candidate genes with potential for further functional genomics analysis.

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Effect of the combination of Mac-2 and Mac-5 QTL on mean percent plant mortality (± standard error) based on genotypic classes carrying both favorable alleles (++, grey bars) and  genotypes (--, white bars) for field experiments in 2006, 2007, and 2008.
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Figure 6: Effect of the combination of Mac-2 and Mac-5 QTL on mean percent plant mortality (± standard error) based on genotypic classes carrying both favorable alleles (++, grey bars) and genotypes (--, white bars) for field experiments in 2006, 2007, and 2008.

Mentions: Eight QTLs (Mac-1 to Mac-8) were selected for the single and pair-wise analysis based on their consistency in map location across experiments. In general, mean percent mortalities for the genotypes were higher than genotypes with favorable alleles. However, in the analysis based on single QTLs, only Mac-1, Mac-2 and Mac-7 showed statistically significant differences out of the eight QTLs (Figure 5), and 15 out of the 28 pair-wise combinations showed significant differences (Table 5). Percent reductions for the pair-wise combinations ranged from -5.8 to 47.6% with six combinations resulting in a reduction of mean percent mortality greater than 40% (Table 5). Five of the six combinations had QTL Mac-7 in common and these ranged from 42.8% to 47.6% reduction in mean percent mortality. The remaining Mac-2/Mac-5 combination resulted in a 41.0% percent reduction, and the genotypes for this combination also had the highest mean percent mortality (18.8% ± 3.37%). Individually, Mac-2 and Mac-5 resulted in reductions of mean percent mortality of 19.6% and 22.5%, respectively, suggesting an additive effect in genotypes carrying both favorable alleles. This QTL combination was chosen for further analysis using the 2006 and 2007 data. The Mac-2/Mac-5 combination resulted in a 65.6% reduction in mean percent mortality based on 2006 data and 58.5% for the 2007 data (Figure 6). Although they exhibited the largest reductions on percent mortality, QTL combinations with Mac-7 were not favored for this analysis due to potential linkage or pleiotropic effects of the Mac-7 locus with maturity which may limit its practical use.


Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.].

Muchero W, Ehlers JD, Close TJ, Roberts PA - BMC Genomics (2011)

Effect of the combination of Mac-2 and Mac-5 QTL on mean percent plant mortality (± standard error) based on genotypic classes carrying both favorable alleles (++, grey bars) and  genotypes (--, white bars) for field experiments in 2006, 2007, and 2008.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3025960&req=5

Figure 6: Effect of the combination of Mac-2 and Mac-5 QTL on mean percent plant mortality (± standard error) based on genotypic classes carrying both favorable alleles (++, grey bars) and genotypes (--, white bars) for field experiments in 2006, 2007, and 2008.
Mentions: Eight QTLs (Mac-1 to Mac-8) were selected for the single and pair-wise analysis based on their consistency in map location across experiments. In general, mean percent mortalities for the genotypes were higher than genotypes with favorable alleles. However, in the analysis based on single QTLs, only Mac-1, Mac-2 and Mac-7 showed statistically significant differences out of the eight QTLs (Figure 5), and 15 out of the 28 pair-wise combinations showed significant differences (Table 5). Percent reductions for the pair-wise combinations ranged from -5.8 to 47.6% with six combinations resulting in a reduction of mean percent mortality greater than 40% (Table 5). Five of the six combinations had QTL Mac-7 in common and these ranged from 42.8% to 47.6% reduction in mean percent mortality. The remaining Mac-2/Mac-5 combination resulted in a 41.0% percent reduction, and the genotypes for this combination also had the highest mean percent mortality (18.8% ± 3.37%). Individually, Mac-2 and Mac-5 resulted in reductions of mean percent mortality of 19.6% and 22.5%, respectively, suggesting an additive effect in genotypes carrying both favorable alleles. This QTL combination was chosen for further analysis using the 2006 and 2007 data. The Mac-2/Mac-5 combination resulted in a 65.6% reduction in mean percent mortality based on 2006 data and 58.5% for the 2007 data (Figure 6). Although they exhibited the largest reductions on percent mortality, QTL combinations with Mac-7 were not favored for this analysis due to potential linkage or pleiotropic effects of the Mac-7 locus with maturity which may limit its practical use.

Bottom Line: Based on annotated genic SNPs as well as synteny with soybean (Glycine max) and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals.Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively.Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nematology Dep., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA.

ABSTRACT

Background: Macrophomina phaseolina is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [Vigna unguiculata (L) Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance to M. phaseolina and the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs).

Results: Nine quantitative trait loci (QTLs), accounting for between 6.1 and 40.0% of the phenotypic variance (R2), were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (Glycine max) and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals. QTL Mac-2 explained the largest percent R2 and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively. Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions. Only three Macrophomina resistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress and Macrophomina infection.

Conclusion: Effective sources of host resistance were identified in this study. QTL mapping and synteny analysis identified genomic loci harboring resistance factors and revealed candidate genes with potential for further functional genomics analysis.

Show MeSH
Related in: MedlinePlus