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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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Percent plant mortality for fourteen diverse cowpea genotypes exposed to Macrophomina phaseolina under drought stress in field experiments conducted at the University of California Riverside in 2006 (vertical) and 2007 (slanted). See text for complete genotype designations. Bars indicate ± standard error. * Mortality for IT98K-499-39 was zero in the 2007 experiment.
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Figure 1: Percent plant mortality for fourteen diverse cowpea genotypes exposed to Macrophomina phaseolina under drought stress in field experiments conducted at the University of California Riverside in 2006 (vertical) and 2007 (slanted). See text for complete genotype designations. Bars indicate ± standard error. * Mortality for IT98K-499-39 was zero in the 2007 experiment.

Mentions: Based on percent plant mortality, there were reproducible differences in genotypic response to drought-enhanced Macrophomina infection among the diverse set of fourteen cowpea genotypes over the two experiments conducted in 2006 and 2007 (Figure 1). Genotypes IT98K-499-39, Suvita 2, IT93K-503-1 and Mouride were the most resistant to disease development with mortality less than 10% in both experiments (Figure 1). Bambey 21 was the most susceptible genotype with a mortality of 25-39%, followed by CB46, UCR232 (IT82E-18), 524B, UCR24, and IT84S-2049. Other genotypes exhibited varying levels of intermediate response over both experiments (Figure 1).


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)

Percent plant mortality for fourteen diverse cowpea genotypes exposed to Macrophomina phaseolina under drought stress in field experiments conducted at the University of California Riverside in 2006 (vertical) and 2007 (slanted). See text for complete genotype designations. Bars indicate ± standard error. * Mortality for IT98K-499-39 was zero in the 2007 experiment.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Percent plant mortality for fourteen diverse cowpea genotypes exposed to Macrophomina phaseolina under drought stress in field experiments conducted at the University of California Riverside in 2006 (vertical) and 2007 (slanted). See text for complete genotype designations. Bars indicate ± standard error. * Mortality for IT98K-499-39 was zero in the 2007 experiment.
Mentions: Based on percent plant mortality, there were reproducible differences in genotypic response to drought-enhanced Macrophomina infection among the diverse set of fourteen cowpea genotypes over the two experiments conducted in 2006 and 2007 (Figure 1). Genotypes IT98K-499-39, Suvita 2, IT93K-503-1 and Mouride were the most resistant to disease development with mortality less than 10% in both experiments (Figure 1). Bambey 21 was the most susceptible genotype with a mortality of 25-39%, followed by CB46, UCR232 (IT82E-18), 524B, UCR24, and IT84S-2049. Other genotypes exhibited varying levels of intermediate response over both experiments (Figure 1).

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