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

Muchero, Wellington; Ehlers, Jeffrey D.; Close, Timothy J.; Roberts, Philip A.

doi:10.1186/1471-2164-12-8

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

Journal Article · Wed Jan 05 00:00:00 EST 2011 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-12-8· OSTI ID:1626411

Muchero, Wellington ^[1]; Ehlers, Jeffrey D. ^[2]; Close, Timothy J. ^[2]; Roberts, Philip A. ^[3]

Univ. of California, Riverside, CA (United States). Nematology Dept.; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Plant Systems Biology Group
Univ. of California, Riverside, CA (United States). Botany and Plant Sciences Dept.
Univ. of California, Riverside, CA (United States). Nematology Dept.

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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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1626411

Journal Information:: BMC Genomics, Vol. 12, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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

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