Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (3 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2008)

Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume worldwide. Cowpea is grown extensively in sub-Saharan Africa where it is an important staple. Root-knot nematode (RKN, Meloidogyne spp.) is a significant pest in cowpea. Several sources of resistance to RKN have been identified in cowpea, including the widely used Rk gene. As part of a study to elucidate the mechanism of Rk -mediated resistance, the histological response to avirulent M. incognita feeding of a resistant cowpea cultivar CB46 was compared with a susceptible near-isogenic line. It was found that the Rk-mediated resistance is a delayed response which lacked an early hypersensitive reaction (HR). Typically in pathogen resistance HR is closely associated with an oxidative burst (OB) in infected tissue. Following a basal OB during early infection in both susceptible and resistant cowpea roots no significant OB was detected, a profile consistent with the histological observations of a delayed resistance response.

As cowpea does not have a microarray platform, a readily available soybean (Glycine max) genome array was used to identify single feature polymorphisms (SFP) in cowpea. An algorithm called Robustified Projection Pursuit was used for data analysis and RNA was used as a surrogate for DNA to detect SFPs between two genetically diverse cowpea genotypes. Cowpea genomic amplicon sequencing was performed for SFP validation and a 71% validation rate was observed. This study demonstrated that the soybean genome array is a satisfactory platform for identification of SFPs in cowpea. Furthermore, this study provided an example of a method to extend genomic resources from well supported species to "orphan" crops like cowpea.

Transcriptome profiles of incompatible and compatible cowpea-RKN interactions for two time points using the Affymetrix soybean GeneChip were generated. The profiles indicated that the RKN resistance pathway was still partially suppressed at 9 days post-inoculation in resistant cowpea roots. Subtle variation of ROS concentration, induction of toxins and other defense related genes were indicated to play a role in this unique resistance mechanism. Further functional analysis of these differentially expressed genes will advance understanding of this intriguing plant-nematode interaction in a more precise manner.

  • 1 supplemental ZIP
Cover page: Characterization of Root-Knot Nematode Resistance in Cowpea and Utilization of Cross-Species Platforms in Legume Genomics
  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2010)
Abstract Background The locus Rk confers resistance against several species of root-knot nematodes (Meloidogyne spp., RKN) in cowpea (Vigna unguiculata). Based on histological and reactive oxygen species (ROS) profiles, Rk confers a delayed but strong resistance mechanism without a hypersensitive reaction-mediated cell death process, which allows nematode development but blocks reproduction. Results Responses to M. incognita infection in roots of resistant genotype CB46 and a susceptible near-isogenic line (null-Rk) were investigated using a soybean Affymetrix GeneChip expression array at 3 and 9 days post-inoculation (dpi). At 9 dpi 552 genes were differentially expressed in incompatible interactions (infected resistant tissue compared with non-infected resistant tissue) and 1,060 genes were differentially expressed in compatible interactions (infected susceptible tissue compared with non-infected susceptible tissue). At 3 dpi the differentially expressed genes were 746 for the incompatible and 623 for the compatible interactions. When expression between infected resistant and susceptible genotypes was compared, 638 and 197 genes were differentially expressed at 9 and 3 dpi, respectively. Conclusions In comparing the differentially expressed genes in response to nematode infection, a greater number and proportion of genes were down-regulated in the resistant than in the susceptible genotype, whereas more genes were up-regulated in the susceptible than in the resistant genotype. Gene ontology based functional categorization revealed that the typical defense response was partially suppressed in resistant roots, even at 9 dpi, allowing nematode juvenile development. Differences in ROS concentrations, induction of toxins and other defense related genes seem to play a role in this unique resistance mechanism.
  • 9 supplemental files
Cover page: Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp) using a soybean genome array
  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2008)

Background

Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.

Results

Here we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max) genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.

Conclusion

We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.
    Cover page: Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array
    Top