Developing Xspecies approaches for genomics and transcriptomics - using resources developed in major species for research in Bambara groundnut
2013
Chai, Hui Hui | Lai, Hung-Ming | Guo, Hui | Basu, S.M. | Massawe, F. | Azam-Ali, S. | Graham, N. | Broadley, M. | May, S. | Mayes, S.
Bambara groundnut (Vigna subterranean L. Verdc.) is a legume mainly grown by subsistence and small-scale farmers in sub-Saharan Africa. This underutilised crop has nutritious and protein-rich seeds, can grow in poor soils and is more tolerant to drought compared to similar major crop species. Like Bambara groundnut, there are many minor and underutilised crops which have not undergone extensive research yet and for which few genomic resources currently exist. We aim to investigate ways to use resources that have already been developed in major species for crop improvement programs in minor and underutilised species. Affymetrix microarrays are powerful and popular tools for genomic and transcriptomic studies, but they require extensive species-specific sequence information to design. Thus, to save time and reduce cost, one option is to use an XSpecies microarray. Here we have used the XSpecies approach to detect genomic differences between two parents of a Bambara groundnut controlled cross between VSSP11 (low stem number per plant) and DipC (high stem number per plant), in order to attempt to develop molecular markers that are linked to the gene(s) controlling stem number as a test case. Bambara groundnut DNA derived from two F2 bulks that are constructed for high and low stem number, respectively, were hybridised separately to the Arabidopsis ATH1 and the Medicago truncatula Affymetrix GeneChips. PCR primers were designed from array probe sequences based on hybridisation signals visualised in the PIGEONS.v1 software. Differences detected between the two parents and the F2 bulks in silico are being tested in the lab to determine whether this is a useful way to generate markers to traits controlled by limited numbers of genes in underutilised and minor crop species. Results to date are presented.
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