A call for Bambara groundnut lines for
- the 100 line genome re-sequencing phase of the African Orphan Crop Consortium (AOCC) Bambara groundnut genome sequencing project
- developing Association Genetics panel of genotype lines.
The African Orphan Crops Consortium (http://africanorphancrops.org/) is in the process of sequencing the Bambara groundnut genome based on a Zimbabwean line. As part of the sequencing effort, they will also be re-sequencing a further 100 lines, with a particular trait focus on nutritional and food security.
In addition, Crops for the Future (CFF ; http://www.cffresearch.org/ ) and Partners, together with the International Institute for Tropical Agriculture (IITA) are establishing an Association Genetics panel of around 500 genotype lines derived from landraces. These will be deep genotyped using Diversity Array Technologies (Dr Andrzej Kilian; DArT Pty Ltd, Canberra, Australia; http://www.diversityarrays.com/ ) to give an expected 5000+ markers per genotype line. The aim is for lines to be multiplied and to be available through the Standard Material Transfer Agreement for research and breeding work under the International Treaty For Plant Genetic Resources (http://www.planttreaty.org/; https://www.croptrust.org/ ).
It would also make sense to ensure that the re-sequence genotypes are present within the Association Genetics panel, to provide a powerful linkage between the genotyping/Association Genetics analysis and the genome sequence, for 100 lines out of 500 to begin with.
Microsatellite work has also shown that Bambara groundnut is strongly inbreeding (single seed from 123 landraces tested with 12 microsatellites marker show a residual heterozygosity of 0.02). This essentially means that seed derived from a single plant is an unselected inbred variety and is likely to be true breeding. This makes it possible for researchers and interested groups to contribute directly to the material which will be selected for resequencing and/or the Association Genetics panel, by providing seed from a landrace. A single plant will be selected for re-sequencing and/or genotyping with DArT markers. Seed from that selected line will then be multiplied and will become available for research use.
As the aim is to get both Genome Sequencing and the Association Genetics panels complete by the end of 2015, the material to be considered for re-sequencing and/or the Association Genetics panel needs to be identified by 1st April 2015.
The criteria for selection are:
- Material can be provided to ICRAF (Kenya) for re-sequencing or CFF (Malaysia)/IITA (Nigeria) for the Association Genetics panel by 1st July 2015. Please be aware that material will need to go through approve quarantine routes to arrive by 1st July
- Coverage of Agroecological zones, to ensure that all environments are represented
- Nutritional value and potential
- Other traits of value, e.g. reduce photoperiod sensitivity, disease resistance, cookability etc
- Geographical spread.
- Lines publicly available and fulfills one of the following (as specified by Dr Allen Van Deynze, on behalf of AOCC for re-sequencing)
- lines important to Africa
- lines with unique nutritional or productivity traits
- a broad representation of diversity worldwide (if available, gbs, ssr and geographical data is helpful)
The potential to integrate research efforts on bambara groundnut and push the genetics and genomics forward in 2015, to make common material available to partners in many countries could lead to a step change in the potential of this crop for addressing world food and nutritional security.
However, the opportunity has arisen at relatively short notice which means that the period for consultation is short. However, we do not wish to delay progress on this crop and must apologise for the short deadlines. Comments and suggestions are more than welcome and BamNetwork (www.bambaragroundnut.org) can form a focus for discussion and dissemination of progress.
Please direct queries or offers of germplasm to Ms Razlin Azman Halimi (email@example.com), in the first instance.
We thank you in advance and hope to hear from you soon
Dr Allen Van Deynze, AOCC
Prof Michael Abberton, IITA
Dr Sean Mayes, CFF