Pre-requisites:
- Species selection based on priority listing from the 101 African Orphan Crops Consortium species
- National partners contacts interested on the species
- Existence of species diversity in natural or cultivated populations
Shortlisted species include:
- Faidherbia albida
- Vitellaria paradoxa
- Moringa oleifera,
- Sclerocarya birrea,
- Annona senegalensis
Each candidate would focus on one of the priority species, with work packages inspired by areas I or II as specified below:
The proposed outline of projects would remain the same as proposed in Area I for any of the species short listed above. For Area II, species for which a mapping population is available can only be used. At present it is available for Vitellaria paradoxa (shea).
Area-1: Applied Ecological Genomics and nutritional characterization
Title of project: To understand genomic, nutritional and phenotypic diversity in species X and developing SNP markers associated with a few important environmental parameters
Objectives:
- To understand and analyze genetic diversity in the natural and domestic stands of species X.
- To understand and analyze nutritional diversity in the fruits of natural and domestic stands of species X.
- To understand and analyze nutritional diversity in the fruits of natural and domestic stands of species X.
- To find out genomics markers associated with environmental variables as quasi-adaptation markers
Expected outcome:
- Understand natural variation in genetic, phenotypic and nutritional diversity of the species
- A few SNP markers (~50) linked with environmental variables that are known to impact adaptation of the species to high temperature, low moisture, and other important contributors.
- These markers help us to screen these populations and select 1/10th of them to go into pre-breeding orchards. This data will also be corroborated with nutritional and phenotypic data.
Tentative time-lines:
- Species distribution modelling and mapping using ensemble suitability modelling approaches[1], mapping of environmental diversity within species distribution range, devising collection strategy based on collection gap analysis, establishing collection and logistics protocols, hands on lab work- 6 months
- Collection of samples (each ecozone represents proportionate diversity to make a total of ~300-400 individuals with location mapping), sending/bringing leaves and fruits to relevant labs, DNA extraction- 8 months (caution- getting samples out of Ethiopia needs to be followed up within Ethiopian framework of law)
- Genotyping data generation- 4 months
- Genotyping data analysis- 4 months
- Nutritional data generation- 4 months
- Nutritional data analysis- 3 months
- Papers and thesis writing- 7 months
Total time: 3 years
Area 2: Applied Genomics
Title of project: Development of genomics resources for species X and its application for developing a linkage map. Species X must have a mapping population-priority to be given Vitellaria paradoxa (shea).
Objectives:
- To phenotype selected mapping population over 2-3 years
- To develop sufficient number of SNP markers for shea linkage mapping (~5000).
- Develop a SNP-marker based linkage map
Expected outcome:
- Development of an array of SNP markers for shea
- To understand phenotyping behavior of the mapping population
- A SNP linkage map for shea.
- Optional- to have QTL map of shea by fusing phenotype and genotype.
- Propose best bi-parental mapping scheme for next level of breeding
Tentative time-lines:
- Reconnaissance and understanding of the population to define proper achievable objectives- 4 months
- Phenotypic data collection- 4 months x 2 years= 8 months
- Genomics data screening to short list SNPs and designing SNP assays- 6 months
- Population screening using SNP markers- 6 months
- Genotype data analysis and linkage map construction- 6 months
- Papers and thesis- 6 months
Total time: 3 years
[1] One of the co-supervisors at ICRAF is the developer and maintainer of the BiodiversityR package in which application the applicants will be trained (see https://doi.org/10.1016/j.envsoft.2017.11.009 or http://www.worldagroforestry.org/atlas-central-america )
Interested candidates should send their CV and a cover letter justifying their candidature suitability to the Program Administrator at ICRAF, Ms. Nelly Mutio (n.mutio@cgiar.org). Deadline for application 22 April 2018. Only shortlisted candidates will be contacted. For further inquiries contact Dr. Alice Muchugi (a.muchugi@cgiar.org).