Molecular Breeding of African Staple Food Crops

Research Interest

I hope to draw on my background in plant breeding, statistical genetics, molecular biology, and bioinformatics as a foundation for studying and applying more advanced functional genomics techniques to develop an efficient and effective marker assisted breeding program for cassava and other IITA mandate crops. I am particularly interested in introducing cost-effective high throughput genotyping techniques feasible in developing countries.
Presently I am working on Rockefeller Foundation funded project “Enhancement of cassava productivity in sub-Saharan Africa”. The aim of the project is to tag all sources of natural resistance to CMD and utilize it to pyramid CMD resistant genes in cassava germplasm. Molecular markers developed will be used to combine different sources of resistance genes into elite parental lines for use in developing durable disease and pest resistant germplasm for several African countries. The end result will be establishment of a protocol for molecular marker-assisted pyramiding of resistance genes. Presently, our focus is on simple sequence repeat (SSR) markers, since SSRs are PCR-based markers that allow high throughput screening with ABI genetic analyzer. We are pursuing various approaches towards achieving our goal including Development of molecular markers for disease resistance genes using BSA, linkage map, resistance gene analogs (RGA), and most recently the TILLING. Furthermore, I collaborate with colleagues in IITA and other partners on projects involving global expression profiling (microarray), EST analysis, SNP and other genomic projects.

Plant Breeding

I have started my career as plant breeder/geneticist work on low land legumes including common bean (Phaseolus vulgaris), soybean (Glycine max), pigeon pea, mung bean, and other minor legumes. My MS thesis was on combining ability for yield and yield components in P. vulgaris. As a leader of crop improvement division in Pawe research station in Ethiopia, I had the opportunity to work on oil crops (sunflower, safflower, noug (Guizota abyssinica)), cereals (maize, sorghum, millet, upland rice).

Molecular Biology

My interest in biotechnology was sparked during my undergraduate time. Because of my enthusiasm for molecular biology, I have rapidly gained extensive laboratory experience in molecular techniques. I was first exposed to molecular biology in 1994 at Oregon State University, department of crop and soil science. Under the guidance of Professor Steve Knapp, I have performed projects involving construction of genetic linkage map, construction and screening of genomic library for simple sequence repeat, and identification of resistance gene analogs in sunflower, Helianthus annuus. As a postdoctoral fellow at IITA, I have worked on mapping of cassava mosaic disease (CMD) resistance gene in cassava, Manihot esculenta.

Bioinformatics

Cognizant of the need for expertise in bioinformatics tools in this post-genomic era, I have developed extensive bioinformatics skills through projects and courses taught by experts from world renowned universities and institutions.

• Statistical analysis of Genchip and cDNA microarray expression data (R/BioConductor, BRB ArrayTools, ScanAnalyze, GCOS, Partek)
• Expertise in genome sequence alignment, contig assembly, homology searching, SNP detection, designing PCR primers for sensitive assays
• Breadth of bioinformatics experience in computational tool development, data mining (curation), data annotation, and visualization
• Extensive use of various public molecular biology databases including, gene prediction, protein domains, protein motifs and active sites, comparative genomics, gene regulatory regions, Gene Ontology, and interspersed repeat elements.
• Working knowledge of programming languages C++ and Perl
• Hands-on experience with UNIX, Mac, Windows/dos environment
• Homology modeling of three-dimensional protein structure and protein-ligand docking
• Construction of genetic linkage map and QTL analysis
• Diversity analysis and clustering