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Integrating genomics and molecular markers into sweetpotato breeding (photo: C. Bukania)

Integrating genomics and molecular markers into sweetpotato breeding

Thirty Sweetpotato SpeedBreeders attended a workshop on the use of genomic and molecular tools in Nairobi’s ILRI campus. The workshop took place from 6th to 7th June, as a prelude to the 15th Sweetpotato Breeders and Genomics annual meeting.


The workshop was organized by the GT4SP project under the theme: ‘an eye opener to integrating genomics and molecular markers into sweetpotato breeding’. The objective is to train a cohort of breeders in Sub-Saharan national research institutes in the use of molecular markers and genomics to accelerate the breeding and release of improved sweetpotato varieties. This particular meeting aimed at getting the breeders to open their eyes to ways in which they can use genomics-assisted breeding. It focussed on making things simple, understandable and doable for the breeders.


The workshop was officially opened by the Biosciences East and Central Africa – International Livestock Research Institute (BecA-ILRI) Hub Director Dr. Appolinaire Djikeng. He set the mood by highlighting the achievements made in breeding, and how molecular breeding would build upon these achievements. Djikeng stated that the partnership between ILRI, BecA and the International Potato Center (CIP) had contributed tremendously to building the region’s capacity in biotechnology and bioinformatics. Through the BecA-Hub capacity building and support to build in-country genotyping platforms, Djikeng expressed his optimism for continued collaboration with the North Carolina State University (NCSU), which is leading the GT4SP project. 


In his remarks, Dr. Craig Yencho, the leader for the GT4SP project, explained that the GT4SP was established in 2012. “It is the largest investment in sweetpotato genomics ever, having 20 principal investigators in seven institutions in six countries across four continents and five time zones. The 12.4 million dollar investment is only for one crop,” he said.


One of the challenges that has hindered the adoption of genomic tools is that genomics experts sometimes use language that a conventional breeder will not understand. This leads to the perception that genomics is a complex area that cannot be applied in practice.


To address this, the participants were exposed to a hands-on practical training. On the first day, they were guided through a lab session where they extracted DNA from sweetpotato leaves and tubers.  On the second day, they used the extracted DNA to create and analyse molecular data using open-source software for phylogenetic analysis. By creating a better understanding of how DNA works, the breeders gained insight into the daily molecular work in genomics.


The GT4SP trainers also discussed some of the bottlenecks in the adoption of molecular breeding in sweetpotato, shortage of well-trained personnel, inadequate high-throughput genotyping capacity, poor phenotyping infrastructure, and the lack of information systems or useful analysis tools in developing countries.


The approach taken by GT4SP in capacity building aims at creating a core of sweetpotato breeders who understand and apply genomics and molecular markers in their breeding programs. Molecular-breeding techniques have the potential to considerably cut the time taken to develop a new crop variety, often by more than half. In the context of the changing climatic conditions and increasing world population, such techniques are crucial for the smallholder farmer.


The breeders who attended the workshop expressed a lot of enthusiasm and interest in the demonstrated techniques. They felt that the hands-on approach simplified what the genomics team had, in previous meetings, been trying to explain to them. As a follow-up to the workshop, the GT4SP team will hold webinars and site visits to train the participants on using data analysis softwares, and to build their confidence in the integration of genomics into their breeding programs.


Highlights from the lab session:


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