Researchers have successfully mapped the genome of African cassava, using the TME 204 variety resistant to Cassava Mosaic Disease-2 (CMD2). This breakthrough is a significant milestone and it will help advance the breeding of new cassava varieties at speed with greater accuracy.
“The genome has a very high quality and accuracy, and the haplotypes of the heterozygous genome have been resolved with high confidence. It is now definitively the gold standard genome for African cassava. Our work has revealed several new and interesting features of the cassava genome that will be of importance for breeders and cassava scientists,” said the principal scientist of the research team, Prof Wilhelm Gruissem of the Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology in Zürich (ETH Zurich).
The work has been published open access in the Oxford Academics journal GIGA Science Press titled “The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features.”
Other researchers include Weihong Qi, Yi-Wen Lim, Andrea Patrignani, Pascal Schläpfer, Anna Bratus-Neuenschwander, Simon Grüter, Christelle Chanez, Nathalie Rodde, Elisa Prat, Sonia Vautrin, Margaux-Alison Fustier, Diogo Pratas, and Ralph Schlapbach.
A genome is the complete set of genes or genetic material present in an organism. It includes all hereditary instructions for creating and maintaining life, reproduction inclusive. Scientists use genome sequencing to find genes much easier and faster and understand how the genes work together for an organism’s growth and development.
Conventionally, cassava breeders rely on phenotypic features of mature plants, as is typical for clonally propagated crops. This is a major drawback as it takes up to six years to produce enough planting material for multi-location trials. The heterozygous nature of the crop and parental lines used to generate new segregating progenies make it difficult to identify parents with good breeding values.
Therefore, new technologies such as genomic selection (GS) and use of inbred progenitors based on doubled haploids are now being used to accelerate genetic gains in cassava, but they have been limited by the highly heterozygous crop with a repetitive and difficult-to-assemble genome. Despite continuous sequencing efforts using different technologies over the past decade, unresolved gaps and haplotypes persist in all chromosomes of currently available cassava genomes.
This new study now becomes handy as it generated phased and annotated chromosome pairs that allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution.
The study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.
Cassava is a vital staple root crop, and almost a billion people worldwide depend on it for food and raw materials. In Africa, the crop is a major source of livelihood for smallholder farmers and a plug for food security owing to its ability to withstand a wide array of environmental conditions. However, because cassava farming is constrained by weeds, pests, and viral diseases, breeders are concentrating on developing improved varieties.