Genomic research improves scientists’ understanding of cassava diversity and domestication


Genomic research improves scientists’ understanding of cassava diversity and domestication

RTB scientists are using next-generation DNA sequencing data to construct more accurate crop and species phylogenies, or evolutionary histories, shedding new light on the relationships among different populations and between cultivated crops and their wild relatives. This knowledge can help breeders locate new sources of desirable traits, or expand the use of interspecific breeding, and will facilitate marker-assisted selection and genomic-assisted breeding to accelerate genetic gains.

A collaboration between CIAT and IITA that included the DNA sequencing of more than 2,500 cassava accessions from Africa and South America – elite breeding clones, landraces and 21 cassava wild relatives – significantly enhanced scientists’ understanding of the structures of African and South American cassava populations and the history of the crop’s domestication. Analysis of genotyping by sequencing (GBS) data showed that accessions of most cultivated varieties (Manihot esculenta) are strongly divergent from the wild cassava relative M. glaziovii, except for improved varieties from IITA, especially Tropical Manioc Selection (TMS) clones. This confirms historical records that TMS clones trace back to an interspecific hybrid derived from backcrosses between M. glaziovii and M. esculenta, carried out in the early 20th century in Tanzania, in order to incorporate mosaic disease resistance into cultivated cassava.

Researchers also identified clones from research center collections with different names that are nearly identical. They determined that the recurrent use of a limited number of genotypes as parents has reduced the genetic diversity in breeding programs, especially in Africa. This knowledge will help breeders to restore genetic diversity in breeding populations.

Analysis of African cassava diversity initially concentrated on accessions from West African collections and farms, but is now being expanded to include 1,045 clones from Tanzanian breeding programs, which will be genotyped and analyzed in 2017. The Tanzanian germplasm is especially important because it contains critical sources of resistance to cassava brown streak virus, which causes major economic losses in East Africa.

Scientists at CIAT used a genome wide sequencing approach on Latin American accessions that provided new insight into cassava’s genetic differentiation in South America, and allowed researchers to revisit the hypotheses of the crop’s center of origin and closest wild relative. An estimation of genome-wide allele range of expansion suggests that cassava was domesticated on the western edge of the Amazon Basin, along the Andes mountain range, rather than the southern border of the Amazon basin, as suggested by previous research. At the same time, a genome-wide excess of shared derived alleles between cultivated cassava and its closest wild relatives using Patterson’s D statistic revealed that cassava’s most likely ancestor was revealed to be M. peruviana Müll.-Arg. rather than M. esculenta ssp flabellifolia, as is widely believed.

According to CIAT molecular geneticist and FP1 leader, Luis Augusto Becerra, this discovery indicates that M. peruviana could be a source of genes for important traits that cultivated M. esculenta lost during domestication. For example, resistance to whiteflies, which are vectors for various cassava diseases, has been reported in M. peruviana.

“We now need to prioritize exploring and preserving M. peruviana germplasm,” Becerra said. He explained that because M. peruviana has largely been ignored by breeders, it is underrepresented in collections, and suggested that an international field collection effort is needed to preserve M. peruviana diversity, since its natural habitat may be threatened by environmental destruction.

As an example of M. peruviana’s potential, Becerra cited the case of the cassava wild relative M. walkerae, which is resistant to postharvest physiological deterioration (PPD)— a process that renders the roots of most cassava varieties inedible within a matter of days. CIAT cassava breeders successfully transferred genes for PPD resistance from M. wankeria into cultivated cassava years ago, and are developing varieties that combine PPD resistance with consumer-preferred traits. CIAT researchers recently characterized some 200 M. wankeria genes linked to PPD resistance.

Such discoveries can help breeders to develop more resilient cassava varieties, with resistance to diseases, pests, or abiotic constraints that could become more intense under climate change.

Photo: Decoding the cassava genome. N.Palmer/CIAT

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