Genetic analysis and genome-wide association mapping of carotenoid and dry matter content in cassava

English: Global efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency (VAD), which has afflicted the health of resource-poor farmers in the developing world. As a staple crop for more than 500 million people in sub-Saharan Africa, cassava (Manihot esculenta Crantz) enriched with provitamin A carotenoids could have a widespread nutritional impact. In Uganda, cassava is the second most consumed crop after bananas. Accordingly, the national cassava programme initiated a breeding pipeline to develop cassava genetic resources combining high carotenoid content with farmer-preferred traits. To advance this initiative, a study was conducted with specific objectives to (1) determine the combining ability of provitamin A genotypes and gene actions in inheritance of carotenoid content and dry matter content (DMC) in cassava, (2) assess the effect of genotype by environment interaction (GEI) on accumulation of carotenoid content and DMC in cassava roots and (3) identify genomic regions and polymorphisms linked to natural variation for carotenoid content and DMC in cassava. A 6x6 partial diallel analysis was conducted to estimate combining ability of six provitamin A clones and gene actions controlling carotenoid content and DMC in cassava roots. Fifteen F1 families generated from diallel crosses were evaluated in two environments in Uganda. General combining ability (GCA) effects were significant for total carotenoid content (TCC) and DMC, suggesting the relative importance of additive gene effects in controlling these traits in cassava. Genotype MH02-073HS was the best general combiner for TCC and fresh root weight (FRW) while NASE 3 was the best general combiner for DMC. Such genotypes with desirable GCA effects could form the genetic basis for breeding programmes targeting improvement of cassava for TCC and DMC. Importantly, 64 genotypes were selected from the 15 F1 families for advancement because of their superior performance for TCC, DMC and FRW. When GEI effects for carotenoid content and DMC were assessed by evaluating 13 advanced provitamin A clones in six environments, additive main effect and multiplicative interaction analysis showed significant variation among genotypes for TCC, FRW and DMC. Environmental effects were non-significant for TCC, but GEI effects were significant for all these traits. From this effort, best performing genotypes were identified for TCC, DMC and FRW and could constitute the genetic material for on-farm testing or further recombination through systematic hybridisation programmes. To survey genetic factors associated with carotenoid content in cassava, a high throughput genotyping-by-sequencing platform was used to genotype a panel of 591 genotypes using 635 247 single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through marker-trait association testing, a genomic region stretching 1.37 Mb on chromosome 1 was identified to contain seven SNPs significantly associated with carotenoid content in cassava. A survey of the cassava genome sequence v6.1 positioned these SNPs in the vicinity of Manes.01G124200.1, a gene known to increase carotenoid concentration in cassava roots. These findings demonstrated the usefulness of GWAS for dissecting the genetic architecture of traits in cassava and could offer practical grounds for improving carotenoid content in cassava through MAS and genomic selection. Overall, a significant negative correlation was found between TCC and DMC, indicating the need for breeders to adopt methods that can combine high levels of these traits, given farmers prefer high DMC. Nonetheless, the study suggested an opportunity for cassava biofortification in eastern Africa. Improved genotypes were identified and genetic information generated, which could form the primary resources for systematic development of carotene-rich cassava varieties for deployment to farmers. Consumption of such nutritious varieties would sustainably reduce VAD among resource-poor peasants, for the benefit of their own physical and economic development.