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

[摘要] English: Global efforts are underway to develop staple crops with improved levels of provitamin Acarotenoids to help combat dietary vitamin A deficiency (VAD), which has afflicted thehealth of resource-poor farmers in the developing world. As a staple crop for more than500 million people in sub-Saharan Africa, cassava (Manihot esculenta Crantz) enrichedwith provitamin A carotenoids could have a widespread nutritional impact. In Uganda,cassava is the second most consumed crop after bananas. Accordingly, the nationalcassava programme initiated a breeding pipeline to develop cassava genetic resourcescombining high carotenoid content with farmer-preferred traits. To advance this initiative, astudy was conducted with specific objectives to (1) determine the combining ability ofprovitamin A genotypes and gene actions in inheritance of carotenoid content and drymatter content (DMC) in cassava, (2) assess the effect of genotype by environmentinteraction (GEI) on accumulation of carotenoid content and DMC in cassava roots and (3)identify genomic regions and polymorphisms linked to natural variation for carotenoidcontent and DMC in cassava.A 6x6 partial diallel analysis was conducted to estimate combining ability of six provitaminA clones and gene actions controlling carotenoid content and DMC in cassava roots.Fifteen F1 families generated from diallel crosses were evaluated in two environments inUganda. General combining ability (GCA) effects were significant for total carotenoidcontent (TCC) and DMC, suggesting the relative importance of additive gene effects incontrolling these traits in cassava. Genotype MH02-073HS was the best general combinerfor TCC and fresh root weight (FRW) while NASE 3 was the best general combiner forDMC. Such genotypes with desirable GCA effects could form the genetic basis forbreeding programmes targeting improvement of cassava for TCC and DMC. Importantly,64 genotypes were selected from the 15 F1 families for advancement because of theirsuperior performance for TCC, DMC and FRW.When GEI effects for carotenoid content and DMC were assessed by evaluating 13advanced provitamin A clones in six environments, additive main effect and multiplicativeinteraction analysis showed significant variation among genotypes for TCC, FRW andDMC. Environmental effects were non-significant for TCC, but GEI effects were significantfor 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 furtherrecombination through systematic hybridisation programmes.To survey genetic factors associated with carotenoid content in cassava, a high throughputgenotyping-by-sequencing platform was used to genotype a panel of 591 genotypes using635 247 single nucleotide polymorphisms (SNPs) distributed across the cassava genome.Through marker-trait association testing, a genomic region stretching 1.37 Mb onchromosome 1 was identified to contain seven SNPs significantly associated withcarotenoid content in cassava. A survey of the cassava genome sequence v6.1 positionedthese SNPs in the vicinity of Manes.01G124200.1, a gene known to increase carotenoidconcentration in cassava roots. These findings demonstrated the usefulness of GWAS fordissecting the genetic architecture of traits in cassava and could offer practical grounds forimproving carotenoid content in cassava through MAS and genomic selection.Overall, a significant negative correlation was found between TCC and DMC, indicating theneed for breeders to adopt methods that can combine high levels of these traits, givenfarmers prefer high DMC. Nonetheless, the study suggested an opportunity for cassavabiofortification in eastern Africa. Improved genotypes were identified and geneticinformation generated, which could form the primary resources for systematic developmentof carotene-rich cassava varieties for deployment to farmers. Consumption of suchnutritious varieties would sustainably reduce VAD among resource-poor peasants, for thebenefit of their own physical and economic development.

[发布机构] University of the Free State