Abstract
The HarvestPlus program for cassava (Manihot esculenta Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies. The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including plant serine–threonine protein kinases (SnRKs), UDP (uridine diphosphate)-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Genes including an acid invertase, a neutral or alkaline invertase, and a glucose-6-phosphate isomerase were validated on the basis of an a priori list for the cassava starch pathway, and also a fructose-biphosphate aldolase from the Calvin cycle pathway. The power of the RHM procedure was estimated as 47% when the causal quantitative trait loci generated 10% of the phenotypic variance (sample size = 451). Cassava DM genetics are complex and RHM may be useful for complex traits.
Highlights
The HarvestPlus program for cassava (Manihot esculenta Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers
Significant genomic segments for the white cassava dry matter (DM) were observed on chromosomes 1, 4, 5, 10, 17, and 18; for the yellow cassava, a significant segment was only observed on chromosome 1 (Fig. 1)
For the top regional heritability mapping (RHM) hits in both cassava gene pools, we identified possible candidate genes and transcriptional regulators adjacent to these hits based on their involvement in the carbohydrate biosynthesis pathway, including members of the serine– threonine protein kinase (SnRK) family, members of the uridine diphosphate (UDP)-glycosyltransferase family, and UDPsugar transporters; specific plant transcriptional factors including members of the β helix-loop-helix family and mini-zinc fingers; and other genes involved in cell wall processes, root storage, and development including pectinases and β-vacuolar processing enzymes
Summary
The HarvestPlus program for cassava (Manihot esculenta Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Cassava currently ranks as the sixth world staple crop consumed by more than 500 million people in Africa, Asia, and South America (El-Sharkawy, 2003) It was originally a perennial shrub but is cultivated as an annual for its starchy root (El-Sharkawy, 2003).
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