Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations

• Published in: The plant genome 2018-03, Vol.11 (1), p.1-18
• Main Authors: Okeke, Uche Godfrey, Akdemir, Deniz, Rabbi, Ismail, Kulakow, Peter, Jannink, Jean‐Luc
• Format: Article
• Language: English
• Subjects: Agricultural production; beta Carotene - genetics; Calvin cycle; Carotenoids; Cassava; Chromosome 1; Cloning; Dry matter; Gene mapping; Genetic control; Genome, Plant; Genomes; Genomics; Glucose isomerase; Heritability; Kinases; Manihot - chemistry; Manihot - genetics; Manihot esculenta; Original Research; Phenotypic variations; Plant Proteins - genetics; Polymorphism; Polymorphism, Single Nucleotide; Population; Protein kinase; Protein-Serine-Threonine Kinases - genetics; Proteins; Quantitative Trait Loci; Reproducibility of Results; Single-nucleotide polymorphism; Starch - genetics; Subpopulations; Threonine; Tubers; Uridine; Vitamin A; β-Carotene
• ISSN: 1940-3372; 1940-3372
• DOI: 10.3835/plantgenome2017.06.0050

Core Ideas Regional heritability mapping (RHM) is effective for understanding the genetic architecture of complex traits in cassava. Prediction accuracies can reflect the impact of genomic segments on cassava dry matter (DM) content. Serine–threonine protein kinases (SnRKs) are candidates positionally associated with cassava DM. The prediction accuracy of SnRKs for cassava DM was 50% of the total accuracy from genome‐wide single nucleotide polymorphisms. 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.