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

ABSTRACT: The HarvestPlus program for cassava ( Crantz) fortifies cassava with ?-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.

SUBMITTER: Okeke UG

PROVIDER: S-EPMC7822058 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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

Okeke Uche Godfrey UG Akdemir Deniz D Rabbi Ismail I Kulakow Peter P Jannink Jean-Luc JL

The plant genome 20180301 1

The HarvestPlus program for cassava ( 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 valid ...[more]

PMID: 29505634

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Project description:Cassava (Manihot esculenta Crantz) is an essential stable food crop in Sub-Saharan Africa commonly consumed amongst the low-income communities in Africa. Though cassava roots and leaf have vast economic and commercial benefits, it produces cyanogenic glycosides, which are toxic and most often responsible for the bitter taste of some cassava cultivars. The study evaluates the cassava roots and leaves' cyanogenic potential and dry matter content of the Genetic Gain Assessment trial grown in a different environment. It establishes the association between the cyanogenic potential (CNP) and the roots and leaves dry matter (DM). Genetic Gain Assessment (GGA) cassava genotypes (N = 400) selected for the Uniform Yield Trial (UYT) breeding stage were planted under IVS (Dry season in Inland Valley Hydromorphic area) and Upland (rain-fed conditions) in two locations of IITA Research Farms, namely; Ibadan (IVS and Upland) and Mokwa (Upland) in Nigeria. The CNP content of cassava leaves in IVS, Mokwa, and Upland ranged from 3.39 to 272.16 mg/100 g, 4.28 to 228.72 mg/100 g, and 13.13 to 127.39 mg/100 g, respectively. However, the respective CNP range in root samples across IVS, Mokwa, and Upland was 0.76-76.31 mg/100 g, 0.94-136.53 mg/100 g, and 2.37-47.11 mg/100 g. Also, the mean ± SD of DM content of leaves were 27.97 ± 3.01%, 28.81 ± 4.01%, and 13.65 ± 3.69%, respectively, in IVS, Mokwa, and Upland, while the root samples had mean ± SD of DM content of 38.09 ± 4.80%, 32.69 ± ,5.93% and 24.63 ± 5.07% respectively. Furthermore, location and genotype had a highly significant effect (p < 0.001) on the CNP and DM of roots and leaves. Also, linear regressions were established between CNP and DM of root and leaf with regression equation; DM-Root = 1.1999*DM-Leaf (r = 0.956) and CNP-Root = 0.29006*CNP-Leaf (r = 0.54). The relationship between the DM (root and leaf) and CNP (root and leaf) could serve as a valuable "inter-prediction" tool for these parameters.

Project description:Storage roots of cassava (Manihot esculenta Crantz), a major subsistence crop of sub-Saharan Africa, are calorie rich but deficient in essential micronutrients, including provitamin A β-carotene. In this study, β-carotene concentrations in cassava storage roots were enhanced by co-expression of transgenes for deoxy-d-xylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin-type 1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 μg/g DW, 15- to 20-fold increases relative to roots from nontransgenic plants. Approximately 85%-90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. β-Carotene-accumulating storage roots displayed delayed onset of postharvest physiological deterioration, a major constraint limiting utilization of cassava products. Large metabolite changes were detected in β-carotene-enhanced storage roots. Most significantly, an inverse correlation was observed between β-carotene and dry matter content, with reductions of 50%-60% of dry matter content in the highest carotenoid-accumulating storage roots of different cultivars. Further analysis confirmed a concomitant reduction in starch content and increased levels of total fatty acids, triacylglycerols, soluble sugars and abscisic acid. Potato engineered to co-express DXS and crtB displayed a similar correlation between β-carotene accumulation, reduced dry matter and starch content and elevated oil and soluble sugars in tubers. Transcriptome analyses revealed a reduced expression of genes involved in starch biosynthesis including ADP-glucose pyrophosphorylase genes in transgenic, carotene-accumulating cassava roots relative to nontransgenic roots. These findings highlight unintended metabolic consequences of provitamin A biofortification of starch-rich organs and point to strategies for redirecting metabolic flux to restore starch production.

Dataset Information

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

Publications

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

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