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Genome-wide association mapping of provitamin A carotenoid content in cassava

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Abstract

Global efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency, which is widespread among 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 immense nutritional impact. To this effort, a genome-wide association study (GWAS) was conducted with the aim of identifying genomic regions controlling variation for carotenoid concentration in cassava as a basis for undertaking systematic genetic improvement for carotenoid content. A high throughput genotyping-by-sequencing platform was used to genotype a diverse association panel of 591 genotypes and identified 179,310 single nucleotide polymorphisms (SNPs) distributed across the cassava genome. A genomic region stretching 1.37 Mb on chromosome 1 was identified with four SNPs significantly associated with carotenoid content in cassava. A survey of cassava genome sequence v6.1 positioned these SNPs in the vicinity of Manes.01G124200.1 locus, which is a known gene responsible for increase in accumulation of provitamin A carotenoids in cassava roots. This study provides one of the pioneer insights into the practical application of GWAS for dissecting the genetic basis of nutritional traits in cassava. Findings presented herein offer practical grounds for improving carotenoid content in cassava through marker-assisted breeding and genomic selection.

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Acknowledgments

The authors are thankful to the East African Agricultural Productivity Project (EAAPP) for funding activities for field trials for this research. All the genotyping and bioinformatics analysis were done with support from the Buckler Laboratory at Cornell University.

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Authors and Affiliations

  1. National Crops Resources Research Institute, 9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala, Uganda

    Williams Esuma, Yona Baguma & Robert Sezi Kawuki

  2. Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa

    Liezel Herselman & Maryke Tine Labuschagne

  3. Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14850, USA

    Punna Ramu, Fei Lu & Edward S. Buckler

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  1. Williams Esuma
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  2. Liezel Herselman
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  3. Maryke Tine Labuschagne
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  4. Punna Ramu
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  5. Fei Lu
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Correspondence to Williams Esuma.

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10681_2016_1772_MOESM3_ESM.tiff

Supplementary Fig. 1 Scatter plot of 591 genotypes based on principal component analysis using GAPIT programme (Lipka et al. 2012). PC1 = principal component 1; PC2 = principal component 2. Supplementary material 3 (TIFF 125 kb)

10681_2016_1772_MOESM4_ESM.tiff

Supplementary Fig. 2 Plot of genome-wide linkage disequilibrium decay based on adjacent pairwise genetic and physical distance. Pairs with distance >60 kb are not shown. Supplementary material 4 (TIFF 357 kb)

10681_2016_1772_MOESM5_ESM.tiff

Supplementary Fig. 3 Manhattan plots for genome-wide diagnosis of association signals based on means of total carotenoid content. P and Q are linkage groups containing unanchored scaffolds in the cassava genome sequence v6.1. Horizontal blue and red lines are the suggestive and 5 % Bonferroni threshold lines, respectively. Supplementary material 5 (TIFF 486 kb)

10681_2016_1772_MOESM6_ESM.tiff

Supplementary Fig. 4 Manhattan plot for genome-wide diagnosis of association signals based and root flesh colour. P and Q are linkage groups containing unanchored scaffolds in the cassava genome sequence v6.1. Horizontal blue and red lines are the suggestive and 5 % Bonferroni threshold lines, respectively. Supplementary material 6 (TIFF 461 kb)

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Esuma, W., Herselman, L., Labuschagne, M.T. et al. Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica 212, 97–110 (2016). https://doi.org/10.1007/s10681-016-1772-5

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