Abstract
Cassava (Manihot esculenta Crantz) is an important crop for starch production, and recently much effort has been directed towards improving its starch properties. Waxy cassava starch has some advantages over starch from other sources due to its neutral flavor and pasting properties. The genetic inheritance of the waxy starch phenotype is considered to be monogenic and recessive; however, it is possible that other genomic regions contribute to the waxy phenotype. The aim of this study was to evaluate the power of genome-wide association studies (GWAS) to detect variants related to waxy starch and to identify alternative genes or genomic regions. For this purpose, a set of 382 samples (waxy and non-waxy) was analyzed using a panel of 20,956 single nucleotide polymorphisms (SNPs). All genotypes were evaluated in relation to the presence of waxy starch, determined using the 2% iodine test. The GWAS was performed using the retrospective CAse–control Retrospective Association Testing (CARAT) model. Kinship and population structure were also investigated and added to the model. Ten SNPs were found to be significant and located on chromosome 2 and co-located in genomic regions. The significant SNPs are in a region near the Granule-bound starch synthase I (GBSSI) and Beta-amylase genes. Additive and epistatic effects were also found among the significant SNPs, and these need to be better investigated in segregant populations of waxy sources. The regions and genes identified in this work may drive further studies and reveal biological processes related to the waxy phenotype.
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Acknowledgements
We particularly wish to express our thanks to Dr. Hernan Ceballos (CIAT) for generating the seeds, and for sharing his expert opinions and insights on the development of waxy cassava clones, and to Dr. Guillaume Bauchet for SNP processing. The authors thank the Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB) (Grant No. PNE 15/2014), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (Grant Doctoral felowship), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (Grant No. 303912/2018-9, Post-doctoral fellowship) for their financial assistance and support.
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CDC and EJO designed this study. CDC and MBeS performed the experiments. CDC, ACB, and EJO analyzed the data. CDC drafted the manuscript. EJO revised the manuscript.
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Table S1:
List of accessions used in the genome-wide association study (GWAS) for identifying genomic regions associated with waxy starch phenotype in cassava (XLSX 14 kb)
Table S2:
List of transcripts related to genomic regions identified by the genome-wide association study (GWAS) as being associated with the waxy starch phenotype in cassava. Source: https://phytozome.jgi.doe.gov/phytomine/begin.do; Starch biosynthesis pathway identifier (Mesculenta PWY-622); Description of enzymes: https://enzyme.expasy.org (XLSX 12 kb)
Table S3:
SNP–SNP interaction under the codominant, additive, dominant, recessive, and overdominant models. The upper triangle contains the p values for the log-likelihood ratio test (LRT) of interaction (epistasis). The lower triangle contains the p values for the LRT comparing the additive probabilities of two SNPs versus the best single-SNP model. The diagonal contains the p values of the LRT for the crude effect of each SNP (XLSX 15 kb)
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do Carmo, C.D., e Sousa, M.B., Brito, A.C. et al. Genome-wide association studies for waxy starch in cassava. Euphytica 216, 82 (2020). https://doi.org/10.1007/s10681-020-02615-9
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DOI: https://doi.org/10.1007/s10681-020-02615-9