Abstract
An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.
Highlights
Cassava (Manihot esculenta Crantz) is one of the most important species globally for starch production
We evaluated a diverse set of cassava accessions to provide a comprehensive view of the population structure and diversity of the species, their effects on genome-wide association study (GWAS), as well as the dynamics of linkage disequilibrium in different chromosomes, and to identify and locate genomic regions associated with the pasting properties of cassava starch
The differences observed in the pasting properties of cassava starch provide an important opportunity for the selection of accessions that can be used for various industrial applications
Summary
Cassava (Manihot esculenta Crantz) is one of the most important species globally for starch production. Starch retrogradation is generally considered to have undesirable effects on food products, but is desirable in some applications, such as in the production of breakfast cereals, dehydrated purees, and resistant starches, which have several nutritional properties [5]. This process in which disaggregate the starch components, amylose and amylopectin chains, in a gelatinized starch paste and reassociate to form more ordered structures. Starch granules are generally composed of an amorphous region interspersed with concentric semicrystalline rings, which exhibit alternating amorphous and crystalline materials [6, 7]
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