Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava

GWAS identified eight yield-related, peak starch type of waxy and wild-type starch and 21 starch pasting property-related traits (QTLs). Prediction ability of eight GS models resulted in low to high predictability, depending on trait, heritability, and genetic architecture. Cassava is both a food and an industrial crop in Africa, South America, and Asia, but knowledge of the genes that control yield and starch pasting properties remains limited. We carried out a genome-wide association study to clarify the molecular mechanisms underlying these traits and to explore marker-based breeding approaches. We estimated the predictive ability of genomic selection (GS) using parametric, semi-parametric, and nonparametric GS models with a panel of 276 cassava genotypes from Thai Tapioca Development Institute, International Center for Tropical Agriculture, International Institute of Tropical Agriculture, and other breeding programs. The cassava panel was genotyped via genotyping-by-sequencing, and 89,934 single-nucleotide polymorphism (SNP) markers were identified. A total of 31 SNPs associated with yield, starch type, and starch properties traits were detected by the fixed and random model circulating probability unification (FarmCPU), Bayesian-information and linkage-disequilibrium iteratively nested keyway and compressed mixed linear model, respectively. GS models were developed, and forward predictabilities using all the prediction methods resulted in values of - 0.001-0.71 for the four yield-related traits and 0.33-0.82 for the seven starch pasting property traits. This study provides additional insight into the genetic architecture of these important traits for the development of markers that could be used in cassava breeding programs.

Enhanced production of raw starch degrading enzyme using agro-industrial waste mixtures by thermotolerant Rhizopus microsporus for raw cassava chip saccharification in ethanol production

In the present study, solid-state fermentation for the production of raw starch degrading enzyme was investigated by thermotolerant Rhizopus microsporus TISTR 3531 using a combination of agro-industrial wastes as substrates. The obtained crude enzyme was applied for hydrolysis of raw cassava starch and chips at low temperature and subjected to nonsterile ethanol production using raw cassava chips. The agro-industrial waste ratio was optimized using a simplex axial mixture design. The results showed that the substrate mixture consisting of rice bran:corncob:cassava bagasse at 8 g:10 g:2 g yielded the highest enzyme production of 201.6 U/g dry solid. The optimized condition for solid-state fermentation was found as 65% initial moisture content, 35°C, initial pH of 6.0, and 5 × 10⁶ spores/mL inoculum, which gave the highest enzyme activity of 389.5 U/g dry solid. The enzyme showed high efficiency on saccharification of raw cassava starch and chips with synergistic activities of commercial α-amylase at 50°C, which promotes low-temperature bioethanol production. A high ethanol concentration of 102.2 g/L with 78% fermentation efficiency was achieved from modified simultaneous saccharification and fermentation using cofermentation of the enzymatic hydrolysate of 300 g raw cassava chips/L with cane molasses.

Characterization and physiological effect of tapioca maltodextrin colloid plasma expander in hemorrhagic shock and resuscitation model

Plasma expanders (PEs) are administered fluids to replace blood volume when massive blood loss has occured. Maltodextrin from tapioca starch was selected as a study candidate to prepare a colloid PE due to an uncomplicated production process. The formulations of mixture between tapioca maltodextrin and 0.9 % sodium chloride solution were prepared and then characterized. This was to investigate the effects of a dextrose equivalent (DE) and the concentration on the physical properties. Storage stability of each formulation was also determined and compared with clinically used PE [6 % hydroxyethyl starch (HES), 130/0.4]. The effects on the circulatory system in hamsters with hemorrhagic shock and resuscitation using prepared PE were also investigated. The results showed that low DE value led to high retrogradation, turbidity and viscosity but low colloid osmotic pressure and poor solubility. Among the prepared solutions, tapioca maltodextrin with DE6 at 10 % w/v concentration had comparable properties with 6 % HES 130/0.4. Animals resuscitated with 10 % DE6 PE had improved mean arterial blood pressure similar to those resuscitated with 6 % HES 130/0.4. However, several parameters in animals resuscitated with 10 % DE6 PE were lower than those resuscitated with 6 % HES 130/0.4, i.e., heart rate, functional capillary density. Therefore, if using tapioca maltodextrin for PE, some properties have to be considered and efficiently optimized.

In vitro Starch Hydrolysis Rate, Physico-chemical Properties and Sensory Evaluation of Butter Cake Prepared Using Resistant Starch Type III Substituted for Wheat Flour

Resistant starch type III (RS III) derived from enzymatically debranched high amylose rice starch was prepared and used to make butter cake at different levels (0, 5, 10, 15 and 20%) in place of wheat flour. Physico-chemical properties, sensory evaluation, and in vitro starch hydrolysis rate of the developed butter cake were investigated. This study showed that the content of resistant starch in butter cake increased significantly (P<0.05) as the level of substitution with RS III increased from 2.1 to 4.4% of resistant starch content. The butter cake with RS III replacement had a significantly lower in vitro starch hydrolysis rate compared to the control cake (0% RS III). The rates of starch hydrolysis from 0 to 180 min digestion time for 0, 5, 10 15, and 20% RS III in place of wheat flour in butter cakes were 3.70 to 67.65%, 2.97 to 64.86%, 2.86 to 59.99%, 2.79 to 55.96 and 2.78 to 53.04% respectively. The physico-chemical properties of 5 to 10% RS III substituted with wheat flour in the butter cake were not significantly different from the control cake and were moderately accepted by panellists in the sensory evaluation test.

Structural and thermodynamic properties of rice starches with different genetic background

High-sensitivity differential scanning microcalorimetry (HSDSC), small-angle X-ray scattering (SAXS), light (LM) and scanning electronic (SEM) microscopy techniques were used to study the defectiveness of different supramolecular structures in starches extracted from 11 Thai cultivars of rice differing in level of amylose and amylopectin defects in starch crystalline lamellae. Despite differences in chain-length distribution of amylopectin macromolecules and amylose level in starches, the invariance in the sizes of crystalline lamellae, amylopectin clusters and granules was established. The combined analysis of DSC, SAXS, LM and SEM data for native starches, as well as the comparison of the thermodynamic data for native and annealed starches, allowed to determine the structure of defects and the localization of amylose chains in crystalline and amorphous lamellae, defectiveness of lamellae, clusters and granules. It was shown that amylose "tie chains", amylose-lipid complexes located in crystalline lamellae, defective ends of double helical chains dangling from crystallites inside amorphous lamellae ("dangling" chains), as well as amylopectin chains with DP 6-12 and 25-36 could be considered as defects. Their accumulation can lead to a formation of remnant granules. The changes observed in the structure of amylopectin chains and amylose content in starches are reflected in the interconnected alterations of structural organization on the lamellar, cluster and granule levels.

Structural and thermodynamic properties of rice starches with different genetic background

A combined DSC - HPAEC-PAD approach, gel permeation chromatography and mild long-term acidic hydrolysis were employed to study the effects of amylopectin chain-length distributional and amylose defects on the assembly structures of amylopectin (crystalline lamellae, amylopectin clusters) in A-type polymorphic starches extracted from 11 Thai cultivars of rice with different amylose level. Joint analysis of the data allowed determining the contributions of different populations of amylopectin chains to the thermodynamic melting parameters of crystalline lamellae. It was shown that amylopectin chains with DP 6-12 and 25<DP<36 as well as amylose-lipid complexes or V-type crystalline structures and apparently amylose "tie-chains" could be considered as defects in the assembly structures of rice starches. Contrary to the defects listed above, amylopectin chains with DP 13-24 and >or=37 could be related to chains stabilizing these structures. The total effect of amylose and amylopectin defects can be described by means of Thomson-Gibbs' equation. The increase of defects in the assembly structures is accompanied by rise of the rates of acidic hydrolysis of both amorphous and crystalline parts in starches.

Aryl thioglycoside-based affinity purification of exo-acting cellulases

The influence of ligand-coupling chemistry and mobile-phase composition on the interaction of exo-acting cellulases with an immobilized complementary ligand was investigated. p-Aminophenyl 1-thio-beta-D-cellobioside (APTC) was used as a representative affinity ligand to which exo-acting cellulases (cellobiohydrolases, CBHs) preferentially bind. A "crude" cellulase preparation from the fungus Trichoderma reesei served as an enzyme source. The adsorption properties of the two principal exo-acting CBHs in this preparation, CBH I and CBH II, are shown to be distinctly different under several scenarios. Their relative affinities, based on column elution behavior and partition equilibrium experiments, are shown to be highly dependent on the functional groups employed for ligand coupling, the extent of functional group hydrolysis, the composition of the mobile phase, and the inherent nature of the enzymes. The dependency on the chemistry of the supporting matrix was illustrated using agarose supports containing cyanate ester, N-hydroxy-succinimide, and epoxy functional groups. When compared under apparent optimal conditions, the affinity of CBH II for immobilized APTC was approximately 10-fold that of CBH I. However, selective adsorption of CBH I or CBH II can be achieved by adjusting experimental parameters.