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

KEY MESSAGE: 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.

Outstanding Characteristics of Thai Non-GM Bred Waxy Cassava Starches Compared with Normal Cassava Starch, Waxy Cereal Starches and Stabilized Cassava Starches.

Waxy cassava roots of nine varieties successfully developed in Thailand by a non-genetic modification (non-GM), conventional breeding method were used for extracting starches and their starch physico-chemical properties were evaluated and compared with normal cassava starches, commercial waxy starches (i.e., waxy maize starch and waxy rice starch) and commercial stabilized starches (i.e., acetylated starch and hydroxypropylated starch). All waxy cassava varieties provided starches without amylose while normal cassava starches contained 18%-20% amylose contents. As determined by a Rapid Visco Analyzer (RVA) at 5% (dry basis), waxy cassava starches had the highest peak viscosity and the lowest setback viscosity. Cooked paste of waxy cassava starches had the greatest clarity and stability among all starches during storage at 4 ℃ for 7 days as evidenced by its high light transmittance (%T) at 650 nm. No syneresis was detected in waxy cassava starch gels after subjecting to four freeze-thaw cycles (4 weeks) indicating high potential use of waxy cassava starches, free from chemicals, to replace stabilized starches as thickening and texturing agents in food products.

Simultaneous saccharification and viscosity reduction of cassava pulp using a multi-component starch- and cell-wall degrading enzyme for bioethanol production.

In this study, an efficient ethanol production process using simultaneous saccharification and viscosity reduction of raw cassava pulp with no prior high temperature pre-gelatinization/liquefaction step was developed using a crude starch- and cell wall-degrading enzyme preparation from Aspergillus aculeatus BCC17849. Proteomic analysis revealed that the enzyme comprised a complex mixture of endo- and exo-acting amylases, cellulases, xylanases, and pectina ses belonging to various glycosyl hydrolase families. Enzymatic hydrolysis efficiency was dependent on the initial solid loading in the reaction. Reduction in mixture viscosity was observed with a rapid decrease in complex viscosity from 3785 to 0.45 Pa s with the enzyme dosage of 2.19 mg/g on a dried weight basis within the first 2 h, which resulted from partial destruction of the plant cell wall fiber and degradation of the released starch granules by the enzymes as shown by scanning electron microscopy. Saccharification of cassava pulp at an initial solid of 16% (w/v) in a bench-scale bioreactor resulted in 736.4 mg glucose/g, which is equivalent to 82.92% glucose yield based on the total starch and glucan in the substrate, after 96 h at 40 °C. Simultaneous saccharification and fermentation of cassava pulp by Saccharomyces cerevisiae with the uncooked enzymatic process led to a final ethanol concentration of 6.98% w/v, equivalent to 96.7% theoretical yield based on the total starch and cellulose content. The results demonstrated potential of the enzyme for low-energy processing of cassava pulp in biofuel industry.

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.

The fine structure of cassava starch amylopectin. Part 2: building block structure of clusters.

The aim of this work was to analyse the organization of unit chains inside clusters of cassava amylopectin. beta-Limit dextrins of the clusters and partly fragmented clusters (sub-clusters) were isolated previously [Laohaphatanaleart et al., Int. J. Biol. Macromol. (2010) doi:10.1016/j.ijbiomac.2010.01.0049] and were now hydrolysed extensively with the alpha-amylase (liquefying type) of Bacillus subtilis into small, branched building blocks. The blocks were size-fractionated and characterized structurally. The smallest blocks predominated in the clusters. They were single branched and possessed a degree of polymerization (DP) of 5-9. Blocks with DP 10-15 were double branched and constituted the second largest group. The clusters of cassava amylopectin, which were of rather uniform size, possessed typically 7-9 building blocks, and all clusters contained similar size-distributions of the blocks. The inter-block chain length was 7-8 residues. The possible mode of attack by the enzyme between the building blocks is discussed. A model of the building block organization in the clusters is presented, in which the structural roles of different sub-groups of clustered chains are suggested. A three-dimensional model suggests a possible organization of the building blocks inside the amorphous lamellae in the granular starch.

The fine structure of cassava starch amylopectin. Part 1: Organization of clusters.

The enzyme alpha-amylase from Bacillussubtilis was applied to partly hydrolyze purified cassava amylopectin into groups of clusters, which were called domains. The domains were further size-fractionated by methanol precipitation and then subjected to a second stage of alpha-amylolysis until the rate of hydrolysis was slow in order to release the single clusters. All domain and cluster fractions were hydrolyzed with beta-amylase into beta-limit dextrins. The size distribution and chain composition of the beta-limit dextrins were analyzed by gel-permeation chromatography and high-performance anion-exchange chromatography with pulsed amperometric detection, respectively. The sizes of the clusters in the form of beta-limit dextrins were uniform with an average degree of polymerization of 67-78. The distribution profiles of B-chains were similar in all cluster fractions, which suggested that the internal structure of the cassava amylopectin clusters was homogenous. Long B-chains were involved in the interconnection of clusters in the domain fractions. These were cleaved and a new group of chains of intermediate length was produced by the alpha-amylase together with short chains. In the isolated clusters, however, some chains corresponding to long B-chains still remained, which is not predicted by the traditional cluster model of the amylopectin structure. Instead, the alternative two-directional backbone model could explain the mode of interconnection between the clusters.

Germination conditions affect physicochemical properties of germinated brown rice flour.

Germinated brown rice has been reported to be nutritious due to increased free gamma-aminobutyric acid (GABA). The physicochemical properties of brown rice (BR) and glutinous brown rice (GNBR) after germination as affected by different steeping times (24, 36, 48, and 72 h depending on the rice variety) and pHs of steeping water (3, 5, 7, and as-is) were determined and compared to those of the nongerminated one (control). As the steeping time increased or pH of steeping water decreased, germinated brown rice flours (GBRF) from both BR and GNBR had greater reducing sugar, free GABA and alpha-amylase activity; while the total starch and viscosity were lower than their respective controls. GBRFs from both BR and GNBR prepared after 24-h steeping time at pH 3 contained a high content of free GABA at 32.70 and 30.69 mg/100 g flour, respectively. The peak viscosity of GBRF obtained from both BR and GNBR (7.42 to 228.22 and 4.42 to 58.67 RVU, respectively) was significantly lower than that of their controls (255.46 and 190.17 RVU, respectively). The principal component analysis indicated that the important variables for discriminating among GBRFs, explained by the first 2 components at 89.82% of total explained variance, were the pasting profiles, alpha-amylase activity, and free GABA.

Application of bipolar electrodialysis on recovery of free lactic acid after simultaneous saccharification and fermentation of cassava starch.

The efficiency of bipolar electrodialysis (BED) for the recovery of lactic acid from fermentation broth was evaluated. Three systems of BED (bipolar-anion, bipolar-cation and bipolar-anion-cation) at fixed voltage (20 V) were compared using a model solution of ammonium lactate (100 g l(-1)). Results showed that bipolar-anion (BED-anion) was the most beneficial in terms of lactate flux, current efficiency, energy consumption and recovery ratio. Consequently, BED-anion was used to purify lactic acid from fermentation broth which had been pre-treated with mono-polar electrodialysis (MED). The final lactic acid concentration and lactate flux obtained were 144 g l(-1) and 393 g m(-2) h(-1), respectively. Using the two-step process (MED and BED-anion) the concentration of fermentation broth was increased by 33% and the total energy consumption was 2.76 kW h kg(-1).

Structural and thermodynamic properties of rice starches with different genetic background Part 2. Defectiveness of different supramolecular structures in starch granules.

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 Part 1. Differentiation of amylopectin and amylose defects.

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 25or=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.