Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root.

BACKGROUND: Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown. RESULTS: We report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance. Me3GT, MeMYB4, and UGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among which CYP79D1, CYP71E7b, and UGT85K5 are highly co-expressed and their allelic combination contributes to low linamarin content. We find MeMYB4 is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate gene MeFLS1 is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant. CONCLUSIONS: These findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.

Magnesium chelatase subunit D is not only required for chlorophyll biosynthesis and photosynthesis, but also affecting starch accumulation in Manihot esculenta Crantz.

BACKGROUND: Magnesium chelatase plays an important role in photosynthesis, but only a few subunits have been functionally characterized in cassava. RESULTS: Herein, MeChlD was successfully cloned and characterized. MeChlD encodes a magnesium chelatase subunit D, which has ATPase and vWA conservative domains. MeChlD was highly expressed in the leaves. Subcellular localization suggested that MeChlD:GFP was a chloroplast-localized protein. Furthermore, the yeast two-hybrid system and BiFC analysis indicated that MeChlD interacts with MeChlM and MePrxQ, respectively. VIGS-induce silencing of MeChlD resulted in significantly decreased chlorophyll content and reduction the expression of photosynthesis-related nuclear genes. Furthermore, the storage root numbers, fresh weight and the total starch content in cassava storage roots of VIGS-MeChlD plants was significantly reduced. CONCLUSION: Taken together, MeChlD located at the chloroplast is not only required for chlorophyll biosynthesis and photosynthesis, but also affecting the starch accumulation in cassava. This study expands our understanding of the biological functions of ChlD proteins.

Numerical Analysis Method That Considers Weathering and Water-Softening Effects for the Slope Stability of Carbonaceous Mudstone.

The mechanical behavior of carbonaceous mudstone deteriorates greatly when exposed to wet environments, and the precise evaluation of its slope stability has been a difficulty. This study aims to establish a numerical analysis method for the instability problems of its slopes; this method considers the effects of weathering and water-softening by establishing their mathematical expressions. The weathering and water-softening effects are reflected by variations in the mechanical properties (e.g., elastic modulus, angle of internal friction, and cohesion) of carbonaceous mudstone, with the depth following a logistic function and the shear strength parameters varying with wetting duration and degree of saturation. Their weathering and water-softening effects are reproduced with the use of the ABAQUS finite-element software and MATLAB programming. The proposed numerical method is applied to analyze the seepage field and stability of a highway cut slope with and without protection structures; the application results show that the proposed numerical method is reliable in analyzing the slope's instability problem. The use of the herringbone skeleton structures can reduce the water-softening effects and thus increase the safety factor of the slope. The findings of this study could provide guidance to the design and construction of highway cut slopes in mountain areas that are rich in carbonaceous mudstone.

Preparation of bio-based modified starch film and analysis of preservation mechanism for sweet cherry.

This study aimed to synthesize packaging films using bioactive ingredients. The composite film was prepared by blending octenyl succinate cassava starch ester (OSCS) with chitosan (CS) nano-ZnO and then adding ε-polylysine (ε-PL). The study also explored the effect of different concentrations of ε-PL on OSCS/CS/ZnO films. Fourier infrared spectroscopyand fluorescence microscopy revealed that the composite film was formed by both hydrogen bonding and a Schiff base reaction. The diffraction peaks of the original materials in X-ray diffraction disappeared after film formation, indicating good miscibility between the materials. Scanning electron microscope showed that the density of its structure increased with increasing the ε-PL content. The thermogravimetric analysis showed that the addition of ε-PL improved the thermal stability of the composite film to some extent. When used in cherry preservation, the bio-based modified starch film effectively reduced cherry decay, stem dryness, and weight loss, maintained surface color, and increased the soluble solid content.

Systematic Analysis of bHLH Transcription Factors in Cassava Uncovers Their Roles in Postharvest Physiological Deterioration and Cyanogenic Glycosides Biosynthesis.

The basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, systematic investigation of bHLH gene family in cassava (Manihot esculenta Crantz) has not been reported. In the present study, we performed a genome-wide survey and identified 148 MebHLHs genes were unevenly harbored in 18 chromosomes. Through phylogenetic analyses along with Arabidopsis counterparts, these MebHLHs genes were divided into 19 groups, and each gene contains a similar structure and conserved motifs. Moreover, many cis-acting regulatory elements related to various defense and stress responses showed in MebHLH genes. Interestingly, transcriptome data analyses unveiled 117 MebHLH genes during postharvest physiological deterioration (PPD) process of cassava tuberous roots, while 65 MebHLH genes showed significantly change. Meanwhile, the relative quantitative analysis of 15 MebHLH genes demonstrated that they were sensitive to PPD, suggesting they may involve in PPD process regulation. Cyanogenic glucosides (CGs) biosynthesis during PPD process was increased, silencing of MebHLH72 and MebHLH114 showed that linamarin content was significantly decreased in the leaves. To summarize, the genome-wide identification and expression profiling of MebHLH candidates pave a new avenue for uderstanding their function in PPD and CGs biosynthesis, which will accelerate the improvement of PPD tolerance and decrease CGs content in cassava tuberous roots.

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity.

BACKGROUND: Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. RESULTS: We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. CONCLUSIONS: This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.