Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0.8 and 0.5 million years ago. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using sequencing of the polyploid organism itself rather than any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.

Considerable knowledge has been accumulated on the lactic acid bacteria (LAB) that affect the aroma and flavour of yogurt. This review focuses on the role of LAB in the production of flavour compounds during yogurt fermentation. The biochemical processes of flavour compound formation by LAB including glycolysis, proteolysis, and lipolysis are summarised, with some key compounds described in detail. The flavour-related activities of LAB mostly depend on the species used for yogurt fermentation, and some strategies have been developed to obtain more control of the flavourforming process. Metabolic engineering can be a powerful tool to reroute the metabolic flux towards the efficient accumulation of the desired flavour compounds with the knowledge of the complex network of flavour-forming pathways and the availability of genetic tools. Further progress made in the omics-based techniques and the use of systems biology approaches are needed to fully understand, control, and steer flavour formation in yogurt fermentation processes. ARTICLE HISTORY

The quality of cassava starch, an important trait in cassava breeding programs, determines its applications in various industries. For example, development of waxy (having a low level of amylose) cassava is in demand. Amylose is synthesized by granule-bound starch synthase I (GBSSI) in plants, and therefore, down-regulation of GBSSI expression in cassava might lead to reduced amylose content. We produced 63 transgenic cassava plant lines that express hair-pin dsRNAs homologous to the cassava GBSSI conserved region under the control of the vascular-specific promoter p54/1.0 from cassava (p54/1.0::GBSSI-RNAi) or cauliflower mosaic virus (CaMV) 35S (35S::GBSSI-RNAi). After the screening storage roots and starch granules from field-grown plants with iodine staining, the waxy phenotype was discovered: p54/1.0::GBSSI-RNAi line A8 and 35S::GBSSI-RNAi lines B9, B10, and B23. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that there was no detectable GBSSI protein in the starch granules of plants with the waxy phenotype. Further, the amylose content of transgenic starches was significantly reduced (<5%) compared with the level in starch granules from the wild-type (about 25%). The inner structure of the waxy starch granules differed from that of the untransformed ones, as revealed by transmission electron microscopy analysis as well as morphological changes in the iodine-starch complex. Endothermic enthalpy was reduced in waxy cassava starches, according to differential scanning calorimeter analysis. Except B9, all waxy starches displayed the A-type X-ray diffraction pattern. Amylogram patterns of the waxy cassava starches were analyzed using a rapid viscosity analyzer and found to have increased values for clarity, peak viscosity, gel breakdown, and swelling index. Setback, consistency, and solubility were notably reduced. Therefore, waxy cassava with novel starch in its storage roots was produced using the biotechnological approach, promoting its industrial utilization.

CRISPR/Cas9-mediated genome editing is a powerful technology that has been used for the genetic modification of a number of crop species. In order to evaluate the efficacy of CRISPR/Cas9 technology in the root crop, sweet potato (Ipomoea batatas), two starch biosynthetic pathway genes, IbGBSSI (encoding granule-bound starch synthase I), and IbSBEII (encoding starch branching enzyme II), were targeted in the starch-type cultivar Xushu22 and carotenoid-rich cultivar Taizhong6. I. batatas was transformed using a binary vector, in which the Cas9 gene is driven by the Arabidopsis AtUBQ promoter and the guide RNA is controlled by the Arabidopsis AtU6 promoter. A total of 72 Xushu22 and 35 Taizhong6 transgenic lines were generated and analyzed for mutations. The mutation efficiency was 62–92% with multi-allelic mutations in both cultivars. Most of the mutations were nucleotide substitutions that lead to amino acid changes and, less frequently, stop codons. In addition, short nucleotide insertions or deletions were also found in both IbGBSSI and IbSBEII. Furthermore, a 2658 bp deletion was found in one IbSBEII transgenic line. The total starch contents were not significantly changed in IbGBSSI- and IbSBEII-knockout transgenic lines compared to the wild-type control. However, in the allopolyploid sweet potato, the IbGBSSI-knockout reduced, while the IbSBEII-knockout increased, the amylose percentage. Our results demonstrate that CRISPR/Cas9 technology is an effective tool for the improvement of starch qualities in sweet potato and breeding of polyploid root crops.

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The objective of this study was to investigate the mechanism of Lactobacillus plantarum (L. plantarum) involved in improving fermentation quality of naturally ensiled alfalfa under poor conditions. High-moisture wilted alfalfa was ensiled without inoculants (CK) or with inoculation of two L. plantarum additives (LPI and LPII). The pH and fermentation products of silage were determined after 30 and 90 days of ensiling. Additionally, the bacterial community compositions were analyzed. The L. plantarum inoculants significantly promoted lactic acid accumulation, and Lactobacillus abundance for both periods. At 90 days, silage in CK exhibited a high pH, a loss in dry matter, and a high concentration of ammoniacal nitrogen. The inoculations of L. plantarum significantly inhibited the growth of Clostridia, and reduced ammoniacal nitrogen concentration in silage (P < 0.05). Thus, inoculation with L. plantarum improved the fermentation quality of alfalfa silage and inhibited the growth of spoilage microorganisms, and further delayed spoilage of alfalfa silage under adverse ensiling conditions.

Biomass is generally believed to be carbon neutral. However, recent studies have challenged the carbon neutrality hypothesis by introducing metric indicators to assess the global warming potential of biogenic CO2 (GWPbio). In this study we calculated the GWPbio factors using a forest growth model and radiative forcing effects with a time horizon of 100 years and applied the factors to five life cycle assessment (LCA) case studies of bioproducts. The forest carbon change was also accounted for in the LCA studies. GWPbio factors ranged from 0.13–0.32, indicating that biomass could be an attractive energy resource when compared with fossil fuels. As expected, short rotation and fast-growing biomass plantations produced low GWPbio. Long-lived wood products also allowed more regrowth of biomass to be accounted as absorption of the CO2 emission from biomass combustion. The LCA case studies showed that the total life cycle GHG emissions were closely related to GWPbio and energy conversion efficiency. By considering the GWPbio factors and the forest carbon change, the production of ethanol and bio-power appeared to have higher GHG emissions than petroleum-derived diesel at the highest GWPbio.

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