Creation of a potato mutant lacking the starch branching enzyme gene StSBE3 that was generated by genome editing using the CRISPR/dMac3-Cas9 system

Understanding starch biosynthesis in potatoes for metabolic engineering to improve starch quality: A detailed review

Potato tubers accumulate substantial quantities of starch, which serves as their primary energy reserve. As the predominant component of potato tubers, starch strongly influences tuber yield, processing quality, and nutritional attributes. Potato starch is distinguished from other food starches by its unique granule morphology and compositional attributes. It possesses large, oval granules with amylose content ranging from 20 to 33 % and high phosphorus levels, which collectively determine the unique physicochemical characteristics. These physicochemical properties direct the utility of potato starch across diverse food and industrial applications. This review synthesizes current knowledge on the molecular factors controlling potato starch biosynthesis and structure-function relationships. Key topics covered are starch granule morphology, the roles and regulation of major biosynthetic enzymes, transcriptional and hormonal control, genetic engineering strategies, and opportunities to tailor starch functionality. Elucidating the contributions of different enzymes in starch biosynthesis has enabled targeted modification of potato starch composition and properties. However, realizing the full potential of this knowledge faces challenges in optimizing starch quality without compromising plant vigor and yield. Overall, integrating multi-omics datasets with advanced genetic and metabolic engineering tools can facilitate the development of elite cultivars with enhanced starch yield and tailored functionalities.

Potato: from functional genomics to genetic improvement

Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.

Cas12a-mediated gene targeting by sequential transformation strategy in Arabidopsis thaliana

Gene targeting (GT) allows precise manipulation of genome sequences, such as knock-ins and sequence substitutions, but GT in seed plants remains a challenging task. Engineered sequence-specific nucleases (SSNs) are known to facilitate GT via homology-directed repair (HDR) in organisms. Here, we demonstrate that Cas12a and a temperature-tolerant Cas12a variant (ttCas12a) can efficiently establish precise and heritable GT at two loci in Arabidopsis thaliana (Arabidopsis) through a sequential transformation strategy. As a result, ttCas12a showed higher GT efficiency than unmodified Cas12a. In addition, the efficiency of transcriptional and translational enhancers for GT via sequential transformation strategy was also investigated. These enhancers and their combinations were expected to show an increase in GT efficiency in the sequential transformation strategy, similar to previous reports of all-in-one strategies, but only a maximum twofold increase was observed. These results indicate that the frequency of double strand breaks (DSBs) at the target site is one of the most important factors determining the efficiency of genetic GT in plants. On the other hand, a higher frequency of DSBs does not always lead to higher efficiency of GT, suggesting that some additional factors are required for GT via HDR. Therefore, the increase in DSB can no longer be expected to improve GT efficiency, and a new strategy needs to be established in the future. This research opens up a wide range of applications for precise and heritable GT technology in plants.

Efficiency of potato genome editing: Targeted mutation on the genes involved in starch biosynthesis using the CRISPR/dMac3-Cas9 system

Potato (Solanum tuberosum L.) has a tetraploid genome. To make a mutant lacking a specific gene function, it is necessary to introduce mutations into all four gene alleles. To achieve this goal, we developed a powerful genome editing tool, CRISPR/dMac3-Cas9, which installed the translation enhancer dMac3 that greatly increased the translation of the downstream open reading frame. The CRISPR/dMac3-Cas9 system employing three guide RNAs (gRNAs) greatly elevated the frequency of the generation rate of mutation. This system enabled to create the 4-allele mutants of granule-bound starch synthase (GBSS) and starch branching enzyme (SBE). These mutants indicated functionally defective features, suggesting that we succeeded in efficient genome editing of the potato tetraploid genome. Here, we show the effect of the number of gRNAs for efficient mutagenesis of the target gene using the mutants of the GBSS1 gene. CRISPR/dMac3-Cas9 employing three gRNA genes achieved a higher mutation efficiency than the CRISPR/dMac3-Cas9 with two gRNAs, suggesting being influenced by the dose effect of the number of gRNAs at the target region. The alleles of the SBE3 gene contained SNPs that caused sequence differences in the gRNAs but these gRNAs functioned efficiently. However, many rearrangement events and large deletions were induced. These results support the importance of accurate binding of gRNA to the target sequence, which may lead to a hint to avoid the unexpected mutation on the off-target sites.

Peculiar properties of tuber starch in a potato mutant lacking the α-glucan water dikinase 1 gene GWD1 created by targeted mutagenesis using the CRISPR/dMac3-Cas9 system

Glucose chains in starch are phosphorylated and contribute to structural stabilization. Phosphate groups contained in starch also play a role in retaining moisture. α-Glucan water dikinase 1 (GWD1) is involved in the phosphorylation of glucose chains in starch. In this study, we generated potato mutants of the GWD1 gene using the CRISPR/dMac3-Cas9 system. Observation of the phenotypes of the GWD1-deficient mutants revealed their physiological roles in tuber starch formation. The 4-allele mutants showed growth retardation and a delay in tuber formation. A significant decrease in phosphorus content was detected in the tuber starch of the gwd1 mutant. This mutant starch showed a higher amylose content than the wild-type starch, whereas its gelatinization temperature was slightly lower than that of the WT starch. The peak viscosity of the mutant starch was lower than that of the WT starch. These observations revealed that the starch of the gwd1 mutants had peculiar and unique properties compared to those of WT, sbe3 and gbss1 mutant starches. The amount of tissue-released water due to freeze-thawing treatment was determined on tubers of the gwd1 mutant and compared with those of WT and the other mutants. Significantly less water loss was found in the gwd1, sbe3 and gbss1 mutant tubers than in the WT tubers. Our results indicate that the GWD1 gene is not only important for potato growth, but also largely effective for the traits of tuber starch.

Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production

Maize accumulates large amounts of starch in seeds which have been used as food for human and animals. Maize starch is an importantly industrial raw material for bioethanol production. One critical step in bioethanol production is degrading starch to oligosaccharides and glucose by α-amylase and glucoamylase. This step usually requires high temperature and additional equipment, leading to an increased production cost. Currently, there remains a lack of specially designed maize cultivars with optimized starch (amylose and amylopectin) compositions for bioethanol production. We discussed the features of starch granules suitable for efficient enzymatic digestion. Thus far, great advances have been made in molecular characterization of the key proteins involved in starch metabolism in maize seeds. The review explores how these proteins affect starch metabolism pathway, especially in controlling the composition, size and features of starch. We highlight the roles of key enzymes in controlling amylose/amylopectin ratio and granules architecture. Based on current technological process of bioethanol production using maize starch, we propose that several key enzymes can be modified in abundance or activities via genetic engineering to synthesize easily degraded starch granules in maize seeds. The review provides a clue for developing special maize cultivars as raw material in the bioethanol industry.

Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects

Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.

CRISPR/Cas mediated genome editing in potato: Past achievements and future directions

Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.

Procedure for the efficient acquisition of progeny seeds from crossed potato plants grafted onto tomato

Potato, Solanum tuberosum L. is an important crop. However, it is difficult to breed potato cultivars by applying conventional crossing methods because potato has a tetraploid genome and is vegetatively propagated. Flower formation and tuber development occur simultaneously. Many potato cultivars hardly produce any fruits after crossing and fail to produce seeds. We report an improved procedure for obtaining progeny seeds by grafting potatoes onto tomatoes. The rate of fruit formation was more than 19% when the grafted potatoes were used for the crossing experiments, whereas crossing using the ungrafted plants showed a rate of 1.1%. This result suggests that our procedure results in the easy acquisition of null-segregant progenies by crossing mutant lines. It is also expected to improve conventional potato breeding.