Efficient transformation and regeneration of transgenic cassava using the neomycin phosphotransferase gene as aminoglycoside resistance marker gene

A Study on Genetically Engineered Foods: Need, Benefits, Risk, and Current Knowledge

Food requirements have always been a top priority, and with the exponential growth of the human population, there is an increasing need for large quantities of food. Traditional cultivation methods are not able to meet the current demand for food products. One significant challenge is the shortened shelf-life of naturally occurring food items, which directly contributes to food scarcity. Contaminating substances such as weeds and pests play a crucial role in this issue. In response, researchers have introduced genetically engineered (GE) food as a potential solution. These food products are typically created by adding or replacing genes in the DNA of naturally occurring foods. GE foods offer various advantages, including increased quality and quantity of food production, adaptability to various climatic conditions, modification of vitamin and mineral levels, and prolonged shelf life. They address the major concerns of global food scarcity and food security. However, the techniques used in the production of GE foods may not be universally acceptable due to the genetic alteration of animal genes into plants or vice versa. Additionally, their unique nature necessitates further long-term studies. This study delves into the procedures and growth stages of DNA sequencing, covering the benefits, risks, industrial relevance, current knowledge, and future challenges of GE foods. GE foods have the potential to extend the shelf life of food items, alleviate food shortages, and fulfill the current nutritional food demand.

Current Advancements and Limitations of Gene Editing in Orphan Crops

Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.

Optimization of parameters to improve transformation efficiency of elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson

Elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson), is an important edible tropical tuber crop, belonging to the family Araceae. Corms produced by this plant is very big and they are rich in starch, protein, mineral, vitamins, and dietary fiber but has acridity problem. This crop is susceptible to virus and phytoplasma diseases which affects crop growth and corm yield. Even though this crop has high commercial value, the problems like susceptibility to viral diseases, acridity problems, and lack of genetic diversity made hindrance in their exploitation. These issues can be resolved only by improving the characters through genetic transformation. To achieve genetic transformation in this important crop, a study was conducted to optimize various parameters for efficient Agrobacterium-mediated genetic transformation using embryogenic calli with vectors having gus reporter gene. Calli were developed using petiole and leaves of in vitro plantlets of elephant foot yam cultivar Gajendra and experiments were conducted to evaluate the sensitivity of calli to different doses of antibiotics viz. geneticin, hygromycin, ticarcillin. It was observed that complete death and discoloration of the calli were obtained with 25 mgl^-1 geneticin and 10 mgl^-1 hygromycin. The lowest lethal concentration of ticarcillin against Agrobacterium growth was found to be 500 mgl^-1 which did not affect calli growth. Optimized parameters for efficient transformation in elephant foot yam include 100 μM acetosyringone concentration with 2 days of co-cultivation at temperature 22 °C using LBA4404 strain. The putative transformants were characterized for the integration of the gus gene using PCR and nucleic acid spot hybridization. The optimized protocol is simple and reproducible and may be adapted for other cultivars also.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02824-6.

Virus-Induced Gene Silencing (VIGS) in Cassava Using Geminivirus Agroclones

Virus-induced gene silencing (VIGS) is an efficient, low-cost, and rapid functional validation tool for candidate genes in planta. The VIGS approach is particularly suitable to perform reverse genetics studies in crop species. Here we present a detailed method to perform VIGS in cassava, from target gene fragment to agroinoculation and VIGS quantitation.

Application of fluorescent and UV-Vis detection methods to profile antimicrobial activity of cassava tissues for an efficient Agrobacterium-mediated transformation

The majority of tissue culture and transformation studies in cassava (Manihot esculenta Crantz) focus on the modification of conditions in order to establish a better protocol. Although this is a standard approach for making progress in genetic transformation technology for a target plant variety, serious difficulty still remains due to the limited applicability and adaptability of the given protocol. In the present study, we aim to develop a new concept that focuses on the development of simple but adaptable genetic transformation technology in cassava. In order to establish an efficient transformation protocol, two local edible cassava varieties, R-type, with a broad leaf with reddish petiole, and S-type, with a thin leaf with shiny greenish petiole, were obtained from Okinawa, Japan. Three detection methods, i.e., fluorescence microscopy, thin-layer chromatography (TLC) with detection under an ultraviolet (UV) illumination (254 nm) and light emitting diode (LED) illuminations (365 nm and 500 nm) without any staining, and a spectrum scanning (250-700 nm) by a microplate reader system were employed to identify a series of unique features of the petioles and leaves. Antimicrobial activity of methanol extracts from the tissues was also assayed. We succeeded in the transient expression of the GUS gene using cassava leaves and also established stable introduction of the GUS gene into three organogenic cassava calli by adapting Agrobacterium-mediated transformation. With all the findings, we have identified a flexible tool to create a better match between explants and Agrobacterium strains.

Genetic Transformation of Recalcitrant Cassava by Embryo Selection and Increased Hormone Levels

Genetic engineering is considered to be an important tool for the improvement of cassava. Cassava is a highly heterozygous crop species for which conventional breeding is a lengthy and tedious process. Robust transformation is based on Agrobacterium-mediated transformation of friable embryogenic callus (FEC). Production of FEC is genotype-dependent and considered to be a major bottleneck for the genetic transformation of cassava. As a consequence, routine genetic transformation has only been established for a handful of cassava cultivars. Therefore, development of procedures enabling efficient production of high-quality cassava FEC is required to allow the translation of research from the model cultivar to farmer-preferred cassava cultivars. Here we study the FEC production capacity of Brazilian cassava cultivars and report the modification of the protocol for the genetic transformation of Verdinha (BRS 222), a recalcitrant cultivar with high potential for protein production that is extensively used by farmers in Brazil.

Modification of Cassava Root Starch Phosphorylation Enhances Starch Functional Properties

Cassava (Manihot esculenta Crantz) is a root crop used as a foodstuff and as a starch source in industry. Starch functional properties are influenced by many structural features including the relative amounts of the two glucan polymers amylopectin and amylose, the branched structure of amylopectin, starch granule size and the presence of covalent modifications. Starch phosphorylation, where phosphates are linked either to the C3 or C6 carbon atoms of amylopectin glucosyl residues, is a naturally occurring modification known to be important for starch remobilization. The degree of phosphorylation has been altered in several crops using biotechnological approaches to change expression of the starch-phosphorylating enzyme GLUCAN WATER DIKINASE (GWD). Interestingly, this frequently alters other structural features of starch beside its phosphate content. Here, we aimed to alter starch phosphorylation in cassava storage roots either by manipulating the expression of the starch phosphorylating or dephosphorylating enzymes. Therefore, we generated transgenic plants in which either the wild-type potato GWD (StGWD) or a redox-insensitive version of it were overexpressed. Further plants were created in which we used RNAi to silence each of the endogenous phosphoglucan phosphatase genes STARCH EXCESS 4 (MeSEX4) and LIKE SEX4 2 (MeLSF), previously discovered by analyzing leaf starch metabolism in the model species Arabidopsis thaliana. Overexpressing the potato GWD gene (StGWD), which specifically phosphorylates the C6 position, increased the total starch-bound phosphate content at both the C6 and the C3 positions. Silencing endogenous LSF2 gene (MeLSF2), which specifically dephosphorylates the C3 position, increased the ratio of C3:C6 phosphorylation, showing that its function is conserved in storage tissues. In both cases, other structural features of starch (amylopectin structure, amylose content and starch granule size) were unaltered. This allowed us to directly relate the physicochemical properties of the starch to its phosphate content or phosphorylation pattern. Starch swelling power and paste clarity were specifically influenced by total phosphate content. However, phosphate position did not significantly influence starch functional properties. In conclusion, biotechnological manipulation of starch phosphorylation can specifically alter certain cassava storage root starch properties, potentially increasing its value in food and non-food industries.

Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots

AIM

We report the construction of a Virus-Induced Gene Silencing (VIGS) vector and an agroinoculation protocol for gene silencing in cassava (Manihot esculenta Crantz) leaves and roots. The African cassava mosaic virus isolate from Nigeria (ACMV-[NOg]), which was initially cloned in a binary vector for agroinoculation assays, was modified for application as VIGS vector. The functionality of the VIGS vector was validated in Nicotiana benthamiana and subsequently applied in wild-type and transgenic cassava plants expressing the uidA gene under the control of the CaMV 35S promoter in order to facilitate the visualization of gene silencing in root tissues. VIGS vectors were targeted to the Mg2+-chelatase gene in wild type plants and both the coding and promoter sequences of the 35S::uidA transgene in transgenic plants to induce silencing. We established an efficient agro-inoculation method with the hyper-virulent Agrobacterium tumefaciens strain AGL1, which allows high virus infection rates. The method can be used as a low-cost and rapid high-throughput evaluation of gene function in cassava leaves, fibrous roots and storage roots.

BACKGROUND

VIGS is a powerful tool to trigger transient sequence-specific gene silencing in planta. Gene silencing in different organs of cassava plants, including leaves, fibrous and storage roots, is useful for the analysis of gene function.

RESULTS

We developed an African cassava mosaic virus-based VIGS vector as well as a rapid and efficient agro-inoculation protocol to inoculate cassava plants. The VIGS vector was validated by targeting endogenous genes from Nicotiana benthamiana and cassava as well as the uidA marker gene in transgenic cassava for visualization of gene silencing in cassava leaves and roots.

CONCLUSIONS

The African cassava mosaic virus-based VIGS vector allows efficient and cost-effective inoculation of cassava for high-throughput analysis of gene function in cassava leaves and roots.

Cassava (Manihot esculenta Crantz)

Genetic transformation of plants is an indispensable technique used for fundamental research and crop improvement. Recent advances in cassava (Manihot esculenta Crantz) transformation have facilitated the effective generation of stably transformed cassava plants with favorable traits. Agrobacterium-mediated transformation of friable, embryogenic callus has evolved to become the most widely used approach and has been adopted by research laboratories in Africa. This procedure utilizes axillary meristem tissue (buds) to produce primary and secondary somatic embryos and subsequently friable, embryogenic callus. Agrobacterium harboring a binary expression cassette is used to transform this tissue, which is regenerated via cotyledons and shoot organogenesis to produce rooted in vitro plantlets. This chapter details each step of the procedure using the model cultivar 60444 and provides supplementary notes to successfully produce transgenic cassava.

Exploiting the combination of natural and genetically engineered resistance to cassava mosaic and cassava brown streak viruses impacting cassava production in Africa

Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are currently two major viral diseases that severely reduce cassava production in large areas of Sub-Saharan Africa. Natural resistance has so far only been reported for CMD in cassava. CBSD is caused by two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). A sequence of the CBSV coat protein (CP) highly conserved between the two virus species was used to demonstrate that a CBSV-CP hairpin construct sufficed to generate immunity against both viral species in the cassava model cultivar (cv. 60444). Most of the transgenic lines showed high levels of resistance under increasing viral loads using a stringent top-grafting method of inoculation. No viral replication was observed in the resistant transgenic lines and they remained free of typical CBSD root symptoms 7 month post-infection. To generate transgenic cassava lines combining resistance to both CBSD and CMD the hairpin construct was transferred to a CMD-resistant farmer-preferred Nigerian landrace TME 7 (Oko-Iyawo). An adapted protocol allowed the efficient Agrobacterium-based transformation of TME 7 and the regeneration of transgenic lines with high levels of CBSV-CP hairpin-derived small RNAs. All transgenic TME 7 lines were immune to both CBSV and UCBSV infections. Further evaluation of the transgenic TME 7 lines revealed that CBSD resistance was maintained when plants were co-inoculated with East African cassava mosaic virus (EACMV), a geminivirus causing CMD. The innovative combination of natural and engineered virus resistance in farmer-preferred landraces will be particularly important to reducing the increasing impact of cassava viral diseases in Africa.

Robust transformation procedure for the production of transgenic farmer-preferred cassava landraces

Recent progress in cassava transformation has allowed the robust production of transgenic cassava even under suboptimal plant tissue culture conditions. The transformation protocol has so far been used mostly for the cassava model cultivar 60444 because of its good regeneration capacity of embryogenic tissues. However, for deployment and adoption of transgenic cassava in the field it is important to develop robust transformation methods for farmer- and industry-preferred landraces and cultivars. Because dynamics of multiplication and regeneration of embryogenic tissues differ between cassava genotypes, it was necessary to adapt the efficient cv. 60444 transformation protocol to genotypes that are more recalcitrant to transformation. Here we demonstrate that an improved cassava transformation protocol for cv. 60444 could be successfully modified for production of transgenic farmer-preferred cassava landraces. The modified transformation method reports on procedures for optimization and is likely transferable to other cassava genotypes reportedly recalcitrant to transformation provided production of high quality FEC. Because the three farmer-preferred cassava landraces selected in this study have been identified as resistant or tolerant to cassava mosaic disease (CMD), the adapted protocol will be essential to mobilize improved traits into cassava genotypes suitable for regions where CMD limits production.