New plant breeding technologies for food security Zaidi, Syed Shan-E-Ali; Vanderschuren, Hervé; Qaim, Matin ...
Science (American Association for the Advancement of Science),
03/2019, Volume:
363, Issue:
6434
Journal Article
To meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of ...climate change. CRISPR genome-editing technology opens new opportunities to engineer disease resistance traits. With precise genome engineering and transgene-free applications, CRISPR is expected to resolve the major challenges to crop improvement. Here, we discuss the latest developments in CRISPR technologies for engineering resistance to viruses, bacteria, fungi, and pests. We conclude by highlighting current concerns and gaps in technology, as well as outstanding questions for future research.
Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling ...virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long.
Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses. Recently, ...the bacterial CRISPR/Cas9 system has been transferred to plants to target and confer immunity to geminiviruses. In this study, we use CRISPR-Cas9 interference in the staple food crop cassava with the aim of engineering resistance to African cassava mosaic virus, a member of a widespread and important family (Geminiviridae) of plant-pathogenic DNA viruses.
Our results show that the CRISPR system fails to confer effective resistance to the virus during glasshouse inoculations. Further, we find that between 33 and 48% of edited virus genomes evolve a conserved single-nucleotide mutation that confers resistance to CRISPR-Cas9 cleavage. We also find that in the model plant Nicotiana benthamiana the replication of the novel, mutant virus is dependent on the presence of the wild-type virus.
Our study highlights the risks associated with CRISPR-Cas9 virus immunity in eukaryotes given that the mutagenic nature of the system generates viral escapes in a short time period. Our in-depth analysis of virus populations also represents a template for future studies analyzing virus escape from anti-viral CRISPR transgenics. This is especially important for informing regulation of such actively mutagenic applications of CRISPR-Cas9 technology in agriculture.
•Cassava genotypes contrasting for drought tolerance were identified through the multi-year and multi-location field trials.•Superior performance under drought stress can be identified based on yield ...data of genotypes under well-watered conditions.•Drought tolerant genotypes display higher stomatal conductance and delayed stomatal closure under water deficit regimes.•Leaf longevity positively contributes to yield in water-deficit conditions.
Understanding drought tolerance mechanisms of cassava is a pre-requisite to improve the performance of the crop in water-scarce regions. Several hypotheses have been formulated to suggest how cassava can withstand a prolonged period of drought. We performed field trials under drought conditions with a selection of 37 cassava genotypes to identify phenotypic and molecular patterns associated with drought tolerance. Plant morphologies varied significantly between cassava genotypes under drought conditions in Kenya, which indicates a strong genetic basis for phenotypic differences. Drought stress reduced yield by 59%, the number of edible storage roots by 43% and leaf retention by 50% on average. Over three years and in two experimental field sites, the most drought tolerant genotype bulked 7.1 (±2.1) t/ha yield while the most drought susceptible genotype yielded 3.3 (±1.4) t/ha under drought conditions. The significant positive correlation of yield under irrigated and non-irrigated conditions suggests that selection of genotypes with high yield performance under well-watered or control conditions should be prioritized to identify genotypes with superior performance under drought stress. The positive correlation between yield and leaf retention provided further evidence that leaf longevity positively contributes to yield in water-deficit conditions. Yield differences could be attributed in part to variation in stomatal conductance (gs) because selected drought tolerant genotypes maintained higher gs and delayed stomatal closure as compared to drought susceptible genotypes. Further analysis revealed that genetic or molecular differences for gs between drought tolerant and susceptible genotypes could be detected at early stages of water deficit. These differences likely involve both abscisic acid (ABA)-dependent and ABA-independent molecular pathways.
Ending all forms of hunger by 2030, as set forward in the UN-Sustainable Development Goal 2 (UN-SDG2), is a daunting but essential task, given the limited timeline ahead and the negative global ...health and socio-economic impact of hunger. Malnutrition or hidden hunger due to micronutrient deficiencies affects about one third of the world population and severely jeopardizes economic development. Staple crop biofortification through gene stacking, using a rational combination of conventional breeding and metabolic engineering strategies, should enable a leap forward within the coming decade. A number of specific actions and policy interventions are proposed to reach this goal.
Cassava is the fourth largest source of calories in the world but is subject to economically important yield losses due to viral diseases, including cassava brown streak disease and cassava mosaic ...disease. Cassava mosaic disease occurs in sub-Saharan Africa and the Asian subcontinent and is associated with nine begomovirus species, whereas cassava brown streak disease has to date been reported only in sub-Saharan Africa and is caused by two distinct ipomovirus species. We present an overview of key milestones and their significance in the understanding and characterization of these two major diseases as well as their associated viruses and whitefly vector. New biotechnologies offer a wide range of opportunities to reduce virus-associated yield losses in cassava for farmers and can additionally enable the exploitation of this valuable crop for industrial purposes. This review explores established and new technologies for genetic manipulation to achieve desired traits such as virus resistance.
PDF
