Archive for the ‘Gene editing’ Category

Thanks to gene editing, another biotech-driven farming revolution might be ‘just around the corner’

Nature | March 26, 2021

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Credit: Research Square
Credit: Research Square

This article or excerpt is included in the GLP’s daily curated selection of ideologically diverse news, opinion and analysis of biotechnology innovation.

The basic principle of crop breeding is to first discover and then select for variants with desired traits. While selection is relatively easy, discovery is more challenging. Conventional breeding for domestication and crop improvement have unquestionably revolutionized agriculture and our society. 

But to further explore the potential of agriculture to feed an ever-growing population, larger crop diversity needs to be unlocked. The gene editing and RNA viral transfection technologies developed over recent years allow precise engineering of desirable variants with unprecedentedly high efficiency and resolution, greatly expanding the range of variations available and reducing our reliance on naturally existing mutations.

CRISPR–Cas breeding is more efficient than mutation breeding because mutagenesis is targeted to genes known to control desirable traits. Moreover, transgene-free plants can be easily obtained by transiently expressing CRISPR proteins or by segregating out constitutively expressed CRISPR. Gene-edited crops could thus avoid regulations against the cultivation of GMOs. 

Crop breeding need no longer rely on naturally occurring mutations, but instead artificially generated variations can be the raw material for further breeding. A much broader spectrum of phenotype space is ready for exploration, allowing development of optimal phenotypes adapted to heterogeneous environments on Earth, or even space. A new biotechnology-driven revolution in agriculture could be just around the corner.

Read the original postRelated article:  ‘Using Nature’s Shuttle’: Judith M. Heimann’s fascinating new book about how scientists learned to create genetically modified crops

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Road map for domesticating multi-genome rice using gene editing

Having more than two sets of chromosomes can help plants to adapt and evolve, but generating new crops with this type of genome is challenging. A road map for doing just that has now been developed using wild rice.

Diane R. Wang

We all sometimes wish we could do more than one thing at once — run errands, catch up on work deadlines and perhaps grab that long-overdue coffee with a friend. A genetic state known as polyploidy helps some plant genomes to do just this. Most plants, like humans, are diploid, with two sets of every chromosome. But polyploid plants have four, six or even eight sets of chromosomes. These additions allow different copies of a gene to take on different roles, and provide a buffer against potentially harmful mutations. Accordingly, polyploidy has served as a common mode of evolution in flowering plants1Writing in Cell, Yu et al.2 outline a viable approach to producing a domesticated form of polyploid rice using gene editing. Their advance could allow us to reap the benefits of polyploidy in one of the world’s most important crop species.Read the paper: A route to de novo domestication of wild allotetraploid rice

All crop species evolved from wild ancestors, as humans saved and propagated plants that had favourable attributes — loss of seed-dispersal mechanisms, for instance, and larger seeds and fruits3 — over hundreds or thousands of years. The world’s main rice crop, the Asian species Oryza sativa, was domesticated about 9,000 years ago from its wild progenitor, Oryza rufipogon, through processes thought to have occurred across multiple regions in Asia4,5. Both species are diploid, carrying two sets of 12 chromosomes.

For rice scientists, the idea of developing polyploid cultivated rice is tantalizing as a potential means for future crop improvement, especially in the face of climate variability6. The plant’s extra gene copies might enable rapid adaptation in response to major changes in the environment without the loss of favourable features7. But generating a polyploid rice from a cultivated diploid plant is hugely technically challenging. With that in mind, Yu et al. took an entirely different approach. The authors started with a distant, wild polyploid cousin of O. sativa and O. rufipogon, and domesticated it using biotechnological approaches (Fig. 1).

Figure 1
Figure 1 | A fast track to cultivated polyploid rice. Yu et al.2 have developed a strategy for rapid domestication of wild polyploid rice (which has more than two sets of chromosomes, unlike the rice commonly grown as a food crop). The first step is to select a wild strain that has favourable characteristics for gene editing and crop production. This is followed by genomic analysis and method optimization. Iterative cycles of genome editing, conventional crossing and testing are then needed before the new crop is rolled out to farmers and evaluated. Red highlights indicate sections of the road map completed by the authors for the wild rice Oryza alta.

The authors first spent time identifying an appropriate starting strain. The ideal candidate needed to be amenable to callus induction and regeneration — a process in which plant tissues are cultured to produce a mass of partially undifferentiated cells called a callus, from which new plants are generated. These properties are essential for gene-editing techniques. The selected individual also needed to have high biomass and tolerance to various abiotic and biotic stresses — heat and insect resistance, for example. After screening 28 polyploid wild rice lines, a strain of Oryza alta was selected, and named polyploid rice 1 (PPR1).

Oryza alta has four sets of chromosomes (it is tetraploid), and is found in Central and South America8. The species arose as a result of hybridization between two ancestors that had diploid genomes, designated C and D. The PPR1 strain selected by Yu et al. looks quite different from cultivated O. sativa. For instance, it is very tall — more than 2.7 metres, compared with 1 metre or less for typical O. sativa. It produces abundant biomass, and has broad leaves and sparse, small seeds adorned with awns (spiky protrusions thought to aid seed dissemination). As such, domesticating this wild relative was no small feat.

Yu and colleagues established methods for gene editing in PPR1, and assembled a high-quality genome for the strain. This acted as a map that helped identify genes to target for domestication. The authors compared PPR1 with an O. sativa genome dubbed Nipponbare. They discovered about 10,000 genes in each of the C and D genomes that did not have equivalents (homologues) in Nipponbare. By contrast, about 39,500 genes in Nipponbare (70.41% of the genome) did have homologues in PPR1.Multiple genomes give switchgrass an advantage

The latter was a promising result, because it meant that the genes responsible for domestication in O. sativa probably had related versions in PPR1. The researchers edited a suite of such genes in PPR1 that were known to have been involved in the domestication of O. sativa. This led to a range of improvements in PPR1: loss of shattering (a seed-dispersal mechanism), so that seeds did not fall off the plant before harvest; reduced awn length to ease post-harvest processing; increased grain length for larger kernels and greater yield; decreased height and thickened stem diameter to support the heavier grains; and modified (both longer and shorter) flowering times, needed for local adaptation to different latitudes.

Together, Yu and colleagues’ efforts led to the production of PPR1 lines with domesticated features in a just few generations, fast-tracking a process that typically occurs over hundreds to thousands of years. The work opens the door to developing plants that not only can better withstand environmental stresses (a crucial characteristic for global food security in the face of changing climates), but also could carry other characteristics — enhanced nutrition and taste, for example — that might help rice to meet evolving consumer preferences in the future. In addition, the strategy the authors have devised could theoretically provide a road map for applying biotechnology to drive the domestication of wild relatives of other present-day crops.Keen insights from quinoa

The techniques established by Yu et al. await testing in other wild, tetraploid rice strains. Successful extension to a broader gene pool will be necessary if researchers and breeders are to generate a diverse repository of domesticated polyploids, which could then be used to generate further improved strains through conventional crosses or genome editing — strains adapted to particular production systems, for instance, or those with high market acceptability. And although wild polyploids hold great promise as yet-untapped sources of genes that confer tolerance to abiotic stresses such as drought, these traits are likely to be complex, as noted by the authors, being influenced by many genes, each of which has only a small effect. A deeper understanding of the genetics of these plants is needed for the full potential of wild rices to be appreciated.

There is a long journey ahead for the breeding of cultivated polyploid rice. But the first seeds have now been sown. As demand for nimble and resilient food systems rises, rapid domestication and improvement of wild plant species, including polyploids, may well become a valuable instrument in agriculture’s toolbox.doi: https://doi.org/10.1038/d41586-021-00589-9

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science daily

Gene-editing protocol for whitefly pest opens door to control

April 23, 2020
Penn State
Whiteflies are among the most important agricultural pests in the world, yet they have been difficult to genetically manipulate and control, in part, because of their small size. An international team of researchers has overcome this roadblock by developing a CRISPR/Cas9 gene-editing protocol that could lead to novel control methods for this devastating pest.

Whiteflies are among the most important agricultural pests in the world, yet they have been difficult to genetically manipulate and control, in part, because of their small size. An international team of researchers has overcome this roadblock by developing a CRISPR/Cas9 gene-editing protocol that could lead to novel control methods for this devastating pest.

According to Jason Rasgon, professor of entomology and disease epidemiology, Penn State, whiteflies (Bemisia tabaci) feed on many types of crop plants, damaging them directly through feeding and indirectly by promoting the growth of fungi and by spreading viral diseases.

“We found a way to genetically modify these insects, and our technique paves the way not only for basic biological studies of this insect, but also for the development of potential genetic control strategies,” he said.

The team’s results appeared on April 21 in The CRISPR Journal.

The CRISPR/Cas9 system comprises a Cas9 enzyme, which acts as a pair of ‘molecular scissors’ that cuts DNA at a specific location on the genome so bits of DNA can be added or removed, and a guide RNA, that directs the Cas9 to the right part of the genome.

“Gene editing by CRISPR/Cas9 is usually performed by injecting the gene-editing complex into insect embryos, but the exceedingly small size of whitefly embryos and the high mortality of injected eggs makes this technically challenging,” said Rasgon. “ReMOT Control (Receptor-Mediated Ovary Transduction of Cargo), a specific type of CRISPR/Cas9 technique developed in my lab, circumvents the need to inject embryos. Instead, you inject the gene-editing complex which is fused to a small ovary-targeting molecule called BtKV, into adult females and the BtKV guides the complex into the ovaries.”

To explore the use of ReMOT Control in whiteflies, the team targeted the “white” gene, which is involved in eye color. When this gene is functioning normally, whiteflies have brown eyes, but when it is non-functional due to mutations, the insects is supposed to have white eyes. The team found that ReMOT Control generated mutations that resulted in juvenile insects with white eyes that turned red as they developed into adults.

“Tangentially, we learned a bit about eye color development,” said Rasgon. “We expected the eyes to remain white and were surprised when they turned red. Importantly, however, we found that the mutations we generated using ReMOT Control were passed on to offspring, which means that a change can be made that is inherited to future generations.”

Rasgon said the team hopes its proof-of-principle study will allow scientists to investigate the same strategy using genes that affect the ability for the insects to transmit viral pathogens of crop plants to help control the insects and protect crops.

“This technique can be used for any application where you want to delete any gene in whiteflies, for basic biology studies or for the development of potential genetic control strategies,” he said.

Story Source:

Materials provided by Penn State. Note: Content may be edited for style and length.

Journal Reference:

  1. Chan C. Heu, Francine M. McCullough, Junbo Luan, Jason L. Rasgon. CRISPR-Cas9-Based Genome Editing in the Silverleaf Whitefly (Bemisia tabaci). The CRISPR Journal, 2020; 3 (2): 89 DOI: 10.1089/crispr.2019.0067

Cite This Page:

Penn State. “Gene-editing protocol for whitefly pest opens door to control.” ScienceDaily. ScienceDaily, 23 April 2020. <www.sciencedaily.com/releases/2020/04/200423130410.htm>.

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