Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology

Disease occurrence adversely affects livestock production and animal welfare, and have an impact on both human health and public perception of food–animals production. Combined efforts from farmers, animal scientists, and veterinarians have been continuing to explore the effective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food–animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance.

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Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system

10.1101/734442 ◽

2019 ◽

Cited By ~ 2

Author(s):

Remi L. Gratacap ◽

Tim Regan ◽

Carola E. Dehler ◽

Samuel A.M. Martin ◽

Pierre Boudinot ◽

...

Keyword(s):

Disease Resistance ◽

Cell Line ◽

Genome Editing ◽

Target Genes ◽

High Efficiency ◽

Genetic Resistance ◽

Model Organisms ◽

Fish Cell ◽

Genome Wide ◽

Lentivirus Transduction

1AbstractGenome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative disease resistance genes in cell lines, and the use of genome-wide CRISPR screens is currently limited by a lack of available tools and techniques. In the current study, an optimised protocol using lentivirus transduction for efficient integration of constructs into the genome of a Chinook salmon (Oncorhynchus tshwaytcha) cell line (CHSE-214) was developed. As proof-of-principle, two target genes were edited with high efficiency in an EGFP-Cas9 stable CHSE cell line; specifically, the exogenous, integrated EGFP and the endogenous RIG-I locus. Finally, the effective use of antibiotic selection to enrich the successfully edited targeted population was demonstrated. The optimised lentiviral-mediated CRISPR method reported here increases possibilities for efficient genome editing in salmonid cells, in particular for future applications of genome-wide CRISPR screens for disease resistance.

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Potential of genomic technologies to improve disease resistance in molluscan aquaculture

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0168 ◽

2021 ◽

Vol 376 (1825) ◽

Cited By ~ 2

Author(s):

Robert W. A. Potts ◽

Alejandro P. Gutierrez ◽

Carolina S. Penaloza ◽

Tim Regan ◽

Tim P. Bean ◽

...

Keyword(s):

Infectious Disease ◽

Disease Resistance ◽

Genome Editing ◽

Selective Breeding ◽

Genetic Resistance ◽

Disease Outbreaks ◽

Commercial Application ◽

Economic Losses ◽

Genomic Technologies ◽

Cost Efficient

Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

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Citizen views on genome editing: effects of species and purpose

Agriculture and Human Values ◽

10.1007/s10460-021-10235-9 ◽

2021 ◽

Author(s):

Gesa Busch ◽

Erin Ryan ◽

Marina A. G. von Keyserlingk ◽

Daniel M. Weary

Keyword(s):

Disease Resistance ◽

Product Quality ◽

Genome Editing ◽

Total Sample ◽

Moral Foundations ◽

Perceived Risks ◽

Public Response ◽

The Public ◽

Wide Range ◽

The Us

AbstractPublic opinion can affect the adoption of genome editing technologies. In food production, genome editing can be applied to a wide range of applications, in different species and with different purposes. This study analyzed how the public responds to five different applications of genome editing, varying the species involved and the proposed purpose of the modification. Three of the applications described the introduction of disease resistance within different species (human, plant, animal), and two targeted product quality and quantity in cattle. Online surveys in Canada, the US, Austria, Germany and Italy were carried out with a total sample size of 3698 participants. Using a between-subject design, participants were confronted with one of the five applications and asked to decide whether they considered it right or wrong. Perceived risks, benefits, and the perception of the technology as tampering with nature were surveyed and were complemented with socio-demographics and a measure of the participants’ moral foundations. In all countries, participants evaluated the application of disease resistance in humans as most right to do, followed by disease resistance in plants, and then in animals, and considered changes in product quality and quantity in cattle as least right to do. However, US and Italian participants were generally more positive toward all scenarios, and German and Austrian participants more negative. Cluster analyses identified four groups of participants: ‘strong supporters’ who saw only benefits and little risks, ‘slight supporters’ who perceived risks and valued benefits, ‘neutrals’ who showed no pronounced opinion, and ‘opponents’ who perceived higher risks and lower benefits. This research contributes to understanding public response to applications of genome editing, revealing differences that can help guide decisions related to adoption of these technologies.

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Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens

Horticulture Research ◽

10.1038/s41438-021-00543-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Ze Peng ◽

Yanhong He ◽

Saroj Parajuli ◽

Qian You ◽

Weining Wang ◽

...

Keyword(s):

Disease Resistance ◽

Downy Mildew ◽

Transcriptome Sequencing ◽

Early Stage ◽

Economic Losses ◽

Potential Candidate ◽

Early Disease ◽

True Leaf ◽

Cotyledon Stage ◽

Wide Range

AbstractDowny mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant–pathogen interactions in the early stage of infection and quickly assess resistance/susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA-Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops.

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Genome Editing to Develop Disease Resistance in Crops

Genome Engineering for Crop Improvement ◽

10.1002/9781119672425.ch14 ◽

2021 ◽

pp. 224-252

Author(s):

Kashaf Zafar ◽

Azka Noureen ◽

Muhammad Jawad Akbar Awan ◽

Naveed Anjum ◽

Muhammad Qasim Aslam ◽

...

Keyword(s):

Disease Resistance ◽

Genome Editing

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Molecular Markers for Powdery Mildew in Pea (Pisum sativum L.): A Review

Legume Research - An International Journal ◽

10.18805/lr-4740 ◽

2021 ◽

Author(s):

Reginah Pheirim ◽

Noren Singh Konjengbam ◽

Mayurakshee Mahanta

Keyword(s):

Disease Resistance ◽

Powdery Mildew ◽

Powdery Mildew Resistance ◽

Genetic Resistance ◽

Disease Resistance Gene ◽

Breeding Programs ◽

Biotic Stresses ◽

Pisum Sativum L ◽

Development And Utilization ◽

Mapping Populations

Powdery mildew is caused by an obligate parasite Erysiphe pisi and considered as one of the most important constraints causing yield reductions in pea. Development and utilization of genetic resistance is acknowledged as the most effective, economic and environmental friendly method of control. Therefore, development of cultivars with improved resistance to biotic stresses is a primary goal of plant breeding programs throughout the world. Three monogenic sources er1, er2 and Er3 have been described to govern the powdery mildew disease resistance. Several markers have been reported linked to resistant genes at varying distances in different mapping populations. Genetic markers linked to the disease resistance gene make the breeding process more efficient for the use of Marker Assisted Selection (MAS) strategy to aid in obtaining a complete powdery mildew resistance in pea.

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Genome editing for plant disease resistance: applications and perspectives

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0322 ◽

2019 ◽

Vol 374 (1767) ◽

pp. 20180322 ◽

Cited By ~ 19

Author(s):

Kangquan Yin ◽

Jin-Long Qiu

Keyword(s):

Disease Resistance ◽

Genome Editing ◽

Plant Disease Resistance ◽

Genetic Improvement ◽

Plant Disease ◽

Resistance Breeding ◽

Global Food Security ◽

Yield And Quality ◽

Genome Modifications ◽

Global Food

Diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant disease resistance is essential for sustainable agriculture. Genome editing has been revolutionizing plant biology and biotechnology by enabling precise, targeted genome modifications. Editing provides new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. Here, we first summarize the challenges for breeding resistant crops. Next, we focus on applications of genome editing technology in generating plants with resistance to bacterial, fungal and viral diseases. Finally, we discuss the potential of genome editing for breeding crops that present novel disease resistance in the future. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.

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Mutation Breeding in Tomato: Advances, Applicability and Challenges

Plants ◽

10.3390/plants8050128 ◽

2019 ◽

Vol 8 (5) ◽

pp. 128 ◽

Cited By ~ 12

Author(s):

Juhi Chaudhary ◽

Alisha Alisha ◽

Vacha Bhatt ◽

Sonali Chandanshive ◽

Nirbhay Kumar ◽

...

Keyword(s):

Genome Editing ◽

Large Scale ◽

Insertional Mutagenesis ◽

Crop Improvement ◽

Mutation Breeding ◽

Tomato Crop ◽

Technological Advances ◽

Trait Improvement ◽

Induced Mutagenesis ◽

Efficient Exploration

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

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Occurrence of mycotoxins in straw used in pig deep litter systems in Australia

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200010139 ◽

2005 ◽

Vol 2005 ◽

pp. 102-102 ◽

Cited By ~ 4

Author(s):

D. D. Moore

Keyword(s):

Disease Resistance ◽

Secondary Metabolites ◽

Feed Intake ◽

Production System ◽

Public Perception ◽

Production Systems ◽

Fusarium Species ◽

Crown Rot ◽

Pig Production ◽

Winter Cereals

Mycotoxins are secondary metabolites produced by fungi under certain stress periods (Smith and Seddon 1998). When ingested, mycotoxins cause insidious losses, ill thrift and reduced disease resistance. Zearalenone is known to cause hyperestrogesium in pigs and hence a reduction in fertility in both sows and boars can occur (Binder 2004). Certain mycotoxins such as zearalenone (ZEA) and deoxinivalenol (DON) are produced by fungi of the fusarium species on crops in the field. Fusarium pseudograminearum (Crown Rot) produces both DON and ZEA in decreasing levels up the tiller of winter cereals (Blaney et al. 1987). Most studies carried out so far analysed the occurrence of mycotoxins in the grain and less is known about the prevalence of mycotoxins in the straw of the crop. Housing of sows during gestation on straw is becoming a favoured production system due to environmental and public perception pressures. The intake of straw by weaners on straw based systems has been found to account for 11.5% of total feed intake (Barneveld et al. 2004), such that there could be a considerable risk for increased ingestion of mycotoxins in animals on straw based systems. The objective of this study was to investigate the occurrence of mycotoxins in straw used for deep litter in Australian deep litter pig production systems.

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