CRISPR-directed mitotic recombination enables genetic mapping without crosses

Sadhu, Meru J.; Bloom, Joshua S.; Day, Laura; Kruglyak, Leonid

doi:10.1126/science.aaf5124

Cited by 90 publications

(104 citation statements)

References 35 publications

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“…Currently, the main factor limiting the resolution of ceX-QTL and other mapping approaches is the highly nonuniform pattern of genetic recombination in C. elegans 46 . Thus, we foresee that future implementations of ceX-QTL could greatly benefit from either targeting recombination to specific loci using CRISPR/Cas9 47…”

Section: Discussionmentioning

confidence: 99%

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk

Burga

Ben-David

Vergara

et al. 2018

Preprint

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Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We used ceX-QTL to map a drug resistance locus with high resolution. We also mapped differences in gene expression in live worms and discovered a regulatory feedback loop that responds to changes in HSP-90 chaperone activity. Lastly, we used ceX-QTL to map loci that influence fitness and discovered that one such locus is caused by a deletion in a highly conserved chromatin reader in the N2 reference strain. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.

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Section: Discussionmentioning

confidence: 99%

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk

Burga

Ben-David

Vergara

et al. 2018

Preprint

Self Cite

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“…It may be feasible to target double-strand breaks to specific regions of chromosomes and then use CRISPR-Cas9 technology to stimulate recombination. Although mitotic recombination can be targeted precisely in yeast cells, and the fine-mapping of loci is also possible 88 , it is difficult to imagine using this approach in multicellular organisms such as plants. It may be possible to use a promoter that is specific to prophase 1 of meiosis or an inducible promoter to express the gene that encodes Cas9 to guide RNAs to create new, targeted patterns of double-strand breaks in the germ line and to promote recombination in new regions of interest during normal meiosis.…”

Section: Crop Breeding As a Dna-assembly Problemmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

342

240

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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“…Thus, the high efficiency of CRISPR-Cas9 mediate recombination events within 20 kb of the targeted site has been demonstrated. Comparing this rate of recombination with that obtained by random meiotic segregation, the later would require more than seven thousand individuals (Sadhu et al, 2016). The application of XP-GWASandCRISPR-Cas9approaches and their potential use in QDR characterization is highly promising.…”

Section: How To Study Complex Traits and Qdrsmentioning

confidence: 99%

“…First, there is extreme-phenotype GWAS (XP-GWAS), a new approach combining bulk segregant analysis (BSA) and GWAS (Yang et al, 2015). The second approach takes advantage of the use of clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) and allow to obtain targeted mitotic recombination events without needing to develop directed crosses (Sadhu et al, 2016).…”

Section: How To Study Complex Traits and Qdrsmentioning

confidence: 99%

Unraveling the molecules hidden in the gray shadows of quantitative disease resistance to pathogens

2018

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One of the most challenging questions in plant breeding and molecular plant pathology research is what are the genetic and molecular bases of quantitative disease resistance (QDR)?. The scarce knowledge of how this type of resistance works has hindered plant breeders to fully take advantage of it. To overcome these obstacles new methodologies for the study of quantitative traits have been developed. Approaches such as genetic mapping, identification of quantitative trait loci (QTL) and association mapping, including candidate gene approach and genome wide association studies, have been historically undertaken to dissect quantitative traits and therefore to study QDR. Additionally, great advances in quantitative phenotypic data collection have been provided to improve these analyses. Recently, genes associated to QDR have been cloned, leading to new hypothesis concerning the molecular bases of this type of resistance. In this review we present the more recent advances about QDR and corresponding application, which have allowed postulating new ideas that can help to construct new QDR models. Some of the hypotheses presented here as possible explanations for QDR are related to the expression level and alternative splicing of some defense-related genes expression, the action of "weak alleles" of R genes, the presence of allelic variants in genes involved in the defense response and a central role of kinases or pseudokinases. With the information recapitulated in this review it is possible to conclude that the conceptual distinction between qualitative and quantitative resistance may be questioned since both share important components. Keywords: breeding, complex traits, genome, gene expression, plant immunity, quantitative disease resistance (QDR), quantitative trait loci (QTL). RESUMENUna de las preguntas más desafiantes del fitomejoramiento y de la fitopatología molecular es ¿cuáles son las bases genéticas y moleculares de la resistencia cuantitativa a enfermedades?. El escaso conocimiento de cómo este tipo de resistencia funciona ha obstaculizado que los fitomejoradores la aprovecharlo plenamente. Para superar estos obstáculos se han desarrollado nuevas metodologías para el estudio de rasgos cuantitativos. Los enfoques como el mapeo genético, la identificación de loci de rasgos cuantitativos (QTL) y el mapeo por asociaciones, incluyendo el enfoque de genes candidatos y los estudios de asociación amplia del genoma, se han llevado a cabo históricamente para describir rasgos cuantitativos y por lo tanto para estudiar QDR. Además, se han proporcionado grandes avances en la obtención de datos fenotípicos cuantitativos para mejorar estos análisis. Recientemente, algunos genes asociados a QDR han sido clonados, lo que conduce a nuevas hipótesis sobre las bases moleculares de este tipo de resistencia. En esta revisión presentamos los avances más recientes sobre QDR y la correspondiente aplicación, que han permitido postular nuevas ideas que pueden ayudar a construir nuevos modelos. Algunas de las hipótesis presen...

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CRISPR-directed mitotic recombination enables genetic mapping without crosses

Cited by 90 publications

References 35 publications

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk

Genomic innovation for crop improvement

Unraveling the molecules hidden in the gray shadows of quantitative disease resistance to pathogens

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