Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

Witek, Kamil; Jupe, Florian; Witek, Agnieszka; Baker, David; Clark, Matt; Jones, Jonathan D. G.

doi:10.1038/nbt.3540

Cited by 253 publications

(252 citation statements)

References 39 publications

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“…In the draft S. verrucosum VER54 assembly, we discovered 409 R-genes in comparison to 502 R-genes, 488 R-genes, and 429 R-genes in the 4-kb, 5-kb, and 7-kb assemblies, respectively. These numbers are similar to the numbers of annotated R-genes for the potato and tomato species: Solanum tuberosum clone DM (704 R-genes) (3), Solanum americanum accession 954750186 (649 R-genes) (17), and Solanum pimponellifolium LA1589 (355 R-genes ) (5). …”

Section: Resultsmentioning

confidence: 90%

“…As the bait library is specifically designed for R-gene coding sequences (17), coding and non-coding regions are unequally covered (Figure 4); therefore, we counted the number of reads mapping to each contig. Contigs of the 4-kb library are supported by an average of 31 RoI, contigs of the 5-kb library by an average of 17 RoI, and contigs of the 7-kb library by an average of 11 RoI.…”

Section: Resultsmentioning

confidence: 99%

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Targeted Capture and Sequencing of Gene-Sized DNA Molecules

et al. 2016

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Targeted capture provides an efficient and sensitive means for sequencing specific genomic regions in a high-throughput manner. To date, this method has mostly been used to capture exons from the genome (the exome) using short insert libraries and short-read sequencing technology, enabling the identification of genetic variants or new members of large gene families. Sequencing larger molecules results in the capture of whole genes, including intronic and intergenic sequences that are typically more polymorphic and allow the resolution of the gene structure of homologous genes, which are often clustered together on the chromosome. Here, we describe an improved method for the capture and single-molecule sequencing of DNA molecules as large as 7 kb by means of size selection and optimized PCR conditions. Our approach can be used to capture, sequence, and distinguish between similar members of the NB-LRR gene family-key genes in plant immune systems.

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Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Targeted Capture and Sequencing of Gene-Sized DNA Molecules

et al. 2016

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“…3b). This approach was used to identify a genetic locus that underlies resistance to late blight in Solanum americanum, a wild relative of the potato, using a combination of genetic mapping and resistance-gene enrichment sequencing (RenSeq) 69 . RenSeq is has now been used to isolate the resistance (R) gene repertoire from populations of wild relatives as well as sequence variation that is associated with phenotypes of disease resistance.…”

Section: Review Insightmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

318

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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“…Molecular tools also permit us to identify R genes that correspond to "core," conserved pathogen effectors [47], which may impose a high fitness cost on virulent pathogen strains. High-throughput techniques for cloning R-genes [123,124] are expected to greatly expand the libraries of R genes available to breeders. Plant artificial chromosomes [125] will likely facilitate stacking of numerous genes performing diverse functions, thus increasing the durability of deployed genes.…”

Section: Deployment Of Ge Traitsmentioning

confidence: 99%

Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-by-Case Decision-Making

Vincelli

2016

Sustainability

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Genetic engineering (GE) offers an expanding array of strategies for enhancing disease resistance of crop plants in sustainable ways, including the potential for reduced pesticide usage. Certain GE applications involve transgenesis, in some cases creating a metabolic pathway novel to the GE crop. In other cases, only cisgenessis is employed. In yet other cases, engineered genetic changes can be so minimal as to be indistinguishable from natural mutations. Thus, GE crops vary substantially and should be evaluated for risks, benefits, and social considerations on a case-by-case basis. Deployment of GE traits should be with an eye towards long-term sustainability; several options are discussed. Selected risks and concerns of GE are also considered, along with genome editing, a technology that greatly expands the capacity of molecular biologists to make more precise and targeted genetic edits. While GE is merely a suite of tools to supplement other breeding techniques, if wisely used, certain GE tools and applications can contribute to sustainability goals.

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Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

Cited by 253 publications

References 39 publications

Targeted Capture and Sequencing of Gene-Sized DNA Molecules

Targeted Capture and Sequencing of Gene-Sized DNA Molecules

Genomic innovation for crop improvement

Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-by-Case Decision-Making

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