Dataset Information

Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.

ABSTRACT: Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a pre-breeding program.

SUBMITTER: Chu J

PROVIDER: S-EPMC7033508 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.

Chu Jianting J Zhao Yusheng Y Beier Sebastian S Schulthess Albert W AW Stein Nils N Philipp Norman N Röder Marion S MS Reif Jochen C JC

Frontiers in plant science 20200214

Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel ...[more]

PMID: 32117381

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Project description:BackgroundThe September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus.MethodThis genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors.ResultEach WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA.ConclusionThe molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough validation study. This method incorporates molecular biology techniques that are already well established in research and diagnostic laboratories, allowing for an easy introduction of this method into existing laboratories.Keywordssingle nucleotide polymorphisms, genotyping, plant pathology, viruses, microbial forensics, Single base primer extension, SNaPshot Multiplex Kit.

Dataset Information

Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.

Publications

Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.

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