Nick Tinker

Nick Tinker
Agriculture and Agri-Food Canada | AAFC · Ottawa Research and Development Centre

PhD

About

164
Publications
34,086
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,535
Citations
Introduction
Nick Tinker works at the Ottawa Research and Development Centre, Agriculture and Agri-Food Canada. He does research in bioinformatics, genetics and molecular biology, primarily on oat.
Additional affiliations
May 1996 - January 2025
Agriculture and Agri-Food Canada
Position
  • Researcher
April 1996 - December 2015
Agriculture and Agri-Food Canada
Position
  • Researcher

Publications

Publications (164)
Article
Full-text available
Key message: Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS a...
Article
Full-text available
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-l...
Article
Full-text available
Background: Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale as...
Article
Full-text available
Oat (Avena sativa L.) is an important and nutritious cereal crop, and there is a growing need to identify genes that contribute to improved oat varieties. Here we utilize a newly sequenced and annotated oat reference genome to locate and characterize quantitative trait loci (QTLs) affecting agronomic and grain-quality traits in five oat populations...
Article
Full-text available
Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a...
Article
Full-text available
Cultivated oat (Avena sativa L.) is an important cereal grown worldwide due to its multifunctional uses for animal feed and human food. Oat has lagged behind other cereals in the genetic and genomic studies attributed to its large and complex genomes. Transposon-based genome characterization has been utilized successfully for identifying and determ...
Article
Full-text available
Key message Comparative sequence analysis was used to design a SNP marker that aided in the identification of new sources of oat stem rust resistance. Abstract New races of Puccinia graminis f. sp. avenae (Pga) threaten global oat production. An A. strigosa accession known to carry the broadly effective oat stem rust resistance gene, Pg6, was cros...
Article
Full-text available
Most oat grains destined for human consumption must possess the ability to pass through an industrial de-hulling process with minimal breakage and waste. Uniform grain size and a high groat to hull ratio are desirable traits related to milling performance. The purpose of this study was to characterize the genetic architecture of traits related to m...
Article
Full-text available
Key message Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. Abstract During the twentieth century, oat landraces have increasing...
Preprint
Full-text available
New races of Puccinia graminis f. sp. avenae ( Pga ) threaten global oat production. An A. strigosa accession known to carry the broadly effective oat stem rust resistance gene, Pg6 , was crossed with two susceptible A. strigosa accessions to generate 198 F 2:3 families and 190 F 5:6 RILs. The RIL population was used to determine that Pg6 was a sin...
Article
Full-text available
Identifying mechanisms and pathways involved in gene-environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework for complex trait dissection and prediction with an environmental dimension. A critical step was to identify an environmental index that is both biologically r...
Article
Full-text available
Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in t...
Article
Full-text available
Key message: Genotyping-by-sequencing (GBS)-derived molecular markers reveal the distinct genetic population structure and relatively narrow genetic diversity of Chinese hulless oat landraces. Four markers linked to the naked grain gene (N1) are identified by genome-wide association study (GWAS). Interest in hulless oat (Avena sativa ssp. nuda), a...
Article
Stem rust is an important disease of cultivated oat (Avena sativa) caused by Puccinia graminis f. sp. avenae. In North America, host resistance is the primary strategy to control this disease and is conferred by a relatively small number of resistance genes. Pg2 is a widely deployed stem rust resistance gene that originates from cultivated oat. Oat...
Article
Full-text available
A barrier to the adoption of genomic prediction in small breeding programs is the initial cost of genotyping material. Although decreasing, marker costs are usually higher than field trial costs. In this study we demonstrate the utility of stratifying a narrow‐base biparental oat population genotyped with a modest number of markers to employ genomi...
Article
Crown rust, caused by Puccinia coronata f. sp. avenae Eriks. (Pca), is among the most important oat diseases resulting in significant yield losses in many growing regions. A gene-for-gene interaction is well established in this pathosystem and has been exploited by oat breeders to control crown rust. Pc39 is a seedling crown rust resistance gene th...
Article
Full-text available
We adapted and tested a Rapture assay as an enhancement of genotyping-by-sequencing (GBS) in oat (Avena sativa). This assay was based on an additional bait-based capture of specific DNA fragments representing approximately 10,000 loci within the enzyme-based complexity reduction provided by GBS. By increasing the specificity of GBS to include only...
Article
Full-text available
Key message The widely deployed, oat stem rust resistance gene Pg13 was mapped by linkage analysis and association mapping, and KASP markers were developed for marker-assisted selection in breeding programs. Abstract Pg13 is one of the most extensively deployed stem rust resistance genes in North American oat cultivars. Identification of markers t...
Article
Full-text available
The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oat...
Article
Full-text available
Oat (Avena sativa L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars w...
Article
Full-text available
Following successful application in dairy cow breeding, genomic selection (GS) has become a hot topic among plant geneticists and breeders. GS and conventional methods have the same goal of identifying best genotypes for a given crop and region, and should follow the same principles, particularly in dealing with genotype-by-environment (GE). Dealin...
Preprint
Full-text available
Oat ( Avena sativa L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars...
Article
GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discove...
Article
Full-text available
Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for molecular characterization of plant germplasm with complex and unsequenced genomes. Here we applied the GBS technology to assess the genetic diversity of 275 hexaploid oat wild relative (Avena sterilis) plants collected from 24 natural p...
Article
We developed 178 recombinant inbred lines from a southern‐by‐spring oat population designated as “TxH.” These lines were genotyped to generate a high‐quality linkage map that resolved 6,902 markers into 21 linkage groups that matched closely with the latest hexaploid oat consensus map. Three major quantitative trait loci (QTLs) affecting heading da...
Article
Full-text available
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C g...
Article
Full-text available
Fluorescence in situ hybridization was used to investigate the physical location of oligo-Am1 and (TTG)6 trinucleotide repeats in the metaphase chromosomes of seven diploid species (AA or CC genomes), seven tetraploid species (AABB or AACC genomes), and two hexaploid species (AACCDD genomes) belonging to the genus Avena. The oligo-Am1 probe produce...
Data
Figure S1 The density of markers in the updated consensus map, based on (a) TL‐haplotype loci and (b) GBS‐SNPs. Figure S2 Mean chromosome haplotype diversity of the three subpopulations. Figure S3 Haplotype diversity of the full set of lines (a), the spring set (b), and the southern set (c) infered using the TL‐haplotype markers. Figure S4 The s...
Data
Appendix S4 The input file used for the Haplotag analysis of the 4657 lines.
Data
Appendix S1 The list of 4657 taxa genotyped and the consensus map. Appendix S2 The genotype data of the 950 lines used to update the consensus map (full data available by accessing haplotag.aowc.ca/SM3_OC_placement_RAW_merged.zip) Appendix S3 Significant GWAS hits of the different comparisons.
Data
Appendix S4 The input file used for the Haplotag analysis of the 4657 lines.
Article
Full-text available
Fluorescence in situ hybridization (FISH) was performed to explore the genomic and species relationships among 17 taxa using Am1 (oligo-Am1) and (GAA)6 oligonucleotide probes. Oligo-Am1 (51 bp) hybridized strongly over almost the entire length of all chromosomes in the C genome. Six translocations between the A and C genomes were found in AACC tetr...
Preprint
Full-text available
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene(Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C ge...
Article
Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic...
Article
Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and assignment to physical chromosomes. Genomic and species relationships among sixteen species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT)6 probes. The Am1 oligonucleotide probe was particularly enr...
Article
Full-text available
Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and their assignment to physical chromosomes. Genomic and species relationships among 16 species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT) 6 probes. The Am1 oligonucleotide probe was particularly e...
Article
Full-text available
Resistance in oats (Avena sativa L.) to Fusarium graminearum was phenotyped in 424 spring oat lines from North America and Scandinavia and genotyped with 2974 SNP markers. Fusarium head blight (FHB), deoxynivalenol (DON) content, days to flowering (DTF) and days to yellow maturity (DTM) were scored in field trials in 2011–12. Trials with phenotypic...
Article
Full-text available
Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat production in many parts of the world. In this first comprehensive multi-environment genomewide association map of oat crown rust, we used 2,972 SNPs genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown...
Article
Full-text available
The Collaborative Oat Research Enterprise (CORE) was initiated in 2009 and ran until approximately 2014. It consisted of a set of coordinated projects, funded investigators, and collaborators who were united by an over-arching goal of developing modern tools for genomics and molecular breeding in oat. Principle outcomes of the CORE included: (1) se...
Article
Full-text available
Six hundred thirty five oat lines and 4,561 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PC nor the cross-validation errors from K=1 to 2...
Article
Full-text available
Genotyping-by-sequencing (GBS) and related methods are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of SNPs within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. How...
Article
Full-text available
Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (~12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density c...
Article
Full-text available
Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this...
Preprint
Full-text available
Genotyping-by-sequencing (GBS) and related methods are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of SNPs within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. How...
Article
Full-text available
The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum L.) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to Fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into comm...
Article
Full-text available
Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference single nucleotide polymorphisms (SNPs), we have developed a 6000 (6K) BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs...
Article
Full-text available
Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.)...
Article
Full-text available
Oat (Avena sativa L.) is a cool season annual grass species produced for grain and forage in many countries. The majority of oat cultivars in the United States are spring types grown primarily for grain production. However, in the southern region of the United States, much of the oat production consists of winter types that are grown for grain or a...
Conference Paper
Full-text available
We report the construction of a new consensus linkage map for hexaploid oat, which is a pre-requisite for the assembly of an oat genome sequence. This map was developed from 12 populations and accurately represents the 21 chromosomes of hexaploid oat. Individual population component maps were constructed using a novel community consensus approach....
Conference Paper
Full-text available
The hexaploid oat (Avena sativa L.) is an important cereal crop worldwide, cultivated to produce grains for the food industry as well as animal feeding. For its importance, oat was chosen as one of the crops of the Plant Pathway Elucidation Project (P2EP), a groundbreaking $1.5 million program that engages college students from across North Carolin...
Article
Full-text available
Cultivated oat (Avena sativa L.) is allohexaploid and contains three genomes (A, C, and D). By using fluorescence in situ hybridization, a 391 bp repetitive DNA fragment (‘A336’) isolated from oat chromosome 18D was predominantly localized in centromeric regions of mitotic metaphase chromosomes of oat accession ‘CN64226’. Assays of simultaneous and...
Article
Full-text available
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP d...
Article
Full-text available
beta-glucan, a soluble fiber found in oat (Avena sativa L.) grain, is good for human health, and selection for higher levels of this compound is regarded as an important breeding objective. Recent advances in oat DNA markers present an opportunity to investigate new selection methods for polygenic traits such as beta-glucan concentration. Our objec...
Article
Full-text available
The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged...