ArticlePlant biotechnology journal2018
Haplotype-based genotyping-by-sequencing in oat genome research.
Article in Plant biotechnology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 1 of them a synthesis that pooled it.
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Who cites it
66 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Narration of Some Key Concepts and Procedures in Plant Breeding.Frontiers in plant science · 2021Pooled it
- Genome-Wide Characterization of Nuclear Factor Y (NF-Y) Transcription Factors in Allohexaploid Oat.Plants (Basel, Switzerland) · 2026Article
- A natural variation within duplicated AsWRKY49-D2 drives the subgenomic functional divergence of homeologs in salt response of allohexaploid oats.Journal of integrative plant biology · 2026Article
- A haplotype-layered GWAS identifies a multi-trait grain mold resistance hub on sorghum chromosome 5.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Unveiling the genetic architecture of stripe rust resistance in wheat: a region-specific GWAS in Xinjiang, China.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- Genomic prediction for stem rust resistance in the southern United States elite oat (Frontiers in plant science · 2026Article
- Uncovering the genetic basis of crown rust resistance in a northern-by-southern oat biparental population.PloS one · 2026Article
- Comparative transcriptome and metabolome analyses reveal the mechanism of silicon to improve stem rust resistance in oat (Avena sativa L.).Scientific reports · 2025Article
- Global genomic population structure of wild and cultivated oat reveals signatures of chromosome rearrangements.Nature communications · 2025Article
- A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment.G3 (Bethesda, Md.) · 2025Article
- Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes.The plant genome · 2025Article
- Review
- Development and accuracy assessment of molecular markers associated with crown rust resistance genes in oat.PloS one · 2025Article
- Proteomic analysis of oat (Avena sativa L.) under drought stress using tandem mass tag labeling.PloS one · 2025Article
- Identification of reference genes for gene expression assessment in Avena sativa under biotic stress triggered by Blumeria graminis.Scientific reports · 2024Article
- Trends and Directions in Oats Research under Drought and Salt Stresses: A Bibliometric Analysis (1993-2023).Plants (Basel, Switzerland) · 2024Review
- Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS.Scientific reports · 2023Article
- Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat.International journal of molecular sciences · 2023Article
- Utilizing Genomics to Characterize the Common Oat Gene Pool-The Story of More Than a Century of Polish Breeding.International journal of molecular sciences · 2023Article
6 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
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-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high-resolution genome analysis and genomic selection in oats. A combined genome-wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component-based genome-wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS-derived markers facilitate genome analysis and genomic selection in oat.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.