T3/Oat Genotype Trial description

Tinker QTL 2021

• Description: GBS PstI-MspI, data called across 5 biparental oat populations
• Publication: Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement
• Filter: heterozygosity was 10%, and minor allele frequency was 10%, minimum complete genotypes: 10%

GBS POGI

• Description: GBS PstI-MspI, Public Oat Genotyping Initiative, Haplotag
• Publication: Haplotag: Software for Haplotype-Based GBS Analysis
• Publication: Haplotype-based GBS in oat genome research
• Filter: Output was filtered across the full population to maintain markers for which genotype calls were 50% or 80% complete, heterozygosity was 10%, and minor allele frequency was 5%. Additional filters for Haplotag included a maximum base difference of three for aligning tags, a maximum of nine tags per cluster, a maximum heterozygote frequency on a haplotype basis of 0.25, and a maximum tolerance for tri-zygotes and multi-zygotes of 1% and 0%, respectively.

GBS POGI 2019

• Description: GBS PstI-MspI, Public Oat Genotyping Initiative, Haplotag, Aligned to PepsiCo OT3098 v1 assembly

GBS Spain

• GBS PstI-MspI, Spain, Haplotag
• Protocol
  
• Accessions
  
• Genotype file
  
• Filter: removed all markers with lower than 80% completeness, less than 5% minor allele frequency, or greater than 10% heterozygosity

GBS Core

• Description: Collaborative Oat Research Enterprise
• Description: GBS data called by TASSEL/UNEAK on 635 CORE diversity lines
• Publication: Using GBS for Genomic Discovery in Cultivated Oat
• GBS sequence reads and a key file for GBS pipeline analysis
• Filter: filtered at >= 95% completeness, >= 1% MAF, >= 5% heterozygous

Infinium 2010

• Publication: A SNP Genotyping Array for Hexaploid Oat
• Filter: filtered SNPs to maximize predicted minor allele frequency (MAF), to minimize heterozygotes within varieties (which could signify miss-assemblies of orthologous and paralogous loci), and to eliminate SNPs that contained multiple variants within the 120- or 200-base context sequence used for assay design

Infinium 2020

• Publication: Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat
• Protocol
  
• Accessions
  
• Genotype file
  
• Filter: no filtering based on MAF for missingness

Working