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Partitioning SNPs Identified By GBS into Genome Annotation Classes and Calculating SNP-Explained Variances for Heading Date and Disease Resistance from the Resulting Genomic Relationship Matrices - Lolium perenne

Research output: Contribution to book/anthology/report/proceedingConference abstract in proceedingsResearch

  • Stephen Byrne, Denmark
  • Fabio Cericola, Denmark
  • Luc Janss
  • Just Jensen
  • Dario Fé
  • Bilal Ashraf, Denmark
  • Adrian Czaban, Denmark
  • Morten Greve-Pedersen, DLF-Trifolium A/S, Denmark
  • Ingo Lenk, DLF-Trifolium A/S Research Division, Højerupvej 31, 4600 Store Heddinge, Denmark, Denmark
  • Christian S Jensen, DLF-Trifolium A/S, Denmark
  • Torben Asp
A draft sequence assembly of the perennial ryegrass genome was annotated with the aid of RNA-seq data from various genotypes, plant components, and treatments. We predicted 39,795 high quality proteins originating from 28,182 genetic loci. There was an average of 5.9 exons per protein, and an average protein Annotation Edit Distance (AED) of 0.14. Genotyping-By-Sequencing (GBS) data was generated after genome complexity reduction with ApeKI for 995 breeding families. Data was aligned against the annotated sequence assembly, and we identified variants at over 1.8 million positions, which were partitioned according to genomic feature. Variants were found in 20,594 (73%) of the gene loci, and these had on average 22.3 SNPs per gene. SNPs were partitioned according to the following annotation features; exon (277,404 SNPs), CDS (221,364 SNPs), 5’UTR (32,551 SNPs), 3’UTR (44,781 SNPs), gene (458,273 SNPs), genes with NB-ARC domains (9,056 SNPs), intron (168,023 SNPs), and inter-genic (1,420,866 SNPs). Genomic relationship matrices were created for each annotation class and SNP-explained variances for heading date and disease resistance were calculated
Original languageEnglish
Title of host publicationFinal Program, Abstract & Exhibit Guide
Number of pages1
Publication year10 Jan 2015
Publication statusPublished - 10 Jan 2015
EventPlant and Animal Genome Conference XIII - Californien, San Diego, United States
Duration: 10 Jan 201514 Jan 2015


ConferencePlant and Animal Genome Conference XIII
LandUnited States
BySan Diego

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