title: SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.
abstract: 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 discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
authors.affiliation: General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America.
authors.forename: Rebekah E
authors.initials: RE
authors.lastname: Oliver
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Tinker
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.forename: Shiaoman
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authors.lastname: Chao
authors.forename: Eric N
authors.initials: EN
authors.lastname: Jellen
authors.forename: Martin L
authors.initials: ML
authors.lastname: Carson
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authors.lastname: Rines
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authors.forename: Joseph D
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authors.lastname: Lutz
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authors.lastname: Shackelford
authors.forename: Abraham B
authors.initials: AB
authors.lastname: Korol
authors.forename: Charlene P
authors.initials: CP
authors.lastname: Wight
authors.forename: Kyle M
authors.initials: KM
authors.lastname: Gardner
authors.forename: Jiro
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authors.lastname: Hattori
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Beattie
authors.forename: Åsmund
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authors.lastname: Bjørnstad
authors.forename: J Michael
authors.initials: JM
authors.lastname: Bonman
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Jannink
authors.forename: Mark E
authors.initials: ME
authors.lastname: Sorrells
authors.forename: Gina L
authors.initials: GL
authors.lastname: Brown-Guedira
authors.forename: Jennifer W
authors.initials: JW
authors.lastname: Mitchell Fetch
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Harrison
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Howarth
authors.forename: Amir
authors.initials: A
authors.lastname: Ibrahim
authors.forename: Frederic L
authors.initials: FL
authors.lastname: Kolb
authors.forename: Michael S
authors.initials: MS
authors.lastname: McMullen
authors.forename: J Paul
authors.initials: JP
authors.lastname: Murphy
authors.forename: Herbert W
authors.initials: HW
authors.lastname: Ohm
authors.forename: Brian G
authors.initials: BG
authors.lastname: Rossnagel
authors.forename: Weikai
authors.initials: W
authors.lastname: Yan
authors.forename: Kelci J
authors.initials: KJ
authors.lastname: Miclaus
authors.forename: Jordan
authors.initials: J
authors.lastname: Hiller
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Maughan
authors.forename: Rachel R
authors.initials: RR
authors.lastname: Redman Hulse
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Anderson
authors.forename: Emir
authors.initials: E
authors.lastname: Islamovic
authors.forename: Eric W
authors.initials: EW
authors.lastname: Jackson
mesh_terms: D018554:Avena / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D026801:Synteny / Q000235:genetics*