title: High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.
abstract: 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 analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.
authors: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.|Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
authors: Honghai
authors: H
authors: Yan
authors: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.
authors: Wubishet A
authors: WA
authors: Bekele
authors: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.
authors: Charlene P
authors: CP
authors: Wight
authors: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
authors: Yuanying
authors: Y
authors: Peng
authors: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK.
authors: Tim
authors: T
authors: Langdon
authors: Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, B3H 4R2, Canada.
authors: Robert G
authors: RG
authors: Latta
authors: Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors: Yong-Bi
authors: YB
authors: Fu
authors: Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
authors: Axel
authors: A
authors: Diederichsen
authors: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK.
authors: Catherine J
authors: CJ
authors: Howarth
authors: Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.
authors: Eric N
authors: EN
authors: Jellen
authors: Plateforme d'analyses génomiques, Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada.
authors: Brian
authors: B
authors: Boyle
authors: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
authors: Yuming
authors: Y
authors: Wei
authors: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada. nick.tinker@canada.ca.
authors: Nicholas A
authors: NA
authors: Tinker
mesh_terms: D018554:Avena / Q000235:genetics*; D020223:Chromosome Painting; D032461:Chromosomes, Plant / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D060005:Genotyping Techniques; D006239:Haplotypes; D011123:Polyploidy
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers