A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement

Full Title: A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement

Journal: The Plant Genome

Year of Publication: 2016

PHHI Author(s): Tzung-Fu Hsieh
Publication Author(s): Ashley S. Chaffin, Yung-Fen Huang, Scott Smith, Wubishet A. Bekele, Ebrahiem Babiker, Belaghihalli N. Gnanesh, Bradley J. Foresman, Steven G. Blanchard, Jeremy J. Jay, Robert W. Reid, Charlene P. Wight, Shiaoman Chao, Rebekah Oliver, Emir Islamovic, Frederic L. Kolb, Curt McCartney, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Tim Langdon, Catherine J. Howarth, Cory R. Brouwer, Eric N. Jellen, Kathy Esvelt Klos, Jesse A. Poland, Tzung-Fu Hsieh, Ryan Brown, Eric Jackson, Jessica A. Schlueter and Nicholas A. Tinker

Abstract:

 

Hexaploid oat (Avena sativa, 2n = 6x = 42) is a member of the Poaceae family and has a large
genome (~12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical
rearrangements among parental genomes have hindered the development of linkage maps in this
species. The objective of this work was to develop a single, high-density, consensus linkage map
that is representative of the majority of commonly grown oat varieties. Data from a cDNA-
derived SNP array and genotyping-by-sequencing were collected from progeny of 12 bi-parental
recombinant inbred line populations derived from 19 parents representing oat germplasm
cultivated primarily in North America. Linkage groups from all mapping populations were
compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster
were then merged into 21 consensus chromosomes, generating a framework consensus map of
7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a
lower degree of certainty. Assignment to physical chromosomes with high confidence was made
for nine chromosomes. Comparison of homeologous regions among oat chromosomes and
matches to orthologous regions of rice reveal that the hexaploid oat genome has been highly
rearranged relative to its ancestral diploid genomes as a result of frequent translocations among
chromosomes. Heterogeneous chromosome rearrangements among populations were also
evident, likely accounting for the failure of some linkage groups to match the consensus. This
work contributes to a further understanding of the organization and evolution of hexaploid grass
genomes.

Link to Article: https://www.researchgate.net/publication/292143479_A_consensus_map_in_cultivated_hexaploid_oat_reveals_conserved_grass_synteny_with_substantial_sub-genome_rearrangement