One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa)

Authors: WIGHT, CHARLENE - Agriculture And Agri-Food Canada; BLAKE, VICTORIA - Montana State University; JELLEN, ERIC - Brigham Young University; YAO, ERIC - University Of California Berkeley; Sen, Taner; TINKER, NICHOLAS - Agriculture And Agri-Food Canada

Submitted to: Crop and Pasture Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/28/2023
Publication Date: 1/19/2024
Citation: Wight, C.P., Blake, V.C., Jellen, E.N., Yao, E., Sen, T.Z., Tinker, N.A. 2024. One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa). Crop and Pasture Science. 75(2). Article CP23246. https://doi.org/10.1071/CP23246.
DOI: https://doi.org/10.1071/CP23246

Interpretive Summary: As the technologies used to discover new information concerning oat genes have evolved, and as the amount of information generated has increased, it has become more and more difficult to keep track of the work that has been done, even when most of it has been collected in one place. This is especially true with the addition of the physical maps. The objectives of this study were to create a guide for users of this information by: (1) linking individual hexaploid oat maps to the consensus map and oat reference genome sequences; (2) locating the markers from the consensus map on the reference genome sequences and visualizing the aligned regions on a genome browser; (3) producing an inventory of genes; and (4) incorporating the above information into GrainGenes through curation. The collected information will provide the oat research community with a guide to which traits are associated with which chromosome regions.

Technical Abstract: Oat researchers have been accumulating information concerning the locations of genes and quantitative trait loci (QTL) for more than 100 years. An inventory of those found in hexaploid oat has now been compiled. To make this resource more useful, a table comparing the major genetic maps of hexaploid oats to each other, to the 2018 oat consensus map, and to physical chromosomes was produced. Using the positions of perfectly matched single nucleotide polymorphism markers, each cM location along the consensus map was assigned to a location on the OT3098 version 2 physical map found on the GrainGenes database website (https://wheat.pw.usda.gov/jb/?data=/ggds/oat-ot3098v2-pepsico). This information was then used to assign physical locations to the genes and QTL in the inventory, where possible. Genome browser tracks aligning the consensus map regions and the locations of the genes and QTL to OT3098 version 2 were added to GrainGenes. Specific examples of identified patterns and validated locations are discussed.