Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity

Juan J. Gutierrez-Gonzalez, Martin Mascher, Jesse Poland, Gary J. Muehlbauer

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17 Scopus citations

Abstract

Wheat (Triticum aestivum) genetic maps are a key enabling tool for genetic studies. We used genotyping-by-sequencing-(GBS) derived markers to map recombinant inbred line (RIL) and doubled haploid (DH) populations from crosses of W7984 by Opata, and used the maps to explore features of recombination control. The RIL and DH populations, SynOpRIL and SynOpDH, were composed of 906 and 92 individuals, respectively. Two high-density genetic linkage framework maps were constructed of 2,842 and 2,961 cM, harboring 3,634 and 6,580 markers, respectively. Using imputation, we added 43,013 and 86,042 markers to the SynOpRIL and SynOpDH maps. We observed preferential recombination in telomeric regions and reduced recombination in pericentromeric regions. Recombination rates varied between subgenomes, with the D genomes of the two populations exhibiting the highest recombination rates of 0.26–0.27 cM/Mb. QTL mapping identified two additive and three epistatic loci associated with crossover number. Additionally, we used published POPSEQ data from SynOpDH to explore the structural variation in W7984 and Opata. We found that chromosome 5AS is missing from W7984. We also found 2,332 variations larger than 100 kb. Structural variants were more abundant in distal regions, and overlapped 9,196 genes. The two maps provide a resource for trait mapping and genomic-assisted breeding.

Original languageEnglish (US)
Article number1793
JournalScientific reports
Volume9
Issue number1
DOIs
StatePublished - Feb 11 2019

Bibliographical note

Funding Information:
This material is based upon work supported by the National Science Foundation under Grant No. (1339389) and partial support provided by Feed the Future through the U.S. Agency for International Development, under the terms of Contract No AID-OAA-A-13-00051. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or U.S. Agency for International Development.

Publisher Copyright:
© 2019, The Author(s).

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