Candidate genes and signatures of directional selection on fruit quality traits during apple domestication

Marshall J. Wedger, Abby C. Schumann, Briana L. Gross

Research output: Contribution to journalArticlepeer-review


PREMISE: During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops. METHODS: We used sequence capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus ×domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis. RESULTS: We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. ×domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low-diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high-diversity genes included a variety of functions. CONCLUSIONS: Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.

Original languageEnglish (US)
JournalAmerican journal of botany
StateAccepted/In press - 2021

Bibliographical note

Funding Information:
The authors thank the University of Minnesota Duluth and the Department of Biology Undergraduate Research in Science and Technology (BURST) program for funding. The University of Minnesota Genomics Center provided assistance with sequence generation, and the Minnesota Supercomputing Institute (MSI) at the University of Minnesota provided resources for data analysis. Special thanks to Ian Misner for offering the Bioinformatics Crash Course through the University of Maryland and to Martin Taylor and Lewis Spurgin for offering the course Introductory Population Genomics: From Data to Inference through Physalia Courses. Finally, thanks to the Gross and Kenneth M. Olsen Lab members, Jared L. Strasburg, Katharine E. Waselkov, Associate Editor Andrew F. Schnabel, and two anonymous reviewers for their thoughtful comments that greatly improved this manuscript.

Publisher Copyright:
© 2021 Botanical Society of America


  • clonal crop
  • crop–wild gene flow
  • diversifying selection
  • Hyb-Seq
  • Malus sieversii
  • Malus ×domestica
  • perennial crop
  • Rosaseae
  • sequence capture
  • unconscious selection

PubMed: MeSH publication types

  • Journal Article

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