Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Cheng Zou, Avinash Karn, Bruce Reisch, Allen Nguyen, Yongming Sun, Yun Bao, Michael S. Campbell, Deanna Church, Stephen Williams, Xia Xu, Craig A. Ledbetter, Sagar Patel, Anne Fennell, Jeffrey C. Glaubitz, Matthew Clark, Doreen Ware, Jason P. Londo, Qi Sun, Lance Cadle-Davidson

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.

Original languageEnglish (US)
Article number413
JournalNature communications
Volume11
Issue number1
DOIs
StatePublished - Dec 1 2020

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.

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    Zou, C., Karn, A., Reisch, B., Nguyen, A., Sun, Y., Bao, Y., Campbell, M. S., Church, D., Williams, S., Xu, X., Ledbetter, C. A., Patel, S., Fennell, A., Glaubitz, J. C., Clark, M., Ware, D., Londo, J. P., Sun, Q., & Cadle-Davidson, L. (2020). Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature communications, 11(1), [413]. https://doi.org/10.1038/s41467-019-14280-1