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 journalArticlepeer-review

19 Scopus citations


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
Issue number1
StatePublished - Jan 21 2020

Bibliographical note

Funding Information:
We would like to thank Linda Cote, Peter Schweitzer, and the Cornell University Biotechnology Resource Center for providing the necessary infrastructure, personnel, and expertise to amplify and sequence the DNA samples. Mike Colizzi and Steve Luce helped maintain vineyard plantings and collect tissue samples at Cornell University. The US Department of Agriculture (USDA)-National Institute of Food and Agriculture (NIFA) Specialty Crop Research Initiative provided funding for this project (award No. 2017-51181-26829). Additional funding supported this work, including USDA-Agricultural Research Service CRIS projects 8062-21000-044-00D and 8060-21220-007-00-D; the National Science Foundation project NPGI PRFB1523793; and the USDA-NIFA Hatch project SD00R668-18. Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. IDT and 10X Genomics co-authors did not have influence over which data was or was not included in the manuscript.

Publisher Copyright:
© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.


  • Alleles
  • Chromosome Mapping/methods
  • DNA, Plant/genetics
  • Genetic Markers/genetics
  • Genome, Plant
  • Genotyping Techniques/methods
  • Haplotypes
  • High-Throughput Nucleotide Sequencing
  • Microsatellite Repeats/genetics
  • Phylogeny
  • Plant Breeding
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA/methods
  • Vitis/genetics

PubMed: MeSH publication types

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


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