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 and Lance Cadle-Davidson ()
Additional contact information
Cheng Zou: Cornell University
Avinash Karn: Cornell University
Bruce Reisch: Cornell University
Allen Nguyen: Integrated DNA Technologies
Yongming Sun: Integrated DNA Technologies
Yun Bao: Integrated DNA Technologies
Michael S. Campbell: 10x Genomics, Inc.
Deanna Church: 10x Genomics, Inc.
Stephen Williams: 10x Genomics, Inc.
Xia Xu: USDA-ARS, Grape Genetics Research Unit
Craig A. Ledbetter: USDA-ARS, Crop Diseases, Pests and Genetics Research
Sagar Patel: South Dakota State University
Anne Fennell: South Dakota State University
Jeffrey C. Glaubitz: Cornell University
Matthew Clark: University of Minnesota
Doreen Ware: Cold Spring Harbor Laboratory
Jason P. Londo: USDA-ARS, Grape Genetics Research Unit
Qi Sun: Cornell University
Lance Cadle-Davidson: USDA-ARS, Grape Genetics Research Unit

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-019-14280-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-14280-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-019-14280-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().