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

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. (January 2020) Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun, 11 (1). p. 413. ISSN 2041-1723 (Public Dataset)

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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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment Investigative techniques and equipment > cloning > PCR Investigative techniques and equipment > assays > cloning > PCR Investigative techniques and equipment > assays Investigative techniques and equipment > cloning Investigative techniques and equipment > assays > cloning bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism > haplotype organism description > plant bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:	Ware, Doreen H.
Communities:	CSHL labs > Ware lab
Depositing User:	Adrian Gomez
Date:	21 January 2020
Date Deposited:	24 Jan 2020 15:48
Last Modified:	01 Feb 2024 19:54
PMCID:	PMC6972940
Related URLs:	Publisher
Dataset ID:	SRA: PRJNA281110 Code: (https://github.com/avinashkarn/analyze_amplicon) (https://bitbucket.org/cornell_bioinformatics/amplicon)
URI:	https://repository.cshl.edu/id/eprint/38926

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