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

• Published in: Nature communications Vol. 11; no. 1; p. 413
• Main Authors: Zou, Cheng, Karn, Avinash, Reisch, Bruce, Nguyen, Allen, Sun, Yongming, Bao, Yun, Campbell, Michael S, Church, Deanna, Williams, Stephen, Xu, Xia, Ledbetter, Craig A, Patel, Sagar, Fennell, Anne, Glaubitz, Jeffrey C, Clark, Matthew, Ware, Doreen, Londo, Jason P, Sun, Qi, Cadle-Davidson, Lance
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 21.01.2020; Nature Publishing Group UK; Nature Portfolio
• Subjects: Alleles; Assemblies; Binding sites; Breeding; Chromosome Mapping - methods; Deoxyribonucleic acid; Disease resistance; Divergence; DNA; DNA, Plant - genetics; DNA, Plant - isolation & purification; Gene sequencing; Genetic Markers - genetics; Genetics; Genome, Plant; Genomes; Genotyping Techniques - methods; Haplotypes; High-Throughput Nucleotide Sequencing; Markers; Microsatellite Repeats - genetics; Phylogeny; Plant Breeding; Polymerase chain reaction; Polymorphism, Single Nucleotide; Sequence Analysis, DNA - methods; Single-nucleotide polymorphism; Species; Strategy; Vitis; Vitis - genetics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-14280-1

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.