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

Authors: ZOU, CHENG - Cornell University; KARN, AVINASH - Cornell University; REISCH, BRUCE - Cornell University; NGUYEN, ALLEN - Integrated Dna Technologies; SUN, YONGMING - Integrated Dna Technologies; BAO, YUN - Integrated Dna Technologies; CAMPBELL, MICHAEL - 10x Genomics, Inc; CHURCH, DEANNA - 10x Genomics, Inc; WILLIAMS, STEPHEN - 10x Genomics, Inc; Xu, Xia; Ledbetter, Craig; PATEL, SAGAR - South Dakota State University; FENNELL, ANNE - South Dakota State University; GLAUBITZ, JEFF - Cornell University; CLARK, MATTHEW - University Of Minnesota; Ware, Doreen; Londo, Jason; SUN, QI - Cornell University; Cadle-Davidson, Lance

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/31/2019
Publication Date: 1/21/2020
Citation: 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., Clark, M., Ware, D., Londo, J.P., Sun, Q., Cadle Davidson, L.E. 2020. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications. https://doi.org/10.1038/s41467-019-14280-1.

Interpretive Summary: DNA markers are widely used for breeding and genetic analyses. However, it can be challenging to develop markers that work well across the diversity of wild and cultivated species. In this study, we applied a new marker strategy targeting core regions of the genome that are maintained across highly diverse grape species. This strategy was enabled by a cost-effective 10x Genomics technology for genome assembly. PCR priming sites were identified in these core regions flanking sequences that were less conserved. For 2,000 such core regions, we used rhAmpSeq marker technology to fingerprint four grape families spanning the diversity of the Vitis genus. In contrast to previous markers, transferability was increased from 2% to 91.4%. This marker development strategy should be widely applicable for breeding and genetic studies in diverse organisms.

Technical Abstract: Molecular markers are essential for dissecting genetic relationships, performing genome-wide association studies, and molecular breeding. Many breeding programs supplement the gene pool by incorporating novel variation from outside the target species. For example, grape breeders utilize disease resistance alleles from congeneric species ~20 million years divergent. This trait introgression would be greatly accelerated by a cross-species, universal marker panel, because existing grape marker platforms, such as genotyping-by-sequencing, have cross-species transfer rates as low as 2%. In this study, we applied a novel marker discovery strategy targeting the core genome that is syntenic across highly diverse grape species. Incorporating seven new grape de novo assemblies generated with linked-read technology and three existing assemblies, the Vitis collinear core genome was estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun whole genome sequencing data from 40 additional accessions enabled identification Molecular markers are essential for dissecting genetic relationships, performing genome-wide association studies, and molecular breeding. Many breeding programs supplement the gene pool by incorporating novel variation from outside the target species. For example, grape breeders utilize disease resistance alleles from congeneric species ~20 million years divergent. This trait introgression would be greatly accelerated by a cross-species, universal marker panel, because existing grape marker platforms, such as genotyping-by-sequencing, have cross-species transfer rates as low as 2%. In this study, we applied a novel marker discovery strategy targeting the core genome that is syntenic across highly diverse grape species. Incorporating seven new grape de novo assemblies generated with linked-read technology and three existing assemblies, the Vitis collinear core genome was estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun whole genome sequencing data from 40 additional accessions enabled identification of conserved PCR primer binding sites flanking polymorphic haplotypes with high information content in the core genome. From these target regions, we developed 2,000 rhAmpSeq markers as a single PCR multiplex and validated the panel in four biparental populations spanning the diversity of the Vitis genus. In stark contrast to previous markers, transferability increased to 91.4%. This core genome marker development strategy, incorporating the high-fidelity rhAmpSeq assays, should be widely applicable for molecular breeding and genetic studies in many crop and animal genera.of conserved PCR primer binding sites flanking polymorphic haplotypes with high information content in the core genome. From these target regions, we developed 2,000 rhAmpSeq markers as a single PCR multiplex and validated the panel in four biparental populations spanning the diversity of the Vitis genus. In stark contrast to previous markers, transferability increased to 91.4%. This core genome marker development strategy, incorporating the high-fidelity rhAmpSeq assays, should be widely applicable for molecular breeding and genetic studies in many crop and animal genera.