Next generation mapping of enological traits in an F2 interspecific grapevine hybrid family

Authors: YANG, SHANSHAN - Cornell University; FRESNEDO, JONATHAN - Cornell University; SUN, QI - Cornell University; MANNS, DAVID - Cornell University; SACKS, GAVIN - Cornell University; AWALE, MANI - South Dakota State University; MANSFIELD, ANNA KATHARINE - Cornell University; LUBY, JIM - University Of Minnesota; Londo, Jason; REISCH, BRUCE - Cornell University; Cadle-Davidson, Lance; FENNELL, ANNE - South Dakota State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2016
Publication Date: 3/14/2016
Citation: Yang, S., Fresnedo, J., Sun, Q., Manns, D., Sacks, G., Awale, M., Mansfield, A., Luby, J., Londo, J.P., Reisch, B., Cadle Davidson, L.E., Fennell, A. 2016. Next generation mapping of enological traits in an F2 interspecific grapevine hybrid family. PLoS One. 11(3):e0149560. doi:10.1371/journal.pone.0149560.

Interpretive Summary: Scientific challenges have limited use of inbred (F2) grape families for genetic mapping, even though that F2 mapping provides opportunities for detailed analysis. This study presents the construction of an F2 grape genetic map using Genotyping-By-Sequencing (GBS) marker technology. This high-resolution map has 1449 markers and covers 95% of the genome. The accuracy of the map was validated using a well-studied trait, berry skin color. Grape quality traits such as berry skin color, malic acid content, and yeast-assimilable nitrogen (nitrogen that is available to yeast during fermentation) are important traits in selecting new hybrid cultivars. The genetic basis of malic acid content and yeast-assimilable nitrogen was studied and narrowed down to candidate genes involved in the malate metabolism regulation pathway. In addition to the utility of these biological findings, the protocols for F2 mapping with GBS markers could be widely applicable for other heterozygous species.

Technical Abstract: Background. In wine grapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are thus important traits in selecting new hybrid wine grape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on double pseudotestcross F1 families with the use of Simple Sequence Repeat (SSR) and a variety of other markers. This study presents the construction of a genetic map by Single Nucleotide Polymorphisms (SNPs) identified through Genotyping-By-Sequencing (GBS) technology in a F2 mapping family of 424 progeny derived from a cross between V. riparia Michx. and the interspecific hybrid wine grape cultivar, ‘Seyval’. Results. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, leading to an average distance between markers of 1.67 cM, covering 95% of the genome. Compared to an SSR map previously developed for this F2 family, these results represent an improved and higher density version. The accuracy of the map was validated using the well-studied trait, berry color. QTLs affecting malic acid content and yeast assimilable nitrogen related traits were detected and narrowed down to candidate genes involved in the malate metabolism regulation pathway. Conclusion. We constructed a high-density linkage map for a large F2 family of the highly heterozygous Vitis genus. This study serves as model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and could accelerate the breeding process by marker-assisted selection (MAS). The protocols for calling intercross GBS markers could be widely applicable for other heterozygous species.