title: Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family.
abstract: In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape 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 F1 families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F2 mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, 'Seyval'. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F2 family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F2 family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species.
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Yang
authors.affiliation: Bioinformatics Facility, Institute of Biotechnology, Cornell University, Rhodes Hall, Ithaca, New York, United States of America.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Fresnedo-Ramírez
authors.affiliation: Bioinformatics Facility, Institute of Biotechnology, Cornell University, Rhodes Hall, Ithaca, New York, United States of America.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.affiliation: Department of Food Science, Cornell University-NYSAES, Geneva, New York, United States of America.
authors.forename: David C
authors.initials: DC
authors.lastname: Manns
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, United States of America.
authors.forename: Gavin L
authors.initials: GL
authors.lastname: Sacks
authors.affiliation: Department of Food Science, Cornell University-NYSAES, Geneva, New York, United States of America.
authors.forename: Anna Katharine
authors.initials: AK
authors.lastname: Mansfield
authors.affiliation: Department of Horticultural Science, University of Minnesota, St. Paul, Minnesota, United States of America.
authors.forename: James J
authors.initials: JJ
authors.lastname: Luby
authors.affiliation: USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America.
authors.forename: Jason P
authors.initials: JP
authors.lastname: Londo
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Bruce I
authors.initials: BI
authors.lastname: Reisch
authors.affiliation: USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America.
authors.forename: Lance E
authors.initials: LE
authors.lastname: Cadle-Davidson
authors.affiliation: Plant Science Department, South Dakota State University, Brookings, South Dakota, United States of America.|BioSNTR, Brookings, South Dakota, United States of America.
authors.forename: Anne Y
authors.initials: AY
authors.lastname: Fennell
mesh_terms: D002678:Chimera / Q000235:genetics*; D005638:Fruit / Q000235:genetics*; D006579:Heterozygote; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D027843:Vitis / Q000235:genetics*