Berry anthocyanin, acid, and volatile trait analyses in a grapevine interspecific F2 population using an integrated GBS and rhAmpSeq genetic map

Authors: ALAHAKOON, DILMINI - South Dakota State University; FENNELL, ANNE - South Dakota State University; HELGET, ZACHARY - South Dakota State University; BATE, TERRY - Cornell University; KARN, AVINASH - Cornell University; MANNS, DAVID - Cornell University; MANSFIELD, ANNA KATHARINE - Cornell University; REISCH, BRUCE - Cornell University; SACKS, GAVIN - Cornell University; SUN, QI - Cornell University; ZOU, CHENG - Cornell University; Cadle-Davidson, Lance; Londo, Jason

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2022
Publication Date: 3/4/2022
Citation: Alahakoon, D., Fennell, A., Helget, Z., Bate, T., Karn, A., Manns, D., Mansfield, A., Reisch, B., Sacks, G., Sun, Q., Zou, C., Cadle Davidson, L.E., Londo, J.P. 2022. Berry anthocyanin, acid, and volatile trait analyses in a grapevine interspecific F2 population using an integrated GBS and rhAmpSeq genetic map. Plants. https://doi.org/10.3390/plants11050696.
DOI: https://doi.org/10.3390/plants11050696

Interpretive Summary: Genetic maps are used to identify DNA markers that predict traits. Increasing the map density by adding more DNA markers increases the precision of trait prediction. Bi-allelic DNA markers only track two versions (alleles) but are cheap to obtain. In contrast, multi-allelic DNA markers provide more specific information, making them more transferable among breeding programs. We combined 1449 bi-allelic and 2000 multi-allelic markers to develop a dense map for a grape family that was derived by selfing a single vine from a Vitis riparia x ‘Seyval blanc’ cross. Berry skin color and flower type correctly mapped to known locations, indicating that the map was high quality. Four multi-allelic markers were identified that can be used in pairs to predict pistillate and hermaphrodite flower type with = 99.7% accuracy. Three important berry chemistry traits were genetically mapped: Anthocyanin diglucosides, malic acid, and the grassy smelling volatile (E)-2-hexenal. Each of these three traits mapped to candidate genes that logically could contribute to these traits. The transferable markers discovered with this approach should be very useful for grape breeders interested in DNA marker-based selection for these important traits.

Technical Abstract: Increased map density and transferability of markers are essential for genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2), that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with = 99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a glucosyltransferase candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two malate dehydrogenase cytoplasmic 1 and aluminum-activated malate transporter 2-like (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another AMLT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a phospholipid hydroperoxide glutathione peroxidase candidate gene near peak markers.