Stable QTL for malate levels in ripe fruit and their transferability across Vitis species

Authors: RESHEF, NOAM - Cornell University; KARN, AVINASH - Cornell University; MANNS, DAVID - Cornell University; MANSFIELD, ANNA KATHARINE - Cornell University; Cadle-Davidson, Lance; REISCH, BRUCE - Cornell University; SACKS, GAVIN - Cornell University

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2021
Publication Date: 2/28/2022
Citation: Reshef, N., Karn, A., Manns, D., Mansfield, A., Cadle Davidson, L.E., Reisch, B., Sacks, G. 2022. Stable QTL for malate levels in ripe fruit and their transferability across Vitis species. Journal of Theoretical and Applied Genetics. https://doi.org/10.1093/hr/uhac009.
DOI: https://doi.org/10.1093/hr/uhac009

Interpretive Summary: Malate has a major role in the sourness of grape berries and their products. Hot or cool climates can cause too little or too much malate, respectively, harming grape and wine quality. Excess malate is also observed in wild grapes, which otherwise have useful traits for grape breeding, like disease resistance and cold hardiness. Several genetic regions controlling grape malate have been reported in the last decade, but these differ from family to family and year to year. This study investigated the genetic basis of malate at harvest for five years in one grape family and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit. Three regions for ripe fruit malate on chromosomes 1, 7, and 17, accounted for 40.6% of the malate variation, explaining a difference of 6.9 grams per liter malate among sibling vines. The accumulation of malate in the first half of grape development caused much of the variation in ripe fruit malate (39%) and was due to the same region on chromosome 7. This is a potential target for breeding, but the same genetic region did not predict malate in a closely related Vitis family. This underscores the complexity of fruit malate regulation in grapes, a conclusion supported by other studies that together show malate concentration can be significantly controlled by genetic regions on all 19 chromosomes.

Technical Abstract: Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Insufficient or excessive malate, associated with hot and cool climates, respectively, are detrimental to both grape and wine quality. Excessive malate at maturity is also observed in wild Vitis grapes, complicating the introgression of valuable disease resistance and cold hardy genes through breeding. Several quantitative trait loci (QTL) for grape malate have been reported in the last decade, but these have generally been unstable and poorly conserved across families. This study investigated an interspecific Vitis mapping population that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for mean differences of 6.9 g/L malate in ripe fruit, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%) and their associated QTL overlapped on chromosome 7, indicating a common genetic basis. Evidence from other fleshy fruit and publicly available transcriptomic data from grape support the involvement of genes associated with malate accumulation in the chromosome 7 locus, and highlight it as a potential target for breeding and further research. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate fruit malate in the Vitis genus, a conclusion supported by a review of over a dozen papers that show malate concentration can be significantly predicted by genetic loci on all 19 chromosomes.