Stable QTL for malate levels in ripe fruit and their transferability acrossVitisspecies

Abstract

Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family 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 over two-fold and 6.9 g/L differences in ripe fruit malate, 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. 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 the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.

Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map

“…This study reports multiple QTL for malic acid and TA in the same growing season with additive QTL modeling of QTL on chromosome 1, 6 and 8 explaining >50% of the malic acid variation. The difference in QTL relative to season GDD supports the suggestion that different physiological mechanisms in different interspecific population may influence the number and stability of QTL found in interspecific populations [ 29 ].…”

“…derived populations, malic acid QTL have been found on chromosome 6 and 8 in multiple years. However, several other malic acid QTL, with varying degrees of stability from year to year, have been identified in grapevine populations with at least one on every chromosome [ 28 , 29 , 30 ]. This study reports multiple QTL for malic acid and TA in the same growing season with additive QTL modeling of QTL on chromosome 1, 6 and 8 explaining >50% of the malic acid variation.…”

“…With many breeding programs focused on increased disease resistance, the introgression of non-vinifera species has also increased the emphasis on berry chemistry traits as non-vinifera species can contribute different fruit characters that may impact product quality. QTL analyses for standard fruit harvest parameters (berry acids, soluble solids, and pH) show multiple loci varying with population and year [ 26 , 27 , 28 , 29 , 30 ]. Fewer volatile QTL have been identified in berries, although many genes and enzymes associated with volatile development in berries have been detected [ 31 ].…”

The Genetic Basis of Anthocyanin Acylation in North American Grapes (Vitis spp.)

“…Multidimensional scaling (MDS) and Mendelian error detection were performed as quality controls ( Supplementary Files S2 and S3 ) to identify vines with genotyping errors due to self-pollination, pollen contamination, or mislabeling as described elsewhere [ 21 ]. An identical by state (IBS) kinship matrix computed in TASSEL 5 [ 22 ] was used to conduct the MDS analysis, which was further visualized using the R ggplot2 package [ 23 ].…”