Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

S. Verma, K. Evans, Y. Guan, J. J. Luby, U. R. Rosyara, N. P. Howard, N. Bassil, M. C.A.M. Bink, W. E. van de Weg, C. P. Peace

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45 Scopus citations


Acidity is a critical component of the apple fruit consumption experience. In previous biparental family studies, two large-effect acidity QTLs were reported using freshly harvested fruit. Objectives of this study were to determine the number and location of QTLs for acidity variation in a large apple breeding program and ascertain the quantitative effects and breeding relevance of QTL allelic combinations at harvest and after commercially relevant periods of cold storage. Pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents, genotyped for the 8K SNP array, was assessed for titratable acidity at harvest and after 10- and 20-week storage treatments, for three successive seasons. Using pedigree-based QTL mapping software, FlexQTL™, evidence was found for only two QTLs, on linkage groups 16 (the reported Ma locus) and LG 8 (here called Ma3) that jointly explained 66 ± 5% of the phenotypic variation. An additive allele dosage model for the two QTLs effectively explained most acidity variation, with an average of + 1.8 mg/L at harvest per high-acidity allele. The more high-acidity alleles, the faster the depletion with storage, with all combinations appearing to eventually converge to a common baseline. All parent cultivars and selections had one or two of the four possible high-acidity alleles. Each QTL had a rare second high-acidity allele with stronger or reduced effect. Diagnostic SNP markers were identified for QTL alleles derived from distinct sources. Combined QTL effects highlighted utility of the DNA-based information in new cultivar development for targeting desired fruit acidity levels before or after storage.

Original languageEnglish (US)
Article number18
JournalTree Genetics and Genomes
Issue number2
StatePublished - Apr 1 2019

Bibliographical note

Funding Information:
Funding information This work was funded by the USDA’s National Institute of Food and Agriculture (NIFA)–Specialty Crop Research Initiative projects BRosBREED: Enabling marker-assisted breeding in Rosaceae^ (2009-51181-05808) and BRosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars^ (2014-51181-22378), and USDA NIFA Hatch projects 0211277 and 1014919.

Publisher Copyright:
© 2019, The Author(s).


  • FlexQTL™
  • Malic acid
  • Malus × domestica
  • Pedigree-Based Analysis
  • RosBREED


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