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

Authors: VERMA, SUJEET - Washington State University; EVANS, KATHERINE - Washington State University; GUAN, Y - Washington State University; LUBY, JAMES - University Of Minnesota; ROSYARA, UMESH - Michigan State University; HOWARD, NICK - University Of Minnesota; Bassil, Nahla; BINK, MARCO - Wageningen University And Research Center; VAN DE WEG, ERIC - Wageningen University; PEACE, CAMERON - Washington State University

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/28/2019
Publication Date: 2/12/2019
Citation: Verma, S., Evans, K., Guan, Y., Luby, J., Rosyara, U., Howard, N., Bassil, N.V., Bink, M., Van De Weg, E., Peace, C. 2019. Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: Breeding insights from a multi-family study. Tree Genetics and Genomes. 15:18. https://doi.org/10.1007/s11295-019-1324-y.
DOI: https://doi.org/10.1007/s11295-019-1324-y

Interpretive Summary: The objective of this study was to understand fruit acidity variation in a large apple breeding program. Pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents, were genotyped and phenotyped for titratable acidity at harvest and after 10- and 20-week storage treatments, for three successive seasons. Using pedigree-based quantitative trait loci mapping software, evidence was found for only two regions in the genome controlling the acidity trait. and that are jointly responsible for 66 +/-5% of the phenotypic variation. Furthermore, we found that 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. Diagnostic markers were identified for acidity alleles derived from distinct sources. This study highlighted the utility of the DNA-based information in new cultivar development for targeting desired fruit acidity levels before or after storage.

Technical Abstract: 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.