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

• Published in: Tree genetics & genomes Vol. 15; no. 2; pp. 1 - 17
• Main Authors: Verma, S., Evans, K., Guan, Y., Luby, J. J., Rosyara, U. R., Howard, N. P., Bassil, N., Bink, M. C. A. M., van de Weg, W. E., Peace, C. P.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.04.2019; Springer Nature B.V
• Subjects: Acidity; Alleles; Apples; Biomedical and Life Sciences; Biotechnology; Breeding; breeding programs; cold; Cold storage; Complex Traits; computer software; Critical components; Cultivars; Deoxyribonucleic acid; Depletion; Diagnostic systems; DNA; Family studies; FlexQTL; Forestry; fruit acids; fruit consumption; Fruits; Gene mapping; genetic traits; genotyping; Germplasm; Life Sciences; linkage groups; loci; Malic acid; Malus × domestica; Mapping; new variety; Original Article; Parents; Pedigree; Pedigree-Based Analysis; phenotypic variation; Phenotypic variations; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Quantitative trait loci; RosBREED; Single-nucleotide polymorphism; titratable acidity; Tree Biology; Malic acid; FlexQTL; ×; RosBREED; Pedigree-Based Analysis
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-019-1324-y

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.