Applications of SNP-based apple pedigree identification to regionally specific germplasm collections and breeding programs

A wealth of previously unknown pedigree information has been generated for apple (Malus × domestica) through recent studies and an ongoing pedigree identification project using SNP array data. This information has been postulated to be useful in a number of ways for germplasm collections and breeding programs. For example, pedigree information is an important part of genetic characterization of material in germplasm collections. Germplasm collections often seek to preserve cultivars that currently lack commercial relevance but have regional or historical significance or are phenotypically interesting. Pedigree information is often limited on such material. With pedigree information, an accurate genetic structure of these collections can be conveyed to breeders who wish to incorporate novel germplasm into new cultivars. To illustrate ways in which this newly generated pedigree information can be used, we provide examples involving accessions from the germplasm collection Ökowerk and the breeding association “apfel:gut e.V.”, which focus in the development of apples for regional organic production. Both organizations are located in northern Germany. Despite focusing on regional apple cultivars and genetic diversity, many of their accessions and breeding lines are common, cosmopolitan, and foundational cultivars. However, the SNP-based analyses also reveal regionally specific founders, not true-to-type accessions, and genetically unique historical cultivars. This new information has benefitted these organizations by providing genetic characterization that was previously lacking, enabling them to better utilize these genetic resources. Additionally, this information will also be useful in the context of an ongoing larger scale apple pedigree reconstruction project.</p

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

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.</p