Extended Pedigrees of Apple Cultivars from the University of Minnesota Breeding Program Elucidated Using SNP Array Markers

Abstract

Apple (Malus ×domestica Borkh.) breeding at the University of Minnesota (UMN) has been ongoing continuously since 1908 when staff originally planted thousands of seedlings from open-pollinated (OP) seeds collected from regional orchards. The first cultivar from the program, ‘Minnehaha’, was introduced in 1920 and several others from these OP seeds followed over the next 3 decades. Controlled crosses were initiated in 1916, and until the time of this publication, 28 cultivars have been introduced. Historical records of parentage, as recorded by staff in notebooks and in 20th-century publications, have been used to inform breeding decisions but might be incorrect as indicated by earlier explorations of parentage using simple sequence repeat (SSR) markers. Our objective was to elucidate parentage and extended pedigrees of all available cultivars introduced from the UMN apple breeding program using evaluations of Mendelian errors and shared haplotype length information based on data from single nucleotide polymorphism (SNP) arrays. Sixteen of the 21 cultivars introduced before ‘Honeycrisp’ (1991) had incorrect or incomplete pedigrees that are now at least partially elucidated. These include the two most important regional cultivars in the 20th century: ‘Haralson’ (parents: ‘Malinda’ and ‘Wealthy’) and ‘Fireside’ (parents: ‘Wealthy’ and ‘Northwest Greening’). ‘Wealthy’, a widely grown cultivar in the United States in the late 19th and early 20th centuries, was a frequent parent of older UMN cultivars. ‘Malinda’ was a less frequent parent than indicated by breeding records. ‘Duchess of Oldenburg’ (synonym ‘Borowitsky’) was revealed as an ancestor of overwhelming importance in the UMN breeding program. It was an ancestor of 27 of the 28 UMN cultivars, including as a parent of two cultivars, and a grandparent of 15 cultivars, including ‘Honeycrisp’.

Apple Fruit Size QTLs on Chromosomes 8 and 16 Characterized in ‘Honeycrisp’-Derived Germplasm

“…The lower fruit weight BLUPs of cultivars Frostbite (86.6 g), Keepsake (109.2 g), and Sweet Sixteen (132.1 g) could partially be explained by the inheritance of haplotype 16A. The other 'Honeycrisp' Chr 16 QTL haplotype, 16B, was significantly associated with higher fruit weights and was traced to 'Honeycrisp's progenitor 'Duchess of Oldenburg', an important progenitor in the UMN apple breeding program [42]. The inheritance of haplotype 16B could partially explain the higher fruit weight BLUPs of 'Minneiska' (158.2 g) and 'MN55' (168.5 g).…”

“…Haplotype 16A, present in 'Honeycrisp' as well as UMN selections MN1836 and MN1915, was significantly associated with lower fruit weights and had a large effect compared to low fruit weight haplotypes 8A, 8B, and 8G (Figure 1; Tables S4 and S5). Haplotype 16A seems to be unique to germplasm derived from 'Frostbite', a smallfruited cultivar that is an important progenitor in the UMN apple breeding program [42]. The lower fruit weight BLUPs of cultivars Frostbite (86.6 g), Keepsake (109.2 g), and Sweet Sixteen (132.1 g) could partially be explained by the inheritance of haplotype 16A.…”

“…If necessary, progenitor and/or offspring SNP data were examined to deduce haplotypes (as in Kostick et al [32]). Parent haplotypes were traced via identityby-descent (IBD) through extended pedigrees, reconstructed by Luby et al [42], to the furthest known ancestor. Pedigree reconstruction of some parents (e.g., 'Pitmaston Pine Apple') was previously done by Howard et al [43] as part of a collaborative apple pedigree reconstruction project.…”

“…'Minneiska's haplotype 8B, inherited from 'Grimes Golden' through 'Golden Delicious', was associated with low relative adjusted fruit weight BLUPs albeit of more moderate effect compared to low fruit weight haplotypes 8G and 16A (Figure 1). Haplotype 8B in 'Grimes Golden' and 'Reinette Franche', reported to be an ancestor of 'Grimes Golden' [42], was likely IBD because homologs of 'Reinette Franche' and 'Grimes Golden' matched from 0 to 22 cM. Haplotype 8B likely segregates in other germplasm sets as 'Golden Delicious' and 'Reinette Franche' are present in the pedigrees of multiple other important cultivars e.g., [32,42,51].…”

“…Haplotype 8B in 'Grimes Golden' and 'Reinette Franche', reported to be an ancestor of 'Grimes Golden' [42], was likely IBD because homologs of 'Reinette Franche' and 'Grimes Golden' matched from 0 to 22 cM. Haplotype 8B likely segregates in other germplasm sets as 'Golden Delicious' and 'Reinette Franche' are present in the pedigrees of multiple other important cultivars e.g., [32,42,51]. 'Minneiska's other Chr 8 QTL haplotype, 8C, was associated with high relative fruit weight BLUPs albeit of more moderate effect compared to high fruit weight haplotypes 16B and 16F.…”