Marker-verified pedigree data

Pedigree data of 220 almond genotypes (169 of known origin and 51 of unknown origin) were compiled from available bibliography and breeding records. From the 220 almond genotypes, 37 genotypes were no longer available (17% of the studied genotypes) as they were eliminated some time ago or were from discontinued breeding programs. To verify parental relationships of the rest of genotypes (183), we used SSRs, SNPs, and self-incompatibility S-allele data from previous studies performed by the breeding programs taking part in this study (Supplementary Material 1). Marker data confirmed both parents of 71 genotypes and one parent of four genotypes (146 confirmed relationships) and found three erroneous parentages. Two wrong parentages were found on the male parent of “Capella” and “Davey”, changing their pedigree to open-pollinated and a third incorrect parentage on “Yosemite” female parent, eliminating this genotype from the analysis.

After the corrections made, pedigrees of 169 genotypes of known origin (77 of them marker-verified, approximately 54% of the available genotypes) were analyzed (Supplementary Material 1). The origin of the genotypes were 59 from Spain, 56 from the USA, 16 from Russia, 11 from Israel, 10 from France, 7 from Australia, 7 from Greece, 2 from Argentina, and 2 from Italy.

A pedigree data file was created. Each record in the file contained one cultivar or selection name, the female parent and the male parent, in that order. Once entered, these data were available for inbreeding analyses such as determining the number of times a cultivar appeared in a pedigree as a male or female genitor. Genotypes of known origin were classified into two groups according to self-compatibility: 104 self-incompatible and 65 self-compatible.