2019 ASHS Annual Conference

Fruit breeding for superior new cultivars is based on creating individuals with improved combinations of genetic factors (alleles) for genomic regions (loci) controlling key traits. Favorable and unfavorable alleles will be passed on to the next generation independently of each other as long as they are located on different chromosomes. However, many loci controlling key traits are located on the same chromosome, such as in quantitative trait locus hotspots. In those cases, a favorable allele for one locus might be physically linked in coupling phase to a second locus’s favorable allele, or favorable alleles might be linked in repulsion phase, and inheritance of the alleles is not independent. However, this linkage relationship can be changed through recombination during gamete formation. When favorable alleles are in coupling phase, this recombination would likely be undesirable, whereas for favorable alleles in repulsion phase recombination is likely desired. Thus, a better understanding of recombination rates is helpful in creating new allelic combinations or maintaining existing combinations.

Accurate information on the location and frequency of recombination events requires genome-wide marker information and pedigreed germplasm to follow these recombination events through generations. Such data is now available for apple, developed by the RosBREED project. In that project, a pedigreed germplasm set was created, representing important parents for the U.S. apple breeding programs and individuals within this germplasm were genome-scanned with the apple 8K SNP array. These SNP data were curated to obtain a high-quality phased data set of genome-wide haplotypes that enables tracing the inheritance of chromosomal segments and identifying recombination events between generations.

The average number of recombination events during gamete formation (as observed through examined offspring) in apple is 10.7 ± 3.1 which corresponds to an average number of recombination events per chromosome of 0.6 ± 0.6. An average of 7.7 ± 2.1 of apple’s 17 chromosomes did not show any recombination during gamete formation. Furthermore, a difference in recombination frequency was found among important breeding parents. The lowest average recombination frequency observed was 8.8 in ‘Gala’ whereas the highest was 14.1 in ‘Cripps Pink’. Knowledge of this difference in recombination frequency will enable development of breeding strategies involving alleles at QTL hotspots and introgression of useful wild alleles.