2017 ASHS Annual Conference

Breeders and their stakeholders can experience (see, taste, etc.) the phenotype of any germplasm individual of interest in its entirety. This experience is critical to goal-setting and knowing when goals are reached. Until now, breeders have not had a sensory connection to genome-wide genotypes of their germplasm. Haploblocking changes that. With pedigree-based haploblocking, the genome of each individual is characterized as discrete segments co-inherited over generations of selection. Key data are genome-spanning marker genotypes for pedigree-connected germplasm, capturing genetic variation and recombination events. Haplotypes, the detected variants of each segment, can be traced through breeding pedigrees to ancestral sources and/or annotated in other useful ways such as phenotypic effect and frequency of occurrence. Genome-wide haplotype mosaics can then be visualized for one or more breeding individuals on a single page or computer screen, enabling various genetic inferences. Genetic relatedness is both qualified and quantified from sets of shared haplotypes among individuals across extended chromosomal regions. Past breeding processes are revealed by frequencies and distributions in germplasm of haplotypes associated with QTL alleles. The genetic virtues and deficiencies of each elite selection are highlighted by the observed mosaic of QTL alleles, embedded in larger ancestral segments, across the genome. For parents, such genomic mosaics display their potential contributions to the next generation. Haploblocking was applied to representative U.S. breeding germplasm of apple and sweet cherry. Genome-scan data for hundreds of individuals of each crop, obtained in the RosBREED project with Illumina Infinium SNP arrays of 8K (apple) and 6K (cherry), were subject to haploblocking with FlexQTL™ and PediHaplotyper software. Numerous new genetic relationships were elucidated among ancestors, revealing for each crop that most breeding individuals are substantially more related than indicated by pedigree records. Introgressed segments from related species into apple were traced, some associated with valuable phenotypic effects. Favorable QTL alleles in important breeding parents often traced to specific sources. At QTL hotspots, haploblocking enabled dissection of linkage relationships among adjacent favorable and unfavorable alleles for breeding individuals. Haploblocking and its associated graphical genotyping of fruit breeding germplasm thus facilitates “breeding by design”. Breeders of apple and cherry can now visually experience the genomes of their germplasm when displayed in a single view, supporting genetic improvement from the holistic perspective of “genotype”.