Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study

摘要

Fourteen founder haplotypes were traced automatically forward to a total of 844 individuals from the combined populations, according to four steps. A famous cultivar ‘Fuji’ is shown as an example. The first step is the phasing and imputation of sporadic missing genotypes of ‘Fuji’. The second step is the estimation of its parental phases. The third step was the estimation of haplotype blocks of ‘Fuji’ inherited from the female ‘Ralls Janet’ and male ‘Delicious’ parents. The final step was to assign the founder haplotypes of ‘Ralls Janet’ and ‘Delicious’ to the haplotype blocks of ‘Fuji’.