Genome-wide estimation of pedigree haplotypes offers genetic compositions and founder origins in Japanese citrus breeding materials

Abstract In fruit crops including citrus, many cultivars have been developed by cross breeding. To determine the genetic composition resulting from cross breeding, we estimated the pedigree haplotypes of Japanese citrus breeding materials. Seventy-eight accessions composed of citrus cultivars, breeding lines, and their founders, as well as 377 F1 seedlings derived from nine parental combinations were genotyped at 285 single nucleotide polymorphism loci. The pedigree haplotypes were estimated by FlexQTL software. The most likely pedigree haplotypes were obtained for all 455 individuals. We believe that the estimated pedigree haplotypes can be useful for the optimization of breeding strategies, such as the efficient accumulation of favorable alleles and prevention of inbreeding depression.