Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)

Breeding of fruit trees is hindered by their large size and long juvenile period. Genome-wide association study (GWAS) and genomic selection (GS) are promising methods for circumventing this hindrance, but preparing new large datasets for these methods may not always be practical. Here, we evaluated...

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Bibliographic Details
Published in:Scientific reports 2018-08, Vol.8 (1), p.11994-12, Article 11994
Main Authors: Minamikawa, Mai F., Takada, Norio, Terakami, Shingo, Saito, Toshihiro, Onogi, Akio, Kajiya-Kanegae, Hiromi, Hayashi, Takeshi, Yamamoto, Toshiya, Iwata, Hiroyoshi
Format: Article
Language:English
Subjects:
45/43
631/208/711
631/449/711
Breeding
Fruit trees
Genetic Linkage
Genetics, Population
Genome, Plant
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Genomics - methods
Humanities and Social Sciences
Humans
Linkage Disequilibrium
Models, Genetic
multidisciplinary
Phenotype
Phenotypes
Pyrus - genetics
Pyrus pyrifolia
Quantitative Trait, Heritable
Science
Science (multidisciplinary)
Selection, Genetic
Single-nucleotide polymorphism
Trees
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Summary:Breeding of fruit trees is hindered by their large size and long juvenile period. Genome-wide association study (GWAS) and genomic selection (GS) are promising methods for circumventing this hindrance, but preparing new large datasets for these methods may not always be practical. Here, we evaluated the potential of breeding populations evaluated routinely in breeding programs for GWAS and GS. We used a pear parental population of 86 varieties and breeding populations of 765 trees from 16 full-sib families, which were phenotyped for 18 traits and genotyped for 1,506 single nucleotide polymorphisms (SNPs). The power of GWAS and accuracy of genomic prediction were improved when we combined data from the breeding populations and the parental population. The accuracy of genomic prediction was improved further when full-sib data of the target family were available. The results suggest that phenotype data collected in breeding programs can be beneficial for GWAS and GS when they are combined with genome-wide marker data. The potential of GWAS and GS will be further extended if we can build a system for routine collection of the phenotype and marker genotype data for breeding populations.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-018-30154-w