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

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Horticulture Research 2021年第1期8卷 614-627页

作者： Mai FMinamikawa Miyuki Kunihisa Koji Noshita Shigeki Moriya Kazuyuki Abe Takeshi Hayashi yuichi katayose Toshimi Matsumoto Chikako Nishitani Shingo Terakami Toshiya Yamamoto Hiroyoshi Iwata Laboratory of Biometry and Bioinformatics Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of Tokyo1-1-1 YayoiBunkyoTokyo 113-8657Japan Institute of Fruit Tree and Tea Science National Agriculture and Food Research Organization(NARO)2-1 FujimotoTsukubaIbaraki 305-8605Japan Division of Apple Research Institute of Fruit Tree and Tea ScienceNARO92-24 Shimokuriyagawa NabeyashikiMoriokaIwate 020-0123Japan Institute of Crop Science NARO2-1-2 KannondaiTsukubaIbaraki 305-8518Japan Institute of Agrobiological Sciences NARO1-2 OwashiTsukubaIbaraki 305-8634Japan

Haplotypes provide useful information for genomics-based approaches,genomic prediction,and genome-wide association *** a small number of superior founders have contributed largely to the breeding history of fruit trees,the information of founder haplotypes may be relevant for performing the genomics-based approaches in these *** this study,we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental(185 varieties)and breeding(659 F 1 individuals from 16 full-sib families)populations based on 11,786 single-nucleotide polymorphisms,by combining multiple ***,92%of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder *** use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this *** also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental *** results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.

关键词： breeding varieties prediction

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