title: Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection.
abstract: 'Fuji' is one of the most popular and highly-produced apple cultivars worldwide, and has been frequently used in breeding programs. The development of genotypic markers for the preferable phenotypes of 'Fuji' is required. Here, we aimed to define the haplotypes of 'Fuji' and find associations between haplotypes and phenotypes of five traits (harvest day, fruit weight, acidity, degree of watercore, and flesh mealiness) by using 115 accessions related to 'Fuji'. Through the re-sequencing of 'Fuji' genome, total of 2,820,759 variants, including single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) were detected between 'Fuji' and 'Golden Delicious' reference genome. We selected mapping-validated 1,014 SNPs, most of which were heterozygous in 'Fuji' and capable of distinguishing alleles inherited from the parents of 'Fuji' (i.e., 'Ralls Janet' and 'Delicious'). We used these SNPs to define the haplotypes of 'Fuji' and trace their inheritance in relatives, which were shown to have an average of 27% of 'Fuji' genome. Analysis of variance (ANOVA) based on 'Fuji' haplotypes identified one quantitative trait loci (QTL) each for harvest time, acidity, degree of watercore, and mealiness. A haplotype from 'Delicious' chr14 was considered to dominantly cause watercore, and one from 'Ralls Janet' chr1 was related to low-mealiness.
authors: NARO Institute of Fruit Tree Science , 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 , Japan.
authors: Miyuki
authors: M
authors: Kunihisa
authors: NARO Institute of Fruit Tree Science , 92-24 Shimokuriyagawa, Morioka, Iwate 020-0123 , Japan.
authors: Shigeki
authors: S
authors: Moriya
authors: NARO Institute of Fruit Tree Science , 92-24 Shimokuriyagawa, Morioka, Iwate 020-0123 , Japan.
authors: Kazuyuki
authors: K
authors: Abe
authors: NARO Institute of Fruit Tree Science , 92-24 Shimokuriyagawa, Morioka, Iwate 020-0123 , Japan.
authors: Kazuma
authors: K
authors: Okada
authors: NARO Institute of Fruit Tree Science , 92-24 Shimokuriyagawa, Morioka, Iwate 020-0123 , Japan.
authors: Takashi
authors: T
authors: Haji
authors: NARO Agricultural Research Center , 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666 , Japan.
authors: Takeshi
authors: T
authors: Hayashi
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Yoshihiro
authors: Y
authors: Kawahara
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan ; DYNACOM Co., Ltd. , E-25F, WBG, 2-6-1 Nakase, Mihama-ku, Chiba 261-7125 , Japan.
authors: Ryutaro
authors: R
authors: Itoh
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Takeshi
authors: T
authors: Itoh
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Yuichi
authors: Y
authors: Katayose
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Hiroyuki
authors: H
authors: Kanamori
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Toshimi
authors: T
authors: Matsumoto
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Satomi
authors: S
authors: Mori
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Harumi
authors: H
authors: Sasaki
authors: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602 , Japan.
authors: Takashi
authors: T
authors: Matsumoto
authors: NARO Institute of Fruit Tree Science , 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 , Japan.
authors: Chikako
authors: C
authors: Nishitani
authors: NARO Institute of Fruit Tree Science , 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 , Japan.
authors: Shingo
authors: S
authors: Terakami
authors: NARO Institute of Fruit Tree Science , 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 , Japan.
authors: Toshiya
authors: T
authors: Yamamoto
keywords:  Malus  ×  domestica ;  SNPs ;  haplotype block ;  mealiness ;  watercore ;  ‘Delicious’ ;  ‘Fuji’ ;  ‘Ralls Janet’ 