Genomic dissection of a 'Fuji' apple cultivar re-sequencing, SNP marker development, definition of haplotypes, and QTL detection

Genomic dissection of a 'Fuji' apple cultivar : re-sequencing, SNP marker development, definition of haplotypes, and QTL detection

'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'...

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Veröffentlicht in:Breeding science. - 1998. - 66(2016), 4 vom: 28. Sept., Seite 499-515
1. Verfasser: Kunihisa, Miyuki (VerfasserIn)
Weitere Verfasser: Moriya, Shigeki, Abe, Kazuyuki, Okada, Kazuma, Haji, Takashi, Hayashi, Takeshi, Kawahara, Yoshihiro, Itoh, Ryutaro, Itoh, Takeshi, Katayose, Yuichi, Kanamori, Hiroyuki, Matsumoto, Toshimi, Mori, Satomi, Sasaki, Harumi, Matsumoto, Takashi, Nishitani, Chikako, Terakami, Shingo, Yamamoto, Toshiya
Format: Aufsatz
Sprache:English
Veröffentlicht: 2016
Zugriff auf das übergeordnete Werk:Breeding science
Schlagworte:Journal Article Malus × domestica SNPs haplotype block mealiness watercore ‘Delicious’ ‘Fuji’ ‘Ralls Janet’
Beschreibung
Zusammenfassung:'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
Beschreibung:Date Revised 01.10.2020
published: Print-Electronic
Citation Status PubMed-not-MEDLINE
ISSN:1344-7610