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.
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DOI：
10.1270/jsbbs.16018
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发表时间：
2016-09
期刊：
影响因子：
2.4
通讯作者：
Yamamoto T
中科院分区：
文献类型：
--
作者：
Kunihisa M;Moriya S;Abe K;Okada K;Haji T;Hayashi T;Kawahara Y;Itoh R;Itoh T;Katayose Y;Kanamori H;Matsumoto T;Mori S;Sasaki H;Matsumoto T;Nishitani C;Terakami S;Yamamoto T
‘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.
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影响因子：
4.4
作者：
Kumar S;Garrick DJ;Bink MC;Whitworth C;Chagné D;Volz RK
通讯作者：
Volz RK
影响因子：
3.7
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
通讯作者：
Peace C
影响因子：
3.7
作者：
Bianco L;Cestaro A;Sargent DJ;Banchi E;Derdak S;Di Guardo M;Salvi S;Jansen J;Viola R;Gut I;Laurens F;Chagné D;Velasco R;van de Weg E;Troggio M
通讯作者：
Troggio M
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
5.4
作者：
Liebhard, R.;Koller, B.;Gessler, C.
通讯作者：
Gessler, C.