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.

Identification of QTLs for Flesh Mealiness in Apple (<i>Malus</i> × <i>domestica</i> Borkh.)

“…We did not detect the chr 1 QTL. This may have been caused by the lack of allelic effect in the OA in the QTL mapping study and the different approaches employed by Kunihisa et al (2016) in the present study.…”

“…4C). However, a relatively high rate of errors in the apple genome assembly means that there are some inconsistencies between the positions obtained by genetic mapping and the positional data in the public database (Antanaviciute et al, 2012;Kunihisa et al, 2016). Thus, to confirm the origin of these regions, a r 2 LD analysis of all the significant SNP pairs was conducted.…”

“…A haplotype-based QTL survey, using only SNPs heterozygous in 'Fuji', has identified one QTL for mealiness in the middle of chr 1 (Kunihisa et al, 2016). The lack of significance of the MdPG1 locus in Kunihisa et al (2016), possibly due to the Md-PG1 SSR 10kd genotype of 'Fuji' (1/2), prevented the detection of QTL.…”

“…The lack of significance of the MdPG1 locus in Kunihisa et al (2016), possibly due to the Md-PG1 SSR 10kd genotype of 'Fuji' (1/2), prevented the detection of QTL. We did not detect the chr 1 QTL.…”

The Long Ashton Legacy: Characterising United Kingdom West Country cider apples using a genotyping by targeted sequencing approach

“…The 487,249 SNPs from the array were filtered to include only robust, poly high resolution markers as defined by Bianco et al (). In addition, we only selected markers with concordant chromosome assignments on the Golden Delicious (Valesco et al, ), Renetta Grigia di Torriana (Falginella et al, ), Fuji (Kunihisa et al, ) and Pinova (Di Pierro et al, ) maps. For SEQSNP® design, additional flanking sequence of 100 bases either side of each Axiom SNP were obtained by cross referencing the Malus domestica sequences (downloaded from https://www.rosaceae.org/species/malus/malus_x_domestica/genome_v3.0.a1).…”