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The effectiveness of detected quantitative trait loci (QTLs) and molecular markers associated with them in tree fruit breeding is measured by the percentages of the variance associated with detected QTL effects accounting for not phenotypic variance, but genetic variance of the trait. The genetic variance can be obtained by subtracting environmental variance from the phenotypic variance. Once accurate environmental variance components are obtained for a given selection field, environmental variances under any number of replications and measurement repetitions can be estimated. We estimated environmental variance components of fruit ripening date measured by days in a Japanese pear (Pyrus pyrifolia Nakai) breeding field in the National Institute of Fruit Tree Science, Tsukuba, Ibaraki, Japan. We estimated variance among fruits within a tree (σ_f ²) as 25.6, among trees within a genotype (σ_t ²) as 0.2, among years (σ_y ²) as 9.4, associated with genotype × year interaction (σ_gy ²) as 7.9, and associated with tree × year interaction (σ_ty ²) as 1.2. Because σ_f ² was the largest environmental variance component, increasing the number of fruit evaluated would most effectively reduce the environmental variance, and tree replication would not because of very small σ_t ² and σ_ty ². The 95% confidence limit of a genotypic value was ± 10 days in the evaluation of five fruits on a single tree in a year and ± 7 days over 2 years. Broad-sense heritability in a family, each offspring in which was evaluated using five fruits on a single tree in a single year, was estimated at 0.83 for three full-sib families analyzed.

Genotypic variations in and environmental variance components of the total sugar content (TSC) and sugar composition, including sucrose (SUC), fructose (FRU), glucose (GLU), and sorbitol (SOR), in the fruit juice of 13 Japanese pear cultivars were analyzed. The TSC of ‘Kanta’ and TSC of ‘Hoshiakari’ were high (both >14.5 g/100 mL). The contents of SUC and FRU were higher than those of the other sugars. The SUC contents were ranked as follows: ‘Gold Nijisseiki’, 7.3 g/100 mL; ‘Shuurei’, 6.2 g/100 mL; and ‘Akizuki’, 6.1 g/100 mL. The FRU content in ‘Kanta’ was the highest among all monomeric sugars evaluated (6.8 g/100 mL). These results suggest that ‘Kanta’ is superior in terms of both TSC and sugar composition, which determine sweetness. The yearly environmental variance components were negligible for all traits. The genotype × year ranged from 4.4% to 13.7% of the total variance. Within-tree variance was 17.1% for TSC, whereas that for the sugar composition ranged from 1.4% to 6.1%. The tree × year ranged from 2.7% to 7.4%. Variance among fruits within trees was the largest environmental variance component—except for FRU—and ranged from 8.8% to 35.6%. Broad-sense heritability (h _B ² ) values based on single tree, single year, and single fruit measurements were 0.33, 0.64, 0.69, 0.71, and 0.76 for TSC, SUC, FRU, GLU, and SOR, respectively. These results suggest that it would be easier to estimate genetic differences in sugar components with a higher level of precision than those in TSC. Increasing the fruit number up to five, in combination with yearly repetition increased to two (without tree repetition), significantly increased the h _B ² of all traits undergoing study. The information obtained during this study will be useful for improving the accuracy of phenotypic selection and future genomic-based breeding studies performed to improve the sweetness of Japanese pear fruits.

We evaluated the nut harvesting date (NHD), nut weight (NW), pericarp splitting (PS), and infestation by insects (II) in eight cultivars/selections of Japanese chestnut, including a Japanese–Chinese hybrid, over 6 years. Data were analyzed by analysis of variance (without transformation for NHD, after log-transformation for NW and PS, and after square root transformation for II). The among-tree variance accounted for only 1.1% to 8.5% of the total variance. The variance component resulting from residual factors for the tree × year interaction and sampling errors was the largest component for NW, PS, and II, accounting for 46% to 54% of the total environmental variance. Because tree replication is costly and time-consuming in chestnut breeding, increasing the number of yearly repetitions is more efficient than increasing the number of tree replicates. Broad-sense heritability was 0.84 for NHD, 0.27 for NW, 0.48 for PS, and 0.17 for II in evaluations with one tree without yearly repetition. It increased to 0.91 for NHD, 0.40 for NW, 0.62 for PS, and 0.29 for II in evaluations with one tree in 2 years. For NHD, the heritabilities are sufficiently high to distinguish genetic differences among cultivars/selection. In contrast, the low heritability of II suggests that this trait should not be evaluated with an emphasis on the initial selection stage but rather with an emphasis on the secondary selection stage based on testing at several locations with a large number of yearly and tree replications.

‘Porotan’ is a Japanese chestnut cultivar (Castanea crenata Sieb. et Zucc.) that was selected from offspring of the cross 550-40 × ‘Tanzawa’ and released in 2006. Its nut is distinguished by a pellicle that is easy to peel after roasting; previously, all Japanese chestnut cultivars were thought to have a pellicle that was difficult to peel. Both 550-40 and ‘Tanzawa’ are Japanese chestnuts, and 550-40 is a selection descended from ‘Tanzawa’. Both 550-40 and ‘Tanzawa’ have a pellicle that is difficult to peel. Among 59 offspring of a cross of 550-40 × ‘Tanzawa’, 12 had an easy-peeling pellicle and 47 had a difficult-peeling pellicle; this ratio is not significantly different from the 1:3 expected ratio for monogenic inheritance based on a chi-square test at P = 0.05. A half-diallel cross without selfings was made among ‘Porotan’, ‘Tanzawa’, and ‘Tsukuba’. All the offspring from ‘Tanzawa’ × ‘Tsukuba’ and from ‘Tsukuba’ × ‘Porotan’ had a difficult-peeling pellicle; in contrast, 39 offspring from ‘Tanzawa’ × ‘Porotan’ segregated in a ratio of 19 difficult-peeling pellicle to 20 easy-peeling pellicle, which is not significantly different from the expected 1:1 ratio for monogenic segregation based on a chi-square test at P = 0.05. These results suggest that the easy-peeling pellicle trait of ‘Porotan’ is controlled by a major recessive gene at a single locus. We designated the pellicle peelability locus as P/p. According to this model, the ‘Tsukuba’ genotype is homozygous-dominant (PP), the ‘Tanzawa’ genotype is heterozygous (Pp), and the ‘Porotan’ genotype is homozygous-recessive (pp).

To understand the role of the MIKC-type dormancy-associated MADS-box (DAM) genes in the regulation of endodormancy in japanese pear (Pyrus pyrifolia), we isolated two DAM genes from ‘Kosui’ and characterized their expression throughout the seasonal endodormancy phases in ‘Kosui’, as well as in TP-85–119 taiwanese pear (P. pyrifolia), which is a less dormant type. Several copies of the corresponding DAM genes are present in the P. pyrifolia genome. Rapid amplification of cDNA ends enabled the isolation of two full-length cDNAs, designated as PpMADS13–1 and PpMADS13–2, with complete open reading frames encoding 227 and 234 amino acids, respectively. Multialignment of the two ‘Kosui’ and the database DAM genes (based on the deduced amino acid sequences) showed that PpMADS13–1 and PpMADS13–2 were highly identical to the Rosaceae DAM genes and encoded the conserved domains characteristic of other MIKC-type MADS-box genes. The phylogenetic relationships showed that PpMADS13–1 and PpMADS13–2 were more closely related to the Prunus DAM, though they formed a unique subclade. The specific expression analysis of PpMADS13–1 and PpMADS13–2 by real-time polymerase chain reaction showed that both DAM genes are gradually down-regulated concomitant with endodormancy breaking. PpMADS13–1 and PpMADS13–2 showed similar fluctuations in expression patterns, although PpMADS13–2 was more highly expressed relative to PpMADS13–1. The expression of PpMADS13–1 and PpMADS13–2 in the less dormant taiwanese pear, TP-85–119, was quite low (nearly zero level), which is consistent with a down-regulated pattern of expression of the DAM genes in japanese pear, peach (Prunus persica), and japanese apricot (Prunus mume). Differential genomic DNA methylation patterns detected in PpMADS13–1 and PpMADS13–2 were not concomitant with seasonal endodormancy transition phases, suggesting that DNA methylation in these loci under investigation may not be linked to endodormancy progression in ‘Kosui’.