Scientia Horticulturae 199 (2016) 9–14 Contents lists available at ScienceDirect Scientia Horticulturae journal homepage: www.elsevier.com/locate/scihorti Validation of molecular markers associated with fruit ripening day of Japanese pear (Pyrus pyrifolia Nakai) using variance components Sogo Nishio a,∗ , Takeshi Hayashi b , Toshiya Yamamoto a , Masahiko Yamada a , Norio Takada a , Hidenori Kato a , Chikako Nishitani a , Toshihiro Saito a a NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan b NARO Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan a r t i c l e i n f o Article history: Received 1 June 2015 Received in revised form 7 December 2015 Accepted 15 December 2015 Keywords: Marker-assisted selection QTL Early ripening Variance component analysis a b s t r a c t One of the most important breeding objectives for Japanese pear (Pyrus pyrifolia Nakai) is to release early-ripening cultivars. To accelerate marker-assisted selection (MAS) for fruit ripening day (FRD), the molecular markers PPACS2 and BGA35, both associated with FRD, were evaluated in six populations by using variance components. The variance explained by PPACS2 ( ACS2 2 ) differed greatly among popu- lations, ranging from 5.7 to 101.9. The percentage of total phenotypic variance accounted for by  ACS2 2 ranged from 8.9% to 40.4%, 22.1% on average. The variance explained by BGA35 ( BGA35 2 ) was 44.4–46.3, and the percentage of the total phenotypic variance accounted for by  BGA35 2 ranged from 18.3% to 24.9%, 21.6% on average. These values are high enough for these markers to be implemented in practical Japanese pear breeding. The 263-bp allele of PPACS2 and the 136-bp allele of BGA35 had early-ripening effects in six populations. No interaction was found between PPACS2 and BGA35, suggesting that the effects of both loci were additive. The 263-bp allele of PPACS2 was previously shown to increase PPACS2 expression and ethylene production, which might have a negative effect on fruit storage and fruit drop, so further investigation of this allele is required. The information obtained in this study will accelerate MAS for FRD using PPACS2 and BGA35 in Japanese pear breeding programs. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Fruit tree species have a long juvenile phase and occupy much more space than annual crops. The time and space needed to grow large seedlings pose the most serious bottleneck in fruit breeding. Marker-assisted selection (MAS), which can be used to evaluate plant genotypes at the seedling stage rather than at fruiting 3–5 years later, has been proposed as a means to speed up the selection process in practical breeding (Luby and Shaw, 2001). Many economically important characteristics of plant species are controlled by major genes (Jiang, 2013). Such characteristics include disease resistance, male sterility, self-incompatibility, and others related to shape, color, and architecture of whole plants. Sev- eral useful DNA markers for major genes have been developed and applied to Japanese pear breeding; these include S 4 sm -haplotype- specific DNA markers to identify self-compatibility (Ishimizu et al., 1999; Okada et al., 2008), a molecular marker associated with ∗ Corresponding author. Fax: +81 29 838 6475. E-mail address: nishios@affrc.go.jp (S. Nishio). the pear scab resistance gene Vnk (Terakami et al., 2006), and a molecular marker associated with resistance to black spot disease (Terakami et al., 2007). However, studies focused on validation of molecular markers representing quantitative trait loci (QTLs) in practical breeding populations have not been reported for fruit tree species. Both genetic variance and genetic background differ among populations, so the effects of candidate QTLs should be elucidated in multiple fruit tree breeding populations. Japanese pear (Pyrus pyrifolia Nakai; Rosaceae) is a traditionally important fruit crop in Japan. The earliest records of pear culti- vation in Japan date back 1300 years. At that time, pears were harvested in fall and eaten soon after harvest or preserved for eat- ing during winter (Tamura, 2006). At present, most Japanese pear fruits are eaten fresh shortly after harvest in August and September because Japanese consumers enjoy eating the juicy fruits when the weather is hot. There are no leading cultivars that are harvested in July, even though they are in demand at that time. Thus, one of the most important objectives in Japanese pear breeding programs is to release early-ripening cultivars (Abe et al., 1995). Fruit ripening day (FRD) was found to be controlled by sev- eral QTLs, and its narrow-sense heritability was estimated in 20 http://dx.doi.org/10.1016/j.scienta.2015.12.032 0304-4238/© 2015 Elsevier B.V. All rights reserved.