BackgroundGenetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions.MethodsA total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR.ResultsA high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity.ConclusionsWe demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.

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Fruit shape is a critical appearance quality in apple. Quantitative trait loci (QTLs) for apple fruit shape index (FSI) traits were previously mapped by our laboratory to linkage group 11 of the maternal parent in a cross population of 'Jonathan' 9 'Golden Delicious' using simple sequence repeat markers. In this study, QTLs for fruit length, diameter, and FSI were identified again using a high-density single nucleotide polymorphism (SNP) genetic linkage map, and candidate genes associated with FSI were screened via whole-genome re-sequencing data for 'Jonathan' and 'Golden Delicious'. Fifteen QTLs, including four for fruit length, one for fruit diameter, and ten for FSI, were identified in three sampling years. Two overlapping year-stable QTL regions related to FSI were anchored on LG 11 of 'Jonathan'. One candidate gene (MDP0000135244) related to FSI in apple and encoding an LysM domain receptor-like kinase protein was predicted and verified in the segregated population. The nonsynonymous SNP (C11.6053728) of MDP0000135244 was present in 23 of 30 individuals with high FSI, demonstrating a close relationship between MDP0000135244 and FSI trait. These results will be useful for the application of marker-assisted selection for FSI trait in apple.

Flesh browning is an important negative trait for quality preservation of fresh-cut fruits. To obtain a better understanding of the inheritance and genetic control of flesh browning in apple, the phenotype of a hybrid population derived from ‘Jonathan’ × ‘Golden Delicious’ was studied for 2 successive years. The inheritance of the flesh browning trait was analyzed by the frequency distribution of the phenotypes. Flesh browning-associated major genes were then mapped by screening genome-wide simple sequence repeat (SSR) markers. Flesh browning is inherited quantitatively and showed a clear bimodal frequency distribution, indicating that the segregation of major genes is involved in the variation. The segregation ratio of light and heavy browning was 7:1 in 2010, 2011, and 2010 + 2011, suggesting that the inheritance of the trait in apple involves three segregated loci of major genes. The heritability of the major gene effect was 72.14% and 72.76% in 2010 and 2011, respectively. SSR markers were screened from 600 pairs of SSR primers located on 17 apple linkage groups (LGs). The three major genes were mapped on LG10, 15, and 17 on the apple genome, respectively, by linkage analysis of flesh browning phenotypes and the genotypes of SSR markers. Two quantitative trait loci (QTLs) for flesh browning were mapped on LG15 of ‘Jonathan’ and LG17 of ‘Golden Delicious’, respectively, which are the same linkage groups that two major genes mapped on.

Cyber-Physical Systems (CPS) are integrations of computation with physical processes. This paper develops a precision agriculture architecture based on CPS technology, including three layers: the physical layer, the network layer and the decision layer. Every layer is analyzed in detail. This paper helps the exploration of CPS in precision agriculture.