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Candidate gene prediction via quantitative trait locus analysis of fruit shape index traits in apple

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Abstract

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’ × ‘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.

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Acknowledgments

This work was supported by the Hi-Tech Research and Development (863) Program of China (2011AA001204); National Special Funds for Scientific Research on Public Causes (Agriculture) Project (200903044); Modern Agricultural Industry Technology System (Apple) (CARS-28); and Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, P. R. China.

Conflict of interest

The authors declare that they have no competing financial interest.

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Authors and Affiliations

  1. Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China

    Ke Cao, Yuansheng Chang, Rui Sun, Fei Shen, Ting Wu, Yi Wang, Xinzhong Zhang & Zhenhai Han

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  1. Ke Cao
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  2. Yuansheng Chang
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  3. Rui Sun
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  4. Fei Shen
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  5. Ting Wu
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  6. Yi Wang
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  7. Xinzhong Zhang
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  8. Zhenhai Han
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Corresponding author

Correspondence to Zhenhai Han.

Electronic supplementary material

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Additional file 1. The detailed gene list of GO annotations of 199 candidate genes

Additional file 2. The GO annotations using WEGO software based on 199 candidate genes

10681_2015_1488_MOESM3_ESM.docx

Additional file 3. The expression result of two candidate genes based on RNAseq analysis of fruit at three fruit development stages in ‘Golden Delicious’. The left-hand y-axis indicates gene expression levels calculated by the RPKM method

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Cao, K., Chang, Y., Sun, R. et al. Candidate gene prediction via quantitative trait locus analysis of fruit shape index traits in apple. Euphytica 206, 381–391 (2015). https://doi.org/10.1007/s10681-015-1488-y

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