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

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.

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The authors declare that they have no competing financial interest.

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Correspondence to Zhenhai Han.

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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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Keywords

  • Candidate gene
  • Fruit shape index
  • Malus × domestica
  • QTLs