Molecular Breeding

, 36:134 | Cite as

Quantitative trait loci mapping of yield and related traits using a high-density genetic map of maize

  • Lin Chen
  • Chunhui Li
  • Yongxiang Li
  • Yanchun Song
  • Dengfeng Zhang
  • Tianyu Wang
  • Yu Li
  • Yunsu Shi


Improving grain yield is the ultimate goal of the maize-breeding programs. In this study, analyses of conditional and unconditional quantitative trait locus (QTL) and epistatic interactions were used to elucidate the genetic architecture of yield and its related traits. A total of 15 traits of a recombinant inbred line population, including yield per plant (YPP), seven ear-related traits, and seven kernel-related traits, were measured in six different environments. Based on the genetic linkage map constructed using 2091 bins as markers, 56 main-effect QTLs for these traits were identified. These QTLs were distributed across eight genomic regions (bin 1.06, bin 4.02/4.05/4.08, bin 5.04, bin 7.04, bin 8.08, and bin 9.04), within the marker intervals of 85.45–6260.66 kb, and the phenotypic variance explained ranging from 5.69 to 11.56 %. One gene (GRMZM2G168229) encoding SBP-box domain protein was located in the small interval of qKRN4-3 and may be involved in patterning of kernel row number. Seventeen conditional QTLs identified for YPP were conditioned on its related traits and explained 6.18–23.15 % of the phenotypic variance. Conditional mapping analysis revealed that qYPP4-1, qYPP6-1, and qYPP8-1 are partially influenced by YPP-related traits at the individual QTL level. Digenic epistatic analysis identified 12 digenic interactions involving 22 loci across the whole genome. In addition, conditional digenic epistatic analysis identified 14 digenic interactions involving 21 loci. This study provides valuable information for understanding the genetic relationship between YPP and related traits and constitutes the first step toward the cloning of the relevant genes.


QTL Yield Genetic relationship Maize Epistasis 



This research was supported by the National Natural Science Foundation (91335206), the Ministry of Science and Technology of China (2014CB138200, 2013BAD01B02), the Ministry of Agriculture of China (2015NWB030), and the CAAS Innovation Program.

Authors contribution

Lin Chen conducted field and genetic experiment, analyzed data, and drafted the manuscript; Chunhui Li and Yongxiang Li phenotyped traits and analyzed data. Yanchun Song and Dengfeng Zhang conducted field trials. Tianyu Wang, Yu Li, and Yunsu Shi designed and supervised the experiment and edited the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The experiments comply with the ethical standards in the country in which they were performed.

Supplementary material

11032_2016_545_MOESM1_ESM.xlsx (36 kb)
Supplementary material 1 (XLSX 35 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Lin Chen
    • 1
  • Chunhui Li
    • 1
  • Yongxiang Li
    • 1
  • Yanchun Song
    • 1
  • Dengfeng Zhang
    • 1
  • Tianyu Wang
    • 1
  • Yu Li
    • 1
  • Yunsu Shi
    • 1
  1. 1.Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina

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