Molecular Genetics and Genomics

, Volume 294, Issue 6, pp 1421–1440 | Cite as

Combination of multi-locus genome-wide association study and QTL mapping reveals genetic basis of tassel architecture in maize

  • Yanli Wang
  • Jie Chen
  • Zhongrong Guan
  • Xiaoxiang Zhang
  • Yinchao Zhang
  • Langlang Ma
  • Yiming Yao
  • Huanwei Peng
  • Qian Zhang
  • Biao Zhang
  • Peng Liu
  • Chaoying Zou
  • Yaou Shen
  • Fei GeEmail author
  • Guangtang PanEmail author
Original Article


Maize tassel architecture is a complex quantitative trait that is significantly correlated with biomass yield and grain yield. The present study evaluated the major trait of maize tassel architecture, namely, tassel branch number (TBN), in an association population of 359 inbred lines and an IBM Syn 10 population of 273 doubled haploid lines across three environments. Approximately 43,958 high-quality single nucleotide polymorphisms were utilized to detect significant QTNs associated with TBN based on new multi-locus genome-wide association study methods. There were 30, 38, 73, 40, 47, and 53 QTNs associated with tassel architecture that were detected using the FastmrEMMA, FastmrMLM, EM-BLASSO, mrMLM, pkWMEB, and pLARmEB models, respectively. Among these QTNs, 51 were co-identified by at least two of these methods. In addition, 12 QTNs were consistently detected across multiple environments. Furthermore, 19 QTLs distributed on chromosomes 1, 2, 3, 4, 6, and 7 were detected in 3 environments and the BLUP model based on 6618 bin markers, which explained 3.64–10.96% of the observed phenotypic variations in TBN. Of these, three QTLs were co-detected in two environments. One QTN associated with TBN was localized to one QTL. Approximately 55 candidate genes were detected by common QTNs and LD criteria. One candidate gene, Zm00001d016615, was identified as a putative target of the RA1 gene. Meanwhile, RA1 was previously validated to plays an important role in tassel development. In addition, the newly identified candidate genes Zm00001d003939, Zm00001d030212, Zm00001d011189, and Zm00001d042794 have been reported to involve in a spikelet meristem identity module. The findings of the present study improve our understanding of the genetic basis of tassel architecture in maize.


Maize Tassel branch number Multi-locus GWAS QTNs QTL 



We thank LetPub ( for its linguistic assistance during the preparation of this manuscript. We thank the “CMplot” package ( for drawing the figure.


The National Basic Research Program of China (2014CB138200) and the Young Scientists Fund of Sichuan Province (2016JQ0008) supported this study.

Compliance with ethical standards

Conflict of interest

G Pan, F Ge, and Y Shen designed the experiments. Y Wang, J Chen, Z Guan, X Zhang, F Ge, and Y Zhang performed the analysis. Y Wang, F Ge, Y Shen, L Ma, Y Yao, H Peng, H Lin, G Pan, Q Zhang, and B Zhang drafted the manuscript. All of the authors critically revised and approval the final version of this manuscript. All of the authors have no conflicts of interest to declare.

Ethical approval

This study did not involve human participants.

Supplementary material

438_2019_1586_MOESM1_ESM.xlsx (485 kb)
Supplementary material 1 (XLSX 486 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Yanli Wang
    • 1
  • Jie Chen
    • 2
  • Zhongrong Guan
    • 5
  • Xiaoxiang Zhang
    • 1
  • Yinchao Zhang
    • 1
  • Langlang Ma
    • 1
  • Yiming Yao
    • 1
  • Huanwei Peng
    • 3
  • Qian Zhang
    • 4
  • Biao Zhang
    • 4
  • Peng Liu
    • 1
  • Chaoying Zou
    • 1
  • Yaou Shen
    • 1
  • Fei Ge
    • 1
    Email author
  • Guangtang Pan
    • 1
    Email author
  1. 1.Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research InstituteSichuan Agricultural UniversityChengduChina
  2. 2.Crop Research InstituteSichuan Academy of Agricultural SciencesChengduChina
  3. 3.Institute of Animal NutritionSichuan Agricultural UniversityChengduChina
  4. 4.Institute of Agro-products Processing Science and TechnologySichuan Academy of Agricultural SciencesChengduChina
  5. 5.Chongqing Yudongnan Academy of Agricultural SciencesChongqingChina

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