Theoretical and Applied Genetics

, Volume 131, Issue 5, pp 1073–1090 | Cite as

Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

  • Kai Liu
  • Xiaoxiao Sun
  • Tangyuan Ning
  • Xixian Duan
  • Qiaoling Wang
  • Tongtong Liu
  • Yuling An
  • Xin Guan
  • Jichun Tian
  • Jiansheng Chen
Original Article


Key message

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map.


The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.



Recombinant inbred line


Quantitative trait locus


Phenotypic variation explained


Significant marker-trait associations


Genome-wide association study


Grain weight


Spike length


Grain number per spike


Fertile spikelet number per spike


Sterile spikelet number per spike


Total spike number per spike


Spikelet density


Genetic distance


Single-nucleotide polymorphism



This work was supported by the Science and Technology of Shandong project GG201703200178, 2017CXGC0308 and the Shandong Major Agricultural Technology Innovation Projects 2017 and 2016LZGC023. The SNP analysis and the construction of genetic maps were kindly conducted by Dr. Mingcheng Luo from the University of California, Davis, and by Dr. Jirui Wang of Sichuan Agricultural University. Prof. Wolfgang Friedt from University Giessen provided valuable revision suggestions.

Compliance with ethical standards

Conflict of interest

We declare no conflicts of interest involving this manuscript.

Ethical standards

We declare that these experiments comply with the ethical standards in China.

Supplementary material

122_2018_3059_MOESM1_ESM.pdf (74 kb)
Supplementary material 1 (PDF 74 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Kai Liu
    • 1
  • Xiaoxiao Sun
    • 1
  • Tangyuan Ning
    • 1
  • Xixian Duan
    • 1
  • Qiaoling Wang
    • 1
  • Tongtong Liu
    • 1
  • Yuling An
    • 1
  • Xin Guan
    • 1
  • Jichun Tian
    • 1
  • Jiansheng Chen
    • 1
  1. 1.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of AgronomyShandong Agricultural UniversityTai’anPeople’s Republic of China

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