, 213:83 | Cite as

Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of three plant morphological traits in upland cotton (Gossypium hirsutum L.)

  • Haikun Qi
  • Ning Wang
  • Wenqing Qiao
  • Qinghua Xu
  • Hong Zhou
  • Jianbin Shi
  • Gentu YanEmail author
  • Qun HuangEmail author


In recent years, the production costs of cotton (Gossypium hirsutum L.) in China have continued to rise, and this has been accompanied by relatively low productivity, diminished enthusiasm of Chinese farmers for planting cotton, and the difficulty caused by high subsidies as well as the high degree of mechanized harvesting for competing crops like grains. Therefore, it is urgent to improve the level of mechanization and the scale of cotton production in China. Morphological traits play an important role in the mechanized harvesting of cotton. Plant height (PH), height of the first fruiting branch node (HFFBN), and the number of vegetative shoot (NOVS) are key cotton morphological traits that influence mechanical harvesting. The genetic basis of PH, HFFBN, and NOVS were examined in the Z571 and CCRI 49 parents as well as 188 individuals comprising the F2 mapping population. This F2 population was examined using genotyping by sequencing (GBS) with 5571 high-density polymorphism single nucleotide polymorphism (SNP) markers to construct a genetic linkage map comprised of 3187 polymorphic markers. The genetic map spanned 3828.551 cM, with an average distance of 0.687 cM between markers. The complete interval mapping method identified 17 quantitative trait loci (QTL) for PH, HFFBN, and NOVS located on chromosomes 3, 4, 5, 7, 9, 17, 19, 23, and 25. Our study provides an efficient approach for fast detection of QTL underlying complex trait variation with high accuracy, thus providing preliminary information that can improve the efficiency of subsequent machine cotton picking through breeding and molecular marker-assisted selection methods.


Cotton Genotyping by sequencing Genetic map Plant morphological traits Quantitative trait loci 



This work was supported by the Basic Scientific Research Budget Increment Project of the Chinese Academy of Agricultural Sciences (1610162016Y02), the National Science and Technology Support Program (2014BAD03B03), and the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences, the Modern Agricultural Industry Technology System in Henan (No. S2013-07-1), and the China Agricultural Research System (No. CARS-18-05).

Author contribution

Conceived and designed the experiments: GTY, QH. Performed the experiments: HKQ, NW, QH, WQQ. Analyzed the data: HKQ, GTY, QH, JBS. Contributed reagents/materials/analysis tools: NW/HZ/QHX. Wrote the paper: HKQ, QH, GTY. Final approval of the version to be published: QH, GTY.

Supplementary material

10681_2017_1867_MOESM1_ESM.xls (38 kb)
Supplementary material 1 (XLS 38 kb). File S1. The progeny SNP detection results
10681_2017_1867_MOESM2_ESM.xls (33.7 mb)
Supplementary material 2 (XLS 34502 kb). File S2. The polymorphic markers of the F2 genomes (1.2 mb)
Supplementary material 3 (ZIP 1182 kb). File S3. All linkage group heatmap analysis
10681_2017_1867_MOESM4_ESM.xls (48 kb)
Supplementary material 4 (XLS 48 kb). File S4. All candidate gene sequences


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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.State Key Laboratory of Cotton BiologyInstitute of Cotton Research of Chinese Academy of Agricultural SciencesAnyangChina

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