, Volume 209, Issue 3, pp 789–804 | Cite as

Genome-wide linkage mapping of QTL for physiological traits in a Chinese wheat population using the 90K SNP array

  • Fengmei Gao
  • Jindong Liu
  • Li Yang
  • Xiaoxia Wu
  • Yonggui Xiao
  • Xianchun Xia
  • Zhonghu HeEmail author


Many physiological traits are associated with grain yield and yield-related traits in wheat. The aim of the present study was to identify quantitative trait loci (QTL) for physiological traits, including ground cover, normalized difference in vegetation index and canopy temperature depression, and closely linked molecular markers for marker-assisted breeding. Two hundred and forty-six F8 recombinant inbred lines (RILs) come from the Zhou 8425B/Chinese Spring cross were genotyped using the high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay. Field trials were conducted under irrigated conditions at Zhengzhou and Zhoukou in Henan province, during the 2012–2013 and 2013–2014 cropping seasons. Analysis of variance of physiological traits showed significant differences (P < 0.01) among RILs, and RILs × environment interactions. Ground cover at late spring (GC-S), normalized difference in vegetation index at late spring (NDVI-S), and ground cover pre-winter (GC-W), had moderate broad-sense heritabilities of 0.66, 0.52 and 0.40, respectively. GC-S, NDVI-S and canopy temperature depression at 10 days post anthesis (CTD-10) were positively correlated with GY. Using a high-density linkage map of 5636 polymorphic SNP markers and composite interval mapping, 24 QTL for GC, NDVI and CTD were identified on 12 chromosomes, explaining 3.4–14.6 % of the phenotypic variance. Five stable QTL were detected across three environments, viz. QGC-W.caas-7AL, QNDVI-S.caas-7AL, QGC-S.caas-3AS, QCTD-A.caas-5BS and QCTD-10.caas-5BS. In addition, 10 QTL clusters were observed on chromosomes 1AL, 2AL, 2BL, 3AS, 3B (2), 4BS, 5B, 7AS, and 7AL. The stable QTL and QTL clusters were linked to SNP markers, with genetic distances to the closest SNPs ranging from 0 to 2.0 cM; these could be used for marker-assisted selection to improve yield-related traits in wheat breeding.


Molecular markers Quantitative trait loci Single nucleotide polymorphism Triticum aestivum 



SPAD value of chlorophyll content at 10 days post anthesis


SPAD value of chlorophyll content at anthesis


Canopy temperature depression


Canopy temperature depression at 10 days post anthesis


Canopy temperature depression at anthesis


Ground cover at late spring


Ground cover pre-winter


Genome-wide association study




Grain yield


Kernel number per spike


Marker-assisted selection


Normalized difference in vegetation index


Normalized difference in vegetation index at late spring


Normalized difference in vegetation index pre-winter


Plant height


Quantitative trait locus/loci


Recombinant inbred line


Spike number per square meter


Single nucleotide polymorphism


Simple sequence repeat


Standard deviation


Thousand kernel weight



We thank Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for review of this manuscript. This work was funded by the National Natural Science Foundation of China (31461143021), Beijing Municipal Science and Technology Project (D151100004415003), and the National High Technology Research and Development Program of China (2012AA10A308).

Supplementary material

10681_2016_1682_MOESM1_ESM.docx (457 kb)
Supplementary material 1 (DOCX 457 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Fengmei Gao
    • 1
    • 2
    • 3
  • Jindong Liu
    • 1
  • Li Yang
    • 1
  • Xiaoxia Wu
    • 2
  • Yonggui Xiao
    • 1
  • Xianchun Xia
    • 1
  • Zhonghu He
    • 1
    • 4
    Email author
  1. 1.National Wheat Improvement Center, Institute of Crop ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
  2. 2.Key Laboratory of Soybean Biology, Soybean Research Institute, Ministry of EducationNortheast Agricultural UniversityHarbinChina
  3. 3.Keshan Agricultural Research InstituteHeilongjiang Academy of Agricultural SciencesKeshanChina
  4. 4.International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAASBeijingChina

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