Skip to main content
SpringerLink
Log in

Identification of the quantitative trait loci controlling spike-related traits in hexaploid wheat (Triticum aestivum L.)

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

Abstract

Main conclusion

Totally, 48 loci responsible for six spike-related traits were identified in wheat, and a major locus QGl-4A for grain length was mapped and validated for marker-assisted selection in breeding.

Abstract

Wheat yield is determined by the number of spikes, number of grains per spike (GN), and one-thousand kernel weight (TKW), among which GN and TKW are greatly related to the spike development and thus the spike-related traits, including spike length (SL), number of spikelet per spike (SN), grain length (GL) and grain width (GW). To identify the key loci governing the spike-related traits (SL, SN, GN, TKW, GL and GW), we conducted the quantitative trait loci (QTL) analysis combined with wheat 660K SNP chip and Kompetitive allele-specific PCR (KASP) assay, using the F2 and F2:3 populations derived from Luohan6 (LH6) with big spike and grain and Zhengmai366 with small spike and grain, and identified a total of 48 QTLs on 18 chromosomes. Moreover, a major stable QTL for GL on chromosome 4A, designated as QGl-4A, was mapped into a 0.37 cM interval between KASP markers Xib4A-10 and Xib4A-12, corresponding to 20 Mb physical region in the Chinese Spring genome. This QTL explained 17.30% and 5.12% of the phenotypic variation for GL in the F2 and F2:3 populations. Further association analysis of flanking markers Xib4A-10 and Xib4A-12 in 192 wheat varieties showed that these two markers could be used for marker-assisted selection in breeding. These results provide valuable information for map-based cloning of the target genes involved in the regulation of spike-related traits in common wheat.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

SL:

Spike length

SN:

Spikelet numbers per spike

GN:

Grain number per spike

TKW:

One-thousand kernel weight

GL:

Grain length

GW:

Grain width

KASP:

Kompetitive allele-specific PCR

ZM366:

Zhengmai366

LH6:

Luohan6

SN8355:

Shannong8355

References

  • Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF (2006) A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc 1:2320–2325

    CAS  PubMed  Google Scholar 

  • Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GLA, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, Griffiths S, Bentley AR, Alda M, Jack P, Phillips AL, Edwards KJ (2017) Characterization of a wheat breeders’ array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J 15:390–401

    CAS  PubMed  Google Scholar 

  • Borrill P, Ramirez-Gonzalez R, Uauy C (2016) expVIP: a customizable RNA-seq data analysis and visualization platform. Plant Physiol 170:2172

    CAS  PubMed  PubMed Central  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    PubMed  PubMed Central  Google Scholar 

  • Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345:1249721

    PubMed  Google Scholar 

  • Cui F, Ding A, Li J, Zhao C, Wang L, Wang X, Qi X, Li X, Li G, Gao J, Wang H (2011) QTL detection of seven spike-related traits and their genetic correlations in wheat using two related RIL populations. Euphytica 186:177–192

    Google Scholar 

  • Deng Z, Cui Y, Han Q, Fang W, Li J, Tian J (2017) Discovery of consistent QTLs of wheat spike-related traits under nitrogen treatment at different development stages. Front Plant Sci 8:2120

    PubMed  PubMed Central  Google Scholar 

  • Ding AM, Li J, Cui F, Zhao CH, Ma HY, Wang HG (2011) Mapping QTLs for yield related traits using two associated RIL populations of wheat. Acta Agron Sin 37:1511–1524

    CAS  Google Scholar 

  • Gasperini D, Greenland A, Hedden P, Dreos R, Harwood W, Griffiths S (2012) Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids. J Exp Bot 63:4419–4436

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hastings KT, Cresswell P (2011) Disulfide reduction in the endocytic pathway: immunological functions of gamma-interferon-inducible lysosomal thiol reductase. Antioxid Redox Signal 15:657–668

    CAS  PubMed  PubMed Central  Google Scholar 

  • International Wheat Genome Sequencing C, IWGSC RefSeq Principal Investigators, Appels R, Eversole K, Feuillet C, Keller B, Rogers J et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:6403

  • Jaiswal V, Gahlaut V, Mathur S, Agarwal P, Khandelwal MK, Khurana JP, Tyagi AK, Balyan HS, Gupta PK (2015) Identification of novel SNP in promoter sequence of TaGW2-6A associated with grain weight and other agronomic traits in wheat (Triticum aestivum L.). PLoS One 10:e0129400

    PubMed  PubMed Central  Google Scholar 

  • Kim YJ, Kim S-I, Kesavan M, Kwak JS, Song JT, Seo HS (2015) Ascorbate peroxidase OsAPx1 is involved in seed development in rice. Plant Breed Biotech 3:11–20

    Google Scholar 

  • Li S, Jia J, Wei X, Zhang X, Li L, Chen H, Fan Y, Sun H, Zhao X, Lei T, Xu Y, Jiang F, Wang H, Li L (2007) A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breed 20:167–178

    Google Scholar 

  • Li C, Bai G, Carver BF, Chao S, Wang Z (2015) Single nucleotide polymorphism markers linked to QTL for wheat yield traits. Euphytica 206:89–101

    Google Scholar 

  • Liu J, Xu Z, Fan X, Zhou Q, Cao J, Wang F, Ji G, Yang L, Feng B, Wang T (2018) A genome-wide association study of wheat spike related traits in China. Front Plant Sci 9:1584

    PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408

    CAS  PubMed  Google Scholar 

  • Lu JL, Chen C, Liu P, He ZH, Xia XC (2016) Identification of a new stripe rust resistance gene in Chinese winter wheat Zhongmai 175. J Integr Agric 15:2461–2468

    CAS  Google Scholar 

  • Manickavelu A, Kawaura K, Imamura H, Mori M, Ogihara Y (2010) Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population. Euphytica 177:179–190

    Google Scholar 

  • Meng L, Li H, Zhang L, Wang J (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283

    Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    CAS  PubMed  PubMed Central  Google Scholar 

  • Narjesi V, Mardi M, Hervan EM, Azadi A, Naghavi MR, Ebrahimi M, Zali AA (2015) Analysis of quantitative trait loci (QTL) for grain yield and agronomic traits in wheat (Triticum aestivum L.) under normal and salt-stress conditions. Plant Mol Biol Rep 33:2030–2040

    CAS  Google Scholar 

  • Neumann K, Kobiljski B, Denčić S, Varshney RK, Börner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed 27:37–58

    Google Scholar 

  • Prashant R, Kadoo N, Desale C, Kore P, Dhaliwal HS, Chhuneja P, Gupta V (2012) Kernel morphometric traits in hexaploid wheat (Triticum aestivum L.) are modulated by intricate QTL × QTL and genotype × environment interactions. J Cereal Sci 56:432–439

    CAS  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    CAS  Google Scholar 

  • Simmonds J, Scott P, Leverington-Waite M, Turner AS, Brinton J, Korzun V, Snape J, Uauy C (2014) Identification and independent validation of a stable yield and thousand grain weight QTL on chromosome 6A of hexaploid wheat (Triticum aestivum L.). BMC Plant Biol 14:191

    PubMed  PubMed Central  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114

    CAS  PubMed  Google Scholar 

  • Su Z, Hao C, Wang L, Dong Y, Zhang X (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122:211–223

    CAS  PubMed  Google Scholar 

  • Su Z, Jin S, Lu Y, Zhang G, Chao S, Bai G (2016) Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat. Mol Breed 36:1–11

    CAS  Google Scholar 

  • Sun XY, Wu K, Zhao Y, Kong FM, Han GZ, Jiang HM, Huang XJ, Li RJ, Wang HG, Li SS (2008) QTL analysis of kernel shape and weight using recombinant inbred lines in wheat. Euphytica 165:615

    Google Scholar 

  • Wang RX, Hai L, Zhang XY, You GX, Yan CS, Xiao SH (2009) QTL mapping for grain filling rate and yield-related traits in RILs of the Chinese winter wheat population Heshangmai × Yu8679. Theor Appl Genet 118:313–325

    CAS  PubMed  Google Scholar 

  • Wang J, Liu W, Wang H, Li L, Wu J, Yang X, Li X, Gao A (2011) QTL mapping of yield-related traits in the wheat germplasm 3228. Euphytica 177:277–292

    Google Scholar 

  • Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    CAS  PubMed  PubMed Central  Google Scholar 

  • Win KT, Vegas J, Zhang C, Song K, Lee S (2017) QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods. Theor Appl Genet 130:199–211

    CAS  PubMed  Google Scholar 

  • Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, King J, West C, Griffiths S, King I, Bentley AR, Edwards KJ (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14:1195–1206

    CAS  PubMed  Google Scholar 

  • Wu X, Cheng R, Xue S, Kong Z, Wan H, Li G, Huang Y, Jia H, Jia J, Zhang L, Ma Z (2013) Precise mapping of a quantitative trait locus interval for spike length and grain weight in bread wheat (Triticum aestivum L.). Mol Breed 33:129–138

    Google Scholar 

  • Wu QH, Chen YX, Zhou SH, Fu L, Chen JJ, Xiao Y, Zhang D et al (2015) High-density genetic linkage map construction and QTL mapping of grain shape and size in the wheat population Yanda 1817 × Beinong 6. PLoS One 10:e0118144

    PubMed  PubMed Central  Google Scholar 

  • Wu J, Wang Q, Liu S, Huang S, Mu J, Zeng Q, Huang L, Han D, Kang Z (2017) Saturation mapping of a major effect QTL for stripe rust resistance on wheat chromosome 2B in cultivar Napo 63 using SNP genotyping rrrays. Front Plant Sci 8:653

    PubMed  PubMed Central  Google Scholar 

  • Xu YF, Li SS, Li LH, Ma FF, Fu XY, Shi ZL, Xu HX, Ma PT, An DG (2017) QTL mapping for yield and photosynthetic related traits under different water regimes in wheat. Mol Breed 37:34

    Google Scholar 

  • Yang Z, Bai Z, Li X, Wang P, Wu Q, Yang L, Li L, Li X (2012) SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theor Appl Genet 125:1057–1068

    CAS  PubMed  Google Scholar 

  • Yang H, Li C, Lam HM, Clements J, Yan G, Zhao S (2015) Sequencing consolidates molecular markers with plant breeding practice. Theor Appl Genet 128:779–795

    CAS  PubMed  Google Scholar 

  • Zhai H, Feng Z, Li J, Liu X, Xiao S, Ni Z, Sun Q (2016) QTL analysis of spike morphological traits and plant height in winter wheat (Triticum aestivum L.) using a high-density SNP and SSR-based linkage map. Front Plant Sci 7:1617

    PubMed  PubMed Central  Google Scholar 

  • Zhai H, Feng Z, Du X, Song Y, Liu X, Qi Z, Song L, Li J, Li L, Peng H, Hu Z, Yao Y, Xin M, Xiao S, Sun Q, Ni Z (2018) A novel allele of TaGW2-A1 is located in a finely mapped QTL that increases grain weight but decreases grain number in wheat (Triticum aestivum L.). Theor Appl Genet 131:539–553

    CAS  PubMed  Google Scholar 

  • Zhang Y, Feng S, Chen F, Chen H, Wang J, McCall C, Xiong Y, Deng XW (2008) Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. Plant Cell 20:1437–1455

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D (2013a) Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 8:e57853

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X, Chen J, Shi C, Chen J, Zheng F, Tian J (2013b) Function of TaGW2-6A and its effect on grain weight in wheat (Triticum aestivum L.). Euphytica 192:347–357

    CAS  Google Scholar 

  • Zou C, Wang P, Xu Y (2016) Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnol J 14:1941–1955

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Kunpu Zhang (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences) for providing the seeds of ZM366, LH6 and SN8355. This work was supported by the Ministry of Agriculture of China (2016ZX08009-003), the National Natural Science Foundation of China (31500298), the National Key Research and Development Program of China (2016YFD0101004) and the Chinese Academy of Science (XDA08010104).

Author information

Authors and Affiliations

  1. Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

    Pei Cao, Xiaona Liang, Hong Zhao, Enjun Xu & Yuxin Hu

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Xiaona Liang & Hong Zhao

  3. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China

    Bo Feng

  4. Henan Science and Technology University, Luoyang, 471023, Henan, China

    Liming Wang

  5. National Center for Plant Gene Research, Beijing, 100093, China

    Yuxin Hu

Authors
  1. Pei Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiaona Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hong Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bo Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Enjun Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Liming Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yuxin Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuxin Hu.

Ethics declarations

Conflict of interest

We declare no conflicts of interest in regards to this manuscript.

Ethical standards

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

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 106 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cao, P., Liang, X., Zhao, H. et al. Identification of the quantitative trait loci controlling spike-related traits in hexaploid wheat (Triticum aestivum L.). Planta 250, 1967–1981 (2019). https://doi.org/10.1007/s00425-019-03278-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00425-019-03278-0

Keywords

Search

Navigation