Skip to main content
SpringerLink
Log in

Identification of genomewide single-nucleotide polymorphisms associated with presummer, summer and autumn bolls in upland cotton

  • Research Article
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Presummer, summer, and autumn bolls (PSB, SB and AB, respectively) in cotton are related to both maturity and yield. Therefore, studying their genetic basis is important for breeding purposes. In this study, we developed an association analysis panel consisting of 169 upland cotton accessions. The panel was phenotyped for PSB, SB and AB across four environments and genotyped using a CottonSNP80K array. Single-nucleotide polymorphisms (SNPs) associated with these three traits were identified by a genomewide association study. A total of 53,848 high-quality SNPs were screened, and 91 significant trait-associated SNPs were detected. Of the 91 SNPs 33 were associated with PSB, 21 with SB and 37 with AB. Three SNPs for PSB (TM10410, TM13158 and TM21762) and five for AB (TM13730, TM13733, TM13834, TM29666 and TM43214) were repeatedly detected in two environments or by two methods. These eight SNPs exhibited high phenotypic variation of more than 10%, thus allowing their use for marker-assisted selection. The candidate genes for target traits were also identified. These findings provide a theoretical basis for the improvement of early maturity and yield in cotton breeding programmes.

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

Similar content being viewed by others

References

  • Abdurakhmonov I. Y., Saha S., Jenkins J. N., Buriev Z. T., Shermatov S. E., Scheffler B. E. et al. 2009 Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136, 401–417.

    Article  Google Scholar 

  • Alexander D. H., Novembre J. and Lange K. 2009 Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664.

    Article  CAS  Google Scholar 

  • An C. F., Jenkins J. N., Wu J. X., Guo Y. F. and McCarty J. C. 2010 Use of fiber and fuzz mutants to detect QTL for yield components, seed, and fiber traits of upland cotton. Euphytica 172, 21–34.

    Article  Google Scholar 

  • Bradbury P. J., Zhang Z., Kroon D. E., Casstevens T. M., Ramdoss Y., Buckler E. S. 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635.

    Article  CAS  Google Scholar 

  • Cai C. P., Ye W. X., Zhang T. Z. and Guo W. Z. 2014 Association analysis of fiber quality traits and exploration of elite alleles in upland cotton cultivars/accessions (Gossypium hirsutum L.). J. Integr. Plant Biol. 56, 51–62.

    Article  CAS  Google Scholar 

  • Cai C. P., Zhu G. Z., Zhang T. Z. and Guo W. Z. 2017 High-density 80K snp array is a powerful tool for genotyping G. hirsutum, accessions and genome analysis. BMC Genomics 18, 654.

    Article  Google Scholar 

  • Cheng H. L. and Yu S. X. 1994 Studies on the earliness inheritance of upland cottons (G. hirsutum L.). Cotton Sci. 6, 9–15.

    Google Scholar 

  • Du L., Cai C., Wu S., Zhang F., Hou S. and Guo W. 2016 Evaluation and exploration of favorable QTL alleles for salt stress related traits in cotton cultivars (G. hirsutum L.). PLoS One 11, e0151076.

    Article  Google Scholar 

  • Fan S. L., Yu S. X., Song M. Z. and Yuan R. H. 2006 Construction of molecular linkage map and QTL mapping for earliness in short-season cotton. Cotton Sci. 18, 135–139.

    Google Scholar 

  • Fang L., Gong H., Hu Y., Liu C., Zhou B., Huang T. et al. 2017 Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biol. 18, 33.

    Article  Google Scholar 

  • Gapare W., Conaty W., Zhu Q. H., Liu S., Stiller W., Llewellyn D. et al. 2017 Genome-wide association study of yield components and fiber quality traits in a cotton germplasm diversity panel. Euphytica 213, 66.

    Article  Google Scholar 

  • Guo Y. F., McCarty J. C., Jenkins J. N. and Saha S. 2008 QTL for node of first fruiting branch in a cross of an upland cotton, Gossypium hirsutum L., cultivar with primitive accession Texas 701. Euphytica 163, 113–122.

    Article  CAS  Google Scholar 

  • Guo Y. F., McCarty J., Jenkins J. N., An C. F. and Saha S. 2009 Genetic detection of node of first fruiting branch in crosses of a cultivar with two exotic accessions of upland cotton. Euphytica 166, 317–329.

    Article  Google Scholar 

  • Gupta P. K., Rustgi S. and Kulwal P. L. 2005 Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57, 461–485.

    Article  CAS  Google Scholar 

  • Hu Y., Huang Y., Zhang L., Zhao H., Liu H., Xing Y. et al. 2016 Genome-wide association analysis reveals flowering-related genes regulating rachis length in rice. Plant Breed. 135, 677–682.

    Article  CAS  Google Scholar 

  • Hu Y., Chen J., Fang L., Zhang Z., Ma W., Niu Y. et al. 2019 Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat. Genet. 51, 739–748.

    Article  CAS  Google Scholar 

  • Huang C., Nie X. H., Shen C., You C. Y., Li W., Zhao W. X. et al. 2017 Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. Plant Biotechnol. J. 15, 1374.

    Article  CAS  Google Scholar 

  • Hulse-Kemp A. M., Lemm J., Plieske J., Ashrafi H., Buyyarapu R., Fang D. D. et al. 2015 Development of a 63K SNP Array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. G3-Genes Genom. Genet. 5, 1187–1209.

    Google Scholar 

  • Islam M. S., Thyssen G. N., Jenkins J. N., Zeng L., Delhom C. D., McCarty J. C. et al. 2016 A MAGIC population-based genome-wide association study reveals functional association of GhRBB1\_A07 gene with superior fiber quality in cotton. BMC Genomics 17, 903.

    Article  Google Scholar 

  • Jia Y., Sun X., Sun J., Pan Z., Wang X., He S. et al. 2014 Association mapping for epistasis and environmental interaction of yield traits in 323 cotton cultivars under 9 different environments. PLoS One 9, e95882.

    Article  Google Scholar 

  • Li C. Q., Wang X. Y., Dong N., Zhao H. H., Xia Z., Wang R. et al. 2013 QTL analysis for early-maturing traits in cotton using two upland cotton (Gossypium hirsutum L.) crosses. Breed. Sci. 63, 154–163.

    Article  Google Scholar 

  • Li C. Q., Xu X. J., Dong N., Ai N. J. and Wang Q. L. 2016a Association mapping identifies markers related to major early-maturating traits in upland cotton (Gossypium hirsutum L.). Plant Breed. 135, 483–491.

    Article  CAS  Google Scholar 

  • Li C. Q., Ai N. J., Zhu Y. J., Wang Y. Q., Chen X. D., Li F. et al. 2016b Association mapping and favorable allele exploration for plant architecture traits in upland cotton (Gossypium hirsutum L.) accessions. J. Agri. Sci. 154, 567–583.

    Article  CAS  Google Scholar 

  • Li H., Zhang L., Hu J., Zhang F., Chen B., Xu K. et al. 2017a Genome-wide association mapping reveals the genetic control underlying branch angle in rapeseed (Brassica napus L.). Front. Plant Sci. 8, 1054.

    Article  Google Scholar 

  • Li T., Ma X., Li N., Zhou L., Liu Z., Han H. et al. 2017b Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol. J. 15, 1520–1532.

    Article  CAS  Google Scholar 

  • Li W., Nan C. X., Wu J. Q., Sun W., Wang Q. and Zhou T. Y. 2001 Autumn boll plays an important role in improving cotton yield of Eastern Hubei cotton region. China Cott. 28, 9–10.

    Google Scholar 

  • Lin Z. X., Feng C. H., Guo X. P. and Zhang X. L. 2009 Genetic analysis of major QTLs and epistasis interaction for yield and fiber quality in upland cotton. Sci. Agric. Sin. 42, 3036–3047.

    Google Scholar 

  • Lipka A. E., Tian F., Wang Q., Peiffer J., Li M., Bradbury P. J. et al. 2012 GAPIT: genome association and prediction integrated tool. Bioinformatics 28, 2397–2399.

    Article  CAS  Google Scholar 

  • Liu G. Z., Mei H. X., Wang S., Li X. H., Zhu X. F. and Zhang T. Z. 2015 Association mapping of seed oil and protein contents in upland cotton. Euphytica 205, 637–645.

    Article  CAS  Google Scholar 

  • Liu R., Wang B., Guo W., Qin Y., Wang L., Zhang Y. et al. 2012 Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Mol. Breed. 29, 297–311.

    Article  CAS  Google Scholar 

  • Mei H. X., Zhu X. F. and Zhang T. Z. 2013 Favorable QTL alleles for yield and its components identified by association mapping in Chinese upland cotton cultivars. PLoS One 8, e82193.

    Article  Google Scholar 

  • Mei H. X., Ai N. J., Zhang X., Ning Z. Y. and Zhang T. Z. 2014 QTLs conferring FOV 7 resistance detected by linkage and association mapping in upland cotton. Euphytica 197, 237–249.

    Article  Google Scholar 

  • Nie X., Huang C., You C., Li W., Zhao W., Shen C. et al. 2016 Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genomics 17, 352.

    Article  Google Scholar 

  • Qin H. D., Guo W. Z., Zhang Y. M. and Zhang T. Z. 2008 QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor. Appl. Genet. 117, 883–894.

    Article  Google Scholar 

  • Qin H. D., Chen M., Yi X. D., Bie S., Zhang C., Zhang Y. C. et al. 2015 Identification of associated SSR markers for yield component and fiber quality traits based on frame map and upland cotton collections. PLoS One 10, e0118073.

    Article  Google Scholar 

  • Saeed M., Guo W. Z. and Zhang T. Z. 2014 Association mapping for salinity tolerance in cotton (Gossypium hirsutum L.) germplasm from US and diverse regions of China. Aust. J. Crop Sci. 8, 338–346.

    CAS  Google Scholar 

  • Su J., Fan S., Li L., Wei H., Wang C., Wang H. et al. 2016a Detection of favorable QTL alleles and candidate genes for lint percentage by GWAS in Chinese upland cotton. Front. Plant Sci. 7, 1576.

    PubMed  PubMed Central  Google Scholar 

  • Su J., Li L., Pang C., Wei H., Wang C., Song M. et al. 2016b Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci. Rep. 6, 38496.

    Article  CAS  Google Scholar 

  • Su J., Pang C., Wei H., Li L., Liang B., Wang C. et al. 2016c Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton. BMC Genomics 17, 687.

    Article  Google Scholar 

  • Sun Z., Wang X., Liu Z., Gu Q., Zhang Y., Li Z. et al. 2017 Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnol. J. 15, 982–996.

    Article  CAS  Google Scholar 

  • Wan J. M. 2006 Perspectives of molecular design breeding in crops. Acta Agron. Sin. 32, 455–462.

    CAS  Google Scholar 

  • Wang M., Tu L., Yuan D., Zhu D., Shen C., Li J. et al. 2019 Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat. Genet. 51, 224–229.

    Article  CAS  Google Scholar 

  • Wang S. B., Feng J. Y., Ren W. L., Huang B., Zhou L., Wen Y. J. et al. 2016 Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci. Rep. 6, 19444.

    Article  CAS  Google Scholar 

  • Wang X. Y., Li C. Q., Xia Z., Dong N. and Wang Q. L. 2012 QTL mapping for pre-summer boll, summer boll and autumn boll traits in cotton. Hereditas 34, 757–764.

    Article  CAS  Google Scholar 

  • Wu Z. B. 2003 Field experimental technology of cotton regional test. J. Hubei Agric. Sci. 2, 37–40.

    Google Scholar 

  • Xu Y., Xu C. and Xu S. 2017 Prediction and association mapping of agronomic traits in maize using multiple omic data. Heredity 119, 174–184.

    Article  CAS  Google Scholar 

  • Yu J., Zhang K., Li S., Yu S., Zhai H., Wu M. et al. 2013 Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum \(\times \) Gossypium barbadense backcross inbred line population. Theor. Appl. Genet. 126, 275–287.

    Article  Google Scholar 

  • Zegeye H., Rasheed A., Makdis F., Badebo A. and Ogbonnaya F. C. 2014 Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat. PLoS One 9, e105593.

    Article  Google Scholar 

  • Zhang T. Z., Qian N., Zhu X. F., Chen H., Wang S., Mei H. X. et al. 2013 Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One 8, e57220.

    Article  CAS  Google Scholar 

  • Zhang J., Song Q., Cregan P. B., Nelson R. L., Wang X., Wu J. et al. 2015a Genome wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm. BMC Genomics 16, 217.

    Article  CAS  Google Scholar 

  • Zhang T. Z., Hu Y., Jiang W. K., Fang L., Guan X. Y., Chen J. D. et al. 2015b Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 33, 531–537.

    Article  CAS  Google Scholar 

  • Zhang X., Zhang J., He X., Wang Y., Ma X. and Yin D. 2017 Genome-wide association study of major agronomic traits related to domestication in peanut. Front. Plant Sci. 8, 1611.

    Article  Google Scholar 

  • Zhao Y., Wang H., Chen W. and Li Y. H. 2014 Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One 9, e86308.

    Article  Google Scholar 

  • Zhou Q., Zhou C., Zheng W., Mason A. S., Fan S., Wu C. et al. 2017 Genome-wide SNP markers based on SLAF-Seq uncover breeding traces in Rapeseed (Brassica napus L.). Front. Plant Sci. 8, 648.

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (grant no. 31371677) and the Middle-aged or Young Leading Talent Project of the Xinjiang Production and Construction Group (grant no. 2016BC001). We thank Liwen Bianji, Edanz Group China (www.liwenbianji.cn.ac), for editing the language of a draft of this manuscript.

Author information

Authors and Affiliations

  1. Shihezi Agricultural Science Research Institute, Shihezi, 832000, Xinjiang Province, People’s Republic of China

    Guo-Li Feng, Hong-Liang Liu & Ni-Jiang Ai

  2. Henan Institute of Science and Technology, Xinxiang, 453003, Henan Province, People’s Republic of China

    Feng-Yan Zhai

Authors
  1. Guo-Li Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Feng-Yan Zhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hong-Liang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ni-Jiang Ai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ni-Jiang Ai.

Additional information

Corresponding Editor: Qingpo Liu

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (xls 123 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Feng, GL., Zhai, FY., Liu, HL. et al. Identification of genomewide single-nucleotide polymorphisms associated with presummer, summer and autumn bolls in upland cotton. J Genet 98, 72 (2019). https://doi.org/10.1007/s12041-019-1118-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12041-019-1118-x

Keywords

Search

Navigation