Skip to main content
SpringerLink
Log in

Genetic diversity and population structure analysis for morphological traits in upland cotton (Gossypium hirsutum L.)

  • Plant Genetics • Original Paper
  • Published:
Journal of Applied Genetics Aims and scope Submit manuscript

Abstract

A total of 96 different genotypes of upland cotton (Gossypium hirsutum) were selected from the breeding material and germplasm available at CCS HAU, India, to find the novel marker-trait associations for morphological traits used for registration of variety in upland cotton. Twenty-three morphological traits of the selected genotypes were recorded in field trials conducted in two replication of randomized block design during Kharif 2018 and 2019. A total of 11 traits showed sufficient variations in the screened germplasm and the same were further used for association mapping. A total of 168 SSRs were used for genotyping, of which 97 SSRs showed polymorphism amplifying 293 different alleles with an average of 3.02 alleles per SSR. Clustering, principal component analysis, and population structure analysis advocated that the current germplasm panel has enough diversity to be considered for association mapping. A total of 20 significant marker-trait associations were identified by the mixed linear model (MLM) and compressed mixed linear model (CMLM), of which 15 were common to both models, hence considered as promising associations. To the best of our knowledge, it is a first attempt to identify the linked markers in relation to morphological traits for the cotton crop. Results of the present study will be highly useful in speeding up variety registration programmes of upland cotton complementing to Distinctiveness, Uniformity, and Stability (DUS) testing.

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
Fig. 7

Similar content being viewed by others

References

  • Abdullaev AA, Salakhutdinov IB, Egamberdiev SS, Khurshut EE, Rizaeva SM, Ulloa M, Abdurakhmonov IY (2017) Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm. Plos One 12:e0188125

    Article  PubMed  PubMed Central  Google Scholar 

  • Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE, Scheffler BE, Pepper AE, John ZY, Kohel RJ, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136:401–417

    Article  PubMed  Google Scholar 

  • Ademe MS, He S, Pan Z, Sun J, Wang Q, Qin H, Liu J, Liu H, Yang J, Xu D (2017) Association mapping analysis of fiber yield and quality traits in upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 292:1267–1280

    Article  CAS  PubMed  Google Scholar 

  • Ali I, Khan NU, Gul S, Khan SU, Tahir I, Bibi Z, Khalil IH, Rahman M-Ur, Ahmed S, Aslam K (2020) Association mapping of QTLs with yield and lint traits in elite upland cotton germplasm. Int J Agric Biol 24:17–28

    CAS  Google Scholar 

  • Anandan A, Anumalla M, Pradhan SK, Ali J (2016) Population structure, diversity and trait association analysis in rice (Oryza sativa L.) germplasm for early seedling vigor (ESV) using trait linked SSR markers. PLoS One 11:e0152406

    Article  PubMed  PubMed Central  Google Scholar 

  • Arens P, Mansilla C, Deinum D, Cavellini L, Moretti A, Rolland S, van der Schoot H, Calvache D, Ponz F, Collonnier C (2010) Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor Appl Genet 120:655–664

    Article  CAS  PubMed  Google Scholar 

  • Balakrishna B, Reddy VC, Reddy KVS (2016) Distinctness, uniformity and stability (DUS) characterization on fiber quality traits of cotton (Gossypium spp.) germplasm. Environ Ecol 34:262–266

    Google Scholar 

  • Bernet GP, Bramardi S, Calvache D, Carbonell EA, Asins MJ (2003) Applicability of molecular markers in the context of protection of new varieties of cucumber. Plant Breed 122:146–152

    Article  Google Scholar 

  • Bonow S, Von Pinho EV, Vieira MG, Vosman B (2009) Microsatellite markers in and around rice genes: applications in variety identification and DUS testing. Crop Sci 49:880–886

    Article  CAS  Google Scholar 

  • Cai C, Ye W, Zhang T, Guo W (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  PubMed  Google Scholar 

  • Cockram J, Norris C, O’Sullivan DM (2009) PCR-based markers diagnostic for spring and winter seasonal growth habit in barley. Crop Sci 49:403–410

    Article  CAS  Google Scholar 

  • Das A, Kumar D (2012) Genetic evaluation and characterization of jute (Corchorus spp. L) genotypes using DUS. SAARC J Agric 10:147–153

    Article  Google Scholar 

  • Earl DA (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Giancola S, Poltri SM, Lacaze P, Hopp HE (2002) Feasibility of integration of molecular markers and morphological descriptors in a real case study of a plant variety protection system for soybean. Euphytica 127:95–113

    Article  CAS  Google Scholar 

  • Gunjaca J, Buhinicek I, Jukic M, Sarcevic H, Vragolovic A, Kozic Z, Jambrovic A, Pejic I (2008) Discriminating maize inbred lines using molecular and DUS data. Euphytica 161:165–172

    Article  CAS  Google Scholar 

  • Hu Z, Zhang D, Zhang G, Kan G, Hong D, Yu D (2014) Association mapping of yield-related traits and SSR markers in wild soybean (Glycine soja Sieb. and Zucc.). Breed Sci 63:441–449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang C, Shen C, Wen T, Gao B, Zhu D, Li X, Ahmed MM, Li D, Lin Z (2018) SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population. Mol Genet Genomics 293:793–805

    Article  CAS  PubMed  Google Scholar 

  • Ibáñez J, Vélez MD, de Andrés MT, Borrego J (2009) Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine. Theor Appl Genet 119:1213

    Article  PubMed  Google Scholar 

  • Iqbal MA, Rahman M (2017) Identification of marker-trait associations for lint traits in cotton. Front Plant Sci 8:86

    Article  PubMed  PubMed Central  Google Scholar 

  • Iquira E, Humira S, François B (2015) Association mapping of QTLs for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach. BMC Plant Biol 15:5

    Article  PubMed  PubMed Central  Google Scholar 

  • ISF (2012) ISF View on Intellectual Property. International Seed Federation. http://www.worldseed.org/wp-content/uploads/2015/10/View_on_Intellectual_Property_2012.pdf

  • Jamali SH, Mohammadi SA, Sadeghzadeh B (2017) Association mapping for morphological traits relevant to registration of barley varieties. Span J Agric Res 15:18

    Google Scholar 

  • Jones H, Norris C, Cockram J, Lee D (2013) Variety protection and plant breeders’ rights in the ‘DNA era,’ in: Diagnostics in plant breeding. Springer, pp. 369–402

  • Kaur B, Tyagi P, Kuraparthy V (2017) Genetic diversity and population structure in the landrace accessions of Gossypium hirsutum. Crop Sci 57:2457–2470

    Article  Google Scholar 

  • Kristensen PS, Jahoor A, Andersen JR, Cericola F, Orabi J, Janss LL, Jensen J (2018) Genome-wide association studies and comparison of models and cross-validation strategies for genomic prediction of quality traits in advanced winter wheat breeding lines. Front Plant Sci 9:69

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar P, Nimbal S, Sangwan RS, Budhlakoti N, Singh V, Mishra DC (2021) Identification of novel marker–trait associations for lint yield contributing traits in upland cotton (Gossypium hirsutum L.) using SSRs. Front Plant Sci 12:e653270

    Article  Google Scholar 

  • Kwon Y-S, Lee J-M, Yi G-B, Yi S-I, Kim K-M, Soh E-H, Bae K-M, Park E-K, Song I-H, Kim B-D (2005) Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol. Cells Springer Sci. Bus. Media BV 19.

  • Li C-Q, Xu X-J, Dong N, Ai N-J, Wang Q-L (2016) 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 W, Yuting B, Wei W, Guorong Y, Yanming M, Zhiyong L (2011) Discuss existing problems on DUS testing guidelines revision of new cotton varieties protection. Chin Agric Sci Bull 2011:56

    Google Scholar 

  • Li X, Zheng H, Zhao H, Wang J, Liu H, Sun J, Li N, Lei L, Zou D (2018) Association analysis of saline-alkali related traits and SSR markers in Japonica rice under soda saline-alkali stress. Acta Agric. Boreali-Sin. 24

  • Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397–2399

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Lombard V, Baril CP, Dubreuil P, Blouet F, Zhang D (2000) Genetic relationships and fingerprinting of rapeseed cultivars by AFLP: consequences for varietal registration. Crop Sci 40:1417–1425

    Article  CAS  Google Scholar 

  • Nie X, Huang C, You C, Li W, Zhao W, Shen C, Zhang B, Wang H, Yan Z, Dai B (2016) Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genomics 17:1–16

    Article  Google Scholar 

  • Noli E, Teriaca MS, Sanguineti MC, Conti S (2008) Utilization of SSR and AFLP markers for the assessment of distinctness in durum wheat. Mol Breed 22:301–313

    Article  CAS  Google Scholar 

  • Perrier X (2006) DARwin software. Httpdarwin Cirad Frdarwin

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin H, Chen M, Yi X, Bie S, Zhang C, Zhang Y, Lan J, Meng Y, Yuan Y, Jiao C (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  PubMed  PubMed Central  Google Scholar 

  • Rotondi A, Magli M, Ricciolini C, Baldoni L (2003) Morphological and molecular analyses for the characterization of a group of Italian olive cultivars. Euphytica 132:129–137

    Article  CAS  Google Scholar 

  • Sagar, Nimbal S, Sangwan RS, Kumar P, Jangid K, Reddy B (2019) DUS characterization of upland cotton (Gossypium hirsutum L.) elite genotypes by qualitative characters. J Pharmacogn Phytochem 8:1100–1103

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RWL (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci 81:8014–8018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santhy V, Rathinavel K, Saravanan M, Meshram M, Priyadharshini C (2020) Genetic diversity assessment of extant cotton varieties based on principal component analysis (PCA) and cluster analysis of enlisted DUS traits. Electron J Plant Breed 11:430–438

    Google Scholar 

  • Schmit F, Cremer S, Gaubatz S (2009) LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner. FEBS J 276:5703–5716

    Article  CAS  PubMed  Google Scholar 

  • Sethi K, Siwach P, Verma SK (2017) Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations. Czech J Genet Plant Breed 53:159–167

    Article  CAS  Google Scholar 

  • Shen X, Guo W, Zhu X, Yuan Y, John ZY, Kohel RJ, Zhang T (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in upland cotton using SSR markers. Mol Breed 15:169–181

    Article  CAS  Google Scholar 

  • Stich B, Melchinger AE (2009) Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 10:1–14

    Article  Google Scholar 

  • Stich B, Melchinger AE, Heckenberger M, Möhring J, Schechert A, Piepho H-P (2008) Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.). Theor Appl Genet 117:1167–1179

    Article  PubMed  Google Scholar 

  • Sun F-D, Zhang J-H, Wang S-F, Gong W-K, Shi Y-Z, Liu A-Y, Li J-W, Gong J-W, Shang H-H, Yuan Y-L (2012) QTL mapping for fiber quality traits across multiple generations and environments in upland cotton. Mol Breed 30:569–582

    Article  Google Scholar 

  • UPOV (1991) International convention for the protection of new varieties of plants, International Union for the Protection of New Varieties of Plants, Publication No. 221 (E), March 19, Geneva. http://www.upov.int/export/sites/upov/upovlex/en/conventions/1991/pdf/act1991.pdf

  • UPOV (2013) Guidance on the use of biochemical and molecular markers in the examination of distinctness, uniformity and stability (DUS). International Union for the Protection of New Varieties of Plants, TGP/15. http://www.upov.int/edocs/tgpdocs/en/tgp_15.pdf

  • Wang M, Jiang N, Jia T, Leach L, Cockram J, Waugh R, Ramsay L, Thomas B, Luo Z (2012) Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124:233–246

    Article  PubMed  Google Scholar 

  • Wu J, Gutierrez OA, Jenkins JN, McCarty JC, Zhu J (2009) Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton. Euphytica 165:231–245

    Article  Google Scholar 

  • Würschum T, Liu W, Gowda M, Maurer HP, Fischer S, Schechert A, Reif JC (2012) Comparison of biometrical models for joint linkage association mapping. Heredity 108:332–340

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33:531–537

    Article  CAS  PubMed  Google Scholar 

  • Zhang T-T, Zhang N-Y, Li W, Zhou X-J, Pei X-Y, Liu Y-G, Ren Z-Y, He K-L, Zhang W-S, Zhou K-H (2020) Genetic structure, gene flow pattern, and association analysis of superior germplasm resources in domesticated Upland Cotton (Gossypium hirsutum L.). Plant Divers

Download references

Acknowledgements

The authors gratefully acknowledge Dr. Rakesh Poonia (Assistant Scientist), Department of Plant Pathology, for his assistance and help to conduct the molecular work in their laboratories and Dr. Dwijesh Chandra Mishra (Scientist), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, for his suggestions and ideas in the analytical part.

Author information

Authors and Affiliations

  1. Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, 125004, India

    Pawan Kumar, Somveer Nimbal & Rajvir Singh Sangwan

  2. ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India

    Neeraj Budhlakoti

  3. Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, 125004, Hisar, India

    Varsha Singh

Authors
  1. Pawan Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Somveer Nimbal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Neeraj Budhlakoti
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Varsha Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rajvir Singh Sangwan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

P.K. has conducted the research and written the manuscript, S. N. and R.S.S. supervised the research and reviewed the manuscript, N.B. analysed the data and V.S. assisted in wet lab work and manuscript writing.

Corresponding author

Correspondence to Somveer Nimbal.

Ethics declarations

Ethics approval

The authors declare that the results described in this article are entirely produced by themselves from their original research work.

Conflict of interest

The authors declare no competing interests.

Additional information

Communicated by: Izabela Pawłowicz

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 305 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar, P., Nimbal, S., Budhlakoti, N. et al. Genetic diversity and population structure analysis for morphological traits in upland cotton (Gossypium hirsutum L.). J Appl Genetics 63, 87–101 (2022). https://doi.org/10.1007/s13353-021-00667-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13353-021-00667-8

Keywords

Search

Navigation