Genetic Diversity Analysis Reveals Strong Population Structure in Sorghum Germplasm Collection

Abstract

Population structure and genetic variability among seven groups of 44 parental lines of sorghum, including mid-season drought-tolerant, mid-season drought-susceptible, stay green lines, terminal drought-tolerant, saline-tolerant, saline-susceptible, high Fe–Zn lines and a wild genotype as an out-group were assessed using three dominant markers namely ISSR, RAPD, and DAMD. Wide range genome coverage of sorghum has been attained using these markers, which produced about 263 fragments of amplified products and the analysis accounted for a higher polymorphism (84.6%) and the polymorphic loci (72.65%) which produced a greater level of genetic distance among the genotypes. These findings are consistent with the UPGMA and neighbor-joining clustering of genotypes by individual markers. The existence of greater genetic variation at an intrapopulation level than at the interpopulation level was indicated by principal coordinate analysis and principal component analysis where the individuals of different groups failed to form distinct clusters rather mixed up along the axis. The Bayesian model-based structure analysis also identified the population structure with high admixture and diversity among the studied populations. The study also showed the non-existence of pure lines from this collection. Therefore, markers used in the study efficiently arrived at the phylogenetic relationships of 44 domesticated sorghum lines, and the obtained information can be implemented in breeding programs of this important food and forage resource for biofortification and the development of varieties with abiotic stress tolerance.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. 1.

    Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Article  CAS  Google Scholar 

  2. 2.

    Reddy BVS, Ramesh S, Reddy PS, Kumar AA (2009) Genetic enhancement for drought tolerance in sorghum. Plant Breed Rev 31:189–222

    CAS  Google Scholar 

  3. 3.

    Duodu KG, Taylor JRN, Beltron PS, Hamaker BR (2003) Factors affecting sorghum protein digestibility. J Cereal Sci 38:117–131

    Article  CAS  Google Scholar 

  4. 4.

    ICRISAT (1996) The world sorghum and millet economies: facts, trends and outlook, ICRISAT/FAO, Patancheru, India/Rome, Italy, pp 1–2

  5. 5.

    Satish L, Shilpha J, Pandian S, Rency AS, Rathinapriya P, Ceasar S, Largia MJV, Ashok AK, Ramesh M (2016) Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods. Gene 576:581–585

    Article  CAS  Google Scholar 

  6. 6.

    Hussain SS, Kayani MA, Amjad M (2011) Transcription factors as tools to engineer enhanced drought stress tolerance in plants. Biotechnol Prog 27:297–306

    Article  CAS  Google Scholar 

  7. 7.

    Burke JJ, Emendack Y, Chad Hayes C, Chen J (2018) Genetic diversity in the environmental conditioning of two Sorghum (Sorghum bicolor L.) Hybrids. Am J Plant Sci 9:817–831

    Article  CAS  Google Scholar 

  8. 8.

    Basnet BR, Ali MB, Ibrahim AM, Payne T, Mosaad MG (2011) Evaluation of genetic bases and diversity of Egyptian wheat cultivars released during the last 50 years using coefficient of parentage. Commun Biom Crop Sci 6:31–47

    Google Scholar 

  9. 9.

    Frankel OH, Brown AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden JHW, Williams JT (eds) Crop genetic resources: conservation and evaluation. George Allen and Unwin, London, UK, pp 249–257

    Google Scholar 

  10. 10.

    Spooner DM, Tivang J, Nienhuis J, Miller JT, Douches DS, Contreras-m A (1996) Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe). Theor Appl Genet 92:532–540

    Article  CAS  Google Scholar 

  11. 11.

    Van Esbroeck G, Bowman DT (1998) Cotton germplasm diversity and its importance in cultivar development. J Cot Sci 2:121–129

    Google Scholar 

  12. 12.

    Uptmoor R, Wenzel W, Friedt W, Donaldson G, Ayisi K, Ordon F (2003) Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theor Appl Genet 106:1316–1325

    Article  CAS  Google Scholar 

  13. 13.

    Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Kapran I, Traore PS, Mamadou A (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 116(7):903–913

    Article  CAS  Google Scholar 

  14. 14.

    Ng’uni D, Geleta M, Bryngelsson T (2011) Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR). Hereditas 148:52–62

    Article  Google Scholar 

  15. 15.

    Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, Jing HC (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12:1

    Article  Google Scholar 

  16. 16.

    Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  CAS  Google Scholar 

  17. 17.

    Akram Z, Khan MM, Shabbir G, Nasir F (2011) Assessment of genetic variability in sorghum genotypes for drought tolerance based on RAPD analysis. J Agric Res 49:455–464

    Google Scholar 

  18. 18.

    Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  PubMed Central  CAS  Google Scholar 

  19. 19.

    Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  20. 20.

    Rohlf FJ (1998) NTSYS-PC. Numerical taxonomy and multivariate analysis system, version 2.02. Exeter Software, Setauket, NY

  21. 21.

    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  PubMed Central  CAS  Google Scholar 

  22. 22.

    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  Google Scholar 

  23. 23.

    Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  CAS  Google Scholar 

  24. 24.

    Uphadyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S (2009) Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci 49:1769–1780

    Article  Google Scholar 

  25. 25.

    Basahi M (2015) ISSR-based analysis of genetic diversity among sorghum landraces growing in some parts of Saudi Arabia and Yemen. CR Biol 338:723–727

    Article  Google Scholar 

  26. 26.

    Desplanque B, Boudry P, Broomberg K, Saumitou-Laprade P, Cuguen J, Van Dijk H (1999) Genetic diversity and gene flow between wild, cultivated and weedy forms of Beta vulgaris L. (Chenopodiaceae), assessed by RFLP and microsatellite markers. Theor Appl Genet 98:1194–1201

    Article  CAS  Google Scholar 

  27. 27.

    Abdel-Fatah BE, Ali EA, El-Din AT, Hessein EM (2013) Genetic diversity among Egyptian sorghum (Sorghum bicolor L. Moench) landraces in agro-morphological traits and molecular markers. Asian J Crop Sci 5:106–124

    Article  Google Scholar 

  28. 28.

    Weerasooriya DK, Maulana FR, Bandara AY, Tirfessa A, Ayana A, Mengistu G, Nouh K, Tesso TT (2016) Genetic diversity and population structure among sorghum (Sorghum bicolor, L.) germplasm collections from Western Ethiopia. Afr J Biotechnol 15:1147–1158

    CAS  Google Scholar 

  29. 29.

    Desmae H, Jordan DR, Godwin ID (2016) DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces. Afr J Biotechnol 15:2301–2311

    Article  CAS  Google Scholar 

  30. 30.

    Gaggiotti OE, Foll M (2010) Quantifying population structure using the F-model. Mol Ecol Res 10:821–830

    Article  Google Scholar 

  31. 31.

    Pandian S, Marichelvam K, Satish L, Ceasar SA, Pandian SK, Ramesh M (2018) SPAR markers-assisted assessment of genetic diversity and population structure in finger millet (Eleusine Coracana (L.) Gaertn) mini-core collection. J Crop Sci Biotechnol 21:469–481

    Article  Google Scholar 

  32. 32.

    Hamrick JL, Godt MJW (1996) Effect of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B Biol Sci 351:1291–1298

    Article  Google Scholar 

Download references

Acknowledgements

One of the authors thanks the University Grants Commission, New Delhi, India for financial support in the form of UGC-BSR SRF (UGC Order No: F.25-1/2014-15 (BSR)/7-326/2011/BSR). The authors thank Dr. Are Ashok Kumar, Sorghum Breeding, International Crops Research Institute from the Semi-Arid Tropics (ICRISAT), Hyderabad, India, and Department of Millets, Tamil Nadu Agricultural University (TNAU), Coimbatore, India, for providing the seed material used in this study. They sincerely acknowledge the Computational and Bioinformatics facility provided by the Alagappa University Bioinformatics Infrastructure Facility (funded by DBT, GOI; File No. BT/BI/25/012/2012,BIF). The authors also thankfully acknowledge RUSA 2.0 [F. 24-51/2014-U, Policy (TN Multi-Gen), Dept of Edn, GOI], DST-FIST (Grant No. SR/FST/LSI-639/2015(C)), UGC-SAP (Grant No. F.5-1/2018/DRS-II (SAP-II)) and DST-PURSE (Grant No. SR/PURSE Phase 2/38 (G)) for providing instrumentation facilities.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Manikandan Ramesh.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest to publish this manuscript.

Additional information

Publisher's Note

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

Significance Statement

Population structure analysis of 45 sorghum germplasm with various agronomic traits has been carried out which provides novel insights into understanding the genetic composition of sorghum collections for crop improvement solutions essential in rapid applications of plant breeding.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 63 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pandian, S., Satish, L., Shilpha, J. et al. Genetic Diversity Analysis Reveals Strong Population Structure in Sorghum Germplasm Collection. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 90, 179–190 (2020). https://doi.org/10.1007/s40011-019-01095-9

Download citation

Keywords

  • Agronomic traits
  • Heterogeneity
  • Molecular markers
  • Population structure
  • Sorghum