Advertisement

Genetic Diversity Analysis Reveals Strong Population Structure in Sorghum Germplasm Collection

  • Subramani Pandian
  • Lakkakula Satish
  • Jayabalan Shilpha
  • Manikandan RameshEmail author
Research Article
  • 36 Downloads

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.

Keywords

Agronomic traits Heterogeneity Molecular markers Population structure Sorghum 

Notes

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.

Compliances with Ethical Standards

Conflict of interest

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

Supplementary material

40011_2019_1095_MOESM1_ESM.docx (63 kb)
Supplementary material 1 (DOCX 63 kb)

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 457:551–556CrossRefGoogle Scholar
  2. 2.
    Reddy BVS, Ramesh S, Reddy PS, Kumar AA (2009) Genetic enhancement for drought tolerance in sorghum. Plant Breed Rev 31:189–222Google Scholar
  3. 3.
    Duodu KG, Taylor JRN, Beltron PS, Hamaker BR (2003) Factors affecting sorghum protein digestibility. J Cereal Sci 38:117–131CrossRefGoogle Scholar
  4. 4.
    ICRISAT (1996) The world sorghum and millet economies: facts, trends and outlook, ICRISAT/FAO, Patancheru, India/Rome, Italy, pp 1–2Google Scholar
  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 576:581–585CrossRefGoogle Scholar
  6. 6.
    Hussain SS, Kayani MA, Amjad M (2011) Transcription factors as tools to engineer enhanced drought stress tolerance in plants. Biotechnol Prog 27:297–306CrossRefGoogle 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 9:817–831CrossRefGoogle 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 6:31–47Google 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 249–257Google 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 92:532–540CrossRefGoogle Scholar
  11. 11.
    Van Esbroeck G, Bowman DT (1998) Cotton germplasm diversity and its importance in cultivar development. J Cot Sci 2:121–129Google 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 106:1316–1325CrossRefGoogle 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):903–913CrossRefGoogle 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 148:52–62CrossRefGoogle 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 12:1CrossRefGoogle 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 18:6531–6535CrossRefGoogle 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 49:455–464Google 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 32:314–331Google Scholar
  19. 19.
    Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Google Scholar
  20. 20.
    Rohlf FJ (1998) NTSYS-PC. Numerical taxonomy and multivariate analysis system, version 2.02. Exeter Software, Setauket, NYGoogle Scholar
  21. 21.
    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959Google 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 14:2611–2620CrossRefGoogle 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 28:2537–2539CrossRefGoogle 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 49:1769–1780CrossRefGoogle 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 338:723–727CrossRefGoogle 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 98:1194–1201CrossRefGoogle 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 5:106–124CrossRefGoogle 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 15:1147–1158Google 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 15:2301–2311CrossRefGoogle Scholar
  30. 30.
    Gaggiotti OE, Foll M (2010) Quantifying population structure using the F-model. Mol Ecol Res 10:821–830CrossRefGoogle 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 21:469–481CrossRefGoogle 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 351:1291–1298CrossRefGoogle Scholar

Copyright information

© The National Academy of Sciences, India 2019

Authors and Affiliations

  1. 1.Department of Biotechnology, Science CampusAlagappa UniversityKaraikudiIndia

Personalised recommendations