Skip to main content
SpringerLink
Log in

Evaluation of Genetic Diversity Among Exotic Sorghum (Sorghum bicolor L. Moench) Genotypes Through Molecular Based Analysis (RAPD-PCR)

Bewertung der genetischen Vielfalt von exotischen Sorghum-Genotypen (Sorghum bicolor L. Moench) durch molekularbiologische Analyse (RAPD-PCR)

  • Original Article
  • Published:
Gesunde Pflanzen Aims and scope Submit manuscript

Abstract

There is a remarkable diversity among sorghum species; hence it requires a powerful marker system for genome characterisation. RAPD (randomly amplified polymorphic DNA) is a very favourable technique used to distinguish the sorghum genotypes due to its clarity and speed. We observed genetic diversity among 30 sorghum (Sorghum bicolor L. Moench) genotypes using RAPD markers. Sixteen RAPD markers produced a total of 148 bands with a mean of 9.25 fragments per loci. Out of the 148, 132 bands showed polymorphism (89.19%), and 16 bands showed monomorphism (10.81%). PIC (polymorphism information content) values were varying from 0.2035 to 0.3438 with a mean of 0.2792. Genetic distance was ranged from 0.013 (for genotype 4 and 8) to 0.807 (for genotype 10 and 27). Cluster analysis exhibited that dendrogram consists of four major groups. Results represent that genotype 1, 3, 5, 15, 6, 11, 4, 8, 26, 29, 20, 24, 14, 25, 19, 23, 2 and 13 were closely related to each other, and genotype 10 was the most diverse genotype among all the studied genotypes by making an independent cluster. The first two factors of principal component analysis (PCA) PC1 (15.06) and PC2 (10.98) had the highest contribution in variability as 10.18 and 7.42%, respectively. Thus, sorghum genotypes can be isolated from each other at the molecular level by using molecular markers.

Zusammenfassung

Es gibt eine bemerkenswerte Vielfalt unter den Sorghum-Arten. Daher ist ein leistungsfähiges Markersystem für die Charakterisierung des Genoms erforderlich. Die RAPD-Technik (RAPD: randomly amplified polymorphic DNA) ist aufgrund ihrer Eindeutigkeit und Schnelligkeit eine sehr günstige Methode, um die Sorghum-Genotypen zu unterscheiden. Wir analysierten die genetische Diversität von 30 Sorghum-Genotypen (Sorghum bicolor L. Moench) unter Verwendung von RAPD-Markern. 16 RAPD-Marker erzeugten insgesamt 148 Banden mit einem Mittelwert von 9,25 Fragmenten pro Loci. Von den 148 zeigten 132 Banden Polymorphismus (89,19 %) und 16 Banden Monomorphismus (10,81 %). Die PIC-Werte (PIC: polymorphism information content) variierten von 0,2035 bis 0,3438, mit einem Mittelwert von 0,2792. Der genetische Abstand lag zwischen 0,013 (für Genotyp 4 und 8) und 0,807 (für Genotyp 10 und 27). Die Clusteranalyse zeigte, dass das Dendrogramm aus vier Hauptgruppen besteht. Die Ergebnisse weisen darauf hin, dass die Genotypen 1, 3, 5, 15, 6, 11, 4, 8, 26, 29, 20, 24, 14, 25, 19, 23, 2 und 13 eng miteinander verwandt waren. Genotyp 10 unterschied sich am meisten von allen anderen untersuchten Genotypen; er bildet ein unabhängiges Cluster. Die ersten beiden Faktoren der Hauptkomponentenanalyse (principal component analysis, PCA) PC1 (15.06) und PC2 (10.98) hatten mit 10,18 % bzw. 7,42 % den höchsten Beitrag zur Varianz. Somit können Sorghum-Genotypen auf molekularer Ebene unter Verwendung molekularer Marker voneinander isoliert werden.

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

Similar content being viewed by others

References

  • Abdel-Mawgood AL (2012) DNA based techniques for studying genetic diversity. In: Genetic diversity in microorganisms. InTech, In

    Google Scholar 

  • Addinsoft SARL (2019) XLSTAT software, version 9.0. Addinsoft. Addinsoft SARL, Paris (https://www.xlstat.com/fr/)

    Google Scholar 

  • Adugna A (2014) Analysis of in situ diversity and population structure in Ethiopian cultivated Sorghum bicolor (L.) landraces using phenotypic traits and SSR markers. Springerplus 3:212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Agrama H, Tuinstra M (2003) Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. Afr J Biotechnol 2:334–340

    Article  CAS  Google Scholar 

  • Akhare AA, Sakhare S, Kulwal P, Dhumale D, Kharkar A (2008) RAPD profile studies in sorghum for identification of hybrids and their parents. Int J Integ Biol 3:18–24

    CAS  Google Scholar 

  • Aliyu B, Ng N, Fawole I (2000) Inheritance of pubescences in crosses between Cowpea (Vigna unquiculata (L) WAIP) and V. Rhomboidea Burtt. Davy. Nig J Genet 15:9–14

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Assar A, Uptmoor R, Abdelmula A, Salih M, Ordon F, Friedt W (2005) Genetic variation in sorghum germplasm from Sudan, ICRISAT, and USA assessed by simple sequence repeats (SSRs). Crop Sci 45:1636–1644

    Article  CAS  Google Scholar 

  • Ayana A, Bekele E, Bryngelsson T (2000) Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD). Hereditas 132:249–254

    Article  CAS  PubMed  Google Scholar 

  • Baenziger S (2014) SSR and SRAP markers-based genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Sudan. Int J Plant Breed Genet 8:89–99

    Article  CAS  Google Scholar 

  • Barnaud A, Deu M, Garine E, McKey D, Joly HI (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248

    Article  PubMed  Google Scholar 

  • Bashasab R, Kuruvinashetti MS (2007) Genetic variability of sorghum charcoal rot pathogen (Macrophomina phaseolina) assessed by random DNA markers. Plant Pathol J 23:45–50

    Article  Google Scholar 

  • Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ (2013) High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array. Plant Biottechnol J 11:1112–1125

    Article  CAS  Google Scholar 

  • Black WC, DuTeau NM, Puterka GJ, Nechols JR, Pettorini JM (1992) Use of the random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) to detect DNA polymorphisms in aphids (Homoptera: Aphididae). Bull Entomol Res 82:151–159

    Article  CAS  Google Scholar 

  • Carvalho VP, Ruas CF, Ferreira JM, Moreira RM, Ruas PM (2004) Genetic diversity among maize (Zea mays L.) landraces assessed by RAPD markers. Genet Mol Biol 27:228–236

    Article  CAS  Google Scholar 

  • Ganapathy K et al (2012) Genetic diversity revealed utility of SSR markers in classifying parental lines and elite genotypes of sorghum (Sorghum bicolor L. Moench). Aus J Crop Sci 6:1486

    Google Scholar 

  • Geleta N, Labuschagne MT, Viljoen CD (2006) Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodivers Conserv 15:3251–3265

    Article  Google Scholar 

  • GoP (2016) Economic survey of Pakistan, 2015–16. Government of Pakistan. Economic Affairs Division, Ministry of Finance, Economic Advisor’s Wing, Islamabad, Pakistan.

    Google Scholar 

  • Habib N, Tahir A, Ain Q (2013) Current situation and future outlook of sorghum area and production in Pakistan. Asian J Agric Rural Develop 3:283

    Google Scholar 

  • Hariprasanna K, Patil J (2015) Sorghum: origin, classification, biology and improvement. In: Sorghum molecular breeding. Springer, Berlin Heidelberg, pp 3–20

    Chapter  Google Scholar 

  • Janda K, Kristoufek L, Zilberman D (2012) Biofuels: policies and impacts. Agric Econ 58:372–386

    Google Scholar 

  • Kamala V, Bramel P, Sivaramakrishnan S, Chandra S, Kannan S, Harikrishna S, Rao DM (2006) Genetic and phenotypic diversity in downy-mildew-resistant sorghum (Sorghum bicolor (L.) Moench) germplasm. Genet Resour Crop Evol 53:1243–1253

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Lázaro A, Aguinagalde I (1998) Genetic diversity in Brassica oleracea L.(Cruciferae) and wild relatives (2 n= 18) using RAPD markers. Ann Bot 82:829–833

    Article  Google Scholar 

  • Mace ES et al (2008) DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genomics 9:26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mehmood S, Bashir A, Ahmad A, Akram Z, Jabeen N, Gulfraz M (2008) Molecular characterization of regional Sorghum bicolor varieties from Pakistan. Pak J Bot 40:2015–2021

    CAS  Google Scholar 

  • Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44:1236–1244

    Article  CAS  Google Scholar 

  • Mutegi E et al (2011) Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers. Theor Appl Genet 122:989–1004

    Article  CAS  PubMed  Google Scholar 

  • Nkongolo K, Nsapato L (2003) Genetic diversity in Sorghum bicolor (L.) Moench accessions from different ecogeographical regions in Malawi assessed with RAPDs. Genetic Resour Crop Evol 50:149–156

    Article  CAS  Google Scholar 

  • Olani Nagara G (2017) Genetic diversity analysis of sorghum [Sorghum bicolor (L.) Moench] races in Ethiopia using SSR markers. Addis Ababa University, Main Campus, Addis Ababa, Ethiopia

    Google Scholar 

  • Prakash SJ, Biji K, Gomez SM, Murthy KG, Babu RC (2006) Genetic diversity analysis of sorghum (Sorghum bicolor L. Moench) accessions using RAPD markers. Ind J Crop Sci 1:109–112

    Google Scholar 

  • Ramu P, Billot C, Rami J‑F, Senthilvel S, Upadhyaya H, Reddy LA, Hash CT (2013) Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor Appl Genet 126:2051–2064

    Article  CAS  PubMed  Google Scholar 

  • Ratnavathi C, Patil JV, Chavan U (2016) Sorghum biochemistry: an industrial perspective. Academic Press, Elsevier, UK

  • Raza A, Mehmood SS, Ashraf F, Khan RS (2019b) Genetic diversity analysis of Brassica species using PCR-based SSR markers. Gesunde Pflanz 71:1–7

    Article  CAS  Google Scholar 

  • Raza A, Razzaq A, Mehmood SS, Zou X, Zhang X, Lv Y, Xu J (2019a) Impact of climate change on crops adaptation and strategies to tackle its outcome: a review. Plants 8:34

    Article  PubMed Central  Google Scholar 

  • Raza A, Shaukat H, Ali Q, Habib M (2018) Assessment of RAPD markers to analyse the genetic diversity among Sunflower (Helianthus annuus L.) genotypes. Turk J Agric Food Sci Technol 6:107–111

    Google Scholar 

  • Reddy BV, Ashok Kumar A, Reddy SP (2008) Genetic improvement of sorghum in the semi-arid tropics. In: Sorghum Improvement in the New Millennium. International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India, pp. 105–123

    Google Scholar 

  • Shengwu H, Ovesna J, Kucera L, Kucera V, Vyvadilova M (2003) Evaluation of genetic diversity of Brassica napus germplasm from China and Europe assessed by RAPD markers. Plant Soil Environ 49:106–113

    Google Scholar 

  • Sifau M, Oduoye O, Oluwasanya O, Aladele S (2017) Assessment of genetic variability in sorghum accessions (Sorghum bicolor L. Moench) at the national centre for genetic resources and biotechnology, Ibadan. Nig J Appl Sci Environ Manag 21:1143–1147

    CAS  Google Scholar 

  • Sinha S, Kumaravadivel N, Eapen S (2014) RAPD Analysis in Sorghum [Sorghum bicolor (L.) Moench] Accessions. Int J Bio-resour Stress Manag 5:381–385

    Article  Google Scholar 

  • Tao Y, Manners J, Ludlow M, Henzell R (1993) DNA polymorphisms in grain sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 86:679–688

    Article  CAS  PubMed  Google Scholar 

  • Taramino G, Tarchini R, Ferrario S, Lee M (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theor Appl Genet 95:66–72

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Wang Y‑H, Gowda C, Sharma S (2013) Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. Theor Appl Genet 126:2003–2015

    Article  CAS  PubMed  Google Scholar 

  • 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  PubMed  Google Scholar 

  • Wang Y‑H, Upadhyaya HD, Kole C (2014) Genetics, genomics and breeding of sorghum. CRC Press, Taylor & Francis group, Boca Raton

    Book  Google Scholar 

  • Wiley EO, Lieberman BS (2011) Phylogenetics: theory and practice of phylogenetic systematics. John Wiley & Sons, New York

    Book  Google Scholar 

  • Yeh F, Yang R, Boyle T, Ye Z, Mao J (2002) Popgen 32, microsoftware windows based freeware for population genetic analysis. Molecular Biology and Biotechnology Center, Edmonton

    Google Scholar 

  • Yue Y, Singh H, Singh B, Mani S (2017) Torrefaction of sorghum biomass to improve fuel properties. Bioresour Technol 232:372–379

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors are grateful to all members of the Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan for their support and motivation to conduct this study.

Author information

Authors and Affiliations

  1. Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, 38040, Faisalabad, Pakistan

    Ali Raza, Farwa Ashraf, Sundas Saher Mehmood & Rao Sohail Ahmad Khan

  2. Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 430062, Wuhan, Hubei, China

    Ali Raza & Sundas Saher Mehmood

Authors
  1. Ali Raza
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Farwa Ashraf
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sundas Saher Mehmood
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rao Sohail Ahmad Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ali Raza.

Ethics declarations

Conflict of interest

A. Raza, F. Ashraf, S.S. Mehmood and R.S.A. Khan declare that they have no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Raza, A., Ashraf, F., Mehmood, S.S. et al. Evaluation of Genetic Diversity Among Exotic Sorghum (Sorghum bicolor L. Moench) Genotypes Through Molecular Based Analysis (RAPD-PCR). Gesunde Pflanzen 71, 187–196 (2019). https://doi.org/10.1007/s10343-019-00464-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10343-019-00464-8

Keywords

Schlüsselwörter

Search

Navigation