SpringerLink
Log in

Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

  • Original Article
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant for its genetic improvement. In the present study, we investigated genetic diversity and population structure among a panel of 145 Indian mustard germplasm accessions using 11 agro-morphological traits and 182 SSR markers. The result of variance analysis exhibited significant differences among the tested genotypes inferring the presence of a high degree of variability. The phenotypic coefficient of variation for seed yield (CV = 28.26%) was the highest among all the studied traits followed by biological yield (CV = 25.72%). Days to maturity ranged from 130 to 141 days (CV = 1.88%), which was the minimum variation exhibited by Indian mustard genotypes. Out of 235 SSR primer pairs evaluated, 182 (77.45%) SSRs resulted in polymorphic amplicons, while 53 (22.55%) SSRs amplified monomorphic loci. Allele number varied from 2 to 7 with 3.97 average number of alleles per SSR marker. PIC value varied from 0.03 (SJ1668I) to 0.71 (EJU4) with an average value of 0.39 per SSR marker. Gene diversity in the present study ranged from 0.03 (SJ1668I) to 0.75 (EJU4) with an average value of 0.46. Cluster analysis using morphological traits and SSR markers grouped all 145 accessions into two major clusters each, respectively. Population structure analysis grouped all the genotypes into three subpopulations with varying degrees of admixture genotypes. Analysis of molecular variance inferred that 88% of the total variation resides within the groups. The resulting estimates of genetic diversity and population structure may be useful for the effective management of Indian mustard germplasm resources and for future mustard breeding programs.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Availability of Data and Materials

All the data and plant material are available with the corresponding author (AKT).

References

  • Banga S, Kumar PR, Bhajan R, Singh D, Banga SS (2015) Brassica oilseeds: breeding and management. In Kumar A, Banga SS, Meena PD, Kumar PR (eds) CAB International, Oxfordshire, UK, 11–41

  • Burton WA, Ripley VL, Potts DA, Salisbury PA (2004) Assessment of genetic diversity in selected breeding lines and cultivars of canola quality Brassica juncea and their implications for canola breeding. Euphytica 136:181–192

    Article  CAS  Google Scholar 

  • Chauhan JS, Singh KH, Singh VV, Kumar S (2011) Hundred years of rapeseed-mustard breeding in India: accomplishments and future strategies. Indian J Agri Sci 81(12):1093–1109

    Google Scholar 

  • Earl DA, vonHoldt BM (2012) Structure harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7

    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. https://doi.org/10.1111/j.1365-294X.2005.02553.x

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    Article  CAS  Google Scholar 

  • Ghosh S, Mazumder M, Mondal B, Mukherjee A, De A, Bose R, Das S, Bhattacharyya S, Basu D (2019) Morphological and SSR marker-based genetic diversity analysis of Indian mustard (Brassica juncea L.) differing in Alternaria brassicicola tolerance. Euphytica 215:206. https://doi.org/10.1007/s10681-019-2523-1

    Article  CAS  Google Scholar 

  • Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int. https://doi.org/10.1155/2015/431487

    Article  PubMed  PubMed Central  Google Scholar 

  • Govt of India (2018) Agricultural statistics at a glance. Directorate of Economics and Statistics, Department of Agriculture and Cooperation, Ministry of Agriculture, Govt. of India, New Delhi. http://cands.daenet.nic.in/PDF. Accessed 21 Jul 2021

  • Habib MA, Manmohan Sharma P, Salgotra RK, Kiran U (2019) Analysis of allelic differentiation and prediction of suitable parents among Brassica juncea L genotypes using microsatellite markers. Int J Curr Microbiol App Sci 8(6):3071–3081

    Article  Google Scholar 

  • Huangfu C, Song X, Qiang SG (2009) ISSR variation within and among wild Brassica juncea populations: implication for herbicide resistance evolution. Genet Resour Crop Evol 56:913–924

    Article  CAS  Google Scholar 

  • Ignjatovic-Micic D, Ristic D, Babic V, Andjelkovic V, Vancetovic J (2015) A simple SSR analysis for genetic diversity estimation of maize landraces. Genetika 47:53–62

    Article  Google Scholar 

  • Jain A, Bhatia S, Banga SS, Prakash S, Lakshmikumaran M (1994) Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis. Theor Appl Genet 88:116–122

    Article  CAS  Google Scholar 

  • Kaur R, Sharma AK, Rani R, Mawlong I, Rai PK (2019) Medicinal qualities of mustard oil and its role in human health against chronic diseases: A review. Asian J Dairy Food Res 382:98–104

    Google Scholar 

  • Khan MA, Rabbani MA, Muhammad M, Ajmal SK, Malik MA (2008) Assessment of genetic variation within Indian mustard germplasm using RAPD markers. J Interg Plant Biol 50:385–392

    Article  CAS  Google Scholar 

  • Kumar N, Avtar R, Ahlawat N, Rakesh (2020) Molecular diversity analysis using simple sequence repeats (SSRs) in ‘A’ and ‘R’ lines of Ogura CMS system in Indian mustard. Int J Chem Stud 8(4):1276-1282

  • Kumari A, Kumari A (2018) Studies on genetic diversity in Indian mustard (Brassica Juncea Czern & Coss) for morphological characters under changed climate in the mid-hills of Himalayas. Pharma Innov J 7(7):290–296

    Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  Google Scholar 

  • Mir JI, Islam I, Kudesia R (2015) Evaluation of genetic diversity in Brassica juncea (L.) using protein profiling and molecular marker (RFLP). Int J Plant Breeding Genet 9(2):77–85

    Article  CAS  Google Scholar 

  • Pandey S, Ansari WA, Pandey M, Singh B (2018) Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers. Physiol Mol Biol Plants 24(1):135–146. https://doi.org/10.1007/s12298-017-0489-9

    Article  CAS  PubMed  Google Scholar 

  • 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. https://doi.org/10.1093/bioinformatics/bts460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin. Accessed 21 Jul 2021

  • Pritchard JK, Wen W (2003) Documentation for the structure software, version 2.3.4. Department of Human Genetics, University of Chicago, Chicago. http://pritch.bsd.uchicago.edu/software. Accessed 21 Jul 2021

  • Qi X, Yang J, Zhang M (2008) AFLP-based genetic diversity assessment among Chinese vegetable mustard (Brassica juncea (L.) Czern.). Genet Resour Crop Evol 55:705–711

    Article  CAS  Google Scholar 

  • Rabbani MA, Iwabuchi A, Murakami Y, Suzuki T, Takayanagi K (1998) Genetic diversity in mustard (Brassica juncea L.) germplasm from Pakistan as determined by RAPDs. Euphytica 103(2):235–242

    Article  CAS  Google Scholar 

  • Saini N, Rai AN (2020) Molecular analysis of diversity present in Brassica juncea genotypes with the help of SSR markers. Int J Curr Microbiol App Sci 9(07):2987–2993. https://doi.org/10.20546/ijcmas.2020.907.352

  • Santos RC, Pires JL, Correa RX (2012) Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma species. Genet Resour Crop Evol 59:327–345

    Article  Google Scholar 

  • Sharma D, Nanjundan J, Singh L, Singh SP, Parmar N, SujithKumar MS, Singh KH, Mishra AK, Singh R, Verma KS, Thakur AK (2020) Genetic diversity in leafy mustard (Brassica juncea var. rugosa) as revealed by agro-morphological traits and SSR markers. Physiol Mol Biol Plants. https://doi.org/10.1007/s12298-020-00883-2

    Article  PubMed  PubMed Central  Google Scholar 

  • Shyam C, Tripathi MK, Tiwari S, Tripathi N, Ahuja A (2020) Molecular characterization and identification of Brassica genotype(s) for low and high erucic acid content using SSR markers. Global J BioSci Biotechnol 9(2):56–66

    Google Scholar 

  • Singh BK, Thakur AK, Tiwari SK, Siddiqui SA, Singh VV, Rai PK (2012) Transferability of Brassica-derived microsatellites to related genera and their implications for phylogenetic analysis. Natl Acad Sci Lett 35(1):37–44

    Article  Google Scholar 

  • Singh KH, Misra AK, Kumar A (2006) Draft guidelines to conduct the tests for distinctness, uniformity and stability in rapeseed and mustard (Brassica). National Research Centre on Rapeseed Mustard, Bharatpur, Rajasthan, India

  • Singh KH, Shakya R, Thakur AK, Chauhan DK, Chauhan JS (2013) Assessment of genetic diversity in Indian mustard (Brassica juncea L Czern & Coss) using morphological traits and RAPD markers. Natl Acad Sci Lett 36(4):419–427

    Article  CAS  Google Scholar 

  • Singh VK, Avtar R, Mahavir NK, Manjeet RK, Rathore V (2020) Assessment of genetic relationship among diverse Indian mustard (Brassica juncea L.) genotypes using XLSTAT. Electronic J Plant Breeding 11(2):674–680. https://doi.org/10.37992/2020.1102.109

  • Srivastava A, Gupta V, Pental D, Pradhan AK (2001) AFLP based genetic diversity assessment amongst agronomically important natural and some newly synthesized lines of Brassica juncea. Theor Appl Genet 102:193–199

    Article  CAS  Google Scholar 

  • Sudan J, Khajuria P, Gupta SK, Singh R (2016) Analysis of molecular diversity in Indian and exotic genotypes of Brassica juncea using SSR markers. Indian J Genet 76(3):361–364. https://doi.org/10.5958/0975-6906.2016.00054.7

    Article  CAS  Google Scholar 

  • Tahira R, Ihsan-Ullah, Saleem M (2013) Evaluation of genetic diversity of raya (Brassica juncea) through RAPD markers. Int J Agric Biol 15:1163–1168

  • Tamanna A, Khan AU (2005) Map** and analysis of simple sequence repeats in the Arabidopsis thaliana genome. Bioinformation 1:64–68

    Article  Google Scholar 

  • Thakur AK, Parmar N, Singh KH, Nanjundan J (2020a) Current achievements and future prospects of genetic engineering in Indian mustard (Brassica juncea L. Czern & Coss.). Planta 252:56. https://doi.org/10.1007/s00425-020-03461-8

    Article  CAS  PubMed  Google Scholar 

  • Thakur AK, Singh BK, Verma V, Chauhan JS (2013) Direct organogenesis in Brassica juncea var. NRCDR-2 and analysis of genetic uniformity using RAPD markers. Natl Acad Sci Lett 36:403–409

    Article  CAS  Google Scholar 

  • Thakur AK, Singh KH, Lal S, Nanjundan J, Yasin JK, Singh D (2018) SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids. Hereditas 155:6. https://doi.org/10.1186/s41065-017-0041-5

    Article  PubMed  Google Scholar 

  • Thakur AK, Singh KH, Parmar N, Sharma D, Mishra DC, Singh L, Nanjundan J, Yadav S (2020b) Population structure and genetic diversity as revealed by SSR markers in Ethiopian mustard (Brassica carinata A. Braun): a potential edible and industrially important oilseed crop. Genet Resour Crop Evol. https://doi.org/10.1007/s10722-020-00988-3

    Article  Google Scholar 

  • Thakur AK, Singh KH, Singh L, Nanjundan J, Khan YJ, Singh D (2017) Patterns of subspecies genetic diversity among oilseed Brassica rapa as revealed by agro-morphological traits and SSR markers. J Plant Biochem Biotechnol 26(3):282–292

    Article  CAS  Google Scholar 

  • Thakur AK, Singh KH, Singh L, Nanjundan J, Rana MK, Singh D (2015) Transferability of SSR markers of Brassica species to some popular varieties of Brassica juncea. Proc Natl Acad Sci India Sect B Biol Sci 85(4):1001–1010. https://doi.org/10.1007/s40011-014-0486

    Article  CAS  Google Scholar 

  • Vinu V, Singh N, Vasodev S, Yadav DK, Kumar S, Naresh S, Bhat SR, Prabhu KV (2013) Assessment of genetic diversity in Brassica juncea (Brassicaceae) genotypes using phenotypic differences and SSR markers. Rev Biol Trop 61(4):1919–1934

    CAS  PubMed  Google Scholar 

  • Yadav M, Rana JS (2012) ISSR markers assisted studies on genetic diversity in Brassica juncea. Int J Pharma Bio Sci 3(2):402

    CAS  Google Scholar 

  • Yadava DK, Parida SK, Dwivedi SK, Varshney A, Ghazi IA, Sujata V, Mohapatra T (2009) Cross-transferability and polymorphic potential of genomic STMS markers of Brassica Species. J Plant Biochem Biotechnol 18(1):29–36

    Article  CAS  Google Scholar 

  • Yang et al (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48:1225–1232. https://doi.org/10.1038/ng.3657

    Article  CAS  PubMed  Google Scholar 

  • Yousuf M, Bhat TM, Kudesia R (2013) Comparative genetic diversity studies in mustard (Brassica juncea) varieties using randomly amplified polymorphic DNA (RAPD) analysis. African J Biotechnol 12(22):3430–3434

    CAS  Google Scholar 

  • Zhu S, Zhang X, Liu Q, Luo T, Tang Z, Zhou Y (2018) The genetic diversity and relationships of cauliflower (Brassica oleracea var. botrytis) inbred lines assessed by using SSR markers. PLoS ONE 13(12):e0208551. https://doi.org/10.1371/journal.pone.0208551

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are thankful to the Director, ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan, for providing funding to carry out this research work. The authors are also thankful to Dr. S.S. Banga, National Professor, PAU, Ludhiana, Punjab, for providing B-genome-specific SSR markers.

Author information

Authors and Affiliations

  1. Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302 006, India

    Deepika Sharma & Kumar Sambhav Verma

  2. ICAR-Indian Agricultural Research Institute-Regional Station, Wellington, 643 231, Tamilnadu, India

    J. Nanjundan

  3. ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, 321 303, Rajasthan, India

    Lal Singh, Nehanjali Parmar, K. H. Singh & Ajay Kumar Thakur

Authors
  1. Deepika Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. Nanjundan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lal Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nehanjali Parmar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. H. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kumar Sambhav Verma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ajay Kumar Thakur
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

AKT, KHS, and JN conceived the idea, developed the work plan, and edited the manuscript. DS, LS, and NP performed the field and lab experiments. KSV helped in the manuscript writing. The authors read and approved the final manuscript.

Corresponding author

Correspondence to Ajay Kumar Thakur.

Ethics declarations

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of Interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

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

Key Message

Genetic diversity in a panel of 145 Indian mustard germplasm accessions was analyzed using agro-morphological traits and SSR markers, which has helped in the identification of genetically diverse lines to be used as donors in future breeding programs aimed at Indian mustard genetic improvement.

Supplementary Information

Below is the link to the electronic supplementary material.

11105_2022_1339_MOESM1_ESM.tiff

Supplementary file1 (TIFF 64 kb). Fig. S1 Graph showing the number of subpopulations in Indian mustard germplasm panel based on Structure analysis

Supplementary file2 (DOCX 34 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sharma, D., Nanjundan, J., Singh, L. et al. Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers. Plant Mol Biol Rep 40, 579–594 (2022). https://doi.org/10.1007/s11105-022-01339-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-022-01339-5

Keywords

Search

Navigation