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Identification and characterization of chickpea genotypes for early flowering and higher seed germination through molecular markers

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Abstract

Background

Chickpea is the fourth most important legume crop contributing 15.42% to the total legume production and a rich source of proteins, minerals, and vitamins. Determination of genetic diversity of wild and elite cultivars coupled with early flowering and higher seed germination lines are quintessential for variety improvement.

Methods and results

In the present study, we have analyzed the genetic diversity, population structure, cross-species transferability, and allelic richness in 50 chickpea collections using 23 Inter simple sequence repeats (ISSR) markers. The observed parameters such as allele number varied from 3 to 16, range of allele size varied from 150 to 1600 bp and polymorphic information content (PIC) range lies in between 0.15 and 0.49. Dendrogram was constructed with ISSR marker genotypic data and classified 50 chickpea germplasms into groups I and II, where the accession P 74 − 1 is in group I and the rest are in group II. Dendrogram, Principal component analysis (PCA), dissimilarity matrix, and Bayesian model-based genetic clustering of 50 chickpea germplasms revealed that P 74 − 1 and P 1883 are very diverse chickpea accessions.

Conclusion

Based on genetic diversity analysis, 15 chickpea germplasm having been screened for early flowering and higher seed germination and found that the P 1857-1 and P 3971 have early flowering and higher seed germination percentage in comparison to P 1883 and other germplasm. These agronomic traits are essential for crop improvement and imply the potential of ISSR markers in crop improvement.

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References

  1. Merga B, Haji J (2019) Economic importance of chickpea: Production, value, and world trade. Cogent Food Agric 5(1):1615718

    Article  Google Scholar 

  2. Sethy NK, Choudhary S, Shokeen B, Bhatia S (2006) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112(2):347–357

    Article  CAS  Google Scholar 

  3. Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112(8):1416–1428

    Article  CAS  Google Scholar 

  4. Kudapa H, Garg V, Chitikineni A, Varshney RK (2018) The RNA-Seq‐based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio‐temporal changes associated with growth and development. Plant Cell Environ 41(9):2209–2225

    CAS  PubMed  Google Scholar 

  5. Kumar K, Bhattacharjee S, Vikuntapu PR, Sharma CL, Jayaswal D, Sharma R, Sundaram RM (2020) Climate change mitigation and adaptation through biotechnological interventions. In: Ch, Srinivasarao et al (eds) Climate change and Indian agriculture: challenges and adaptation strategies. ICAR-National Academy of Agricultural Research Management, Hyderabad, Telangana, India, pp 1–22

    Google Scholar 

  6. Mainkar PS, Manoj ML, Jayaswal D, Agarwal Y (2020) Identification and in-silico characterization of serpin genes in legumes genomes. Indian J Agri Sci 90(9):1763–1768

    CAS  Google Scholar 

  7. Varshney RK, Roorkiwal M, Sun S, Bajaj P, Chitikineni A, Thudi M, Liu X et al (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 599(7886):622–627

    Article  CAS  Google Scholar 

  8. Kumar SP, Susmita C, Agarwal DK, Pal G, Rai AK, Simal-Gandara J (2021) Assessment of genetic purity in rice using polymorphic SSR markers and its economic analysis with grow-out-test. Food Anal Methods 14(5):856–864

    Article  Google Scholar 

  9. 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, 2015: Article ID 431487

  10. Kumar SP, Susmita C, Sripathy KV, Agarwal DK, Pal G, Singh AN, Simal-Gandara J (2021) Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers. Mol Biol Rep 1–12

  11. Ahmad F (1999) Random amplified polymorphic DNA (RAPD) analysis reveals genetic relationships among the annual Cicer species. Theor Appl Genet 98(3–4):657–663

    Article  CAS  Google Scholar 

  12. Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genom 271(1):91–97

    Article  CAS  Google Scholar 

  13. Schulman AH (2007) Molecular markers to assess genetic diversity. Euphytica 158(3):313–321

    Article  CAS  Google Scholar 

  14. Gill-Langarica HR, Muruaga-Martínez JS, Vargas-Vázquez ML, Rosales-Serna R, Mayek-Pérez N (2011) Genetic diversity analysis of common beans based on molecular markers. Genet Mol Biol 34(4):595–605

    Article  CAS  Google Scholar 

  15. Mohammadi NZ, Sheidai M, Ghasemzadeh-Baraki S, Alishah O (2013) Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers. Genet Mol Res 12(1):256–269

    Article  Google Scholar 

  16. Bonman JM, Babiker EM, Cuesta-Marcos A, Esvelt‐Klos K, Brown‐Guedira G et al (2015) Genetic diversity among wheat accessions from the USDA national small grains collection. Crop Sci 55(3):1243–1253

    Article  Google Scholar 

  17. Mogga M, Sibiya J, Shimelis H, Lamo J, Yao N (2018) Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers. PLoS ONE 13(6):e0198012

    Article  Google Scholar 

  18. Elshafei AA, Afiah SAEA, Al-Doss AA, Ibrahim EI (2019) Morphological variability and genetic diversity of wheat genotypes grown on saline soil and identification of new promising molecular markers associated with salinity tolerance. J Plant Interact 14(1):564–571

    Article  CAS  Google Scholar 

  19. Delfini J, Moda-Cirino V, dos Santos Neto J, Ruas PM, Sant’Ana GC, Gepts P, Gonçalves LSA (2021) Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Sci Rep 11(1):1–12

    Article  Google Scholar 

  20. Abdelaziz SM, Medraoui L, Alami M, Pakhrou O, Makkaoui M, Boukhary AOMS, Filali-Maltouf A (2020) Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration. Sci Rep 10:14948

    Article  Google Scholar 

  21. Rao LS, Rani PU, Deshmukh PS, Kumar PA, Panguluri SK (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum L. Genet Resour Crop Evol 54(6):1235–1244

    Article  CAS  Google Scholar 

  22. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4326

    Article  CAS  Google Scholar 

  23. Perrier X, Jacquemoud-Collet JP (2006) DARwin software: Dissimilarity analysis and representation for windows. Website http://darwin.cirad.fr/darwin [accessed 1 March 2013]

  24. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67(1):170–181

    Article  CAS  Google Scholar 

  25. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: Dominant markers and null alleles. Mol Ecol Notes 7(4):574–578

    Article  CAS  Google Scholar 

  26. Howe EA, Sinha R, Schlauch D, Quackenbush J (2011) RNASeq analysis in MeV. Bioinformatics 27(22):3209–3210. https://doi.org/10.1093/bioinformatics/btr490.WOS. : 000296637500022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gowda B, Naik AK, Mathad C, Ganiger BS, Lokesh GY, Raghu BN (2018) An improved method of seed germination testing in Kabuli chickpea. Indian J Agric Res 52(4):456–459

    Google Scholar 

  28. Singh R, Sharma P, Varshney RK, Sharma SK, Singh NK (2008) Chickpea improvement: role of wild species and genetic markers. Biotechnol Genet Eng Rev 25(1):267–314

    Article  CAS  Google Scholar 

  29. Gautam AK, Gupta N, Bhadkariya R, Srivastava N, Bhagyawant SS (2016) Genetic diversity analysis in chickpea employing ISSR markers. Agrotechnology 5(2):2168–9881

    Google Scholar 

  30. Jayaswall K, Bhandawat A, Sharma H, Yadav VK, Mahajan V, Singh M (2019) Characterization of Allium germplasms for conservation and sustainable management using SSR markers. Indian J Tradit Knowl 18(1):193–199

    Google Scholar 

  31. Jayaswall K, Sharma H, Bhandawat A, Sagar R, Yadav VK, Sharma V, Singh M (2019) Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives. Genet Resour Crop Evol 66(7):1379–1388

    Article  CAS  Google Scholar 

  32. Chakraborty D, Wang T, Andre K, Konnert M, Lexer MJ, Matulla C, Schueler S (2016) Adapting Douglas-fir forestry in Central Europe: Evaluation, application, and uncertainty analysis of a genetically based model. Eur J For Res 135(5):919–936

    Article  Google Scholar 

  33. Wei X, Jackson PA, McIntyre CL, Aitken KS, Croft B (2006) Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor Appl Genet 114(1):155–164

    Article  CAS  Google Scholar 

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Acknowledgements

Financial assistance for research by Indian Council of Agricultural Research-Indian Institute of Seed Sciences, Mau is gratefully acknowledged. Further ICRISAT, Hyderabad is gratefully acknowledged for providing chickpea germplasms.

Funding

No funding was received for the current research.

Author information

Authors and Affiliations

  1. ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India

    Garima Yadav, Deepanshu Jayaswal, Kuldip Jayaswall, ArvindNath Singh, Abhishek Kumar Rai, Ashutosh Kumar & Sanjay Kumar

  2. Department of Botany, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India

    Kuldip Jayaswall

  3. Agri-Biotechnology Department, National Agri-Food Biotechnology Institute, 140507, Mohali, Punjab, India

    Abhishek Bhandawat

  4. ICAR- National Bureau of Agriculturally Important Microorganisms, 275103, Mau, Uttar Pradesh, India

    Jyotsana Tilgam & Rachna Chaturvedi

  5. Amity Institute of Biotechnology, Amity University, 226028, Lucknow, Uttar Pradesh, India

    Jyotsana Tilgam & Rachna Chaturvedi

  6. ICAR- Directorate of Floricultural Research, 411005, Pune, Maharashtra, India

    S. P. Jeevan Kumar

Authors
  1. Garima Yadav
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  2. Deepanshu Jayaswal
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  3. Kuldip Jayaswall
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  4. Abhishek Bhandawat
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  5. ArvindNath Singh
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  6. Jyotsana Tilgam
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  7. Abhishek Kumar Rai
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  8. Rachna Chaturvedi
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  9. Ashutosh Kumar
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  10. Sanjay Kumar
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  11. S. P. Jeevan Kumar
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Contributions

DJ and KJ Conceived and designed the study. GY, AK, and JT performed the experiments. ANS, AK, RC, AK, SK, and JK helped in the preparation of the draft manuscript. SK and JK performed the critical revision of the article. SPJK edited the final draft. All authors approved the final version of the article.

Corresponding authors

Correspondence to Deepanshu Jayaswal or S. P. Jeevan Kumar.

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The authors declare that they have no conflict of interest.

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

Pre-print Submission

The pre-print of the research article has been submitted to bioRxiv platform with the DOI (https://doi.org/10.1101/2021.08.04.455107) and made available under CC-BY 4.0 International license.

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Yadav, G., Jayaswal, D., Jayaswall, K. et al. Identification and characterization of chickpea genotypes for early flowering and higher seed germination through molecular markers. Mol Biol Rep 49, 6181–6188 (2022). https://doi.org/10.1007/s11033-022-07410-4

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  • DOI: https://doi.org/10.1007/s11033-022-07410-4

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