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Development of a set of SSR markers for characterization of Indian mustard germplasm and varieties

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Abstract

Simple sequence repeat (SSR) markers can serve as an important tool for characterization and genetic diversity evaluation in Indian mustard germplasm and varieties. For DNA fingerprinting of various Indian mustard varieties, it is necessary that a common set of SSRs be used by various laboratories so that the developed genetic profiles of various genotypes can be compared with one another. In this study, we evaluated the polymorphic potential of 350 SSR markers to derive a set of SSR markers for characterization of Indian mustard germplasm and varieties. Out of a total of 350 SSR markers evaluated, 310 (88.57%) SSRs produced polymorphic amplicons, while remaining 40 (11.43%) SSRs resulted into monomorphic products. The allele number varied from 2 to 7 with 3.22 average number of alleles per locus. Polymorphism information content (PIC) value ranged from 0.24 (Ol09A01) to 0.75 (nia-m141a) with an average PIC value of 0.40 per locus. A total of 95 (31%) SSR markers evaluated were having PIC values more than the average PIC value, which constitute the representative set of SSR markers. Unweighted pair group method with arithmetic averages (UPGMA)-dendrogram grouped all the 46 genotypes into two main clusters, while STRUCTURE analysis formed three subpopulations having admixture of alleles. This SSR marker set will facilitate systematic characterization and classification of various Indian mustard germplasm accessions and varieties.

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Abbreviations

SSR:

Simple sequence repeat

ISSR:

Inter simple sequence repeat

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

AFLP:

Amplified fragment length polymorphism

PIC:

Polymorphic information content

UPGMA:

Unweighted pair group method with arithmetic averages

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Acknowledgements

Authors are thankful to the Science & Engineering Research Board (SERB), New Delhi for providing funding for this work.

Funding

Funds for this research work was provided under the ‘Start-up Research Grant No. SB/YS/LS-86/2014’ received by AKT from Science & Engineering Research Board (SERB), New Delhi.

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Authors and Affiliations

  1. Manipal University Jaipur, Jaipur, Rajasthan, 303 007, India

    Lal Singh & Rohit Jain

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

    J. Nanjundan

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

    K. H. Singh, Deepika Sharma, Nehanjali Parmar & Ajay Kumar Thakur

  4. ICAR-National Institute for Plant Biotechnology, New Delhi, 110 012, India

    Anshul Watts

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  1. Lal Singh
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  4. Deepika Sharma
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Correspondence to Ajay Kumar Thakur.

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13562_2021_737_MOESM1_ESM.tif

Fig. S4 Principal co-ordinate analysis (PCoA) of 46 Indian mustard accessions base on selected 95 microsatellite loci (TIF 150 kb)

13562_2021_737_MOESM2_ESM.tif

Fig. S1 UPGMA dendrogram depicting the genetic inter-relationship among different accessions of Indian mustard based on the allelic data of selected set of 95 SSR markers (TIF 148 kb)

13562_2021_737_MOESM3_ESM.tif

Fig. S2 Population genetic structure and relationships among 46 Indian mustard accessions based on the allelic data of selected set of 95 SSR markers. Values of delK with its modal value detecting a true K of three groups (K = 3) (TIF 106 kb)

13562_2021_737_MOESM4_ESM.tif

Fig.S3 The three subgroups inferred from the STRUCTURE analysis using the allelic data of selected 95 microsatellite loci (TIF 216 kb)

Supplementary file5 (DOCX 36 kb)

Supplementary file6 (DOCX 37 kb)

Supplementary file7 (DOCX 22 kb)

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Singh, L., Nanjundan, J., Singh, K.H. et al. Development of a set of SSR markers for characterization of Indian mustard germplasm and varieties. J. Plant Biochem. Biotechnol. 31, 581–591 (2022). https://doi.org/10.1007/s13562-021-00737-2

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