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Identification, characterization, validation and cross-species amplification of genic-SSRs in Indian Mustard (Brassica juncea)

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Abstract

Brassica juncea is an economically important oilseed crop worldwide. It has limited genomic resources at present. We generated 47,962,057 expressed sequence reads which were assembled into 45,280 unigenes. A total of 4108 SSR loci (≥10 bp) were identified in these unigenes. Trinucleotide was the most frequent repeat unit (59.91 %) followed by di- (38.66 %), tetra - (0.71 %), hexa - (0.49 %) and pentanucleotide repeats (0.24 %). Primers were designed for 2863 SSR loci among which 460 were selected for primer synthesis. A total of 339 loci amplified successfully of which 134 (39.5 %) exhibited polymorphism among six B. juncea genotypes with PIC values ranging from 0.18 to 0.81. Further, 25 polymorphic SSRs were used for analysis of genetic variability in 25 genotypes of Brassicas and their wild relatives. Two to five alleles with PIC values 0.22–0.66 were detected at these loci. The dendrogram grouped the genotypes according to their known pedigree/systematic position.

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Acknowledgments

We sincerely acknowledge Director, ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur-321303, Rajasthan, India, for providing financial support and the facilities to carry out this research work. We also gratefully acknowledge Director, ICAR - Indian Agricultural Statistics Research Institute, New Delhi - 110 012, India, for providing computational facilities of Centre for Agricultural Bioinformatics, and Dr. S.R. Bhatt (Principal Scientist), ICAR- National Research Centre on Plant Biotechnology, New Delhi – 110012, India, for providing seed materials of wild species used in this study.

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Authors and Affiliations

  1. ICAR - Indian Institute of Agricultural Biotechnology, Ranchi, 834 010, Jharkhand, India

    Binay K. Singh & Kishor U Tribhuvan

  2. ICAR - Indian Agricultural Statistics Research Institute, New Delhi, 110 012, India

    Dwijesh C. Mishra, Sanjeev Kumar, K. K. Chaturvedi & Anil Rai

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

    Sushma Yadav, Supriya Ambawat, Era Vaidya, Arun Kumar, Sujith Kumar, Reema Rani, Prashant Yadav, P. K. Rai, V. V. Singh & Dhiraj Singh

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  1. Binay K. Singh
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Correspondence to Binay K. Singh.

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Supplementary Information Available

Supplementary information is included with this article.

Supplementary Table 1

Brassicas and wild relative species used for the validation of genic-SSRs (DOC 59 kb)

Supplementary Table 2

Particulars of 2863 genic-SSR loci (≥10 bp) in Brassica juncea for which primers were designed (XLS 629 kb)

Supplementary Table 3

Particulars of 339 validated genic-SSRs of Brassica juncea and predicted function of their genes (XLS 116 kb)

Supplementary Table 4

Particulars of 134 genic-SSR loci showing polymorphism among six Brassica juncea genotypes (XLS 37 kb)

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Singh, B.K., Mishra, D.C., Yadav, S. et al. Identification, characterization, validation and cross-species amplification of genic-SSRs in Indian Mustard (Brassica juncea). J. Plant Biochem. Biotechnol. 25, 410–420 (2016). https://doi.org/10.1007/s13562-016-0353-y

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