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Patterns of subspecies genetic diversity among oilseed Brassica rapa as revealed by agro-morphological traits and SSR markers

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Abstract

Brassica rapa (2n = 20, AA genome) is an important oil yielding species of the family Brassicaceae and characterized by wide range of genetic and morphological subtypes suitable for cultivation under diverse agro-climatic regions of India. In this study, genetic diversity among three subspecies of B. rapa including yellow sarson, toria and outlier brown sarson was estimated using various agro-morphological traits and simple sequence repeat (SSR) markers. Maximum variability was recorded for siliqua angle (Coefficient of variation = 30.9%), followed by seeds/siliqua (CV = 18.8%), leaf length (CV = 10%) and plant height (CV = 16.8%). Principal component analysis explained more than 50% of the total observed morphological variability for first two components. Of the 107 SSR markers tested, 80 generated reproducible, clear and distinct amplicons of which, 65 (81.25%) were found polymorphic. The number of alleles at each locus ranged from 2 to 7, with an average of 3.03 alleles per marker. A total of 197 alleles were detected at 65 SSR loci with average PIC value of 0.457 and a mean resolving power of 3.04. Neighbor-Joining cluster analysis based on morphological traits and SSR markers separately classified all the 28 genotypes into five major groups. The population structure analysis resulted into three sub-populations with certain extent of admixture among the earlier established taxonomic sub-groups. Twenty-three unique alleles were detected in thirteen B. rapa varieties. The clustering analysis and principal coordinate analysis outlined the genetic relationships among different varieties belonging to the three subspecies of B. rapa. Genetically diverse genotypes as illustrated by score plots and from the clustering patterns brought out the wide range of diversity present among B. rapa genotypes and the underlying options available for selecting parental genotypes for hybridization and developing high yielding cultivars suitable for Indian conditions.

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Abbreviations

CV:

Coefficient of variation

PC:

Principal component

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

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Acknowledgements

We sincerely thank the Director, ICAR-DRMR, Bharatpur, Rajasthan for providing all the necessary facilities to carry out this work. The authors acknowledge Indian Council of Agricultural Research, New Delhi for funding this research.

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Authors and Affiliations

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

    Ajay Kumar Thakur, Kunwar Harendra Singh, Lal Singh & Dhiraj Singh

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

    Joghee Nanjundan

  3. Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110 012, India

    Yasin Jeshima Khan

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  1. Ajay Kumar Thakur
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  2. Kunwar Harendra Singh
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  3. Lal Singh
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  4. Joghee Nanjundan
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  5. Yasin Jeshima Khan
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  6. Dhiraj Singh
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Correspondence to Ajay Kumar Thakur.

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Thakur, A.K., Singh, K.H., Singh, L. et al. Patterns of subspecies genetic diversity among oilseed Brassica rapa as revealed by agro-morphological traits and SSR markers. J. Plant Biochem. Biotechnol. 26, 282–292 (2017). https://doi.org/10.1007/s13562-016-0390-6

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