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Development and validation of donor-specific STS markers for tracking alien introgressions into Brassica juncea (L.) Czern

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Abstract

Alien introgressions into crop plants rely on phenotypic evaluation. Employing molecular markers could greatly accelerate this and help discover new alleles/QTLs. We report here a new strategy to develop markers for tracking introgression using genome survey sequence. We demonstrate this using an advanced backcross population of Brassica juncea involving the wild species Diplotaxis erucoides. To develop D. erucoides-specific markers, 72 million single end reads were obtained using Ion-Torrent platform. Quality reads (67.6 million) were checked against Brassica database and the redundant reads were eliminated. De novo assembly of the remaining 14.6 million reads gave 3895 contigs (> 1 kb), which were used to design 101 donor-specific (DS) STS markers. Of these, 89 markers showed polymorphism between D. erucoides and B. juncea. Genotyping of 90 randomly picked plants with 31 donor-specific STS markers detected 22 plants containing 17 markers. Alien introgression was also detected in eight of the 22 lines displaying phenotypes deviating from B. juncea parent. The marker DSSTS 70 was found in six of the nine lines showing glossy leaf suggesting its association with the trait. This is the first study demonstrating the use of molecular markers for implementing reverse genetics approach for alien introgression into crop plants.

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Acknowledgements

We thank NPTC-ICAR, Government of India for funding this work. We are grateful to Dr. T. R. Sharma, Project Director, NRCPB for access to CLC Genomics Workbench V7.5.1 software.

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Authors and Affiliations

  1. ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110012, India

    Naresh Vasupalli, Mahesh Rao, Rohit Chamola, Ramcharan Bhattacharya & Shripad Ramachandra Bhat

  2. Department of Genetics and Plant Breeding, College of Agriculture, GBPUA&T, Pantnagar, Uttarakhand, 263153, India

    Usha Pant

Authors
  1. Naresh Vasupalli
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  2. Mahesh Rao
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  3. Rohit Chamola
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  4. Usha Pant
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  5. Ramcharan Bhattacharya
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  6. Shripad Ramachandra Bhat
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Contributions

NV- bioinformatics, design of primers, laboratory work and draft manuscript preparation; RC, MR and UP- population development, maintenance and phenotyping; RB- design of experiments and data analysis; SRB- conceptualization and design of experiments, development of basic material, phenotyping, data analysis, manuscript preparation and finalization.

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Correspondence to Shripad Ramachandra Bhat.

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Key Message

The study demonstrates for the first time an efficient reverse genetics approach for alien gene introgression into cultivated species.

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Vasupalli, N., Rao, M., Chamola, R. et al. Development and validation of donor-specific STS markers for tracking alien introgressions into Brassica juncea (L.) Czern. Mol Breeding 37, 110 (2017). https://doi.org/10.1007/s11032-017-0714-9

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  • DOI: https://doi.org/10.1007/s11032-017-0714-9

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