Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha

Soham Ray, Lotan K. Bose, Joshitha Ray, Umakanta Ngangkham, Jawahar L. Katara, Sanghamitra Samantaray, Lambodar Behera, Mahender Anumalla, Onkar N. Singh, Meingsheng Chen, Rod A Wing, Trilochan Mohapatra

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.

Original languageEnglish (US)
Pages (from-to)1783-1794
Number of pages12
JournalMolecular Genetics and Genomics
Volume291
Issue number4
DOIs
StatePublished - Aug 1 2016

Keywords

  • Cleaved amplified polymorphic sequence (CAPS)
  • Cross-transferable co-dominant molecular markers
  • Monosomic alien addition line (MAAL)
  • Oryza brachyantha
  • Oryza sativa
  • Relative gene enrichment index (RGEI)
  • Sequence tagged microsatellite (STMS)
  • Sequence tagged sites (STS)
  • Simple sequence repeats (SSR)
  • Whole genome sequence (WGS)

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

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  • Cite this

    Ray, S., Bose, L. K., Ray, J., Ngangkham, U., Katara, J. L., Samantaray, S., Behera, L., Anumalla, M., Singh, O. N., Chen, M., Wing, R. A., & Mohapatra, T. (2016). Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha. Molecular Genetics and Genomics, 291(4), 1783-1794. https://doi.org/10.1007/s00438-016-1214-z