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

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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.

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Acknowledgments

The authors acknowledge the financial support provided by Director, NRRI to conduct this work.

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Authors and Affiliations

  1. National Rice Research Institute, Cuttack, 753006, Odisha, India

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

  2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China

    Meingsheng Chen

  3. Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA

    Rod A. Wing

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  1. Soham Ray
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Correspondence to Trilochan Mohapatra.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by B. Yang.

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Fig. S1

Comparative analysis of O. sativa and O. brachyantha genomes. A. Chromosome-size (in Mb) variations in O. sativa (red) and O. brachyantha (blue). B. Relative contribution (in percentage) of each chromosome to constitute the genomes of O. sativa (red) and O. brachyantha(blue). C. Gene content in each chromosome (expressed in terms of percentage of total gene content) of O. sativa (red) and O. brachyantha (red) (JPEG 792 kb)

Fig. S2

PCR analysis using genic STS and CAPS markers belonging to different chromosomes. Name of the markers mentioned at the top of the parentheses. Lanes: Os: Oryza sativa; Ob: Oryza brachyantha; 48: B2-48; M1: 100 bp ladder (Fermentas); M2: 1 kb ladder (Fermentas); M3: 50 bp ladder (Fermentas). (JPEG 1493 kb)

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Ray, S., Bose, L.K., Ray, J. et al. Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha . Mol Genet Genomics 291, 1783–1794 (2016). https://doi.org/10.1007/s00438-016-1214-z

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