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Cloning of genome-specific repetitive DNA sequences in wild rice (O. rufipogon Griff.), and the development of Ty3-gypsy retrotransposon-based SSAP marker for distinguishing rice (O. sativa L.) indica and japonica subspecies

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Abstract

In the rice genome, insertions and eliminations of transposable elements have generated numerous transposon insertion polymorphisms (TIPs). Common wild rice (O. rufipogon Griff.), the ancestor of Asian cultivated rice (O. sativa L.), carries abundant genetic variations. To find subspecies-specific (SS) markers that can distinguish O. sativa ssp. indica and ssp. japonica, some long terminal repeat (LTR) sequences (sc1-14) of AA genome-specific RIRE retrotransposon were isolated from O. rufipogon genome. Sequences sc1 and sc12 were successfully utilized to develop the SS marker system based on retrotransposon inserted position polymorphisms. Twenty-two SS markers (ssi1-9, ssj1-13) were developed, where ssi1-9 are the indica-specific types, and ssj1-13 the japonica-specific types. The average accuracy of these markers in distinguishing the two subspecies is over 85%. SS marker ssj-10 can distinguish the two subspecies at 100% accuracy. Principal component analysis (PCA) showed that these markers could successfully distinguish indica from japonica varieties, regardless of their geographical origin.

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Abbreviations

SS marker:

Subspecies-specific markers

LTR:

Retrotransposon long terminal repeat

PCA:

Principal component analysis

RBIPs:

Retrotransposon-based insertion polymorphisms

ICD:

Integrase coding domain

TEs:

Transposable elements

RT:

Reverse transcriptase

RFLP:

Restriction fragment length polymorphism

RAPD:

Random amplified polymorphic DNA

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

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Acknowledgments

The research was supported by IAEA (12228/RO).

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Authors and Affiliations

  1. College of Bioscience and Biotechnology, Yangzhou University, 88 Daxue Road, 225009, Yangzhou, China

    Ning **ao, Yihuan Hong, Ruixiang **a, Chao Zhang, Yan Su & Jianmin Chen

  2. Lixiahe Region Agricultural Research Institute of Jiangsu, 225000, Yangzhou, China

    Ning **ao

  3. Department of Biology, Saint Mary’s University, Halifax, NS, Canada

    Genlou Sun

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  1. Ning **ao
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  2. Genlou Sun
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  3. Yihuan Hong
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  4. Ruixiang **a
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  6. Yan Su
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  7. Jianmin Chen
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Correspondence to Jianmin Chen.

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**ao, N., Sun, G., Hong, Y. et al. Cloning of genome-specific repetitive DNA sequences in wild rice (O. rufipogon Griff.), and the development of Ty3-gypsy retrotransposon-based SSAP marker for distinguishing rice (O. sativa L.) indica and japonica subspecies. Genet Resour Crop Evol 58, 1177–1186 (2011). https://doi.org/10.1007/s10722-010-9651-8

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