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Alipour A, Tsuchimoto S, Sakai H, et al. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels. 2013;6(1):129doi: 10.1186/1754-6834-6-129.
Alipour, A., Tsuchimoto, S., Sakai, H., Ohmido, N., & Fukui, K. (2013). Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnology for biofuels, 6(1), 129. https://doi.org/10.1186/1754-6834-6-129
Alipour, Atefeh, et al. "Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L." Biotechnology for biofuels vol. 6,1 (2013): 129. doi: https://doi.org/10.1186/1754-6834-6-129
Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels. 2013 Sep 10;6(1):129. doi: 10.1186/1754-6834-6-129. PMID: 24020916; PMCID: PMC3852365.
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Biotechnol Biofuels. 2013 Sep 10;6(1):129. doi: 10.1186/1754-6834-6-129.

Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

Biotechnology for biofuels

Atefeh Alipour, Suguru Tsuchimoto, Hiroe Sakai, Nobuko Ohmido, Kiichi Fukui

Affiliations

  1. Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. [email protected].

PMID: 24020916 PMCID: PMC3852365 DOI: 10.1186/1754-6834-6-129

Abstract

BACKGROUND: Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop.

RESULTS: In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions.

CONCLUSION: This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA markers. Distinct dynamics of individual copia-type families, feasibility of a retrotransposon-based insertion polymorphism marker system in examining genetic variability, and approaches for the development of breeding strategies in jatropha using copia-type retrotransposons are discussed.

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