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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

Title: Retrotransposon- and microsatellite sequence-associated genomic changes in early 2 generations of a newly synthesized allotetraploid cucumis × hytivus Chen & Kirkbride

Authors
item Jiang, Biao -
item Lou, Qunfeng -
item Wang, Dong -
item Wu, Zhiming -
item Zhang, Wamping -
item Mbira, Kere -
item Weng, Yiqun
item Chen, Jinfeng -

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 28, 2011
Publication Date: August 5, 2011
Citation: Jiang, B., Lou, Q., Wang, D., Wu, Z., Zhang, W., Mbira, K.G., Weng, Y., Chen, J. 2011. Retrotransposon- and microsatellite sequence-associated genomic changes in early 2 generations of a newly synthesized allotetraploid cucumis × hytivus Chen & Kirkbride. Plant Molecular Biology. Available: http://www.springerlink.com/content/2155j32p4h574585/export-citation/.

Interpretive Summary: Allopolyploidization is an important event in plant evolution, which can trigger genomic shock in allopolyploid genome through activation of transcription of retrotransposons. Two retrotransposon-based markers, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) and a microsatellite-based marker, inter-simple sequence repeat (ISSR) were employed to investigate genomic changes in the early generations of a newly synthesized allotetraploid Cucumis hytivus, which was derived from crossing between cultivated cucumber and its wild relative C. hystrix. Extensive genomic changes were observed, most of which involved the loss of parental DNA fragments and gain of novel fragments in the allotetraploid. Among the 28 fragments examined, 24 were lost while 4 were novel, suggesting that DNA sequence elimination is a relatively frequent event during polyploidization. Interestingly, of the 24 lost fragments, 18 were of C. hystrix origin, 4 were cucumber-specific, and the remaining 2 were shared by both species, implying that fragment loss may be correlated with haploid DNA content (genome size) of diploid parents. Most changes were observed in the first generation after polyploidization (S1) and stably inherited in the subsequent three generations (S2-S4), indicating that genomic changes may be a rapid driving force for the stabilization of allotetraploids. Sequence analysis of 11 of the 28 altered DNA fragments showed that genomic changes in the allotetraploid occurred in both coding and non-coding regions, which might suggest that retrotransposons inserted into genome randomly and had a genome-wide effect on the allotetraploid evolution. Fluorescence in situ hybridization (FISH) analysis revealed a unique distribution of retrotransposon and/or microsatellite flanking sequences in mitotic and meiotic chromosomes, where the preferential FISH signals occurred in the centromeric and telomeric regions, implying that these regions were the possible hotspots for genomic changes.

Technical Abstract: Allopolyploidization is considered an essential evolutionary process in plants that could trigger genomic shock in allopolyploid genome through activation of transcription of retrotransposons, which may be important in plant evolution. Two retrotransposon-based markers, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) and a microsatellite-based marker, inter-simple sequence repeat (ISSR) were employed to investigate genomic changes in the early generations of a newly synthesized allotetraploid Cucumis × hytivus Chen & Kirkbride (2n=4x=38) which was derived from crossing between cultivated cucumber C. sativus L. (2n = 2x = 14) and its wild relative C. hystrix Chakr. (2n = 2x = 24). Extensive genomic changes were observed, most of which involved the loss of parental DNA fragments and gain of novel fragments in the allotetraploid. Among the 28 fragments examined, 24 were lost while 4 were novel, suggesting that DNA sequence elimination is a relatively frequent event during polyploidization in Cucumis. Interestingly, of the 24 lost fragments, 18 were of C. hystrix origin, 4 were C. sativus-specific, and the remaining 2 were shared by both species, implying that fragment loss may be correlated with haploid DNA content (genome size) of diploid parents. Most changes were observed in the first generation after polyploidization (S1) and stably inherited in the subsequent three generations (S2-S4), indicating that genomic changes may be a rapid driving force for the stabilization of allotetraploids. Sequence analysis of 11 of the 28 altered DNA fragments showed that genomic changes in the allotetraploid occurred in both coding and non-coding regions, which might suggest that retrotransposons inserted into genome randomly and had a genome-wide effect on the allotetraploid evolution. Fluorescence in situ hybridization (FISH) analysis revealed a unique distribution of retrotransposon and/or microsatellite flanking sequences in mitotic and meiotic chromosomes, where the preferential FISH signals occurred in the centromeric and telomeric regions, implying that these regions were the possible hotspots for genomic changes.

Last Modified: 7/24/2014
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