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ARS Home » Pacific West Area » Logan, Utah » Forage and Range Research » Research » Publications at this Location » Publication #338218
Title: The diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation

Author
item ZHANG, YINGXIN - Chinese Academy Of Agricultural Sciences
item FAN, CHENGMING - Chinese Academy Of Agricultural Sciences
item CHEN, YUHONG - Chinese Academy Of Agricultural Sciences
item Wang, Richard
item ZHANG, XIANGQI - Chinese Academy Of Agricultural Sciences
item HAN, FANGPU - Chinese Academy Of Agricultural Sciences
item HU, ZANMIN - Chinese Academy Of Agricultural Sciences

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2017
Publication Date: 10/4/2017
Citation: Zhang, Y., Fan, C., Chen, Y., Wang, R., Zhang, X., Han, F., Hu, Z. 2017. The diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation. Frontiers in Plant Science. 8:1706. https://doi.org/10.3389/fpls.2017.01706.
DOI: https://doi.org/10.3389/fpls.2017.01706

Interpretive Summary: The tribe Triticeae contains annual cereal crop species and perennial forage crop species made of a diverse of genetic compositions scientifically called genomes. Chromosomes of different genomes differ in structural features and DNA sequences. Characteristics of DNA sequences are important in maintaining chromosome integrity and stability during cell division in reproductive organs. It is highly desirable to understand similarities and differences between two genomes so that we can foresee what could be done to manipulate the species possessing these genomes. We isolated and studied the characteristics of transposable elements in rye genome (designated as R) in comparison to those in common wheat genomes (as A, B, and D). Findings in this study enhance our knowledge on the structure and organization of chromosomes in rye, which in turn can aid in the wheat improvement efforts.

Technical Abstract: The rye genome features a high percentage of repetitive elements, especially transposable elements (TEs). However, studies about the constitution and organization of TEs on rye chromosomes are limited. In this study, 97 unique TE segments were isolated and characterized; 50 TE segmemts showed varying degrees of homology to the previously identified TEs (>80%), and 47 TE segments are defined as new. All the TEs are class I elements, except for six class II elements. Among these TEs, 68 are rye genome-specific, of which 57 are dispersed on the chromosome arms, 7 are mainly distributed on the pericentromeric regions and only 4 are located at the centromeric regions. Of the TEs, 29 hybridized to both wheat and rye chromosomes. Our results indicated that the retrotransposons compose the majority of the isolated TEs, which were localized from the distal to centromeric regions; some centromere-located Ty3/gypsy elements may play an important role in the establishment of functional centromeres, and the pericentromeric regions are enriched with more Ty1/copia elements and SINE elements compared with the centromeric regions. These findings provide new insights into the constitution and distribution of TEs in the rye genome, which will help to understand their structure and organization.