Scientists from the CAS Center for Excellence in Molecular Plant Sciences, Henan Agricultural University, Chinese Academy of Agricultural Sciences and Henan Institute of Science and Technology revealed that homologous transposable elements play important roles in maintaining the higher-order chromatin structure and subgenome stability. This work was published online in Genome biology entitled “Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression” on January 8^th.

Polyploidization is a major factor driving plant genome evolution and influencing crop breeding.  Common wheat (Triticum aestivum; AABBDD, 2n？=？6x？=？42)  is a widely cultivated hexaploid species that contains three similar but not identical subgenomes (A, B, D) evolved via two polyploidization events. The A, B, and D subgenomes are relatively independent in the cell. Meiotic pairing is limited to homologous chromosomes, and homoeologous chromosomes generally do not pair. But so far, there have been few reports on the exploration of the interaction mechanism within and between subgenomes.

Bainong Aikang 58 (AK58) is an excellent wheat variety cultivated by Professor Ru Zhengang of Henan Institute of Science and Technology after 30 years of breeding. It has a high and stable yield, considerable adaptability to environmental conditions, and resistance to biotic and abiotic stresses. Its breeding and application won the first prize of the National Science and Technology Progress Award in 2013. Since 2015, Henan Agricultural University, Chinese Academy of Agricultural Sciences, and Henan Institute of Science and Technology have jointly assembled the AK58 genome, the whole genome sequence has been released in China ahead of schedule. This article is one of the AK58 series of articles.

In this study, the authors first analyzed the AK58 3D chromatin structure and found that the chromatin of different subgenomes is relatively independent, and the interaction between chromosomes within the subgenome is much greater than the interaction between chromosomes between subgenomes. Combining with genome sequence comparison, they found that the interaction between chromosomes within the subgenome is closely related to the existence of subgenome-biased transposons, indicating that the interactions among the chromosomes of a subgenome are potentially mediated by subgenome-biased homologous transposable elements. The internal interaction of 1BL/ 1RS translocation chromosomes is apparent, but the interaction between 1RS and other wheat chromosomes is significantly reduced, which may be related to the special transposon composition. In summary, these results reveal that specific transposons are involved in maintaining the stability of the polyploid subgenome and the independence of introgressed chromosome segments, as well as the important role of specific transposons in stabilizing the polyploid subgenome (Model Figure). It is worth pointing out that different parameters can lead to completely different conclusions. Setting appropriate alignment parameters is crucial to the research results. It also hints that the influence of parameters on the results can be used in the analysis process to reveal the underlying molecular mechanisms.

This work was completed by the cooperation of Henan Agricultural University, Chinese Academy of Agricultural Sciences, Henan Institute of Science and Technology, and Center for Excellence in Molecular Plant Science of Chinese Academy of Sciences. Researcher Zhang Yijing of the CAS Center for Excellence in Molecular Plant Sciences, Researcher Jia Jizeng and Zhao Guangyao of the Chinese Academy of Agricultural Sciences, Professor Wang Daowen of Henan Agricultural University, and Professor Ru Zhengang of Henan Institute of Science and Technology are the co-corresponding authors of the paper. Jia Jizeng, PhD student Xie Yilin, Cheng Jingfei and Kong Chuizheng are the co-first authors of the paper. Professor Cui Dangqun of Henan Agricultural University and Professor Hu Tiezhu of Henan Institute of Science and Technology jointly participated in this work. This project was supported by National Key Research and Development Program of China, Construction Funds for the Collaborative Innovation Center of Henan Grain Crops under the National “2011” Plan of China, Strategic Priority Research Program of the Chinese Academy of Sciences.

Contact:
Dr. Yijing Zhang, Professor
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academic of Sciences
Tel: 86-21-54924206
Email: zhangyijing@cemps.ac.cn