Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication afte
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RESEARCH ARTICLE
Open Access
Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization Yan Zhao1†, Luhao Dong1†, Conghui Jiang2†, Xueqiang Wang2†, Jianyin Xie2, Muhammad Abdul Rehman Rashid3, Yanhe Liu1, Mengyao Li1, Zhimu Bu1, Hongwei Wang1, Xin Ma1, Silong Sun1, Xiaoqian Wang1, Cunyao Bo1, Tingting Zhou1 and Lingrang Kong1*
Abstract Background: The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individualstrand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Results: Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. (Continued on next page)
* Correspondence: [email protected] † Yan Zhao, Luhao Dong, Conghui Jiang and Xueqiang Wang contributed equally to this work. 1 State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, Shandong, People’s Republic of China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproducti
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