title: Evolution of the BBAA component of bread wheat during its history at the allohexaploid level.
abstract: Subgenome integrity in bread wheat (Triticum aestivum; BBAADD) makes possible the extraction of its BBAA component to restitute a novel plant type. The availability of such a ploidy-reversed wheat (extracted tetraploid wheat [ETW]) provides a unique opportunity to address whether and to what extent the BBAA component of bread wheat has been modified in phenotype, karyotype, and gene expression during its evolutionary history at the allohexaploid level. We report here that ETW was anomalous in multiple phenotypic traits but maintained a stable karyotype. Microarray-based transcriptome profiling identified a large number of differentially expressed genes between ETW and natural tetraploid wheat (Triticum turgidum), and the ETW-downregulated genes were enriched for distinct Gene Ontology categories. Quantitative RT-PCR analysis showed that gene expression differences between ETW and a set of diverse durum wheat (T. turgidum subsp durum) cultivars were distinct from those characterizing tetraploid cultivars per se. Pyrosequencing revealed that the expression alterations may occur to either only one or both of the B and A homoeolog transcripts in ETW. A majority of the genes showed additive expression in a resynthesized allohexaploid wheat. Analysis of a synthetic allohexaploid wheat and diverse bread wheat cultivars revealed the rapid occurrence of expression changes to the BBAA subgenomes subsequent to allohexaploidization and their evolutionary persistence.
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Huakun
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China.
authors.forename: Bao
authors.initials: B
authors.lastname: Qi
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Xiaowan
authors.initials: X
authors.lastname: Gou
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Yuzhu
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011.
authors.forename: Chunming
authors.initials: C
authors.lastname: Xu
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Bangjiao
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Xutong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Chunwu
authors.initials: C
authors.lastname: Yang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Life Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel.
authors.forename: Khalil
authors.initials: K
authors.lastname: Kashkush
authors.affiliation: Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Moshe
authors.initials: M
authors.lastname: Feldman
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011.
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China baoliu@nenu.edu.cn.
authors.forename: Bao
authors.identifier: http://orcid.org/0000-0001-5481-1675
authors.initials: B
authors.lastname: Liu
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics*; D042822:Genomic Instability; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D056626:Inflorescence / Q000235:genetics; D059785:Karyotype; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA; D057891:Tetraploidy; D059467:Transcriptome; D014908:Triticum / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D018749:RNA, Plant