title: The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat.
abstract: The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoeologues. Here, RNA-Seq was used to obtain the genome-wide leaf transcriptome of two independent Triticum turgidum × Aegilops tauschii allotriploids (F1), along with their spontaneous allohexaploids (S1) and their parental lines. The resulting sequence data were then used to characterize variation in homoeologue transcript abundance.
  
  
  
  The hybridization event strongly down-regulated D-subgenome homoeologues, but this effect was in many cases reversed by whole genome doubling. The suppression of D-subgenome homoeologue transcription resulted in a marked frequency of parental transcription level dominance, especially with respect to genes encoding proteins involved in photosynthesis. Singletons (genes where no homoeologues were present) were frequently transcribed at both the allotriploid and allohexaploid plants.
  
  
  
  The implication is that whole genome doubling helps to overcome the phenotypic weakness of the allotriploid, restoring a more favourable gene dosage in genes experiencing transcription level dominance in hexaploid wheat.
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Hao
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Aili
authors.initials: A
authors.lastname: Li
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, China.
authors.forename: Tongwei
authors.initials: T
authors.lastname: Shi
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Jiangtao
authors.initials: J
authors.lastname: Luo
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Lianquan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, China.
authors.forename: Xuechuan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Shunzong
authors.initials: S
authors.lastname: Ning
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Zhongwei
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Deying
authors.initials: D
authors.lastname: Zeng
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Xingchen
authors.initials: X
authors.lastname: Kong
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Li
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, China.
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Xiujin
authors.initials: X
authors.lastname: Lan
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
authors.forename: Huaigang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
authors.forename: Youliang
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. maolong@caas.cn.
authors.forename: Long
authors.initials: L
authors.lastname: Mao
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China. dcliu7@yahoo.com.|Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China. dcliu7@yahoo.com.
authors.forename: Dengcai
authors.initials: D
authors.lastname: Liu
mesh_terms: D015536:Down-Regulation / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D006824:Hybridization, Genetic; D010641:Phenotype; D011123:Polyploidy; D012333:RNA, Messenger / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D014908:Triticum / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: Genome duplication; Interspecific hybridization; Polyploidy; Synthetic wheat; Transcriptome evolution