Identification and characterization of genes on a single subgenome in the hexaploid wheat (Triticum aestivum L.) genotype ‘Chinese Spring’

J. Ma; Z. Zheng; J. Stiller; X-J Lan; Y. Liu; M. Deng; P. Wang; Z. Pu; G. Chen; Q-T Jiang; Y. Wei; Y-L Zheng; F. Belzile

doi:10.1139/gen-2016-0076

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Identification and characterization of genes on a single subgenome in the hexaploid wheat (Triticum aestivum L.) genotype ‘Chinese Spring’

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Identification and characterization of genes on a single subgenome in the hexaploid wheat (Triticum aestivum L.) genotype ‘Chinese Spring’

J. Ma, Z. Zheng, J. Stiller, X-J Lan, Y. Liu, M. Deng, P. Wang, Z. Pu, G. Chen, Q-T Jiang, …

Genome, Vol.60(3), pp.208-215

2017

DOI: https://doi.org/10.1139/gen-2016-0076

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Abstract

Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat. Unexpectedly, no bias in expression breadth or in the distribution patterns of GO (gene ontology) terms for these genes was detected among the high-confidence genes. Further, network and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses indicated that most of these genes were not functionally related to each other. Interestingly, 30.7% of these SSG genes were most highly expressed in root, showing biased distribution given the distribution of the whole high-confidence genes. Collectively, these results facilitate our understanding of the loss of the genes that were retained in a SSG during the formation of hexaploid wheat.

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Title: Identification and characterization of genes on a single subgenome in the hexaploid wheat (Triticum aestivum L.) genotype ‘Chinese Spring’
Authors/Creators: J. Ma (Author/Creator) - Sichuan Agricultural University
Z. Zheng (Author/Creator) - Commonwealth Scientific and Industrial Research Organisation
J. Stiller (Author/Creator) - Hebei Academy of Agriculture and Forestry Sciences
X-J Lan (Author/Creator) - Sichuan Agricultural University
Y. Liu (Author/Creator) - Sichuan Agricultural University
M. Deng (Author/Creator) - Sichuan Agricultural University
P. Wang (Author/Creator) - Murdoch University
Z. Pu (Author/Creator) - Sichuan Agricultural University
G. Chen (Author/Creator) - Sichuan Agricultural University
Q-T Jiang (Author/Creator) - Sichuan Agricultural University
Y. Wei (Author/Creator) - Sichuan Agricultural University
Y-L Zheng (Author/Creator) - Sichuan Agricultural University
F. Belzile (Author/Creator)
Publication Details: Genome, Vol.60(3), pp.208-215
Publisher: NRC Research Press
Identifiers: 991005545325207891
Copyright: © 2017 Published by NRC Research Press.
Murdoch Affiliation: School of Veterinary and Life Sciences
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics