Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Hongjun Liu; Xuerong Yang; Xinhui Liao; Tao Zuo; Cheng Qin; Shiliang Cao; Ling Dong; Huangkai Zhou; Yongzhong Zhang; Sisi Liu; Yaou Shen; Haijian Lin; Thomas Lübberstedt; Zhiming Zhang; Guangtang Pan

doi:10.1016/j.ygeno.2015.03.005

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Genomics. 2015 Jul;106(1):52-60. doi: 10.1016/j.ygeno.2015.03.005. Epub 2015 Apr 3.

Authors

Hongjun Liu¹, Xuerong Yang², Xinhui Liao³, Tao Zuo⁴, Cheng Qin⁵, Shiliang Cao⁶, Ling Dong⁷, Huangkai Zhou³, Yongzhong Zhang¹, Sisi Liu¹, Yaou Shen¹, Haijian Lin¹, Thomas Lübberstedt⁸, Zhiming Zhang⁹, Guangtang Pan¹⁰

Affiliations

¹ Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
² Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China.
³ BGI-Shenzhen, Shenzhen 518083, China.
⁴ Interdepartmental Genetics Program, Iowa State University, Ames 50011, USA.
⁵ Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China; Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
⁶ Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China.
⁷ Department of Agronomy, Northeast Agricultural University, 150030 Harbin, China.
⁸ Department of Agronomy, Iowa State University, Ames 50011, USA.
⁹ Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China. Electronic address: zzmmaize@gmail.com.
¹⁰ Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China. Electronic address: pangt@sicau.edu.cn.

PMID: 25847872
DOI: 10.1016/j.ygeno.2015.03.005

Abstract

The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.

Keywords: DGE; Ear development; Maize; MicroRNA156; Transcriptional factor.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling / methods
Gene Expression Regulation, Plant
Genome, Plant
RNA, Antisense / analysis
Real-Time Polymerase Chain Reaction
Sequence Alignment
Transcription Factors / genetics
Transcription Factors / metabolism
Transcriptome*
Zea mays / genetics*
Zea mays / growth & development*
Zea mays / metabolism

Substances

RNA, Antisense
Transcription Factors