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Molecular & cellular proteomics : MCP
02, 2019;18 (2): 263-276.

Characterization of Proteome Variation During Modern Maize Breeding.

Lu-Guang Jiang, Bo Li, Sheng-Xue Liu, Hong-Wei Wang, Cui-Ping Li, Shu-Hui Song, Mary Beatty, Gina Zastrow-Hayes, Xiao-Hong Yang, Feng Qin, Yan He
Author Information
  1. Lu-Guang Jiang: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
  2. Bo Li: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
  3. Sheng-Xue Liu: College of Biological Sciences, China Agricultural University, Beijing 100094, China.
  4. Hong-Wei Wang: Agricultural College, Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Hubei 434000, China.
  5. Cui-Ping Li: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  6. Shu-Hui Song: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  7. Mary Beatty: DuPont Pioneer, Johnston, IA 50131.
  8. Gina Zastrow-Hayes: DuPont Pioneer, Johnston, IA 50131.
  9. Xiao-Hong Yang: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
  10. Feng Qin: College of Biological Sciences, China Agricultural University, Beijing 100094, China;. Electronic address: qinfeng@cau.edu.cn.
  11. Yan He: MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China;. Electronic address: yh352@cau.edu.cn.
PMID: 30409858 DOI: 10.1074/mcp.RA118.001021

Abstract

The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.

Keywords

Gene Expression Proteome RNA SEQ Statistics Temperate Adaptation Transcriptional Regulation Zea mays eQTL iTRAQ pQTL

References

Science. 2015 Feb 6;347(6222):664-7 [PMID: 25657249]
Science. 2007 Feb 16;315(5814):972-6 [PMID: 17218491]
PLoS Biol. 2011 Sep;9(9):e1001144 [PMID: 21909241]
Plant Physiol. 2006 Jul;141(3):957-65 [PMID: 16698901]
Mol Cell Biol. 1999 Mar;19(3):1720-30 [PMID: 10022859]
Genomics Proteomics Bioinformatics. 2017 Feb;15(1):14-18 [PMID: 28387199]
Genome Res. 2013 Sep;23(9):1496-504 [PMID: 23720455]
Stat Appl Genet Mol Biol. 2005;4:Article17 [PMID: 16646834]
Plant J. 2014 May;78(3):424-40 [PMID: 24547885]
Bioinformatics. 2009 Nov 15;25(22):3043-4 [PMID: 19717575]
Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11878-83 [PMID: 22753482]
Nature. 2016 Jun 15;534(7608):500-5 [PMID: 27309819]
BMC Genomics. 2011 Jun 30;12:336 [PMID: 21718468]
Mol Cell Proteomics. 2014 Feb;13(2):397-406 [PMID: 24309898]
PLoS Genet. 2011 Jun;7(6):e1001393 [PMID: 21695224]
BMC Genomics. 2017 Apr 18;18(1):305 [PMID: 28420336]
Nature. 2016 May 25;534(7605):55-62 [PMID: 27251275]
PLoS Comput Biol. 2011 Jan 20;7(1):e1001057 [PMID: 21283776]
BMC Bioinformatics. 2007 Jan 24;8:22 [PMID: 17250769]
Cancer Cell. 2010 Jan 19;17(1):98-110 [PMID: 20129251]
Nat Genet. 2013 Jan;45(1):43-50 [PMID: 23242369]
Science. 2016 Aug 19;353(6301):814-8 [PMID: 27540173]
Bioinformatics. 2010 Jun 15;26(12):1572-3 [PMID: 20427518]
Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12420-5 [PMID: 22802642]
Cell. 2014 Sep 11;158(6):1415-1430 [PMID: 25215496]
Nat Genet. 2006 May;38(5):500-1 [PMID: 16642009]
Nature. 2014 Feb 27;506(7489):494-7 [PMID: 24402228]
Nat Commun. 2017 Mar 28;8:14864 [PMID: 28348404]
Mol Cell Proteomics. 2014 Mar;13(3):907-17 [PMID: 24443746]
Bioinformatics. 2003 Dec 12;19(18):2502-4 [PMID: 14668247]
Bioinformatics. 2007 Oct 1;23(19):2633-5 [PMID: 17586829]
Plant Physiol. 2015 May;168(1):233-46 [PMID: 25780097]
Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5014-8 [PMID: 19307573]
Plant Cell. 2014 Sep;26(9):3472-87 [PMID: 25248552]
Genome Res. 2014 Aug;24(8):1363-70 [PMID: 24823668]
Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4673-8 [PMID: 23487758]
Cell. 2016 Jul 28;166(3):755-765 [PMID: 27372738]
Science. 2016 Jun 10;352(6291):aad0189 [PMID: 27284200]
Nat Genet. 2012 Jun 03;44(7):812-5 [PMID: 22660547]
Mol Syst Biol. 2010 Aug 24;6:400 [PMID: 20739923]
J Proteome Res. 2018 Feb 2;17(2):822-833 [PMID: 29250956]
Sci Rep. 2017 May 18;7(1):2077 [PMID: 28522839]
Cell. 2013 Oct 24;155(3):713-24 [PMID: 24243024]
Nucleic Acids Res. 2017 Jan 4;45(D1):D18-D24 [PMID: 27899658]
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6567-72 [PMID: 12011421]
Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2655-62 [PMID: 23803858]
Nat Biotechnol. 2015 Mar;33(3):290-5 [PMID: 25690850]
Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5019-24 [PMID: 19307570]
Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16969-74 [PMID: 24089449]
Science. 2002 Aug 30;297(5586):1551-5 [PMID: 12202830]
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W352-7 [PMID: 15980487]
Genome Biol. 2016 Jul 13;17(1):155 [PMID: 27411931]
Nat Rev Genet. 2012 Mar 13;13(4):227-32 [PMID: 22411467]
Genome Res. 2015 Nov;25(11):1610-21 [PMID: 26297486]
Mol Biosyst. 2009 Dec;5(12):1512-26 [PMID: 20023718]
PLoS Genet. 2017 Mar 16;13(3):e1006666 [PMID: 28301472]
BMC Genomics. 2016 Feb 20;17:125 [PMID: 26897027]
Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12698-703 [PMID: 20616000]
Nat Genet. 2016 Oct;48(10):1233-41 [PMID: 27526320]
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4808-17 [PMID: 24248366]
Bioinformatics. 2008 Mar 1;24(5):719-20 [PMID: 18024473]
Annu Rev Genet. 2004;38:37-59 [PMID: 15568971]
Mol Plant. 2015 Jun;8(6):871-84 [PMID: 25620769]
Nat Genet. 2015 Feb;47(2):151-7 [PMID: 25531751]
PLoS One. 2012;7(5):e36807 [PMID: 22615816]
J Math Psychol. 2000 Mar;44(1):108-132 [PMID: 10733860]
Science. 2013 Nov 29;342(6162):1100-4 [PMID: 24136357]
Am J Hum Genet. 2007 Sep;81(3):559-75 [PMID: 17701901]
BMC Bioinformatics. 2008 Dec 29;9:559 [PMID: 19114008]
Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
Nat Commun. 2015 Sep 21;6:8326 [PMID: 26387805]
Nature. 2013 Jul 4;499(7456):79-82 [PMID: 23676674]
Plant Physiol. 2016 Jan;170(1):136-46 [PMID: 26556794]
Proteomics. 2010 Dec;10(23):4209-12 [PMID: 21089048]
Nature. 2014 Sep 18;513(7518):382-7 [PMID: 25043054]
Nat Genet. 2010 Apr;42(4):355-60 [PMID: 20208535]
Plant J. 2017 May;90(3):447-465 [PMID: 28161902]
Bioinformatics. 2011 Sep 1;27(17):2463-4 [PMID: 21737437]
Nucleic Acids Res. 2017 Jul 3;45(W1):W122-W129 [PMID: 28472432]
Nat Commun. 2013;4:2832 [PMID: 24343161]
Nat Genet. 2006 Feb;38(2):203-8 [PMID: 16380716]
Am J Bot. 2008 Oct;95(10):1240-53 [PMID: 21632329]
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70 [PMID: 20435677]
Genome Biol. 2016 Jul 08;17(1):137 [PMID: 27387028]
Nat Commun. 2014 Mar 17;5:3438 [PMID: 24633423]

MeSH Term

Evolution, Molecular
Gene Expression Profiling
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Plant Breeding
Plant Proteins
Protein Interaction Maps
Proteomics
Quantitative Trait Loci
Zea mays

Chemicals

Plant Proteins
Comparative Study Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GSA: CRA000334 (Genetic Components Controlling Drought Responsiveness in Maize Seedlings)
GSA: CRA002002 (Unraveling Regulatory Variants Controlling Gene Expression in Drought Response in Maize)
BioProject: PRJCA000509 (Genetic Components Controlling Drought Responsiveness in Maize Seedlings)

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