title: Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen.
abstract: BACKGROUND
  Nitrogen (N) is the most common limiting factor for crop productivity worldwide. An effective approach to solve N deficiency is to develop low N (LN) tolerant crop cultivars. Tibetan annual wild barley is well-known for its wide genetic diversity and high tolerance to poor soil fertility. Up to date, no study has been done to illustrate the mechanism of LN tolerance underlying the wild barley at transcriptional level.
  
  
  RESULTS
  In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two Tibetan wild barley genotypes differing in LN tolerance (XZ149, tolerant and XZ56, sensitive). A total of 1469 differentially expressed genes (DEGs) were identified in the two genotypes at 6 h and 48 h after LN treatment. Genetic difference existed in DEGs between XZ149 and XZ56, including transporters, transcription factors (TFs), kinases, antioxidant stress and hormone signaling related genes. Meanwhile, 695 LN tolerance-associated DEGs were mainly mapped to amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and involved in transporter activity, antioxidant activities, and other gene ontology (GO). XZ149 had a higher capability of N absorption and use efficiency under LN stress than XZ56. The higher expression of nitrate transporters and energy-saving assimilation pattern could be attributed to its more N uptake and higher LN tolerance. In addition, auxin (IAA) and ethylene (ETH) response pathways may be also related to the genotypic difference in LN tolerance.
  
  
  CONCLUSIONS
  The responses of XZ149 and XZ56 to LN stress differed dramatically at transcriptional level. The identified candidate genes related to LN tolerance may provide new insights into comprehensive understanding of the genotypic difference in N utilization and LN tolerance.
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. qdxiaoyan_cool@126.com.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Quan
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. zengjb@zju.edu.cn.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Zeng
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. mylz1987@163.com.
authors.forename: Lingzhen
authors.initials: L
authors.lastname: Ye
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. chenguang0915@zju.edu.cn.
authors.forename: Guang
authors.initials: G
authors.lastname: Chen
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. hanzg@zju.edu.cn.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Han
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. Shah8712@yahoo.com.
authors.forename: Jawad Munawar
authors.initials: JM
authors.lastname: Shah
authors.affiliation: Agronomy Department, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. zhanggp@zju.edu.cn.
authors.forename: Guoping
authors.initials: G
authors.lastname: Zhang
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005838:Genotype; D001467:Hordeum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D013312:Stress, Physiological; D018609:Tibet
chemical_list: D009584:Nitrogen
references.citation: Plant Cell Physiol. 2006 Jan;47(1):74-83
references.pmid: 16284408
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references.pmid: 10592173
references.citation: Ann Bot. 2005 Oct;96(5):925-30
references.pmid: 16103036
references.citation: Plant Mol Biol. 2007 Dec;65(6):775-97
references.pmid: 17885809
references.citation: Bioinformatics. 2010 Jan 1;26(1):139-40
references.pmid: 19910308
references.citation: Plant J. 2014 Oct;80(2):230-41
references.pmid: 25065551
references.citation: Plant Physiol. 2011 May;156(1):144-64
references.pmid: 21427279
references.citation: J Exp Bot. 2008;59(11):2933-44
references.pmid: 18552353
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: Plant Cell Environ. 2013 Jul;36(7):1328-37
references.pmid: 23305042
references.citation: J Exp Bot. 2004 Feb;55(396):321-36
references.pmid: 14739259
references.citation: Trends Plant Sci. 2002 Sep;7(9):405-10
references.pmid: 12234732
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 2001 Jun;52:163-210
references.pmid: 11337396
references.citation: Plant Physiol. 2005 Jun;138(2):1083-96
references.pmid: 15923334
references.citation: Mol Ecol. 2015 Feb;24(3):610-27
references.pmid: 25524431
references.citation: Nat Protoc. 2008;3(6):1101-8
references.pmid: 18546601
references.citation: Cold Spring Harb Perspect Biol. 2009 Dec;1(6):a001586
references.pmid: 20457562
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Annu Rev Plant Biol. 2002;53:247-73
references.pmid: 12221975
references.citation: Annu Rev Plant Biol. 2010;61:291-315
references.pmid: 20192745
references.citation: BMC Plant Biol. 2015;15:134
references.pmid: 26055625
references.citation: BMC Genomics. 2014;15:179
references.pmid: 24597475
references.citation: Genome Biol. 2010;11(3):R25
references.pmid: 20196867
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18524-9
references.pmid: 22025711
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: J Mol Evol. 2000 Feb;50(2):103-15
references.pmid: 10684344
references.citation: Science. 1988 Jul 1;241(4861):42-52
references.pmid: 3291115
references.citation: BMC Genomics. 2007;8:281
references.pmid: 17705847
references.citation: Cell. 1992 Aug 7;70(3):375-87
references.pmid: 1643656
references.citation: Arabidopsis Book. 2002;1:e0011
references.pmid: 22303192
references.citation: Plant Cell Physiol. 2015 Mar;56(3):455-67
references.pmid: 25432971
references.citation: J Exp Bot. 2000 Jan;51(342):9-17
references.pmid: 10938791
references.citation: Proc Natl Acad Sci U S A. 1999 May 25;96(11):6001-8
references.pmid: 10339531
references.citation: Plant Cell Environ. 2009 Sep;32(9):1147-60
references.pmid: 19183294
references.citation: J Proteomics. 2015 Aug 3;126:1-11
references.pmid: 26021476
references.citation: Plant Cell. 2012 Jan;24(1):245-58
references.pmid: 22227893
references.citation: J Agric Food Chem. 2000 Jul;48(7):2663-9
references.pmid: 10898604
references.citation: Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1175-80
references.pmid: 9989997
references.citation: PLoS One. 2014;9(6):e100567
references.pmid: 24949953
references.citation: Mol Plant. 2010 Nov;3(6):973-96
references.pmid: 20926550
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16969-73
references.pmid: 23033493
references.citation: New Phytol. 2010 Dec;188(4):960-76
references.pmid: 21039567
references.citation: Plant Cell. 1995 Jul;7(7):1085-1097
references.pmid: 12242399
references.citation: Plant Cell Physiol. 2013 Dec;54(12):1976-88
references.pmid: 24058150
references.citation: Gene. 2015 Jan 25;555(2):305-17
references.pmid: 25447912
references.citation: J Exp Bot. 2012 May;63(9):3401-12
references.pmid: 22231501
references.citation: J Biosci. 2012 Sep;37(4):731-47
references.pmid: 22922198
references.citation: Trends Plant Sci. 2006 Sep;11(9):440-8
references.pmid: 16899391
references.citation: Plant Cell Physiol. 2005 Aug;46(8):1350-7
references.pmid: 15946982
references.citation: Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12548-53
references.pmid: 19592510
references.citation: J Plant Res. 2003 Jun;116(3):253-7
references.pmid: 12836045
references.citation: Trends Plant Sci. 2006 Dec;11(12):610-7
references.pmid: 17092760