title: Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis.
abstract: BACKGROUND
  Primary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Its molecular basis has been identified as a nested Gypsy-44 retrotransposon insertion; however the link between the insertion and the phenotype as well as the timing of the phenotype emergence are as yet unclear. We extend the transcriptomic studies of columnar tissues to the radicles, which are the earliest developmental stage and investigate whether homozygous columnar seedlings are viable.
  
  
  RESULTS
  Radicles mainly express genes associated with primary metabolism, growth and development. About 200 genes show differential regulation in a comparison of heterozygous columnar radicles with non-columnar radicles, whereas the comparison of homozygous columnar radicles with non-columnar radicles yields about 300 differentially regulated genes. Genes involved in cellulose and phenylpropanoid biosynthesis, cell wall modification, transcription and translation, ethylene and jasmonate biosynthesis are upregulated in columnar radicles. Genes in the vicinity of the columnar-specific Gypsy-44 insertion experience an especially strong differential regulation: the direct downstream neighbor, dmr6-like, is downregulated in heterozygous columnar radicles, but strongly upregulated in columnar shoot apical meristems.
  
  
  CONCLUSIONS
  The transcriptomic profile of primary roots reflects their pivotal role in growth and development. Homozygous columnar embryos are viable and form normal radicles under natural conditions, and selection towards heterozygous plants most likely occurs due to breeders' preferences. Cell wall and phytohormone biosynthesis and metabolism experience differential regulation in columnar radicles. Presumably the first step of the differential regulation most likely happens within the region of the retrotransposon insertion and its tissue-specificity suggests involvement of one (or several) tissue-specific regulator(s).
authors: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. peterser@uni-mainz.de.
authors: Romina
authors: R
authors: Petersen
authors: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. dj-haris@gmx.de.
authors: Haris
authors: H
authors: Djozgic
authors: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. riegerb@uni-mainz.de.
authors: Benjamin
authors: B
authors: Rieger
authors: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. rapps@uni-mainz.de.
authors: Steffen
authors: S
authors: Rapp
authors: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. eschmidt@uni-mainz.de.
authors: Erwin Robert
authors: ER
authors: Schmidt
mesh_terms: D020869:Gene Expression Profiling; D017343:Genes, Plant; D027845:Malus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction
references: Plant Cell. 2007 Jul;19(7):2169-85
references: 17630276
references: Genome Res. 2013 Feb;23(2):396-408
references: 23149293
references: J Plant Physiol. 2013 Mar 15;170(5):480-8
references: 23347818
references: Plant J. 2004 Mar;37(6):914-39
references: 14996223
references: Proteomics. 2008 Sep;8(18):3882-94
references: 18704907
references: Plant Physiol. 2001 Jun;126(2):524-35
references: 11402184
references: Plant Physiol. 2009 Apr;149(4):1797-809
references: 19176718
references: BMC Bioinformatics. 2006;7:474
references: 17064419
references: Planta. 1998 Aug;205(4):483-91
references: 9684353
references: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11376-81
references: 17595297
references: Planta. 2010 Nov;232(6):1397-407
references: 20830596
references: BMC Genomics. 2009;10:399
references: 19709400
references: Genome Biol. 2010;11(10):R106
references: 20979621
references: Plant J. 2008 Jun;54(5):785-93
references: 18248595
references: Development. 1993 Sep;119(1):71-84
references: 8275865
references: Nat Genet. 2011 Feb;43(2):109-16
references: 21186353
references: Plant Mol Biol. 2013 Feb;81(3):211-20
references: 23306528
references: Science. 2007 Nov 2;318(5851):801-6
references: 17975066
references: J Integr Plant Biol. 2010 Jan;52(1):98-111
references: 20074144
references: BMC Plant Biol. 2010;10:87
references: 20470375
references: Am J Bot. 2012 Feb;99(2):248-56
references: 22268221
references: Plant Cell. 2000 Jul;12(7):1117-26
references: 10899978
references: Planta. 2013 Jul;238(1):1-22
references: 23695821
references: Development. 2013 Apr;140(7):1373-83
references: 23482484
references: Trends Plant Sci. 2007 Dec;12(12):556-63
references: 18198522
references: Nature. 1997 Nov 20;390(6657):287-9
references: 9384380
references: Plant Cell Physiol. 2000 Mar;41(3):354-62
references: 10805599
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Plant Physiol. 2008 May;147(1):41-57
references: 18354039
references: BMC Res Notes. 2014;7:488
references: 25084827
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Plant Physiol. 1983 Jul;72(3):750-3
references: 16663079
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Plant J. 2013 May;74(3):398-410
references: 23398045
references: Planta. 2007 Mar;225(4):1051-7
references: 17260145
references: Plant Signal Behav. 2009 Dec;4(12):1121-7
references: 20514226
references: Planta. 2010 Sep;232(4):999-1005
references: 20628761
references: PLoS One. 2013;8(12):e80961
references: 24324652
references: Plant Cell. 2005 Jul;17(7):1908-25
references: 15937229
references: Gene. 2012 May 1;498(2):223-30
references: 22353365
references: Front Zool. 2012 Nov 29;9(1):33
references: 23190771
references: Int J Plant Genomics. 2008;2008:619832
references: 18483572
references: Annu Rev Plant Biol. 2012;63:563-90
references: 22404466
references: FEBS Lett. 2003 May 8;542(1-3):37-41
references: 12729894
references: Science. 2003 Dec 12;302(5652):1956-60
references: 14671301
references: BMC Genomics. 2014;15:148
references: 24559402
references: Nat Genet. 2013 May;45(5):487-94
references: 23525075
references: Nat Genet. 2010 Oct;42(10):833-9
references: 20802477
references: New Phytol. 2013 Dec;200(4):993-9
references: 24571666
references: Genome Res. 1999 Sep;9(9):868-77
references: 10508846
references: Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47:245-271
references: 15012289
references: Plant Physiol. 2007 Nov;145(3):575-88
references: 17766395
references: Plant Physiol. 2006 May;141(1):147-66
references: 16531485
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
references: 15215394