Comparative transcriptome analysis of root hairs proliferation induced by water deficiency in maize

다국어 초록 (Multilingual Abstract)

Root hairs functions as water channels and nutritional components transporters in plants. It has been shown to enhance nutrient uptake including phosphate, nitrogen, potassium and calcium. In the experiment, the droughtinduced root hairs were collected. By transcriptome sequence and analysis, the molecular mechanisms and differentially expressed genes related to root hairs growth and development were studied. As a result, by using the HiSeq 2500 platform, 61,872,790 clean reads with 96.23% Q20 bases and 9.28 Gb clean bases with 58.88% GC ratio were obtained for normal root. In contrast with Control group, 67,650,572 clean reads with 96.43% Q20 bases and 10.15 Gb clean bases with 58.3% GC content were obtained for drought-induced root hairs. Totally, 323 differentially expressed genes (DEGs) were identified. Among these DEGs, 109 genes were upregulated and 214 genes were downregulated in drought-induced root hairs. Moreover, metabolic pathway enrichment analysises on the 323 DEGs revealed that totally 10 metabolic pathways were distinctly regulated. In details, alanine, aspartate and alutamate metabolism, galactose metabolism and nitrogen metabolism were significantly upregulated. 7 metabolic pathways such as phenylpropanoid biosynthesis, phenylalanine metabolism, biosynthesis of secondary metabolites and flavonoid biosynthesis were significantly downregulated. Furthermore, functional genes and transcription factors were both found to be involved in drought-induced root hair proliferation. These results will help us understand better the molecular mechanism of maize root hair growth and development.

참고문헌 (Reference)

1 Brown LK, "What are the implications of variation in root hair length on tolerance to phosphorus deficiency in combination with water stress in barley (Hordeum vulgare)?" 110 : 319-328, 2012

2 Kim DC, "TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions" 14 : R36-, 2013

3 Gilroy S, "Through form to function: root hair development and nutrient uptake" 5 : 56-60, 2000

4 Stenzel I, "The type B phosphatidylinositol-4-phosphate 5-kinase 3 is essential for root hair formation in Arabidopsis thaliana" 20 : 124-141, 2008

5 White RG, "The distribution and abundance of wheat roots in a dense, structured subsoil—implications for water uptake" 33 : 133-148, 2010

6 Lothier J, "The cytosolic glutamine synthetase GLN1; 2 plays a role in the control of plant growth and ammonium homeostasis in Arabidopsis rosettes when nitrate supply is not limiting" 62 : 1375-1390, 2011

7 Kato M, "The Ca2+-binding protein PCaP2 located on the plasma membrane is involved in root hair development as a possible signal transducer" 74 : 690-700, 2013

8 Schnable PS, "The B73 maize genome" 326 : 1112-1115, 2009

9 Konno M, "Temporal and positional relationships between Mn uptake and low-pH-induced root hair formation in Lactuca sativa cv. Grand Rapids seedlings" 119 : 439-447, 2006

10 Datta S, "Root hairs: development, growth and evolution at the plant-soil interface" 346 : 1-14, 2011

11 Vandamme E, "Root hairs explain P uptake efficiency of soybean genotypes grown in a P-deficient Ferralsol" 369 : 269-282, 2013

12 Libault M, "Root hair systems biology" 15 : 641-650, 2010

13 Li T, "Relative importance of an arbuscular mycorrhizal fungus (Rhizophagus intraradices) and root hairs in plant drought tolerance" 24 : 595-602, 2014

14 Tominaga R, "Regulation of root hair cell differentiation by R3 MYB transcription factors in tomato and Arabidopsis" 5 : 91-, 2014

15 Wang Z, "RNA-Seq: a revolutionary tool for transcriptomics" 10 : 57-63, 2009

16 Boron AK, "Proline-rich proteinlike PRPL1 controls elongation of root hairs in Arabidopsis thaliana" 65 : 5485-5495, 2014

17 Yang TJ, "Manganese deficiency alters the patterning and development of root hairs in Arabidopsis" 59 : 3453-3464, 2008

18 Cao X, "Influence of nutrient deficiency on root architecture and root hair morphology of trifoliate orange (Poncirus trifoliata L. Raf.) seedlings under sand culture" 162 : 100-105, 2013

19 Hao J, "GbTCP, a cotton TCP transcription factor, confers fiber elongation and root hair development by a complex regulating system" 63 : 6267-6281, 2012

20 Lin Q, "GLABRA2 directly suppresses basic Helix-Loop-Helix transcription factor genes with diverse functions in root hair development" 27 : 2894-2906, 2015

21 Mackay AD, "Effect of cyclic wetting and drying of a soil on root hair growth of maize roots" 104 : 291-293, 1987

22 Anders S, "Differential expression analysis for sequence count data" 11 : R106-, 2010

23 Tang QY, "Data Processing System (DPS) software with experimental design, statistical analysis and data mining developed for use in entomological research" 20 : 254-260, 2013

24 Xu C, "Cooperative action of the paralogous maize lateral organ boundaries (LOB) domain proteins RTCS and RTCL in shoot-borne root formation" 207 : 1123-1133, 2015

25 Benjamini Y, "Controlling the false discovery rate: a practical and powerful approach to multiple testing" 57 : 289-300, 1995

26 Jones M, "Analysis of the root-hair morphogenesis transcriptome reveals the molecular identity of six genes with roles in root-hair development in Arabidopsis" 45 : 83-100, 2006

27 Andriankaja A, "AP2-ERF transcription factors mediate nod factor–dependent Mt ENOD11 activation in root hairs via a novel cis-regulatory motif" 19 : 2866-2885, 2007

28 Yoo C, "AGD1, a class 1 ARF-GAP, acts in common signaling pathways with phosphoinositide metabolism and the actin cytoskeleton in controlling Arabidopsis root hair polarity" 69 : 1064-1076, 2012

29 An LJ, "A zinc finger protein gene ZFP5 integrates phytohormone signaling to control root hair development in Arabidopsis" 72 : 474-490, 2012

30 Ding W, "A transcription factor with a bHLH domain regulates root hair development in rice" 19 : 1309-1311, 2009

31 Yi K, "A basic helix-loop-helix transcription factor controls cell growth and size in root hairs" 42 : 264-267, 2010