Abstract：Abstract Longping206 (Zea mays), a spreading hybrid in south areas of the Yellow River, Huai and Hai Rivers, with conspicuous growth heterosis and higher yield production, provides us an opportunity to explore the potential molecular mechanism for heterosis. In this study, the new technology Illumina Hiseq2500 was applied to explore the transcription level in sixth leaves stage between Longping206 and its parents (L7221 and L239). Gene expression level and function prediction were analysed with a lot of bioinformatic methods. From the comparison of phenogram, the hybrid was stronger than its paternal line in sixth leaves stage. The measurement of biomass had the same results with the phenogram. After the RNA-Seq sequencing, approximately 12.52 Gb clean data was generated after removing low-quality read. At least 69% read could be mapped into the reference genome of maize B73 with the software Tophat2. With the module Cuffdiff of Cufflinks, gene expression quantity was obtained. Then EBSeq software was used to calculate the differential expression. A total of 3 005 differentially expressed genes (DEGs) was discovered between Longping206 and its parental lines. All 1 788 DEGs were up-regulated in hybrid with 925 DEGs were down-regulated. To calculate the gene expression level in heterosis, traditional quantitative genetic parameters were used as the quantitative traits. To classify the function of DEGs, Gene Ontology (GO) analysis was used. In total, 2 399 of 3 005 DGHP (different expression genes in hybrid and parents) were assigned to at least one term in GO database including molecular function, biological process and cellular component. Most of important biological processes were enriched in hybrid such as hormone signal conditioning, energy metabolism, materials transport, stress threaten etc. To identify the metabolic pathways which the DGHP were involved and enriched, Kyoto Encyclopedia of Genes and Genomes (KEGG) database was performed to analyze the pathway. The results showed that at least 255 DGHP were classified into one functional category. 5.88% and 8.24% of these DEGs were involved in the carbon metabolism and plant signal transduction pathways, respectively. Interestingly, most of the DEGs were up-regulated, which revealed that the two ways were important to the formation of heterosis. qRT-PCR was performed to validate the consistence of transcriptome analysis with 10 random different expression genes. The extensive transcriptome data which was obtained from high-throughput sequencing given the comprehensive overview of the leaf transcriptomes at Longping206 and its parents in a heterotic maize cross. This study provides a useful resource for molecular mechanisms of the maize heterosis research.
[1]黄泾.玉米新品种隆平的特征特性及高产栽培技术[J].安徽农学通报, 2012, 18(9):77-78 [2]Huang J.The characteristics and high yield cultivation techniques of new variety longping206"[J].Anhui Agricultural Science Bulletin, 2012, 18(9):77-78 [3]黄泾.玉米新品种隆平在阜阳市最佳种植密度试验[J].安徽农学通报, 2012, 18(11):57-57 [4]Huang J.The best planting density test of longping 206 in Fuyang"[J][J].Anhui Agricultural Science Bulletin, 2012, 18(11):57-57 [5]姜涛，王丕武，张君.玉米差异显示与杂种优势关系的研究[J].玉米科学, 2013, 21(05):41-45 [6]Jiao T, Wang P W, Zhang J.Relationship Between mRNA Differential Gene Expression and Heterosis in Maize”[J].J].Journal of Maize Sciences, 2013, 21(5):41-45 [7] 刘天骄.2013. 玉米杂交种及其亲本DNA胞嘧啶甲基化模式和水平变化研究[D]. 硕士毕业论文，吉林大学.导师：原亚萍. [8]Liu T J.2013.Research of DNA Cytosine Methylation Patterns and Levels in Maize Hybirds and Their Parents[D]. Thesis for M.S., JiLin University ( in Chinese ). Supervisor: Yuan Y P. [9]刘洋，林希昊, 姚艳丽, 等.高等植物蔗糖代谢研究进展[J].中国农学通报, 2012, 28(06):145-152 [10]Liu Y, Lin X H, Yao Y L, et al.Sucrose Metabolism in Higher Plants[J].J].Chinese Agricultural Science Bulletin, 2012, 28(06):145-152 [11]刘振华，于延冲，向凤宁.生长素响应因子与植物的生长发育[J].遗传, 2011, 33(12):1335-1346 [12]Liu Z H, Yu Y C, Xiang F N.Auxin response factors to plant growth and development[J].J].Genetics, 2011, 33(12):1335-1346 [13]汪尚，徐鹭芹，张亚仙, 等.白菜与芜菁亚种间杂交种及其亲本莲座期基因差异表达[J].园艺学报, 2016, 52(5):581-590 [14]Wang S, Xu L Q, Zhang Y X, et al.Recent advance of salicylic acid signaling in plant disease resistance[J].J].Acta Phytophysiologica Sinica, 2016, 52(5):581-590 [15]吴才君，曹家树，何勇, 等.白菜与芜菁亚种间杂交种及其亲本莲座期基因差异表达[J].园艺学报, 2004, 31(04):508-510 [16]Wu C J, Cao J S, He Y, et al.The Relationship between Differential Gene Expression Patterns in Rosette Stages and Heterosis in Chinese Cabbage-pakchoi,Turnip and Their Hybrids[J].J].Acta Horticulturae Sinica, 2004, 31(04):508-510 [17]翟荣荣.2013. 超级稻协优9308根系杂种优势的转录组分析[D].博士毕业论文，中国农业科学院，导师：程式华. [18]Zhai R R.2013.Transcriptome analysis of rice root heterosis by RNA-Seq. [D] Thesis for D.S., Chinese Academy of Agricultural Sciences ( in Chinese ). Supervisor:Chen S H. [19]张富.2004. 玉米苗期根系杂种优势及根系基因表达谱分析[D]. 硕士毕业论文, 中国农业大学. 导师：李建生. [20]Zhang F.2004. Gene expression profile analysis of root Heterosis in maize. [D] Thesis for M.S., China Agricultural University ( in Chinese ). Supervisor:Li J S. [21]X.S.,ZN?,YYao,et al."Wheat ( Triticum aestivum L.) root proteome and differentially expressed root proteins between hybrid and parents."[J].Proteomics, 2007, 7(19):3538-3557 [22]Baute, J, D.Herman,FCoppens,et al"Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population"[J].Genome Biology, 2014, 16(1):1-26 [23]Birchler, JA.H. Yao,SChudalayandi,et al"Heterosis"[J].Plant Cell, 2010, 22(7):2105-2112 [24]Blum, A.Heterosis,stress,and the environment: a possible road map towards the general improvement of crop yield"[J].J].Journal of Experimental Botany, 2013, 64(16):4829-4837 [25]Bruce, AB.The Mendelian Theory of Heredity and the Augmentation of Vigor"[J].Science, 1910, 32(827):627-628 [26]Busov, VB.A. MBrunner and SHStrauss"Genes for control of plant stature and form."[J].New Phytologist, 2008, 177(3):589-607 [27] Charles, VA, LDanielle, B,Jean-Michel, et al..Saccharose-Phosphat-Synthase (SPS), ihr Verfahren zur Herstellung, ihr cDNA und Verwendung von cDNA zur Ver?nderung der SPS-Expression in Pflanzenzellen, EP.[J]., 2004, :- [28]Chen, J, B.Zeng,MZhang,et al"Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development"[J].Plant Physiology, 2014, 166(1):252-264 [29]Cheverud, JM.and EJRoutman"Epistasis and its contribution to genetic variance components"[J].Genetics, 1995, 139(3):1455-1461 [30]Cho, WK, S.Lian,SMKim,et al"Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection."[J].Plos One, 2015, 10(8):e-0136736 [31]Conesa, A, S.G?tz,JMGarcía-Gómez,et al"Blast2GO: a universal tool for annotation,visualization and analysis in functional genomics research."[J].Bioinformatics, 2005, 21(18):3674-3676 [32]East, EM.Heterosis"[J].Genetics, 1936, 21(4):375-397 [33]Farrokhi, N, R.A. Burton,LBrownfield,et al"Plant cell wall biosynthesis: genetic,biochemical and functional genomics approaches to the identification of key genes"[J].Plant Biotechnology Journal, 2006, 4(2):145-167 [34]Galtier, N, C.H. Foyer,EMurchie,et al"Effects of light and atmospheric carbon dioxide enrichment on photosynthesis and carbon partitioning in the leaves of tomato (Lycopersicon esculentum L) plants over-expressing sucrose phosphate synthase."[J].Journal of Experimental Botany, 1995, 46(special):1335-1344 [35]Groszmann, M, R.Gonzalez-Bayon,RLLyons,et al"Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids."[J].Proceedings of the National Academy of Sciences, 2015, 112(46):6397-6406 [36]Hou, J, Q.Wu,TZuo,et al"Genome-wide transcriptomic profiles reveal multiple regulatory responses of poplar to Lonsdalea quercina infection"[J].Trees, 2016, 30(4):1389-1402 [37]Jiang, H and WH.Wong"Statistical inferences for isoform expression in RNA-Seq"[J].Bioinformatics, 2009, 25(8):1026-1032 [38]Kanehisa, M, M.Araki,SGoto,et al"KEGG for linking genomes to life and the environment"[J].Nucleic Acids Research, 2008, 36(Database issue):480-484 [39]Kim, D.TopHat2: accurate alignment of transcriptomes in the presence of insertions,deletions and gene fusions"[J].Genome Biology, 2013, 14(4):R36-R49 [40]Leng, N, J.A. Dawson,JAThomson,et al"EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments."[J].Bioinformatics, 2013, 29(8):1035-1043 [41]Li, J, L.Wang,QZhan,et al"Sorghum bmr6 mutant analysis demonstrates that a shared MYB1 transcription factor binding site in the promoter links the expression of genes in related pathways"[J].J].Functional & Integrative Genomics, 2013, 13(4):445-453 [42]Li, S, S.Zachgo,SLi,et al"TCP3 interacts with R2R3-MYB proteins,promotes flavonoid biosynthesis and negatively regulates the auxin response in"[J].The Plant Journal, 2013, 76(6):901-913 [43]Mcgonigle, B.and DPO'Keefe"A genomics approach to the comprehensive analysis of the glutathione S-transferase gene family in soybean and maize"[J].Plant Physiology, 2000, 124(3):1105-1120 [44]Miura, K, J.Lee,TMiura,et al"SIZ1 controls cell growth and plant development in Arabidopsis through salicylic acid"[J].Plant & Cell Physiology, 2010, 51(1):103-113 [45]Omholt, SW.E. Plahte,LOyehaug,et al"Gene regulatory networks generating the phenomena of additivity,dominance and epistasis"[J].Genetics, 2000, 155(2):969-980 [46]Peng, Y, G.Wei,LZhang,et al"Comparative transcriptional profiling of three super-hybrid rice combinations"[J].International Journal of Molecular Sciences, 2014, 15(3):3799-3815 [47]Qin, L, J.Trouverie,SChateau-Joubert,et al"Involvement of the Ivr2 -invertase in the perianth during maize kernel development under water stress"[J].Plant Science, 2004, 166(2):371-379 [48]Romagnoli, S, M.Maddaloni,CLivini,et al"Relationship between gene expression and hybrid vigor in primary root tips of young maize (Zea mays L) plants."[J].Theoretical & Applied Genetics, 1990, 80(6):769-775 [49]Schnable, P, D.Ware,RFulton,et al"The B73 maize genome: complexity,diversity,and dynamics"[J].Science, 2009, 326(5956):1112-1115 [50] Shull, GH.“The composition of a field of maize.”[J]., 1908, :- [51]Somerville, C, S.Bauer,GBrininstool,et al"Toward a systems approach to understanding plant cell walls"[J].Science, 2004, 306(5705):2206-2211 [52]Vicente, RS.and JPlasencia "Salicylic acid beyond defence: its role in plant growth and developmentJ Exp Bot"[J].Journal of Experimental Botany, 2011, 62(10):3321-3338 [53]Wang, J, H.Ding,AZhang,et al"A Novel Mitogen-Activated Protein Kinase Gene in Maize (Zea mays),ZmMPK3,is Involved in Response to Diverse Environmental Cues"[J].植物学报英文版, 2010, 52(5):442-452 [54]Ye, J, L.Fang,HZheng,et al"WEGO: a web tool for plotting GO annotations"[J].Nucleic Acids Research, 2006, 34(suppl 2):W293-W297 [55]Zhai, R, F, Yue, H.Wang,et al"Transcriptome analysis of rice root heterosis by RNA-Seq"[J].Bmc Genomics, 2013, 14(3):19-33
