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ハクサイのヘテロシスを示すF1とその親系統を用いたゲノムワイドなヒストン修飾解析

HASAN MEHRAJ 神戸大学

2022.03.25

概要

Brassica rapa is a diploid (AA genome) thought to be one of the ancestral species of both B.juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Chinese cabbage (B. rapa var. pekinensis) is an economically important leafy vegetable. Heterosis is the superiority of the Fi hybrid compared with its parental lines, which is important for crop breeding. The molecular mechanism of heterosis might regulate by the modifications of chromatin marks. At first, two active histone marks (H3K4me3 and H3K36me3) were characterized in the parental lines (female parent; RJKB-T24, and male parent; RJKB-T23) and were reported the distribution in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing (ChlP-seq). Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be susceptible to changes by abiotic (Fusarium oxysporum f. sp. conglutinans, Foe) and biotic (vernalization) stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes. These results suggested that covalent modification δ of histone proteins act as epigenetic regulators of gene expression. The Fi hybrid showed heterosis compared to its parental lines in different phenotypes at early and final yield stages of Chinese cabbage, suggesting the fitness of the current genetic materials for heterosis study. H3K4me3-, H3K9me2-, H3K27me3- and H3K36me3-marks through the genome of F)hybrid and its parental lines were then examined by ChlP-seq. Differentially modified histone marked genes (DMGs) were identified for all four histone marks, and parental lines had a difference in genes having DMGs. A small number of genes showed Fi hybrid-specific histone modification. For all four histone marks, most DMGs of between Fi hybrid and each of parental line showed high-parent specific pattern while a small subset of DMGs showed intermediate or low parent pattern, suggesting that high parent-specific inheritance of histone marks might be associated with the heterotic growth in Chinese cabbage Fi hybrid. Long noncoding RNAs (IncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. LncRNAs of B. rapa were classified into long intergenic noncoding RNAs (lincRNAs), natural antisense RNAs (NATs), and intronic noncoding RNAs (incRNAs) and their expression analyzed in relation to H3K27me3 marks. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. Both H3K4me3 and H3K36me3 marks were enriched in chromatin regions encoding IncRNAs, especially around the transcription start site. The transcription level of lincRNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in NATs and incRNAs. Using previous datasets of Foe inoculation and paired genes overlapping IncRNAs,12 mRNA and NAT pairs in 14-day leaves in RJKB-T24 were identified and examined the H3K4me3, H3K36me3, and H3K27me3 marks. Three pairs did not have any histone modifications, one pair had only H3K4me3 or H3K27me3 and four pairs had H3K4me3 and H3K36me3. Two pairs (BraO16382/MSTRG. 19710 and BraO33549/MSTRG.1355) had bivalent active and repressive histone modifications H3K4me3 and H3K27me3. This result suggests that the bivalent modification might have some role in the transcriptional regulation in biotic stress. The outcomes of my dissertation provide significant insights into the epigenetic mechanisms of heterosis in B. rapa.

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Akter A, Takahashi S, Deng W, Shea DJ, Itabashi E, Shimizu M, Miyaji N, Osabe K, Nishida N., Suzuki Y, Helliwell CA, Seki M, Peacock WJ, Dennis ES, Fujimoto R. The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L. DNA Research 2019, 26, 433-443.

Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M. Battles and hijacks: noncoding transcription in plants. Trends Plant Science 2015, 20, 362-71.

Asensi-Fabado MA, Amtmann A, Perrella G. Plant responses to abiotic stress: The chromatin context of transcriptional regulation. Biochim. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2017, 1860, 106-122.

Au PCK, Dennis ES, Wang MB. Analysis of argonaute 4-associated long non-coding RNA in Arabidopsis thaliana sheds novel insights into gene regulation through RNA-directed DNA methylation. Genes 2017, 8, 198.

Bailey CD, Koch MA, Mayer M, Mummenhoff K, O’Kane SL, Warwick SI, Al-Shehbaz IA. Toward a global phylogeny of the Brassicaceae. Molecular Biology and Evolution 2006, 23, 2142-2160.

Bannister A, Kouzarides T. Regulation of chromatin by histone modifications. Cell Research 2011, 21, 381-395.

Baranwal VK, Mikkilineni V, Zehr UB, Tyagi AK, Kapoor S. Heterosis: emerging ideas about hybrid vigor. Journal of Experimental Botany 2012, 63, 6309-6314.

Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 2012, 9, 671-675.

Barth S, Busimi AK, Utz HF, Melchinger AE. Heterosis for biomass yield and related traits in five hybrids of Arabidopsis thaliana L. Heynh. Heredity 2003, 91, 36-42

Basunanda P, Radoev M, Ecke W, Friedt W, Becker HC, Snowdon RJ. Comparative mapping of quantitative trait loci involved in heterosis for seedling and yield traits in oilseed rape (Brassica napus L.). Theoretical and Applied Genetics 2010, 120, 271–281.

Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 2008, 3, e3156.

Berr A, Shafiq S, Pinon V, Dong A, Shen WH. The trxG family histone methyltransferase SET DOMAIN GROUP 26 promotes flowering via a distinctive genetic pathway. The Plant Journal 2015, 81, 316-328.

Bewick AJ, Schmitz RJ. Gene body DNA methylation in plants. Current Opinion in Plant Biology 2017, 36, 103-110.

Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA. Heterosis. The Plant Cell 2010, 22, 2105-2112.

Black JC, Van RechemC, Whetstine JR. Histone lysine methylation dynamics: Establishment, regulation, and biological impact. Molecular Cell 2012, 48, 491-507.

Blanc G, Hokamp K, Wolfe KH. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research 2003, 13, 137-144.

Blanco E, González-Ramírez M, Alcaine-Colet A, Aranda S, Croce LD. The bivalent genome: Characterization, structure, and regulation. Trends in genetics 2020, 36, 118-131.

Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. Elife 2015, 4, e09591.

Böhmdorfer G, Sethuraman S, Jordan Rowley M, Krzyszton M, Hafiz Rothi M, Bouzit L, Wierzbicki AT. Long noncoding RNA produced by RNA polymerase V determines boundaries of heterochromatin. Elife 2016, 5, e19092.

Bologna NG, Voinnet O. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annual Review of Plant Biology 2014, 65, 473-503.

Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science 2010, 330, 612- 616.

Bowers JE, Chapman BA, Rong J, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422, 433-438.

Bruce AB. The mendelian theory of heredity and the augmentation of vigor. Science 1910, 32, 627-628.

Budak H, Kaya SB and Cagirici HB. Long non-coding RNA in plants in the era of reference sequences. Frontiers in Plant Science 2020, 11, 276.

Buzas DM, Robertson M, Finnegan EJ, Helliwell CA. Transcription-dependence of histone H3 lysine 27 trimethylation at the Arabidopsis polycomb target gene FLC. The Plant Journal 2011, 65, 872-881.

Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 2014, 157, 77-94.

Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345, 950- 953.

Chekanova JA. Long non-coding RNAs and their functions in plants. Current Opinion in Plant Biology 2015, 27, 207-216.

Chen L, Zhu QH, Kaufmann K. Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. Planta 2020, 252, 92.

Chen Q, Liu K, Yu R, Zhou B, Huang P, Cao Z, Zhou Y, Wang J. From “Dark Matter” to “Star”: Insight into the regulation mechanisms of plant functional long non-coding RNAs. Frontiers in Plant Science 2021, 12, 650926.

Chen R, Li M, Zhang H, Duan L, Sun X, Jiang Q, Zhang H, Hu Z. Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. BMC Genomics 2019, 20, 730.

Chen ZJ. Molecular mechanisms of polyploidy and hybrid vigor. Trends in Plant Science 2010, 15, 57-71.

Chen ZJ. Genomic and epigenetic insights into the molecular bases of heterosis. Nature Reviews Genetics 2013, 14, 471-482

Chen X, Ge X, Wang J, Tan C, King GJ, Liu K. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Frontiers in Plant Science 2015, 6, 836.

Chen ZJ, Mas P. Interactive roles of chromatin regulation and circadian clock function in plants. Genome Biology 2019, 20, 62.

Cheng F, Liang J, Cai C, Cai X, Wu J, Wang X. Genome sequencing supports a multi-vertex model for Brassiceae species. Current Opinion in Plant Biology 2017, 36, 79-87.

Cheng F, Sun C, Wu J, Schnable J, Woodhouse MR, Liang J, Cai C, Freeling M, Wang X. Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. The New Phytologist 2016b, 211, 288-299.

Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y, Liu B, Liang J, Zhuang M, Liu Y, Liu D, Wang X, Li P, Liu Y, Lin K, Bucher J, Zhang N, Wang Y, Wang H, Deng J, Liao Y, Wei K, Zhang X, Fu L, Hu Y, Liu J, Cai C, Zhang S, Zhang S, Li F, Zhang H, Zhang J, Guo N, Liu Z, Liu J, Sun C, Ma Y, Zhang H, Cui Y, Freeling MR, Borm T, Bonnema G, Wu J, Wang X. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nature Genetics 2016a, 48, 1218-1224.

Cheng F, Wu J, Wang X. Genome triplication drove the diversification of Brassica plants. Horticulture Research 2014, 1, 14024.

Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang X. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 2012, 7, e36442.

Cheng K, Xu Y, Yang C, Ouellette L, Niu L, Zhou X, Chu L, Zhuang F, Liu J, Wu H, Charron JB, Luo M. Histone tales: lysine methylation, a protagonist in Arabidopsis development. Journal of Experimental Botany 2020, 71, 793-807.

Cho J. Transposon-derived non-coding RNAs and their function in plants. Frontiers in Plant Science 2018, 9, 600.

Collins LJ, Penny D. The RNA infrastructure: dark matter of the eukaryotic cell? Trends in Genetics 2009, 25, 120-128.

Crick F. Central dogma of molecular biology. Nature 1970, 227, 561-563.

Crow JF. Alternative hypothesis of hybrid vigor. Genetics 1948, 33, 477-487.

Dapp M, Reinders J, Bédiée A, Balsera C, Bucher E, Theiler G, Granier C, Paszkowski J. Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nature Plants 2015, 1, 15092.

Darwin CR. The effects of cross and self fertilization in the vegetable kingdom. John Murray: London, UK. 1876.

Davenport CB. Degeneration, albinism and inbreeding. Science 1908, 28, 454-455.

Demetriadou C, Koufaris C, Kirmizis A. Histone N-alpha terminal modifications: genome regulation at the tip of the tail. Epigenetics Chromatin 2020, 13, 29.

Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 2013, 503, 371-376.

Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q. A long noncoding RNA regulates photoperiod sensitive male sterility, an essential component of hybrid rice. Proceedings of the National Academy of Sciences of USA 2012, 109, 2654-2659.

Dixon GR. Vegetable brassicas and related crucifers. In Dixon GR (ed.), Origins and diversity of Brassica and its relatives. CABI: Wallingford, UK. 2006, pp 1-33.

Dong X, Reimer J, Göbel U, Engelhorn J, He F, Schoof H, Turck F. Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements. Genome Biology 2012, 13, R117.

Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research 2010, 38, W64–W70.

Duvick DN. Biotechnology in the 1930s: the development of hybrid maize. Nature Reviews Genetics 2001, 2, 69-74.

East EM. Heterosis. Genetics 1936, 21, 375-397.

Engelhorn J, Blanvillain R, Kröner C, Parrinello H, Rohmer M, Posé D, Ott F, Schmid M, Carles CC. Dynamics of H3K4me3 chromatin marks prevails over H3K27me3 for gene regulation during flower morphogenesis in Arabidopsis thaliana. Epigenomes 2017, 1, 8.

Fedak H, Palusinska M, Krzyczmonik K, Brzezniak L, Yatusevich R, Pietras Z, Kaczanowski S, Swiezewski S. Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript. Proceedings of the National Academy of Sciences of USA 2016, 113, E7846-E7855.

Finnegan EJ, Bond DM, Buzas DM, Goodrich J, Helliwell CA, Tamada Y, Yun JY, Amasino RM, Dennis ES. Polycomb proteins regulate the quantitative induction of VERNALIZATION INSENSITIVE 3 in response to low temperatures. The Plant Journal 2011, 65, 382-391.

Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM. Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS One 2009, 4, e7433.

Footitt S, Müller K, Kermode AR, Finch-Savage WE. Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. The Plant Journal 2015, 81, 413-425.

Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. Journal of Applied Genetics 2015, 56, 1-13.

Fuchs J, Demidov D, Houben A, Schubert I. Chromosomal histone modification patterns - from conservation to diversity. Trends in Plant Science 2006, 11, 199-208.

Fujimoto R, Sasaki T, Ishikawa R, Osabe K, Kawanabe T, Dennis ES. Molecular mechanisms of epigenetic variation in plants. International Journal of Molecular Sciences 2012a, 13, 9900-9922.

Fujimoto R, Taylor JM, Shirasawa S, Peacock WJ, Dennis ES. Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proceedings of the National Academy of Sciences of USA 2012b, 109, 7109-7114.

Fujimoto R, Uezono K, Ishikura S, Osabe K, Peacock WJ, Dennis ES. Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems. Breeding Science 2018, 68, 145-158.

Fukushima S, Mori M, Sugano S, Takatsuji H. Transcription factor WRKY62 plays a role in pathogen defense and hypoxia-responsive gene expression in rice. Plant and Cell Physiology 2016, 57, 2541-2551.

Gaiti, F., Degnan, B. M., & Tanurdžić, M. Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity. RNA Biology 2018, 15, 696-702.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004, 5, R80.

Greaves IK, Gonzalez-Bayon R, Wang L, Zhu A, Liu PC, Groszmann M, Peacock WJ, Dennis ES. Epigenetic changes in hybrids. Plant Physiology 2015, 168, 1197-1205.

Groszmann M, Gonzalez-Bayon R, Greaves IK, Wang L, Huen AK, Peacock WJ, Dennis ES. Intraspecific Arabidopsis hybrids show different patterns of heterosis despite the close relatedness of the parental genomes. Plant Physiology 2014, 166, 265-280.

Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES. Changes in 24- nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proceedings of the National Academy of Sciences of USA 2011, 108, 2617-2622.

Guo Y, Chen S, Li Z, Cowling WA. Center of origin and centers of diversity in an ancient crop, Brassica rapa (Turnip Rape), Journal of Heredity 2014, 105, 555-565,

Guo Z, Song G, Liu Z, Qu X, Chen R, Jiang D, Sun Y, Liu C, Zhu Y, Yang D. Global epigenomic analysis indicates that epialleles contribute to Allele-specific expression via Allele- specific histone modifications in hybrid rice. BMC Genomics 2015, 16, 232.

He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. The Plant Cell 2010, 22, 17-33.

Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011, 331, 76-79.

Huang L, Dong H, Zhou D, Li M, Liu Y, Zhang F, Feng Y, Yu D, Lin S, Cao J. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. The Plant Journal 2018, 96, 203-222.

Huang CH, Sun R, Hu Y, Zeng L, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP, Pires JC, Tan DY, Zhong Y, Ma H. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular Biology and Evolution 2016, 33, 394-412.

Hung FY, Chen C, Yen MR, Hsieh JA, Li C, Shih YH, Chen FF, Chen PY, Cui Y, Wu K. The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genomics and Bioinformatics 2020, 2, lqaa066.

Itabashi E, Osabe K, Fujimoto R, Kakizaki T. Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Reports 2018, 27, 87-101.

Jakobsen MK, Poulsen LR, Schulz A, Fleurat-Lessard P, Møller A, Husted S, Schiøtt M, Amtmann A, Palmgren MG. Pollen development and fertilization in Arabidopsis is dependent on the MALE GAMETOGENESIS IMPAIRED ANTHERS gene encoding a type V P-type ATPase. Genes and Development 2005, 19, 2757-2769.

Jenuwein T, Allis CD. Translating the histone code. Science 2001, 293, 1074-1080.

Jha UC, Nayyar H, Jha R, Khurshid M, Zhou M, Mantri N, Siddique KHM. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC Plant Biology 2020, 20, 466.

Johnson C, Conrad LJ, Patel R, Anderson S, Li C, Pereira A, Sundaresan V. Reproductive long intergenic noncoding RNAs exhibit male gamete specificity and polycomb repressive complex 2-mediated repression. Plant Physiology 2018, 177, 1198-1217.

Jones DF. Dominance of linked factors as a means of accounting for heterosis. Genetics 1917, 2, 466-479.

Joshi RK, Megha S, Basu U, Rahman MH, Kav NNV. Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus. PloS One 2016, 11, e0158784.

Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. Biotechnology and Biotechnological Equipment 2019, 33, 429-439.

Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R. Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. Plant Gene 2016, 5, 1-7

Kawanabe T, Osabe K, Itabashi E, Okazaki K, Dennis ES, Fujimoto R. Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in Brassica rapa L. Genes Genetic Systems 2016b, 91, 1-10.

Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of USA 2016a, 113, E6704-E6711.

Kim DH, Sung S. Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Developmental Cell 2017, 40, 302-312.

Kim DH, Xi Y, Sung S. Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genetics 2017, 13, e1006939.

Kim JA, Kim HS, Choi SH, Jang JY, Jeong MJ, Lee SI. The Importance of the Circadian Clock in Regulating Plant Metabolism. International Journal of Molecular Sciences 2017, 18, 2680.

Kim CK, Seol YJ, Perumal S, Lee J, Waminal NE, Jayakodi M, Lee SC, Jin S, Choi BS, Yu Y, Ko HC, Choi JW, Ryu KY, Sohn SH, Parkin I, Yang TJ. Re-exploration of U’s Triangle Brassica species based on chloroplast genomes and 45S nrDNA sequences. Scientific Reports 2018, 8, 7353.

Kim JH. Multifaceted chromatin structure and transcription changes in plant stress response. International Journal of Molecular Sciences 2021, 22, 2013. 427

Kim JM, Sasaki T, Ueda M, Sako K, Seki M. Chromatin changes in response to drought, salinity, heat, and cold stresses in plants. Frontiers in Plant Science 2015, 6, 114.

Ko DK, Rohozinski D, Song Q, Taylor SH, Juenger TE, Harmon FG, Chen ZJ. Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids. PLoS Genetics 2016, 12, e1006197.

Koenig D, Weigel D. Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. Nature Reviews Genetics 2015, 16, 285-298.

Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research 2007, 35, W345-W349.

Kopp F, Mendell JT. Functional classification and experimental dissection of long noncoding RNAs. Cell 2018, 172, 393-407.

Kouzarides T. Chromatin modifications and their function. Cell 2007, 128, 693-705.

Kung JTY, Colognori D, Lee JT. Long noncoding RNAs: Past, present, and future. Genetics 2013, 193, 651-669.

Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F. Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiology 2018, 176, 1627-1645.

Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 2010, 11, 204-220.

Li JR, Liu CC, Sun CH, Chen YT. Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. BMC Genomics, 2018, 19, 966.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biology 2014, 15, R40.

Li S, Vandivier LE, Tu B, Gao L, Won SY, Li S, Zheng B, Gregory BD, Chen X. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Research 2015, 25, 235-245.

Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007, 128, 707- 719.

Li P, Su T, Zhang D, Wang W, Xin X, Yu Y, Zhao X, Yu S, Zhang F. Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass. Horticulture Research 2021, 8, 39.

Lippman ZB, Zamir D. Heterosis: revisiting the magic. Trends in Genetics 2007, 23, 60-66.

Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 2012, 24, 4333-4345.

Liu J, Wang H, Chua NH. Long noncoding RNA transcriptome of plants. Plant Biotechnology Journal 2015, 13, 319-328.

Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 2014, 5, 3930.

Liu X, Hao L, Li D, Zhu L, Hu S. Long non-coding RNAs and their biological roles in plants.

Genomics Proteomics and Bioinformatics 2015, 13, 137-147.

Liu ZW, Zhao N, Su YN, Chen SS, He XJ. Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis. Scientifc Reports 2020, 10, 3094.

Liu L, Chen X. Intercellular and systemic trafficking of RNAs in plants. Nature Plants 2018, 4, 869-878.

Liu Y, Liu K, Yin L, Yu Y, Qi J, Shen WH, Zhu J, Zhang Y, Dong A. H3K4me2 functions as a repressive epigenetic mark in plants. Epigenetics and Chromatin 2019, 12, 40.

Lu K, Wei L, Li X, Wang Y, Wu J, Liu M, Zhang C, Chen Z, Xiao Z, Jian H, Cheng F, Zhang K, Du H, Cheng X, Qu C, Qian W, Liu L, Wang R, Zou Q, Ying J, Xu X, Mei J, Liang Y, Chai YR, Tang Z, Wan H, Ni Y, He Y, Lin N, Fan Y, Sun W, Li NN, Zhou G, Zheng H, Wang X, Paterson AH, Li J. Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement. Nature Communications 2019, 10, 1154.

Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Research 2020, 30, 497-513.

Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. The Plant Journal 2013, 73, 77-90.

Lv H, Miyaji N, Osabe K, Akter A, Mehraj H, Shea DJ, Fujimoto R. The importance of genetic and epigenetic research in the Brassica vegetables in the face of climate change. In Kole C (ed.), Genomic designing of climate-smart vegetable crops. Springer: Cham, Switzerland. 2020, pp. 161-255.

Ma Q, Hedden P, Zhang QF. Heterosis in rice seedlings: its relationship to gibberellin content and expression of gibberellin metabolism and signaling genes. Plant Physiology 2011, 156, 1905-1920.

Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM. Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 2013, 25, 780-793.

Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nature Structural and Molecular Biology 2015, 22, 5-7.

Matzke MA, Kanno T, Matzke AJM. RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annual Review of Plant Biology 2015, 66, 243-267.

Mehraj H, Takahashi S, Miyaji N, Akter A, Suzuki Y, Seki M, Dennis ES, Fujimoto R. Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L. Frontiers in Plant Science 2021, 12, 659634.

Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T. Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. The Plant Journal 2012, 71, 669-683.

Meyer RC, Törjék O, Becher M, Altmann T. Heterosis of biomass production in Arabidopsis. Establishment during early development. Plant Physiology 2004, 134, 1813-1823.

Meyer P. Epigenetic variation and environmental change. Journal of Experimantal Botany 2015, 66, 3541-3548.

Miller M, Zhang C, Chen ZJ. Ploidy and hybridity effects on growth vigor and gene expression in Arabidopsis thaliana hybrids and their parents. Genes Genomes Genetics 2012, 2, 505- 513.

Miyaji N, Shimizu M, Miyazaki J, Osabe K, Sato M, Ebe Y, Takada S, Kaji M, Dennis ES, Fujimoto R, Okazaki K. Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa

L. Plant Cell Reports 2017, 36, 1841-1854.

Moghaddam AM, Roudier F, Seifert M, Bérard C, Magniette ML, Ashtiyani RK, Houben A, Colot V, Mette MF. Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. The Plant Journal 2011, 67, 691-700.

Moreno-Romero J, Jiang H, Santos-González J, Köhler C. Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. The EMBO Journal 2016, 35, 1298-1311.

Mukhtar MS, Deslandes L, Auriac MC, Marco Y, Somssich IE. The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. The Plant Journal 2008, 56, 935-947.

Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 1980, 8, 4321-4326.

Nakamura S, Hosaka K. DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis. Theoretical and Applied Genetics 2010, 120, 205-214

Ng DW, Zhang C, Miller M, Palmer G, Whiteley M, Tholl D, Chen ZJ. cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell 2011, 23, 1729-1740.

Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 2009, 457, 327-331.

Nowak R. Mining treasures from “junk DNA”. Science 1994, 263, 608-610.

Oh S, Park S, van Nocker S. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genetics 2008, 4, e1000077.

Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 2014, 15, R77.

Payá-Milans M, Poza-Viejo L, Martín-Uriz PS, Lara-Astiaso D, Wilkinson MD, Crevillén P. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. GigaScience 2019, 8, giz147.

Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009, 136, 629-41.

Powers L. An expansion of Jones’s theory for the explanation of heterosis. The American Naturalist 1944, 78, 275-280.

Prakash S. Wu X. Bhat SR. History, evolution and domestication of Brassica crops. Plant Breeding Reviews 2012, 35, 19-84.

Qi X, Li ZH, Jiang LL, Yu XM, Ngezahayo F, Liu B. Grain-yield heterosis in Zea mays L. shows positive correlation with parental difference in CHG methylation. Crop Science 2010, 50, 2338-2346

Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X, Du J. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nature Communications 2018, 9, 2425.

Quadrana L, Colot V. Plant transgenerational epigenetics. Annual Review of Genetics 2016, 50, 467-491.

Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019, 111, 997-1005.

Regulski M, Lu Z, Kendall J, Donoghue MTA, Reinders J, Llaca V, et al. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research 2013, 23, 1651-1662.

Richey FD. Mock-dominance and hybrid vigor. Science 1942, 96, 280-281.

Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. The EMBO Journal 2011, 30, 1928-1938.

Ryder P, McKeown PC, Fort A, Spillane C. Epigenetics and heterosis in crop plants. In Alvarez-Venegas R, De-la-Peña C, Casas-Mollano J (eds.), Epigenetics in plants of agronomic importance: Fundamentals and applications. Springer: Cham, Switzerland. 2019, pp. 129-148.

Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC Plant Biology 2016, 16, 45.

Sampath P, Murukarthick J, Izzah NK, Lee J, Choi HI, Shirasawa K, Choi BS, Liu S, Nou IS, Yang TJ. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea. PLoS One 2014, 9, e94499.

Schmitz RJ, Ecker JR. Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends in Plant Science 2012, 17, 149-154

Schnable PS, Springer NM. Progress toward understanding heterosis in crop plants. Annual Review of Plant Biology 2013, 64, 71–88.

Seo JS, Sun HX, Park BS, Huang CH, Yeh SD, Jung C, Chua NH. ELF18-INDUCED LONG-NONCODING RNA associates with mediator to enhance expression of innate immune response genes in Arabidopsis. Plant Cell 2017, 29, 1024-1038.

Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C. The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. Plant Cell 2014, 26, 2351-2366.

She R, Chu JSC, Wang K, Pei J, Chen N. genBlastA: Enabling BLAST to identify homologous gene sequences. Genome Research 2009, 19, 143-149.

Shea DJ, Nishida N, Takada S, Itabashi E, Takahashi S, Akter A, Miyaji N, Osabe K, Mehraj H, Shimizu M, Seki M, Kakizaki T, Okazaki K, Dennis ES, Fujimoto R. Long noncoding RNAs in Brassica rapa L. following vernalization. Scientific Reports 2019, 9, 9302.

Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R. Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of commercial F1 hybrid cultivar of Chinese cabbage. Breeding Science 2018, 68, 375-380.

Shen E, Zhu X, Hua S, Chen H, Ye C, Zhou L, et al. Genome-wide identification of oil biosynthesis related long non-coding RNAs in allopolyploid Brassica napus. BMC Genomics 2018, 19, 745.

Shen G, Hu W, Zhang B, Xing Y. The regulatory network mediated by circadian clock genes is related to heterosis in rice. Journal of Integrative Plant Biology, 2015, 57, 300-312.

Shen H, He H, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 2012, 24, 875-892.

Shen X, Xu L, Liu Y, Dong H, Zhou D, Zhang Y, Lin S, Cao J, Huang L. Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa. BMC Genomics 2019, 20, 264.

Shen Y, Sun S, Hua S, Shen E, Ye CY, Cai D, Timko MP, Zhu QH, Fan L. Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. The Plant Journal 2017, 91, 874-893.

Shi J, Li R, Zou J, Long Y, Meng J. A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.). PLoS One 2011, 6, e21645.

Shimizu M, Fujimoto R, Ying H, Pu ZJ, Ebe Y, Kawanabe T, Saeki N, Taylor JM, Kaji M, Dennis ES, Okazaki K. Identification of candidate genes for Fusarium yellows resistance in Chinese cabbage by differential expression analysis. Plant Molecular Biology 2014, 85, 247-257.

Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. The EMBO Journal 2012, 31, 257-266.

Shull GH. The composition of a field of maize. Journal of Heredity 1908, 4, 296-301. Shull GH. What Is “Heterosis”? Genetics 1948, 33, 439-446.

Song L, Fang Y, Chen L, Wang J, Chen X. Role of non-coding RNAs in plant immunity. Plant Communications 2021, 2, 100180.

Song X, Liu G, Huang Z, Duan W, Tan H, Li Y, Hou X. Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage. BMC Genomics 2016, 17, 297.

Strahl B, Allis C. The language of covalent histone modifications. Nature 2000, 403, 41-45.

Swiezewski S, Liu F, Magusin A, Dean C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 2009, 462, 799-802.

Takahashi S, Osabe K, Fukushima N, Takuno S, Miyaji N, Shimizu M, Takasaki-Yasuda T, Suzuki Y, Dennis ES, Seki M, Fujimoto R. Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L. DNA Research 2018, 25, 511-520.

Talbert PB, Henikoff S. Histone variants at a glance. Journal of Cell Science 2021, 134, jcs244749.

Tang X, Lim MH, Pelletier J, Tang M, Nguyen V, Keller WA, Tsang EW, Wang A, Rothstein SJ, Harada JJ, Cui Y. Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings. Journal of Experimantal Botany 2012, 63, 1391-1404.

Tian Y, Zheng H, Zhang F, Wang S, Ji X, Xu C, He Y, Ding Y. PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR. Science Advvances 2019, 5, eaau7246.

Tong C, Wang X, Yu J, Wu J, Li W, Huang J, Dong C, Hua W, Liu S. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics 2013, 14, 689.

Tu S, Yuan GC, Shao Z. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Scientific Reports 2017, 7, 41669.

Turck F, Coupland G. Natural variation in epigenetic gene regulation and its effects on plant developmental traits. Evolution 2014, 68, 620-631.

Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genetics 2007, 3, e86.

U N. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Japanese Journal of Botany 1935, 7, 389-452.

Vandivier LE, Anderson SJ, Foley SW, Gregory BD. The conservation and function of RNA secondary structure in plants. Annual Review of Plant Biology 2016, 67, 463-488.

Wang A, Hu J, Gao C, Chen G, Wang B, Lin C, Song L, Ding Y, Zhou G. Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp. chinensis). Scientific Reports 2019, 9, 5002.

Wang C, Wang L, Ding Y, Lu X, Zhang G, Yang J, Zheng H, Wang H, Jiang Y, Xu L. LncRNA structural characteristics in epigenetic regulation. International Journal of Molecular Sciences 2017, 18, 2659.

Wang D, Qu Z, Yang L, Zhang Q, Liu ZH, Do T, Adelson DL, Wang ZY, Searle I, Zhu JK. Transposable elements (TEs) contribute to stress related long intergenic noncoding RNAs in plants. The Plant Journal 2017, 90, 133-146.

Wang H, Chung PJ, Liu J, Jang IC, Kean MJ, Xu J, Chua NH. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Research 2014, 24, 444-453.

Wang L, Liu PC, Wu LM, Tan J, Peacock WJ, Dennis ES. Cotyledons contribute to plant growth and hybrid vigor in Arabidopsis. Planta 2019, 249, 1107-1118.

Wang R, Zou J, Meng J, Wang J. Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids. Ecology and Evolution 2018, 8, 6034-6052.

Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 2011, 43, 1035-1040.

Wang Y, Fan X, Lin F, He G, Terzaghi W, Zhu D, Deng XW. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proceedings of the National Academy of Sciences of USA 2014, 111, 10359-10364.

Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, Wu WH. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiology 2008, 148, 1201-1211.

Williams W. Heterosis and the genetics of complex characters. Nature 1959, 184, 527-530.

Wu CT, Morris JR. Genes, genetics, and epigenetics: A correspondence. Science 2001, 293, 1103-1105.

Wu H, Yang L, Chen LL. The diversity of long noncoding RNAs and their generation. Trends in Genetics 2017, 33, 540-52.

Wu X, Liu Y, Zhang Y, Gu R. Advances in research on the mechanism of heterosis in plants. Frontiers in Plant Science 2021, 12, 745726.

Xi Y, Park SR, Kim DH, Kim, ED, Sung S. Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana. The Plant Journal 2020, 103, 1490-1502.

Xiao J, Lee US, Wagner D. Tug of war: adding and removing histone lysine methylation in Arabidopsis. Current Opinion in Plant Biology 2016, 34, 41-53.

Xue JY, Wang Y, Chen M, Dong S, Shao ZQ, Liu Y. Maternal inheritance of U’s Triangle and evolutionary process of Brassica mitochondrial genomes. Frontiers in Plant Science 2020, 11, 805.

Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302, 842-846.

Yan H, Bombarely A, Xu B, Frazier TP, Wang C, Chen P, Chen J, Hasing T, Cui C, Zhang X, Zhao B, Huang L. siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. Biotechnology for Biofuels 2018, 11, 208.

Yang J, Liu D, Wang X, Ji C, Cheng F, Liu B, Hu Z, Chen S, Pental D, Ju Y, Yao P, Li X, Xie K, Zhang J, Wang J, Liu F, Ma W, Shopan J, Zheng H, Mackenzie SA, Zhang M. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nature Genetics 2016b, 48, 1225- 1232.

Yang J, Liu G, Zhao N, Chen S, Liu D, Ma W, Hu Z, Zhang M. Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica. Plant Biology 2016a, 18, 527-536.

Yang M, Wang X, Ren D, Huang H, Xu M, He G, Deng XW. Genomic architecture of biomass heterosis in Arabidopsis. Proceedings of the National Academy of Sciences of USA 2017, 114, 8101-8106.

Yang H, Howard M, Dean C. Antagonistic roles for H3K36me3 and H3K27me3 in the cold induced epigenetic switch at Arabidopsis FLC. Current Biology 2014, 24, 1793-1797.

Yang L, Liu P, Wang X, Jia A, Ren D, Tang Y, Tang Y, Deng XW, He G. A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs. Nature Communications 2021, 12, 2317.

Yang M, Wang X, Huang H, Ren D, Su Y, Zhu P, Zhu D, Fan L, Chen L, He G, Deng XW. Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid. Journal of Integrative Plant Biology 2016, 58, 466-474.

Yu D, Gu X, Zhang S, Dong S, Miao H, Gebretsadik K, Bo K. Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding. Horticulture Research 2021, 8, 120.

Yu J, Zhao M, Wang X, Tong C, Huang S, Tehrim S, Liu Y, Hua W, Liu S. Bolbase: A comprehensive genomics database for Brassica oleracea. BMC Genomics 2013, 14, 664.

Yu X, Yang J, Li X, Liu X, Sun C, Wu F, He Y. Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa. BMC Plant Biology 2013, 13, 208.

Yu Y, Zhang Y, Chen X, Chen Y. Plant noncoding RNAs: hidden players in development and stress responses. Annual Review of Cell and Developmental Biology 2019, 35, 407-31.

Zeng Z, Zhang W, Marand AP, Zhu B, Buell CR, Jiang J. Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biology 2019, 20, 123.

Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C, Chen X, Park SY, Liu L, Gallego- Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE. A one precursor one siRNA model for Pol Iv dependent siRNA biogenesis. Cell 2015, 163, 445-455.

Zhang J, Wei L, Jiang J, Mason AS, Li H, Cui C, Chai L, Zheng B, Zhu Y, Xia Q, Jiang L, Fu D. Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species. Scientific Reports 2018, 8, 4960.

Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biology 2009, 10, R62.

Zhang P, Wu W, Chen Q, Chen M. Non-Coding RNAs and their Integrated Networks. Journal of Integrative Bioinformatics 2019, 16, 20190027.

Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biology 2007, 5, e129.

Zhao X, Li J, Lian B, Gu H, Li Y, Qi Y. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nature Communications 2018, 9, 5056.

Zhao XX, Chai Y, Liu B. Epigenetic inheritance and variation of DNA methylation level and pattern in maize intra-specific hybrids. Plant Science 2007, 172, 930-938

Zhao T, Zhan Z, Jiang D. Histone modifications and their regulatory roles in plant development and environmental memory. Journal of Genetics and Genomics 2019, 46, 467-476.

Zhu A, Greaves IK, Dennis ES, Peacock WJ. Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage. BMC Genomics 2017, 18, 137.

Zhu W, Hu B, Becker C, Doğan ES, Berendzen KW, Weigel D, Liu C. Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biology 2017, 18, 157.

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