{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T22:42:10Z","timestamp":1788302530611,"version":"build-2803163510"},"reference-count":54,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Earmarked Fund for China Agriculture Research System","award":["CARS-13"],"award-info":[{"award-number":["CARS-13"]}]},{"DOI":"10.13039\/501100013077","name":"National Science and Technology Support Project of China","doi-asserted-by":"publisher","award":["2014BAD11B03"],"award-info":[{"award-number":["2014BAD11B03"]}],"id":[{"id":"10.13039\/501100013077","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oil Crop Innovation Team in Yunnan Province, China","award":["2017HC021"],"award-info":[{"award-number":["2017HC021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Nitrate (NO3\u2212) and ammonium (NH4+) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted \u201c15\u201d) and 814 (low N efficiency, denoted \u201c814\u201d), were inhibited under NH4+ nutrition, though both cultivars grew normally under NO3\u2212 nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO3\u2212 (NT), and NH4+ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and CESA genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment.<\/jats:p>","DOI":"10.3390\/genes10050391","type":"journal-article","created":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T03:22:03Z","timestamp":1558581723000},"page":"391","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Comparative Transcriptome Analysis in Oilseed Rape (Brassica napus) Reveals Distinct Gene Expression Details between Nitrate and Ammonium Nutrition"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5883-9744","authenticated-orcid":false,"given":"Weijie","family":"Tang","sequence":"first","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"},{"name":"College of Agronomy and Biotechnology, Yunan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"He","sequence":"additional","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"},{"name":"Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lunwen","family":"Qian","sequence":"additional","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"},{"name":"Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Wang","sequence":"additional","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8877-1090","authenticated-orcid":false,"given":"Zhenhua","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Agronomy and Biotechnology, Yunan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangbin","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Agronomy and Biotechnology, Yunan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyun","family":"Guan","sequence":"additional","affiliation":[{"name":"National Center of Oilseed Crops Improvement, Hunan Branch, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s11104-008-9733-y","article-title":"Effects of different nitrogen forms on the growth and cytokinin content in xylem sap of tomato (Lycopersicon esculentum Mill.) seedlings","volume":"315","author":"Lu","year":"2009","journal-title":"Plant Soil"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.gene.2014.11.021","article-title":"RNA-seq analysis of differentially expressed genes in rice under varied nitrogen supplies","volume":"555","author":"Yang","year":"2015","journal-title":"Gene"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/aob\/mcl258","article-title":"Effect of nitrogen form and root-zone ph on growth and nitrogen uptake of tea (Camellia sinensis) plants","volume":"99","author":"Ruan","year":"2006","journal-title":"Ann. Bot."},{"key":"ref_4","first-page":"48","article-title":"Blueberry physiological ecology research progress in our country","volume":"3","author":"Wu","year":"2006","journal-title":"North. Hortic."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s11104-009-0110-2","article-title":"Wheat growth in a saline sandy loam soil as affected by N form and application rate","volume":"328","author":"Elgharably","year":"2010","journal-title":"Plant Soil"},{"key":"ref_6","first-page":"14","article-title":"Effect of nitrate\/ammonium ratios on growth, root morphology and nutrient elements uptake of watermelon (Citrullus lanatus) seedlings","volume":"37","author":"Liu","year":"2014","journal-title":"J. Plant Nutr."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1093\/pcp\/pcs012","article-title":"Nitrate addition alleviates ammonium toxicity without lessening ammonium accumulation, organic acid depletion and inorganic cation depletion in Arabidopsis thaliana shoots","volume":"53","author":"Hachiya","year":"2012","journal-title":"Plant Cell Physiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.agee.2006.04.006","article-title":"Integrated nitrogen management strategies to improve seed yield, oil content and nitrogen efficiency of winter oilseed rape (Brassica napus L.). A review","volume":"117","author":"Rathke","year":"2006","journal-title":"Agric. Ecosyst. Environ."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1626\/pps.15.265","article-title":"Responses of seed yield and quality to nitrogen application levels in two oilseed rape (Brassica napus L.) varieties differing in nitrogen efficiency","volume":"15","author":"Zhang","year":"2012","journal-title":"Plant Prod. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2546","DOI":"10.2135\/cropsci2012.02.0134","article-title":"Nitrogen use efficiency in a genetically diverse set of winter oilseed rape (Brassica napus L.)","volume":"52","author":"Kessel","year":"2012","journal-title":"Crop Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/BF00329797","article-title":"Interspecies differences in the preference of ammonium and nitrate in vascular plants","volume":"102","author":"Falkengrengrerup","year":"1995","journal-title":"Oecologia"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/B978-0-444-88900-3.50033-3","article-title":"Dissimilative nitrate reduction to ammonium in different soils in waterlogged conditions","volume":"6","author":"Correa","year":"1991","journal-title":"Develop. Geochem."},{"key":"ref_13","first-page":"1338","article-title":"Effects of nitrate and ammonium supply ratios on growth, physiology and yield of oilseed rape (Brassica napus L.)","volume":"24","author":"Tang","year":"2018","journal-title":"J. Plant Nutr. Fert."},{"key":"ref_14","first-page":"1486","article-title":"Distinct signalling pathways and transcriptome response signatures differentiate ammonium- and nitrate-supplied plants","volume":"33","author":"Patterson","year":"2010","journal-title":"Plant Cell Environ."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/s11738-018-2701-0","article-title":"Transcriptome analysis using RNA-seq revealed the effects of nitrogen form on major secondary metabolite biosynthesis in tea (Camellia sinensis) plants","volume":"40","author":"Yang","year":"2018","journal-title":"Acta Physiol. Plant."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1104\/pp.15.01377","article-title":"Nitrogen use efficiency is mediated by vacuolar nitrate sequestration capacity in roots of Brassica napus","volume":"170","author":"Han","year":"2016","journal-title":"Plant Physiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.1080\/00103624.2010.489134","article-title":"Nitrogen redistribution characteristics of oilseed rape varieties with different nitrogen use efficiencies during later growth period","volume":"41","author":"Zhang","year":"2010","journal-title":"Commun. Soil Sci. Plant Anal."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1007\/s11105-013-0696-7","article-title":"Evidence for apoplasmic phloem unloading in pear fruit","volume":"32","author":"Zhang","year":"2014","journal-title":"Plant Mol. Biol. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1126\/science.1253435","article-title":"Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome","volume":"345","author":"Chalhoub","year":"2014","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript level expression analysis of RNA-seq experiments with hisat, stringtie and ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"Stringtie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"Go:: Termfinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3493","DOI":"10.3390\/ijms16023493","article-title":"Transcriptome profiling and identification of transcription factors in ramie (Boehmeria nivea L. gaud) in response to peg treatment, using illumina paired-end sequencing technology","volume":"16","author":"An","year":"2015","journal-title":"Int. J. Mol. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s11104-009-0245-1","article-title":"Ammonium nutrition increases water absorption in rice seedlings (Oryza sativa L.) under water stress","volume":"331","author":"Gao","year":"2010","journal-title":"Plant Soil"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/289292a0","article-title":"Vacuoles as storage compartments for nitrate in barley leaves","volume":"289","author":"Martinoia","year":"1981","journal-title":"Nature"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1093\/pcp\/pcd059","article-title":"Transport processes of solutes across the vacuolar membrane of higher plants","volume":"41","author":"Martinoia","year":"2000","journal-title":"Plant Cell Physiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Jian, S.F., Liao, Q., Song, H.X., Liu, Q., Lepo, J.E., Guan, C.Y., Zhang, J.H., Ismail, A.M., and Zhang, Z.H. (2018). NRT1.1-related NH4+ toxicity is associated with a disturbed balance between NH4+ uptake and assimilation. Plant Physiol.","DOI":"10.1101\/241174"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"562","DOI":"10.2134\/agronj1982.00021962007400030037x","article-title":"Analysis and interpretation of factors which contribute to efficiency of nitrogen utilization","volume":"74","author":"Moll","year":"1982","journal-title":"Agron. J."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Sinha, S.K., Sevanthi, V.A.M., Chaudhary, S., Tyagi, P., Venkadesan, S., Rani, M., and Mandal, P.K. (2018). Transcriptome Analysis of two rice varieties contrasting for nitrogen use efficiency under chronic N starvation reveals differences in chloroplast and starch metabolism-related genes. Genes, 9.","DOI":"10.3390\/genes9040206"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2757","DOI":"10.1534\/g3.118.200481","article-title":"Genomics-assisted identification and characterization of the genetic variants underlying differential nitrogen use efficiencies in allotetraploid rapeseed genotypes","volume":"8","author":"Hua","year":"2018","journal-title":"G3"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Zhang, Z.H., Zhou, T., Liao, Q., Yao, J.Y., Liang, G.H., Song, H.X., Guan, C.Y., and Hua, Y.P. (2018). Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation. BMC Plant Biol., 18.","DOI":"10.1186\/s12870-018-1507-y"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Wittgenstein, N.J.V., Le, C.H., Hawkins, B.J., and Ehlting, J. (2014). Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants. BMC Evol. Biol., 14.","DOI":"10.1186\/1471-2148-14-11"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1007\/s004250050372","article-title":"Regulation of GmNRT2 expression and nitrate transport activity in roots of soybean (Glycine max)","volume":"206","author":"Amarasinghe","year":"1998","journal-title":"Planta"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/pcp\/pcg036","article-title":"Regulation of NRT1 and NRT2 gene families of Arabidopsis thaliana: Responses to nitrate provision","volume":"44","author":"Okamoto","year":"2003","journal-title":"Plant Cell Physiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1046\/j.1365-3040.2003.01023.x","article-title":"Differential expression of three members of the AMT1 gene family encoding putative high-affinity NH4+ transporters in roots of Oryza sativa subspecies indica","volume":"26","author":"Kumar","year":"2010","journal-title":"Plant Cell Environ."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1105\/tpc.108.060244","article-title":"Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport","volume":"20","author":"Lin","year":"2008","journal-title":"Plant Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1105\/tpc.110.075242","article-title":"The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and mediates cadmium tolerance","volume":"22","author":"Li","year":"2010","journal-title":"Plant Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.plaphy.2013.04.027","article-title":"Genotypic differences in nitrate uptake, translocation and assimilation of two Chinese cabbage cultivars [Brassica campestris L. ssp. Chinensis (L.)]","volume":"70","author":"Tang","year":"2013","journal-title":"Plant Physiol. Bioch."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/nature05013","article-title":"The nitrate\/proton antiporer AtCLC a mediates nitrate accumulation in plant vacuoles","volume":"442","author":"Angeli","year":"2006","journal-title":"Nature"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1093\/pcp\/pcq062","article-title":"CLC-b mediated NO3\u2212\/H+ exchange across the tonoplast of Arabidopsis vacuoles","volume":"51","author":"Fechtbartenbach","year":"2010","journal-title":"Plant Cell Physiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/BF00281630","article-title":"Identification and characterization of a chlorate-resistant mutant of Arabidopsis thaliana with mutations in both nitrate reductase structural genes NIA1 and NIA2","volume":"239","author":"Wilkinson","year":"1993","journal-title":"Mol. Gen. Genet. MGG"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1111\/j.1399-3054.1992.tb04712.x","article-title":"Structure, function and regulation of nitrate reductase in higher plants","volume":"84","author":"Hoff","year":"1992","journal-title":"Physilol. Plantarum"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1104\/pp.111.1.39","article-title":"Development stage-specific and nitrate-independent regulation of nitrate reductase gene expression in rapeseed","volume":"111","author":"Fukuoka","year":"1996","journal-title":"Plant Physiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4308","DOI":"10.1104\/pp.104.047548","article-title":"Glutamatedehydrogenase of tobacco (Nicotiana tabacum L.) is mainly induced in the cytosol of phloem companion cells whenammonia is provided either externally or released during photorespiration","volume":"136","author":"Dubois","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/S0176-1617(99)80110-2","article-title":"Cd-stress on nitrogen assimilation","volume":"155","author":"Boussama","year":"1994","journal-title":"J. Plant Physiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.plantsci.2014.12.005","article-title":"Overcoming ammonium toxicity","volume":"231","author":"Pilinszkya","year":"2015","journal-title":"Plant Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.3389\/fpls.2017.01079","article-title":"Nitrogen metabolism in adaptation of photosynthesis to water stress in rice grown under different nitrogen levels","volume":"8","author":"Zhong","year":"2017","journal-title":"Front. Plant Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.plantsci.2017.12.012","article-title":"Root cell wall solutions for crop plants in saline soils","volume":"269","author":"Byrt","year":"2018","journal-title":"Plant Sci."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Irshad, M., Canut, H., Borderies, G., Pont-Lezica, R., and Jamet, E. (2008). A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers. BMC Plant Biol., 8.","DOI":"10.1186\/1471-2229-8-94"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1104\/pp.124.2.495","article-title":"The cellulose synthase superfamily","volume":"124","author":"Richmond","year":"2000","journal-title":"Plant Physiol."},{"key":"ref_53","first-page":"33","article-title":"Cellulose and cell elongation","volume":"5","year":"2006","journal-title":"Plant Cell Monogr."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1093\/pcp\/pcf164","article-title":"Cellulose biosynthesis in plants: From genes to rosettes. A review","volume":"43","author":"Doblin","year":"2002","journal-title":"Plant Cell Physiol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/5\/391\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:54:20Z","timestamp":1760187260000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/5\/391"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":54,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5]]}},"alternative-id":["genes10050391"],"URL":"https:\/\/doi.org\/10.3390\/genes10050391","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,22]]}}}