Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (3): 365-380.doi: 10.3724/SP.J.1006.2019.84099

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Bioinformatics analysis and response to nitrate-cadmium stress of NRT1.5 and NRT1.8 family genes in Brassica napus

Gui-Hong LIANG1,2,Ying-Peng HUA1,2,Ting ZHOU1,2,Qiong LIAO1,2,Hai-Xing SONG1,2,Zhen-Hua ZHANG1,2,*()   

  1. 1 College of Resource and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
    2 Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
  • Received:2018-07-18 Accepted:2018-10-08 Online:2019-03-12 Published:2018-11-02
  • Contact: Zhen-Hua ZHANG E-mail:zhzh1468@163.com
  • Supported by:
    This study was supported by the National Key R&D Program of China(2017YFD0200100);This study was supported by the National Key R&D Program of China(2017YFD0200103);the China Agriculture Research System

Abstract:

The absorption and transportation of nitrate in plants require the assistance of nitrate transporters (NRTs). The expression of two members of the NRT1 family, including NRT1.5 and NRT1.8 genes was strongly induced by nitrate, and regulated the long-distance transport and distribution of nitrate between roots and shoots in Arabidopsis. NRT1.5 and NRT1.8 homologous genes in B. rapa, B. oleracea, and B. napus were identified by bioinformatics with the basic sequences of AtNRT1.5 and AtNRT1.8 and analyzed in gene structures and proteins molecular characterization, gene copy number variations, chromosome locations, evolutionary relationship tree, proteins conservative sequence alignment and the transmembrane domains. NRT1.5 and NRT1.8 responsive to the low concentration nitrate and cadmium stress were also determined by transcriptome analysis and co-expression network analysis, showing that NRT1.5 and NRT1.8 proteins belong to major facilitator superfamily (MFS) and peptide transporter (PTR) with the conservative transmembrane domains and motifs (F-Y-L-A-L-N-L-G-S-L) in B. rapa, B. oleracea, and B. napus. High-throughput transcriptome analysis showed that the expression of NRT1.5 gene was up-regulated and the NRT1.8 was down-regulated by low concentration nitrate treatment for 72 h in roots, which caused more nitrate transferred from roots to shoots. On the contrary, the ethylene/jasmonic acid-NRT signaling module could promote NRT1.8 up-regulation and inhibit the expression of NRT1.5 by cadmium treatment. So that more nitrate transported from shoots to roots and improved the ability of plants to resist cadmium stress. This study is valuable for the research of biological functions of NRT1.5 and NRT1.8 family genes in B. napus and the responses to nitrate-cadmium stress. Our results also provide references for the bioinformatic study of NRT1.5 and NRT1.8 family genes in other plant species.

Key words: Brassica napus, bioinformatics, NRT1.5, NRT1.8, nitrate, cadmium

Table 1

Molecular characterization of NRT1.5 and NRT1.8 genes in B. rapa, B. oleracea, and B. napus"

基因名
Gene name
基因编号
Gene ID
分区
Block
亚类
Subgenome
物理位置
Physical position
编码区长度
CDS (bp)
外显子/内含子Exon/intron
NRT1.5
BraA5.NRT1.5 Bra010165 B MF2 15109908-15113350 1815 5/4
BraA9.NRT1.5 Bra023267 B LF 20166714-20170510 1833 5/4
BolC5.NRT1.5a Bol020904 B MF2 13227461-13230901 1812 5/4
BolC5.NRT1.5b Bol022226 B LF 10183303-10186752 1236 5/4
BnaA5.NRT1.5 BnaA05g35790D B MF2 1269482-1274007 1845 6/5
BnaA9.NRT1.5 BnaA09g24330D B LF 17085147-17089456 1863 6/5
BnaC5.NRT1.5a BnaC05g28620D B MF2 26898087-26903213 1845 6/5
BnaC5.NRT1.5b BnaC05g24580D B LF 19037761-19041900 1860 6/5
NRT1.8
BraA1.NRT1.8 Bra013547 U LF 6243271-6245298 1752 4/3
BraA3.NRT1.8 Bra038763 U MF1 24230588-24232594 1752 4/3
BolC1.NRT1.8 Bol028440 U LF 8086050-8088075 1752 4/3
BolC6.NRT1.8 Bol024295 U MF1 42081659-42082729 897 3/2
BnaA1.NRT1.8 BnaA01g11510D U LF 5715790-5718126 1752 4/3
BnaA3.NRT1.8 BnaA03g44820D U MF1 22774854-22776862 1752 4/3
BnaC7.NRT1.8 BnaC07g36810D U MF1 38737319-38739325 1752 4/3
BnaCn.NRT1.8 BnaCnng78690D U LF 80520183-80521816 1167 3/2

Table 2

Molecular characterization of NRT1.5 and NRT1.8 proteins in B. rapa, B. oleracea, and B. napus"

基因名
Gene name
氨基酸数Amino acids 主要氨基酸 Major amino acids 碱性氨基酸Arg+Lys 酸性氨基酸Asp+Glu 分子量MW(kD) 等电点pI 不稳定系数Instability index 亲水性GRAVY 脂肪指数Aliphatic index
NRT1.5
BraA5.NRT1.5 604 Leu, Ser 58 63 67.64 5.93 34.13 0.096 88.79
BraA9.NRT1.5 610 Leu, Ser 59 62 68.17 6.29 31.20 0.073 89.18
BolC5.NRT1.5a 603 Leu, Ser 58 63 67.45 5.93 33.33 0.094 88.77
BolC5.NRT1.5b 411 Leu, Ser 38 44 45.80 5.63 27.54 -0.006 86.13
BnaA5.NRT1.5 614 Leu, Ser 59 64 68.72 5.93 34.82 0.094 88.62
BnaA9.NRT1.5 620 Leu, Ser 60 64 69.41 6.14 32.08 0.082 89.47
BnaC5.NRT1.5a 614 Leu, Ser 59 64 68.71 5.93 34.68 0.094 88.45
BnaC5.NRT1.5b 619 Leu, Ser 59 62 69.35 6.35 33.07 0.094 89.77
NRT1.8
BraA1.NRT1.8 583 Leu, Ser 48 51 64.72 6.22 27.23 0.209 91.66
BraA3.NRT1.8 583 Leu, Ala 51 51 64.55 7.06 29.40 0.218 94.70
BolC1.NRT1.8 583 Leu, Ser 48 52 64.67 6.05 28.13 0.211 92.16
BolC6.NRT1.8 298 Leu, Ala 26 24 32.84 8.18 18.64 0.088 88.36
BnaA1.NRT1.8 583 Leu, Ser 48 51 64.60 6.22 27.84 0.211 91.17
BnaA3.NRT1.8 583 Leu, Ala 52 51 64.60 7.52 27.69 0.208 94.70
BnaC7.NRT1.8 583 Leu, Ser 53 50 64.67 8.18 27.88 0.207 94.85
BnaCn.NRT1.8 388 Leu, Ser 37 38 43.81 6.60 32.07 0.110 87.96

Fig. 1

Copy number variations of NRT1.5 and NRT1.8 genes in B. rapa, B. oleracea, B. napus, and A. thaliana The number at the top of the histogram is the number of genes copied for that species."

Fig. 10

Supplementary fig. 1 Chromosomal localization of NRT1.5 and NRT1.8 genes in B. rapa, B. oleracea, B. napus, and A. thaliana. Fig. a shows the chromosomal localization of NRT1.5 genes in A. thaliana, B. napus, B. oleracea, and B. rapa. Fig. b shows the chromosomal localization of NRT1.8 genes in A. thaliana, B. napus, B. oleracea, and B. rapa."

Fig. 2

Gene structure characteristics of NRT1.5 and NRT1.8 in B. rapa, B. oleracea, B. napus, and A. thaliana. Fig. a and Fig. b show the gene structure characteristics of NRT1.5 and NRT1.8 respectively in A. thaliana, B. rapa, B. oleracea, and B. napus. The yellow parts represent the CDS sequence and the blue parts represent the upstream and downstream genes. The black lines represent the intron of genes."

Fig. 3

Phylogenetic relationships of the NRT1.5 and NRT1.8 proteins in diverse species. Fig.a and Fig.b show the phylogenetic relationships of NRT1.5 and NRT1.8 proteins respectively in dicots and monocots. The green parts represent the dicots, including Arabidopsis thaliana, Brassica rapa, Brassica oleracea, Brassica napus, and Populus euphratica. The red parts represent the monocots, including Sorghum bicolor, Oryza sativa, Setaria italica, Zea mays, and Brachypodium distachyon."

Fig. 4

Synonymous nucleotide substitution rates (Ks) and non-synonymous nucleotide substitution rates (Ka) of NRT1.5 and NRT1.8 proteins in B. rapa, B. oleracea, and B. napus Fig. a, Fig. b, and Fig. c show synonymous nucleotide substitution rates and non-synonymous nucleotide substitution rates of NRT1.5 proteins in B. rapa, B. oleracea, and B. napus, respectively. Fig. d, Fig. e, and Fig. f show synonymous nucleotide substitution rates and non-synonymous nucleotide substitution rates of the NRT1.8 proteins in B. rapa, B. oleracea, and B. napus, respectively."

Fig. 5

Conservative sequence alignment of NRT1.5 and NRT1.8 proteins in B. rapa, B. oleracea, B. napus, and A. thaliana. Fig. a and Fig. b show the conservative sequence alignment of NRT1.5 and NRT1.8 proteins respectively in A. thaliana, B. rapa, B. oleracea, and B. napus. The blue parts show the conservative sequence (F-Y-L-A-L-N-L-G-S-L) of peptide transporter."

Fig. 6

Characterization of conserved motifs in the NRT1.5 and NRT1.8 proteins in B. rapa, B. oleracea, B. napus, and A. thaliana. Fig. a and Fig. d show the phylogenetic relationships of NRT1.5 and NRT1.8 proteins respectively in A. thaliana, B. rapa, B. oleracea, and B. napus. Fig. b and Fig. e show the motives of NRT1.5 and NRT1.8 proteins respectively in A. thaliana, B. rapa, B. oleracea, and B. napus. Fig. c and Fig. f show the sequence of conserved motif of NRT1.5 and NRT1.8 proteins."

Fig. 7

Transmembrane domains of NRT1.5 and NRT1.8 proteins in B. napus Fig. a to Fig. d show four transmembrane domains of NRT1.5 protein in B. napus. Fig. a, Fig. b, Fig. c, and Fig. d show the protein of Bna.A5.NRT1.5, Bna.A9.NRT1.5, Bna.C5.NRT1.5a, and Bna.C5.NRT1.5b, respectively. Fig. e to Fig. h show four transmembrane domains of NRT1.8 protein in B. napus. Fig. e, Fig.f, Fig. g, and Fig. h show the protein of Bna.A1.NRT1.8, Bna.A3.NRT1.8, Bna.C7.NRT1.8, and Bna.Cn.NRT1.8, respectively."

Fig. 8

Response to low concentration nitrate and co-expression network analysis of NRT1.5 and NRT1.8 genes in B. napus Fig. a shows the gene expression abundance of NRT1.5 family genes in shoots and roots of B. napus with low nitrate treatment for 0 h, 3 h, 72 h. Fig. b shows the co-expression network analysis of NRT1.5 family genes with low nitrate treatment. Fig. c shows the gene expression abundance of NRT1.8 family genes in shoots and roots of B. napus with low nitrate treatment for 0 h, 3 h, 72 h. Fig. d shows the co-expression network analysis of NRT1.8 family genes with low nitrate treatment. FPKM means the fragments per kilobase of exon model per million mapped reads."

Fig. 9

Response to cadmium stress and co-expression network analysis of NRT1.5 and NRT1.8 genes Fig. a and Fig. b show the gene expression abundance of NRT1.5 family genes in shoots and roots of B. napus with cadmium stress. Fig. c shows the co-expression network analysis of NRT1.5 family genes with cadmium stress. Fig. d and Fig. e show the gene expression abundance of NRT1.8 family genes in shoots and roots of B. napus with cadmium stress. Fig. f shows the co-expression network analysis of NRT1.8 family genes with cadmium stress. FPKM means the fragments per kilobase of exon model per million mapped reads. The significant difference shown in the figure is the pairwise comparison between control and cadmium treatment, and the figure without significant difference is not marked. Data are shown as means±SE (n = 3) and the different lowercases above text are used to show statistical significance (Ρ < 0.05)."

[1] 李建勇, 龚继明 . 植物硝酸根信号感受与传导途径. 植物生理学报, 2011,47:111-118.
Li J Y, Gong J M . Nitrate signal sensing and transduction in higher plants. Plant Physiol J, 2011,47:111-118 (in Chinese with English abstract).
[2] Tang Y, Sun X C, Hu C X, Tan Q L, Zhao X H . Genotypic differences in nitrate uptake, translocation and assimilation of two Chinese cabbage cultivars [ Brassica campestris L. ssp. Chinesnsis( L.)]. Plant Physiol Biochem, 2013,70:14-20.
[3] Fan S C, Lin C S, Hsu P K, Lin S H, Tsay Y F . The Arabidopsis nitrate transporter NRT1.7, expressed in phloem, is responsible for source-to-sink remobilization of nitrate. Plant Cell, 2009,21:2750-2761.
doi: 10.1105/tpc.109.067603 pmid: 19734434
[4] Orsel M, Chopin F, Leleu O, Smith S J, Krapp A, Daniel-Vedele F, Miller A J . Characterization of a two-component high-affinity nitrate uptake system in Arabidopsis. Physiology and protein- protein interaction. Plant Physiol, 2006,142:1304-1317.
doi: 10.1104/pp.106.085209 pmid: 17012411
[5] Møller A L, Pedas P, Andersen B, Svensson B, Schjoerring J K, Finnie C . Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium. Plant Cell Environ, 2011,34:2024-2037.
doi: 10.1111/j.1365-3040.2011.02396.x pmid: 21736591
[6] 张振华 . 作物硝态氮转运利用与氮素利用效率的关系. 植物营养与肥料学报, 2017,23:217-223.
doi: 10.11674/zwyf.15357
Zhang Z H . The relationship between nitrate transport and utilization in crop and nitrogen utilization efficiency. J Plant Nutr, 2017,23:217-223 (in Chinese with English abstract).
doi: 10.11674/zwyf.15357
[7] Dechorgnat J, Nguyen C T, Armengaud P, Jossier M, Diatloff E, Filleur S, Daniel-Vedele F . From the soil to the seeds: the long journey of nitrate in plants. J Exp Bot, 2011,62:1349-1359.
doi: 10.1093/jxb/erq409 pmid: 21193579
[8] Lin S H, Kuo H F, Canivenc G, Lin C S, Lepetit M, Hsu P K, Tillard P, Lin H L, Wang Y Y, Tsai C B, Gojon A, Tsay Y F . Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport. Plant Cell, 2008,20:2514-2528.
doi: 10.1105/tpc.108.060244 pmid: 18780802
[9] Chen C Z, Lv X F, Li J Y, Yi H Y, Gong J M . Arabidopsis NRT1.5 is another essential component in the regulation of nitrate reallocation and stress tolerance. Plant Physiol, 2012,159:1582-1590.
doi: 10.1104/pp.112.199257 pmid: 22685171
[10] Li J Y, Fu Y L, Pike S M, Bao J, Tian W, Zhang Y, Chen C Z, Zhang Y, Li H M, Huang J, Li L G, Schroeder J I, Gassmann W, Gong J M . The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and mediates cadmium tolerance. Plant Cell, 2010,22:1633-1646.
doi: 10.1105/tpc.110.075242 pmid: 20501909
[11] Zhang G B, Yi H Y, Gong J M . The Arabidopsis ethylene/jasmonic acid-NRT signaling module coordinates nitrate reallocation and the trade-off between growth and environmental adaption. Plant Cell, 2014,26:3984-3998.
doi: 10.1105/tpc.114.129296 pmid: 25326291
[12] Léran S, Varala K, Boyer J C, Chiurazzi M, Crawpord N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong J M, Halkier B A, Harris J M, Hedrich R, Limami A M, Rentsch D, Seo M, Tsay Y F, Zhang M, Coruzzi G, Lacombe B . A unified nomenclature of nitrate transporter 1/peptide transporter family members in plants. Trends Plant Sci, 2014,19:5-9.
doi: 10.1016/j.tplants.2013.08.008 pmid: 24055139
[13] 宋田丽, 周建建, 徐晨曦, 蔡晓锋, 戴绍军, 王全华, 王小丽 . 植物硝酸盐转运蛋白功能及表达调控研究进展. 上海师范大学学报(自然科学版), 2017,46:740-750.
doi: 10.3969/J.ISSN.1000-5137.2017.05.019
Song T L, Zhou J J, Xu C X, Cai X F, Dai S J, Wang Q H, Wang X L . Progress in function and regulation of nitrate transporters in plants. J Shanghai Nor Univ ( Nat Sci), 2017,46:740-750 (in Chinese with English abstract).
doi: 10.3969/J.ISSN.1000-5137.2017.05.019
[14] 殷艳, 陈兆波, 余健, 王汉中, 冯中朝 . 我国油菜生产潜力分析. 中国农业科技导报, 2010,12(3):16-21.
doi: 10.3969/j.issn.1008-0864.2010.03.03
Yin Y, Chen Z B, Yu J, Wang H Z, Feng Z C . Analysis of potential for rapeseed production in China. J Agric Sci Tech, 2010,12(3):16-21 (in Chinese with English abstract).
doi: 10.3969/j.issn.1008-0864.2010.03.03
[15] Blackshaw R E, Johnson E N, Gan Y T, May W E ,McAndrew D W, Barthet V, McDonald T, Wispinski D. Alternative oilseed crops for biodiesel feedstock on the Canadian prairies. Plant Sci, 2011,91:889-896.
doi: 10.4141/cjps2011-002
[16] Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J H, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires J C, Paterson A H, Chalhoub B, Wang B, Hayward A, Sharpe A G, Park B S, 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 G J, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin I A, Batley J, Kim J S, Just J, Li J, Xu J, Deng J, Kim J A, 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 M G, Zhao M, Jin M, Ramchiary N, Drou N, Berkman P J, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S J, Choi S R, Lee T H, 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. Nat Genet, 2011,43:1035-1039.
[17] Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin I A, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang T J, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King G J, Pires J C, 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 A G, Park B S, Ruperao P, Cheng F, Waminal N E, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee T H, 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 H H, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson A H . The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun, 2014,5:3930.
[18] Bayer P E, Hurgobin B, Golicz A A, Chen C K, Yuan Y, Lee H, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King G J, Batley J, Edwards D . Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J, 2017,15:1602-1610
doi: 10.1111/pbi.12742 pmid: 5698052
[19] Chalhoub B, Denoeud F, Liu S, Parkin I A, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh C S, 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 P P, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N ,Le Paslier M C, Fan G, Renault V, Bayer P E, Golicz A A, Manoli S, Lee T H, Thi V H, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom C H, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim Y P, Lyons E, Town C D, Bancroft I, Wang X, Meng J, Ma J, Pires J C, King G J, Brunel D, Delourme R, Renard M, Aury J M, Adams K L, Batley J, Snowdon R J, Tost J, Edwards D, Zhou Y, Hua W, Sharpe A G, Paterson A H, Guan C, Wincker P. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014,345:950-953.
[20] 轩红梅, 王永华, 魏利婷, 杨莹莹, 王利娜, 康国章, 郭天财 . 小麦幼苗叶片中硝酸盐转运蛋白NRT1NRT2家族基因对氮饥饿响应的表达分析. 麦类作物学报, 2014,34:1019-1028.
doi: 10.7606/j.issn.1009-1041.2014.08.01
Xuan H M, Wang Y H, Wei L T, Yang Y Y, Wang L N, Kang G Z, Guo T C . Transcription analysis of the genes encoding nitrate transporter NRT1 and NRT2 family in response to nitrogen starvation in wheat seedlings leaves. J Triticeae Crops, 2014,34:1019-1028 (in Chinese with English abstract).
doi: 10.7606/j.issn.1009-1041.2014.08.01
[21] 马翠 . 水稻硝酸盐转运蛋白基因OsNRT1.2OsNRT1.5超量表达材料的功能鉴定. 南京农业大学硕士论文, 江苏南京, 2011.
doi: 10.7666/d.Y2038161
Ma C . Characteristics of Over-expression for Nitrate Transporter Genes OsNRT1.2 and OsNRT1.5 in Rice. MS Thesis of Nanjing Agricultural University, Nanjing, Jiangsu, China, 2011 (in Chinese with English abstract).
doi: 10.7666/d.Y2038161
[22] 李红 . 拟南芥转运蛋白NRT1.5/NPF7.3调控K+在木质部装载的分子机制研究. 中国农业大学博士学位论文,北京, 2016.
Li H . Mechanism analyses of NRT1.5/NPF7.3-mediated K + release into the xylem in Arabidopsis. ChinaPhD Dissertation of China Agricultural University, Beijing, 2016 (in Chinese with English abstract).
[23] Wang X B, Wu J, Liang J L, Cheng F, Wang X W . Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. Database, 2015, 1-8.
[24] Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins M R, Appel R D, Bairoch A. Protein identification and analysis tools on the ExPASy server. In: Walker J M ed. The Proteomics Protocols Handbook. Totowa, NJ, USA: Humana Press Inc, 2005. pp 571-607.
[25] Hu B, Jin J, Guo A Y, Zhang H, Luo J, Gao G . GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 2015,31:1296-1297
doi: 10.1093/bioinformatics/btu817 pmid: 25504850
[26] Smith T F, Waterman M S . Identification of common molecular subsequences. J Mol Biol, 1981,147, 195-197.
doi: 10.1016/0022-2836(81)90087-5 pmid: 7265238
[27] Tamura K, Stecher G, Peterson D, Filipski A, Kumar S . MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 2013,30:2725-2729.
doi: 10.1093/molbev/mst197
[28] Larkin M A, Blackshields G, Brown N P, Chenna R ,McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. Clustal W and clustal X version 2.0. Bioinformatics, 2007,23:2947-2948.
doi: 10.1093/bioinformatics/btm404 pmid: 17846036
[29] Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987,4:406-425.
[30] Bailey T L, Boden M, Buske F A, Frith M, Grant C E, Clementi L, Ren J, Li W W, Noble W S . MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 2009,37(Web Server issue):W202-W208.
doi: 10.1093/nar/gkp335 pmid: 19458158
[31] Hofmann K, Stoffel W . TMBase: a database of membrane spanning protein segments. Biol Chem Hoppe Seyler, 1993,374:166
[32] Hoagland D R, Arnon D I . The water culture method for growing plants without soil. California Agric Exp Stn Cireular, 1950,347:1-32.
doi: 10.1016/S0140-6736(00)73482-9
[33] Morin R D, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T J ,McDonald H, Varhol R, Jones S J, Marra M A. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Bio Techniques, 2008,45:81-94.
[34] Hua Y P, Zhou T, Xu F S . Genome-scale mRNA transcriptomic insights into the responses of oilseed rape ( Brassica napus L.) to varying boron availabilities. Plant Soil, 2017,416:205-225.
doi: 10.1007/s11104-017-3204-2
[35] Guruprasad K, Reddy B V, Pandit M W . Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng, 1990,4:155-161.
doi: 10.1093/protein/4.2.155
[36] 王占军, 金伦, 徐忠东, 欧祖兰 . 麻风树LEC1基因的生物信息学分析. 生物学杂志, 2014,31(4):68-72.
doi: 10.3969/j.issn.2095-1736.2014.04.068
Wang Z J, Jin L, Xu Z D, Ou Z L . Bioinformatics analysis of gene LEC1 from Jatropha curcas. J Biol, 2014,31(4):68-72 (in Chinese with English abstract).
doi: 10.3969/j.issn.2095-1736.2014.04.068
[37] Hua Y P, Zhou T, Song H X, Guan C Y, Zhang Z H . Integrated genomic and transcriptomic insights into the two-component high-affinity nitrate transporters in allotetraploid rapeseed. Plant Soil, 2018,427:245-268.
doi: 10.1007/s11104-018-3652-3
[38] Cheng F, Wu J, Fang L, Wang X . Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci, 2012,3:198.
[39] Nekrutenko A, Makova K D, Li W H . The Ka/Ks ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res, 2002,12:198-202.
doi: 10.1101/gr.200901
[40] Forde B G . Nitrate transporters in plants: structure, function and regulation. Biochim Biophys Acta, 2000,1465:219-235.
doi: 10.1016/S0005-2736(00)00140-1 pmid: 10748256
[41] Chakrabarti S, Bryant S H, Panchenko A R . Functional specificity lies within the properties and evolutionary changes of amino acids. J Mol Biol, 2007,373:801-810.
doi: 10.1016/j.jmb.2007.08.036 pmid: 2605514
[42] Tsay Y F, Chiu C C, Tsai C B, Ho C H, Hsu P K . Nitrate transporters and peptide transporters. FEBS Lett, 2007,581:2290-2300.
doi: 10.1016/j.febslet.2007.04.047 pmid: 17481610
[43] 尹辉, 牟书勇, 李冠 . 植物硝酸盐转运体的功能及其调控. 南方农业学报, 2012,43:425-430.
doi: 10.3969/j:issn.2095-1191.2012.04.425
Yin H, Mu S Y, Li G . Function and regulation of nitrate transporters in plants. J Southern Agric, 2012,43:425-430 (in Chinese with English abstract).
doi: 10.3969/j:issn.2095-1191.2012.04.425
[44] 汪进, 添先凤, 江昌俊, 李叶云 . 茶树硝酸盐转运蛋白基因的克隆和表达分析. 植物生理学报, 2014,50:983-988.
Wang J, Tian X F, Jiang C J, Li Y Y . Cloning and expression analysis of nitrate transporter gene in Camellia sinensis. Plant Physiol J, 2014,50:983-988 (in Chinese with English abstract).
[45] Almagro A, Lin S H, Tsay Y F . Characterization of the Arabidopsis nitrate transporter NRT1.6 reveals a role of nitrate in early embryo development. Plant Cell, 2008,20:3289-3299.
[46] 童依平, 蔡超, 刘全友, 李继云, 李振声 . 植物吸收硝态氮的分子生物学进展. 植物营养与肥料学报, 2004,10:433-440.
doi: 10.3321/j.issn:1008-505X.2004.04.018
Tong Y P, Cai C, Liu Q Y, Li J Y, Li Z S . Recent advances in molecular biology of nitrate transporters in higher plants. J Plant Nutr, 2004,10:433-440 (in Chinese with English abstract).
doi: 10.3321/j.issn:1008-505X.2004.04.018
[47] Theissen G, Becker A, Di Rosa A, Kanno A, Kim J T, Münster T, Winter K U, Saedler H . A short history of MADS-box genes in plants. Plant Mol Biol, 2000,42:115-149.
doi: 10.1023/A:1006332105728
[48] Kaufmann K, Melzer R, Theissen G . MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene, 2005,347:183-198.
doi: 10.1016/j.gene.2004.12.014 pmid: 15777618
[49] Wang P, Wang Z L, Cai R G, Li Y, Chen X G, Yin Y P . Physiological and molecular response of wheat roots to nitrate supply in seedling stage. Agric Sci China, 2011,10:695-704.
doi: 10.1016/S1671-2927(11)60052-7
[1] CHEN Song-Yu, DING Yi-Juan, SUN Jun-Ming, HUANG Deng-Wen, YANG Nan, DAI Yu-Han, WAN Hua-Fang, QIAN Wei. Genome-wide identification of BnCNGC and the gene expression analysis in Brassica napus challenged with Sclerotinia sclerotiorum and PEG-simulated drought [J]. Acta Agronomica Sinica, 2022, 48(6): 1357-1371.
[2] YUAN Da-Shuang, DENG Wan-Yu, WANG Zhen, PENG Qian, ZHANG Xiao-Li, YAO Meng-Nan, MIAO Wen-Jie, ZHU Dong-Ming, LI Jia-Na, LIANG Ying. Cloning and functional analysis of BnMAPK2 gene in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(4): 840-850.
[3] WU Yan-Fei, HU Qin, ZHOU Qi, DU Xue-Zhu, SHENG Feng. Genome-wide identification and expression analysis of Elongator complex family genes in response to abiotic stresses in rice [J]. Acta Agronomica Sinica, 2022, 48(3): 644-655.
[4] HUANG Cheng, LIANG Xiao-Mei, DAI Cheng, WEN Jing, YI Bin, TU Jin-Xing, SHEN Jin-Xiong, FU Ting-Dong, MA Chao-Zhi. Genome wide analysis of BnAPs gene family in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(3): 597-607.
[5] WANG Rui, CHEN Xue, GUO Qing-Qing, ZHOU Rong, CHEN Lei, LI Jia-Na. Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(3): 759-769.
[6] JIAN Hong-Ju, SHANG Li-Na, JIN Zhong-Hui, DING Yi, LI Yan, WANG Ji-Chun, HU Bai-Geng, Vadim Khassanov, LYU Dian-Qiu. Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 86-98.
[7] WANG Yan-Hua, LIU Jing-Sen, LI Jia-Na. Integrating GWAS and WGCNA to screen and identify candidate genes for biological yield in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(8): 1491-1510.
[8] LI Jie-Hua, DUAN Qun, SHI Ming-Tao, WU Lu-Mei, LIU Han, LIN Yong-Jun, WU Gao-Bing, FAN Chu-Chuan, ZHOU Yong-Ming. Development and identification of transgenic rapeseed with a novel gene for glyphosate resistance [J]. Acta Agronomica Sinica, 2021, 47(5): 789-798.
[9] HUANG Ning, HUI Qian-Long, FANG Zhen-Ming, LI Shan-Shan, LING Hui, QUE You-Xiong, YUAN Zhao-Nian. Identification, localization and expression analysis of beta-carotene isomerase gene family in sugarcane [J]. Acta Agronomica Sinica, 2021, 47(5): 882-893.
[10] TANG Xin, LI Yuan-Yuan, LU Jun-Xing, ZHANG Tao. Morphological characteristics and cytological study of anther abortion of temperature-sensitive nuclear male sterile line 160S in Brassica napus [J]. Acta Agronomica Sinica, 2021, 47(5): 983-990.
[11] ZHOU Xin-Tong, GUO Qing-Qing, CHEN Xue, LI Jia-Na, WANG Rui. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 587-598.
[12] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[13] TANG Jing-Quan, WANG Nan, GAO Jie, LIU Ting-Ting, WEN Jing, YI Bin, TU Jin-Xing, FU Ting-Dong, SHEN Jin-Xiong. Bioinformatics analysis of SnRK gene family and its relation with seed oil content of Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(3): 416-426.
[14] MENG Jiang-Yu, LIANG Guang-Wei, HE Ya-Jun, QIAN Wei. QTL mapping of salt and drought tolerance related traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(3): 462-471.
[15] WEI Li-Juan, SHEN Shu-Lin, HUANG Xiao-Hu, MA Guo-Qiang, WANG Xi-Tong, YANG Yi-Ling, LI Huan-Dong, WANG Shu-Xian, ZHU Mei-Chen, TANG Zhang-Lin, LU Kun, LI Jia-Na, QU Cun-Min. Genome-wide association analysis reveals zinc-tolerant loci of rapeseed at germination stage [J]. Acta Agronomica Sinica, 2021, 47(2): 262-274.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!