Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (4): 86-96.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0185
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WANG Rong-hua(), WANG Shu-bin, ZHANG Zhi-gang, ZHAO Zhi-zhong, LI Qiao-yun, WANG Li-hua, LIU Shuan-tao
Received:
2022-02-15
Online:
2022-04-26
Published:
2022-05-06
WANG Rong-hua, WANG Shu-bin, ZHANG Zhi-gang, ZHAO Zhi-zhong, LI Qiao-yun, WANG Li-hua, LIU Shuan-tao. Genome-wide Characterization of KCS Gene Family in Brassica rapa and Their Expression Profiling in Waxy Near-isogenic Lines[J]. Biotechnology Bulletin, 2022, 38(4): 86-96.
基因名称Gene | 正向引物Forward primer sequence(5'-3') | 反向引物Reverse primer sequence(5'-3') |
---|---|---|
BrKCS1a | CCGCTACAAGATGAGAGAAGACA | GGTTAGAGAGGAGAATCGCTGC |
BrKCS2a | CGTCCTCGCAAAGTATTCCTC | GGAAAGTAAGTCTTCTGTCCTAAACCG |
BrKCS5 | GCTATTCACTACATCCCTCCAACTC | CGAGAGAGAAGGCGTTGGT |
BrKCS6a | CCTCAACGACAAGCCTAAGC | GCCTCACTTGTAGCCTCGTTC |
BrKCS6b | GTGTCCCCTTCGCAACTTTC | GGTTGGTGTCGGAGGAATG |
BrKCS7a | GGGAGCAAGACAAGCCTAATG | TGAGGACCTAACTCCACCACG |
BrKCS7b | ACCCTGATGATGCTCGCCT | GTAAGTGCCCTTGTGCTCATCA |
BrKCS9a | GGTGTAGTGCTGGTGTTATCTCC | GGATCAGCATCGCCTTCTTA |
BrKCS9b | TGAGGGTTTGCACTGCGT | GTCGGGTTGAACAAGCTGC |
BrKCS9c | GCGAGGAGTCGTCTTTGGA | CTGGAGAGGTGGAACGCTATG |
BrKCS10a | GTTTCTTTAGGATGGGGTGCTC | GTCGGCAGCCTTATGAGTC |
BrKCS10b | CGACTCCGTCACTATCTGCCA | GGCTATGATTCCCGCTGAG |
BrKCS13 | GCCAAAGGTGCTCAACTCTACA | GAGGTCAGCATGCAACGTG |
BrKCS20a | CTATCCTCTACAACCACCTCCG | AAGACACGGCGAGGACGA |
G6PD | GGGTATGCCAGGACTAAGCTC | GAATCATAAGGGCCACTCACAT |
Table 1 Primer sequences for qRT-PCR analysis
基因名称Gene | 正向引物Forward primer sequence(5'-3') | 反向引物Reverse primer sequence(5'-3') |
---|---|---|
BrKCS1a | CCGCTACAAGATGAGAGAAGACA | GGTTAGAGAGGAGAATCGCTGC |
BrKCS2a | CGTCCTCGCAAAGTATTCCTC | GGAAAGTAAGTCTTCTGTCCTAAACCG |
BrKCS5 | GCTATTCACTACATCCCTCCAACTC | CGAGAGAGAAGGCGTTGGT |
BrKCS6a | CCTCAACGACAAGCCTAAGC | GCCTCACTTGTAGCCTCGTTC |
BrKCS6b | GTGTCCCCTTCGCAACTTTC | GGTTGGTGTCGGAGGAATG |
BrKCS7a | GGGAGCAAGACAAGCCTAATG | TGAGGACCTAACTCCACCACG |
BrKCS7b | ACCCTGATGATGCTCGCCT | GTAAGTGCCCTTGTGCTCATCA |
BrKCS9a | GGTGTAGTGCTGGTGTTATCTCC | GGATCAGCATCGCCTTCTTA |
BrKCS9b | TGAGGGTTTGCACTGCGT | GTCGGGTTGAACAAGCTGC |
BrKCS9c | GCGAGGAGTCGTCTTTGGA | CTGGAGAGGTGGAACGCTATG |
BrKCS10a | GTTTCTTTAGGATGGGGTGCTC | GTCGGCAGCCTTATGAGTC |
BrKCS10b | CGACTCCGTCACTATCTGCCA | GGCTATGATTCCCGCTGAG |
BrKCS13 | GCCAAAGGTGCTCAACTCTACA | GAGGTCAGCATGCAACGTG |
BrKCS20a | CTATCCTCTACAACCACCTCCG | AAGACACGGCGAGGACGA |
G6PD | GGGTATGCCAGGACTAAGCTC | GAATCATAAGGGCCACTCACAT |
拟南芥A. thaliana | 大白菜B. rapa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
基因名称 Gene Name | 基因编号 Gene ID | 基因名称 Gene name | 基因编号 Gene ID | 染色体 Chromosome | 亚基因组 Subgenome | 氨基酸大小 No. of amino acids/ aa | 分子量 Molecular weight/kD | 理论等电点 pI | ||
AtKCS1 | AT1G01120 | BrKCS1a | BraA10g000750.3C | A10 | LF | 523 | 59.36 | 8.57 | ||
BrKCS1b | BraA09g065990.3C | A09 | MF2 | 491 | 55.11 | 9.02 | ||||
AtKCS2 | AT1G04220 | BrKCS2a | BraA10g002770.3C | A10 | LF | 529 | 59.58 | 9.27 | ||
BrKCS2b | BraA08g034990.3C | A08 | MF1 | 181 | 20.54 | 9.34 | ||||
AtKCS3 | AT1G07720 | BrKCS3a | BraA06g005040.3C | A06 | LF | 427 | 48.19 | 9.31 | ||
BrKCS3b | BraA08g033410.3C | A08 | MF1 | 391 | 43.97 | 8.92 | ||||
AtKCS4 | AT1G19440 | BrKCS4a | BraA06g015010.3C | A06 | LF | 506 | 56.71 | 9.17 | ||
BrKCS4b | BraA09g056620.3C | A09 | MF2 | 511 | 57.13 | 9.01 | ||||
AtKCS5 | AT1G25450 | BrKCS5 | BraA09g037930.3C | A09 | LF | 497 | 56.26 | 9.02 | ||
AtKCS6 | AT1G68530 | BrKCS6a | BraA02g018480.3C | A02 | MF1 | 231 | 25.68 | 9.19 | ||
BrKCS6b | BraA07g030740.3C | A07 | MF2 | 497 | 56.36 | 9.03 | ||||
AtKCS7 | AT1G71160 | BrKCS7a | BraA02g020280.3C | A02 | MF1 | 449 | 50.04 | 8.01 | ||
BrKCS7b | BraA07g029700.3C | A07 | MF2 | 755 | 84.83 | 8.41 | ||||
AtKCS8 | AT2G15090 | BrKCS8 | BraA07g005530.3C | A07 | LF | 461 | 51.80 | 9.00 | ||
AtKCS9 | AT2G16280 | BrKCS9a | BraA07g004540.3C | A07 | LF | 507 | 57.08 | 9.18 | ||
BrKCS9b | BraA09g010440.3C | A09 | MF1 | 456 | 51.26 | 8.87 | ||||
BrKCS9c | BraA03g043030.3C | A03 | MF2 | 487 | 54.81 | 9.27 | ||||
AtKCS10 | AT2G26250 | BrKCS10a | BraA09g052820.3C | A09 | LF | 547 | 61.48 | 9.10 | ||
BrKCS10b | BraA04g019210.3C | A04 | MF1 | 549 | 61.81 | 9.14 | ||||
AtKCS11 | AT2G26640 | NA | NA | NA | NA | NA | NA | NA | ||
AtKCS12 | AT2G28630 | BrKCS12a | BraA07g018970.3C | A07 | LF | 437 | 49.39 | 9.27 | ||
BrKCS12b | BraA04g020490.3C | A04 | MF1 | 476 | 54.00 | 9.15 | ||||
AtKCS13 | AT2G46720 | BrKCS13 | BraA05g001130.3C | A05 | LF | 587 | 65.18 | 9.39 | ||
AtKCS14 | AT3G10280 | NA | NA | NA | NA | NA | NA | NA | ||
AtKCS15 | AT3G52160 | BrKCS15 | BraA03g045900.3C | A03 | MF2 | 457 | 51.92 | 9.40 | ||
AtKCS16 | AT4G34250 | BrKCS16a | BraA01g004000.3C | A01 | LF | 459 | 51.60 | 9.25 | ||
BrKCS16b | BraA03g058730.3C | A03 | MF1 | 482 | 53.97 | 9.19 | ||||
AtKCS17 | AT4G34510 | BrKCS17 | BraA08g015890.3C | A08 | MF2 | 506 | 56.37 | 9.26 | ||
AtKCS18 | AT4G34520 | BrKCS18 | BraA08g015900.3C | A08 | MF2 | 474 | 53.81 | 9.31 | ||
AtKCS19 | AT5G04530 | BrKCS19a | BraA10g031780.3C | A10 | LF | 463 | 52.25 | 8.81 | ||
BrKCS19b | BraA02g001400.3C | A02 | MF2 | 429 | 48.3 | 8.79 | ||||
AtKCS20 | AT5G43760 | BrKCS20a | BraA06g043600.3C | A06 | LF | 526 | 58.99 | 9.21 | ||
BrKCS20b | BraA02g030820.3C | A02 | MF1 | 526 | 58.99 | 9.10 | ||||
AtKCS21 | AT5G49070 | BrKCS21 | BraA02g039980.3C | A02 | MF1 | 457 | 51.55 | 9.17 |
Table 2 Corresponding relationship between B. rapa and A. thaliana KCS genes and basic information of KCS genes in B. rapa
拟南芥A. thaliana | 大白菜B. rapa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
基因名称 Gene Name | 基因编号 Gene ID | 基因名称 Gene name | 基因编号 Gene ID | 染色体 Chromosome | 亚基因组 Subgenome | 氨基酸大小 No. of amino acids/ aa | 分子量 Molecular weight/kD | 理论等电点 pI | ||
AtKCS1 | AT1G01120 | BrKCS1a | BraA10g000750.3C | A10 | LF | 523 | 59.36 | 8.57 | ||
BrKCS1b | BraA09g065990.3C | A09 | MF2 | 491 | 55.11 | 9.02 | ||||
AtKCS2 | AT1G04220 | BrKCS2a | BraA10g002770.3C | A10 | LF | 529 | 59.58 | 9.27 | ||
BrKCS2b | BraA08g034990.3C | A08 | MF1 | 181 | 20.54 | 9.34 | ||||
AtKCS3 | AT1G07720 | BrKCS3a | BraA06g005040.3C | A06 | LF | 427 | 48.19 | 9.31 | ||
BrKCS3b | BraA08g033410.3C | A08 | MF1 | 391 | 43.97 | 8.92 | ||||
AtKCS4 | AT1G19440 | BrKCS4a | BraA06g015010.3C | A06 | LF | 506 | 56.71 | 9.17 | ||
BrKCS4b | BraA09g056620.3C | A09 | MF2 | 511 | 57.13 | 9.01 | ||||
AtKCS5 | AT1G25450 | BrKCS5 | BraA09g037930.3C | A09 | LF | 497 | 56.26 | 9.02 | ||
AtKCS6 | AT1G68530 | BrKCS6a | BraA02g018480.3C | A02 | MF1 | 231 | 25.68 | 9.19 | ||
BrKCS6b | BraA07g030740.3C | A07 | MF2 | 497 | 56.36 | 9.03 | ||||
AtKCS7 | AT1G71160 | BrKCS7a | BraA02g020280.3C | A02 | MF1 | 449 | 50.04 | 8.01 | ||
BrKCS7b | BraA07g029700.3C | A07 | MF2 | 755 | 84.83 | 8.41 | ||||
AtKCS8 | AT2G15090 | BrKCS8 | BraA07g005530.3C | A07 | LF | 461 | 51.80 | 9.00 | ||
AtKCS9 | AT2G16280 | BrKCS9a | BraA07g004540.3C | A07 | LF | 507 | 57.08 | 9.18 | ||
BrKCS9b | BraA09g010440.3C | A09 | MF1 | 456 | 51.26 | 8.87 | ||||
BrKCS9c | BraA03g043030.3C | A03 | MF2 | 487 | 54.81 | 9.27 | ||||
AtKCS10 | AT2G26250 | BrKCS10a | BraA09g052820.3C | A09 | LF | 547 | 61.48 | 9.10 | ||
BrKCS10b | BraA04g019210.3C | A04 | MF1 | 549 | 61.81 | 9.14 | ||||
AtKCS11 | AT2G26640 | NA | NA | NA | NA | NA | NA | NA | ||
AtKCS12 | AT2G28630 | BrKCS12a | BraA07g018970.3C | A07 | LF | 437 | 49.39 | 9.27 | ||
BrKCS12b | BraA04g020490.3C | A04 | MF1 | 476 | 54.00 | 9.15 | ||||
AtKCS13 | AT2G46720 | BrKCS13 | BraA05g001130.3C | A05 | LF | 587 | 65.18 | 9.39 | ||
AtKCS14 | AT3G10280 | NA | NA | NA | NA | NA | NA | NA | ||
AtKCS15 | AT3G52160 | BrKCS15 | BraA03g045900.3C | A03 | MF2 | 457 | 51.92 | 9.40 | ||
AtKCS16 | AT4G34250 | BrKCS16a | BraA01g004000.3C | A01 | LF | 459 | 51.60 | 9.25 | ||
BrKCS16b | BraA03g058730.3C | A03 | MF1 | 482 | 53.97 | 9.19 | ||||
AtKCS17 | AT4G34510 | BrKCS17 | BraA08g015890.3C | A08 | MF2 | 506 | 56.37 | 9.26 | ||
AtKCS18 | AT4G34520 | BrKCS18 | BraA08g015900.3C | A08 | MF2 | 474 | 53.81 | 9.31 | ||
AtKCS19 | AT5G04530 | BrKCS19a | BraA10g031780.3C | A10 | LF | 463 | 52.25 | 8.81 | ||
BrKCS19b | BraA02g001400.3C | A02 | MF2 | 429 | 48.3 | 8.79 | ||||
AtKCS20 | AT5G43760 | BrKCS20a | BraA06g043600.3C | A06 | LF | 526 | 58.99 | 9.21 | ||
BrKCS20b | BraA02g030820.3C | A02 | MF1 | 526 | 58.99 | 9.10 | ||||
AtKCS21 | AT5G49070 | BrKCS21 | BraA02g039980.3C | A02 | MF1 | 457 | 51.55 | 9.17 |
[1] |
Kunst L, Samuels AL. Biosynjournal and secretion of plant cuticular wax[J]. Prog Lipid Res, 2003, 42(1):51-80.
pmid: 12467640 |
[2] |
Haslam TM, Kunst L. Extending the story of very-long-chain fatty acid elongation[J]. Plant Sci, 2013, 210:93-107.
doi: 10.1016/j.plantsci.2013.05.008 pmid: 23849117 |
[3] |
Denic V, Weissman JS. A molecular caliper mechanism for determining very long-chain fatty acid length[J]. Cell, 2007, 130(4):663-677.
doi: 10.1016/j.cell.2007.06.031 URL |
[4] |
James DW Jr, Lim E, Keller J, et al. Directed tagging of the Arabidopsis FATTY ACID ELONGATION1(FAE1)gene with the maize transposon activator[J]. Plant Cell, 1995, 7(3):309-319.
pmid: 7734965 |
[5] |
Joubès J, Raffaele S, Bourdenx B, et al. The VLCFA elongase gene family in Arabidopsis thaliana:phylogenetic analysis, 3D modelling and expression profiling[J]. Plant Mol Biol, 2008, 67(5):547-566.
doi: 10.1007/s11103-008-9339-z URL |
[6] |
Todd J, Post-Beittenmiller D, Jaworski JG. KCS1 encodes a fatty acid elongase 3-ketoacyl-CoA synthase affecting wax biosynjournal in Arabidopsis thaliana[J]. Plant J, 1999, 17(2):119-130.
pmid: 10074711 |
[7] |
Franke R, Höfer R, Briesen I, et al. The DAISY gene from Arabidopsis encodes a fatty acid elongase condensing enzyme involved in the biosynjournal of aliphatic suberin in roots and the chalaza-micropyle region of seeds[J]. Plant J, 2009, 57(1):80-95.
doi: 10.1111/j.1365-313X.2008.03674.x URL |
[8] | Costaglioli P, Joubès J, Garcia C, et al. Profiling candidate genes involved in wax biosynjournal in Arabidopsis thaliana by microarray analysis[J]. Biochim Biophys Acta BBA Mol Cell Biol Lipids, 2005, 1734(3):247-258. |
[9] |
Hooker TS, Millar AA, Kunst L. Significance of the expression of the CER6 condensing enzyme for cuticular wax production in Arabidopsis[J]. Plant Physiol, 2002, 129(4):1568-1580.
pmid: 12177469 |
[10] |
Kim J, Jung JH, Lee SB, et al. Arabidopsis 3-ketoacyl-coenzyme a synthase9 is involved in the synjournal of tetracosanoic acids as precursors of cuticular waxes, suberins, sphingolipids, and phospholipids[J]. Plant Physiol, 2013, 162(2):567-580.
doi: 10.1104/pp.112.210450 URL |
[11] |
Pruitt RE, Vielle-Calzada JP, Ploense SE, et al. FIDDLEHEAD, a gene required to suppress epidermal cell interactions in Arabidopsis, encodes a putative lipid biosynthetic enzyme[J]. Proc Natl Acad Sci USA, 2000, 97(3):1311-1316.
doi: 10.1073/pnas.97.3.1311 URL |
[12] |
Gray JE, Holroyd GH, van der Lee FM, et al. The HIC signalling pathway links CO2 perception to stomatal development[J]. Nature, 2000, 408(6813):713-716.
doi: 10.1038/35047071 URL |
[13] |
Lee SB, Jung SJ, Go YS, et al. Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynjournal, but differentially controlled by osmotic stress[J]. Plant J, 2009, 60(3):462-475.
doi: 10.1111/j.1365-313X.2009.03973.x URL |
[14] |
Lee SB, Suh MC. Recent advances in cuticular wax biosynjournal and its regulation in Arabidopsis[J]. Mol Plant, 2013, 6(2):246-249.
doi: 10.1093/mp/sss159 URL |
[15] |
Millar AA, Kunst L. The natural genetic variation of the fatty-acyl composition of seed oils in different ecotypes of Arabidopsis thaliana[J]. Phytochemistry, 1999, 52(6):1029-1033.
pmid: 10643668 |
[16] |
Fiebig A, Mayfield JA, Miley NL, et al. Alterations in CER6, a gene identical to CUT1, differentially affect long-chain lipid content on the surface of pollen and stems[J]. Plant Cell, 2000, 12(10):2001-2008.
pmid: 11041893 |
[17] |
Qin YM, Hu CY, Pang Y, et al. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynjournal[J]. Plant Cell, 2007, 19(11):3692-3704.
doi: 10.1105/tpc.107.054437 URL |
[18] |
Chai MF, Queralta Castillo I, Sonntag A, et al. A seed coat-specific β-ketoacyl-CoA synthase, KCS12, is critical for preserving seed physical dormancy[J]. Plant Physiol, 2021, 186(3):1606-1615.
doi: 10.1093/plphys/kiab152 URL |
[19] | Yang HB, Mei WJ, Wan HL, et al. Comprehensive analysis of KCS gene family in Citrinae reveals the involvement of CsKCS2 and CsKCS11 in fruit cuticular wax synjournal at ripening[J]. Plant Sci, 2021, 310:110972. |
[20] | 武玉花. 甘蓝型油菜KCS基因家族表达及功能分析[D]. 北京:中国农业科学院, 2012. |
Wu YH. Expression profile and functional characterization of KCS gene family in Brassica napus[D]. Beijing:Chinese Academy of Agricultural Sciences, 2012. | |
[21] | 易婷, 张志硕, 汤冰倩, 等. 辣椒β-酮脂酰辅酶A合酶基因家族的鉴定与表达分析[J]. 园艺学报, 2020, 47(2):370-380. |
Yi T, Zhang ZS, Tang BQ, et al. Identification and expression analysis of the KCS gene family in pepper[J]. Acta Hortic Sin, 2020, 47(2):370-380. | |
[22] | 张高阳, 单士莲, 邓接楼, 等. 黄麻β-酮脂酰-CoA合酶(KCS)基因分离与功能鉴定[J]. 分子植物育种, 2018, 16(20):6718-6722. |
Zhang GY, Shan SL, Deng JL, et al. The segregation and functional identification of jute β-ketoyl-CoA synthase gene(KCS)[J]. Mol Plant Breed, 2018, 16(20):6718-6722. | |
[23] | 王荣花, 王树彬, 刘栓桃, 等. 大白菜花茎蜡粉近等基因系转录组分析[J]. 园艺学报, 2022, 49(1):62-72. |
Wang RH, Wang SB, Liu ST, et al. Transcriptome analysis of waxy near-isogenic lines in Chinese cabbage floral axis[J]. Acta Hortic Sin, 2022, 49(1):62-72. | |
[24] |
Liu ST, Wang RH, Zhang ZG, et al. High-resolution mapping of quantitative trait loci controlling main floral stalk length in Chinese cabbage(Brassica rapa L. ssp. pekinensis)[J]. BMC Genomics, 2019, 20(1):437.
doi: 10.1186/s12864-019-5810-2 URL |
[25] |
Ayaz A, Saqib S, Huang HD, et al. Genome-wide comparative analysis of long-chain acyl-CoA synthetases(LACSs)gene family:a focus on identification, evolution and expression profiling related to lipid synjournal[J]. Plant Physiol Biochem, 2021, 161:1-11.
doi: 10.1016/j.plaphy.2021.01.042 URL |
[26] |
Zhang L, Cai X, Wu J, et al. Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies[J]. Hortic Res, 2018, 5:50.
doi: 10.1038/s41438-018-0071-9 URL |
[27] |
Liu SY, Liu YM, Yang XH, et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes[J]. Nat Commun, 2014, 5:3930.
doi: 10.1038/ncomms4930 URL |
[28] |
Kumar S, Stecher G, Tamura K. MEGA7:molecular evolutionary genetics analysis version 7. 0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7):1870-1874.
doi: 10.1093/molbev/msw054 URL |
[29] |
Artimo P, Jonnalagedda M, Arnold K, et al. ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Res, 2012, 40(Web Server issue):W597-W603.
doi: 10.1093/nar/gks400 URL |
[30] |
Chen CJ, Chen H, Zhang Y, et al. TBtools:an integrative toolkit developed for interactive analyses of big biological data[J]. Mol Plant, 2020, 13(8):1194-1202.
doi: 10.1016/j.molp.2020.06.009 URL |
[31] |
Hu B, Jin JP, Guo AY, et al. GSDS 2. 0:an upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8):1296-1297.
doi: 10.1093/bioinformatics/btu817 URL |
[32] |
Yang SJ, Liu HL, Wei XC, et al. BrWAX2 plays an essential role in cuticular wax biosynjournal in Chinese cabbage(Brassica rapa L. ssp. pekinensis)[J]. Theor Appl Genet, 2022, 135(2):693-707.
doi: 10.1007/s00122-021-03993-x URL |
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