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Acta Agron Sin ›› 2015, Vol. 41 ›› Issue (11): 1758-1766.doi: 10.3724/SP.J.1006.2015.01758

• RESEARCH ACTIVITIES • Previous Articles     Next Articles

Expression Analysis and eQTL Mapping of BnTT3 Gene in Brassica napus L.

LU Kun1,2,**,QU Cun-Min1,2,**,LI Sha1,2,ZHAO Hui-Yan1,2,WANG Rui1,2,XU Xin-Fu1,2,LIANG Ying1,2,LI Jia-Na1,2,*   

  1. 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; 2 Chongqing Rapeseed Engineering Research Center, Chongqing 400715, China
  • Received:2015-01-19 Revised:2015-07-20 Online:2015-11-12 Published:2015-08-12
  • Contact: 李加纳, E-mail: ljn1950@swu.edu.cn, Tel: 023-68250642 E-mail:drlukun@swu.edu.cn


In flavonoid biosynthesis pathway, the key enzyme dihydroflavonol 4-reductase (DFR) involved in the proanthocyanidin and anthocyanin biosynthesis pathway is encoded by TRANSPARENT TESTA 3 (TT3) gene. The objective of this research was to identify the upstream regulatory networks of BnTT3 using the composite interval mapping method (CIM). Hence, we performed an eQTL analysis for the transcript-level variation of BnTT3 gene in seeds at 40 days after flower (DAF) in 94 recombinant inbred lines (RILs) derived from a cross between the yellow-seeded female parent GH06 and black-seeded male parent ZY821. Five eQTLs for expression levels of BnTT3 were detected on four different chromosomes (A03, A08, A09, and C01) in B. napus, accounting for 5.22% to 24.05% of phenotypic variation. Two major eQTLs were found and located among the markers KS10260–KBrB019I24.15 and B055B21-5–KS30880 of chromosome A09, with explained 24.05% and 16.55% of phenotypic variation, respectively. Three minor eQTLs were also detected to be located on chromosomes A03, A08 and C01. The flanking sequences with 200 kb of two major eQTLs on chromosome A09 of B. napus showed well synteny to those of A. thaliana, Brassica rapa, Brassica oleracea and other Brassiceae relatives. Furthermore, the annotation results showed that they belong to the trans-QTL, containing 78 genes in the two trans-QTL regions. Some transcription factors (MYB51, MYB52, and bZIP5) might be upstream regulatory factors associated with transcriptional regulation of BnTT3. Therefore, further study about these genes function will be helpful to elucidate the molecular mechanism of the seed coat colour formation, as well as lay the foundation for selecting candidate genes of seed coat colour in B. napus.

Key words: Brassica napus L., Seeds, TRANSPARENT TESTA 3, Recombinant inbred lines (RILs), Expression quantitative trait locus (eQTL)

[1]Winkel-Shirley B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol, 2001, 126: 485–493

[2]Winkel-Shirley B. Biosynthesis of flavonoids and effects of stress. Curr Opin Plant Biol, 2002, 5: 218–223

[3]Lepiniec L, Debeaujon I, Routaboul J M, Baudry A, Pourcel L, Nesi N, Caboche M. Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol, 2006, 57: 405–430

[4]Routaboul J M, Kerhoas L, Debeaujon I, Pourcel L, Caboche M, Einhorn J, Lepiniec L. Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Planta, 2006, 224: 96–107

[5]Haughn G, Chaudhury A. Genetic analysis of seed coat development in Arabidopsis. Trends Plant Sci, 2005, 10: 472–477

[6]Zhang J, Lu Y, Yuan Y, Zhang X, Geng J, Chen Y, Cloutier S, McVetty P B, Li G. Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Mol Biol, 2009, 69: 553–563

[7]Padmaja L K, Agarwal P, Gupta V, Mukhopadhyay A, Sodhi Y S, Pental D, Pradhan A K. Natural mutations in two homoeologous TT8 genes control yellow seed coat trait in allotetraploid Brassica juncea (AABB). Theor Appl Genet, 2014, 127: 339–347

[8]Fu F Y, Liu L Z, Chai Y R, Chen L, Yang T, Jin M Y, Ma A F, Yan X Y, Zhang Z S, Li J N. Localization of QTLs for seed color using recombinant inbred lines of Brassica napus in different environments. Genome, 2007, 50: 840–854

[9]Chai Y R, Lei B, Huang H L, Li J N, Yin J M, Tang Z L, Wang R, Chen L. TRANSPARENT TESTA12 genes from Brassica napus and parental species: cloning, evolution, and differential involvement in yellow seed trait. Mol Genet Genom, 2009, 281: 109–123

[10]Stein A, Wittkop B, Liu L, Obermeier C, Friedt W, Snowdon R J. Dissection of a major QTL for seed colour and fibre content in Brassica napus reveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition. Plant Breed, 2013, 132: 382–389

[11]Chen A H, Chai YR, Li J N, Chen L. Molecular cloning of two genes encoding cinnamate 4-hydroxylase (C4H) from oilseed rape (Brassica napus). J Biochem Mol Biol, 2007, 40: 247–260

[12]Wei Y L, Li J N, Lu J, Tang Z L, Pu D C, Chai Y R. Molecular cloning of Brassica napus TRANSPARENT TESTA 2 gene family encoding potential MYB regulatory proteins of proanthocyanidin biosynthesis. Mol Biol Rep, 2007, 34: 105–120

[13]Xu B B, Li J N, Zhang X K, Wang R, Xie L L, Chai Y R. Cloning and molecular characterization of a functional flavonoid 3'-hydroxylase gene from Brassica napus. J Plant Physiol, 2007, 164: 350–363

[14]Jansen R C, Nap J P. Genetical genomics: the added value from segregation. Trends Genet, 2001, 17: 388–391

[15]陈颖, 汪旭升, 许玲莉, 沈勤, 王晓冬, 陆璐. 基因表达数量性状定位的研究进展. 生命科学, 2009, 21: 38–42

Chen Y, Wang X S, Xu L L, Shen Q, Wang X D, Lu L. Advance in study of gene expression quantitative trait loci (eQTL). Chin Bull Life Sci, 2009, 21: 38–42 (in Chinese with English abstract)

[16]Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet, 2009, 10: 184–194

[17]Kliebenstein D. Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. Annu Rev Plant Biol, 2009, 60: 93–114

[18]Michaelson J J, Loguercio S, Beyer A. Detection and interpretation of expression quantitative trait loci (eQTL). Methods, 2009, 48: 265–276

[19]曲存民, 卢坤, 刘水燕, 卜海东, 付福友, 王瑞, 徐新福, 李加纳. 黄黑籽甘蓝型油菜类黄酮途径基因SNP位点检测分析. 作物学报, 2014, 40: 1914–1924

Qu C, Lu K, Liu S Y, Bu H D, Fu F Y, Wang R, Xu X F, Li J N. SNP detection and analysis of genes for flavonoid pathway in yellow- and black-seeded Brassica napus L. Acta Agron Sin, 2014, 40: 1914–1924 (in Chinese with English abstract)

[20]Li T, Jia K P, Lian H L, Yang X, Li L, Yang H Q. Jasmonic acid enhancement of anthocyanin accumulation is dependent on phytochrome A signaling pathway under far-red light in Arabidopsis. Biochem Biophys Res Commun, 2014, 454: 78–83

[21]Qu C, Fu F, Lu K, Zhang K, Wang R, Xu X, Wang M, Lu J, Wan H, Tang Z, Li J. Differential accumulation of phenolic compounds and expression of related genes in black-and yellow-seeded Brassica napus. J Exp Bot, 2013, 64: 2885–2898

[22]Wu G, Li Z, Yuhua W, Yinglong C, Changming L. Comparison of five endogenous feference Genes for specific PCR detection and quantification of Brassica napus. J Agric Food Chem, 2010, 58: 2812–2817

[23]曲存民, 付福友, 刘列钊, 王家丰, 毛丽佳, 原小燕, 谌利, 李加纳. 甘蓝型油菜胚色素成分的QTL定位. 作物学报, 2009, 35: 286–294

Qu C M, Fu F Y, Liu L Z, Wang J F, Mao L J, Yuan X Y, Chen L, Li J N. QTL mapping of embryonic pigment components in Brassica napus. Acta Agron Sin, 2009, 35: 286–294 (in Chinese with English abstract)

[24]曲存民, 付福友, 卢坤, 谢景梅, 刘晓兰, 黄杰恒, 李波, 王瑞, 谌利, 唐章林. 不同环境中甘蓝型油菜种皮木质素含量的QTL定位. 作物学报, 2011, 37: 1398–1405

Qu C M, Fu F Y, Lu K, Xie, J M, Liu X L, Huang J H, Li B, Wang R, Chen L, Tang Z L, Li J N. Identification of QTLs for lignin content of seed coat in Brassica napus L. in different environments. Acta Agron Sin, 2011, 37: 1398–1405 (in Chinese with English abstract)

[25]Lander E S, Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 1989, 121: 185–199

[26]刘仕芸, 黄艳岚, 张树珍. 植物花青素生物合成中的调控基因. 植物生理学通讯, 2006, 42: 747–754

Liu S Y, Huang Y L, Zhang S Z. Regulatory gene of anthocyanin biosynthesis in plant. Plant Physiol Commun, 2006, 42: 747–754 (in Chinese with English abstract)

[27]沈忠伟, 许昱, 夏犇, 李建粤. 植物类黄酮次生代谢生物合成相关转录因子及其在基因工程中的应用. 分子植物育种, 2008, 6: 542–548

Shen Z W, Xu Y, Xia B, Li J Y. Transcription factors involved in plant flavonoid biosynthesis of secondary metabolismand its application in genetic engineering. Mol Plant Breed, 2008, 6: 542–548 (in Chinese with English abstract)

[28]Qi T, Song S, Ren Q, Wu D, Huang H, Chen Y, Fan M, Peng W, Ren C, Xie D. The Jasmonate-ZIM-domain proteins interact with the WD-Repeat/bHLH/MYB complexes to regulate Jasmonate-mediated anthocyanin accumulation and trichome initiation in Arabidopsis thaliana. Plant Cell, 2011, 23:1795–1814

[29]Marles M, Gruber MY. Histochemical characterisation of unextractable seed coat pigments and quantification of extractable lignin in the Brassicaceae. J Sci Food Agric, 2004, 84: 251–262

[30]叶小利, 李加纳, 唐章林, 梁颖, 谌利. 甘蓝型油菜种皮色泽及相关性状的研究. 作物学报, 2001, 27: 550–556

Ye X L, Li J N, Tang Z L, Liang Y, Chen L. Study on seed coat color and related characters of Brassica napus. Acta Agron Sin, 2001, 27: 550–556 (in Chinese with English abstract)

[31]Kim S, Binzel M L, Park S, Yoo K S, Pike L M. Inactivation of DFR (Dihydroflavonol 4-reductase) gene transcription results in blockage of anthocyanin production in yellow onions (Allium cepa). Mol Breed, 2004, 14: 253–263

[32]Furukawa T, Maekawa M, Oki T, Suda I, Iida S, Shimada H, Takamure I, Kadowaki Ki. The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J, 2007, 49: 91–102

[33]Park K I, Ishikawa N, Morita Y, Choi J D, Hoshino A, Iida S. A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation. Plant J, 2007, 49: 641–654

[34]Marles M, Gruber M Y, Scoles G J, Muir A D. Pigmentation in the developing seed coat and seedling leaves of Brassica carinata is controlled at the dihydroflavonol reductase locus. Phytochemistry, 2003, 62: 663–672

[35]Yan M L, Liu X J, Liu Z S, Guan C Y, Yuan M Z, Xiong X H. Cloning and expression analysis of Dihydroflavonol 4-Reductase gene in Brassica juncea. Acta Agron Sin, 2008, 34: 1–7

[36]曲存民. 甘蓝型油菜种皮色泽形成机理研究. 西南大学博士学位论文, 重庆, 2012. pp 55–62

Qu C M. Studies on the Mechanism of Formation of Seed Coat Colour in Brassica napus L. PhD Disseration of Southwest University, Chongqing, China, 2012. pp 55–62 (in Chinese with English abstract)

[37]Frerigmann H, Gigolashvili T. MYB34, MYB51 and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana. Mol Plant, 2014, 7: 814–828

[38]Park M Y, Kang J Y, Kim S Y. Overexpression of AtMYB52 confers ABA hypersensitivity and drought tolerance. Mol Cells, 2011, 31: 447–454

[39]Borevitz J O, Xia Y, Blount J, Dixon R A, Lamb C. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell, 2000, 12: 2383–2393

[40]Stracke R, Werber M, Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol, 2001, 4: 447–456

[41]Lewis D R, Ramirez M V, Miller N D, Vallabhaneni P, Ray W K, Helm R F, Winkel B S, Muday G K. Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiol, 2011, 156:144–164

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