Please wait a minute...
Journal of Integrative Agriculture  2022, Vol. 21 Issue (8): 2211-2226    DOI: 10.1016/S2095-3119(21)63656-0
Special Issue: 油料作物合辑Oil Crops
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Transcriptional profiling between yellow- and black-seeded Brassica napus reveals molecular modulations on flavonoid and fatty acid content

RONG Hao1, YANG Wen-jing1, XIE Tao1, WANG Yue1, WANG Xia-qin1, JIANG Jin-jin1, WANG You-ping1, 2

1 Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, P.R.China

2 Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, P.R.China 

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

本研究通过RNA-seq分析比较了甘蓝型油菜-白芥属间杂种后代的黄籽材料及其褐籽亲本间的基因表达差异,并与类黄酮和脂肪酸含量变化进行关联分析。通过HPLC-PDA-ESI(−)/MSn分析,我们发现黄籽中苯丙烷和类黄酮类物质(如异鼠李素、表儿茶素、山奈酚和其它衍生物)的含量显著低于褐籽材料。黄籽材料的脂肪酸含量较褐籽高,主要是由于C16:0、C18:0、C18:1、C18:2和C18:3的含量变化所导致。通过授粉后4周(4 WAF)和5周种子的RNA-seq分析,我们发现黄、褐籽间的差异表达基因(DEGs)主要富集于类黄酮和脂肪酸合成相关的路径,包括BnTT3BnTT4BnTT18BnFAD2。此外,我们发现黄籽中脂肪酸合成、去饱和、延伸相关的基因(FAD3LEC1FUS3LPAT2)较褐籽上调表达,而与β氧化相关的基因(AIM1KAT2)在黄籽中下调表达。这些与类黄酮、苯丙烷、脂肪酸含量变化相关的DEGs将有助于解释黄籽甘蓝型油菜的表型变化,且对于油菜的遗传改良也具有一定的意义


Brassica napus is an important cash crop broadly grown for the vegetable and oil values.  Yellow-seeded Bnapus is preferred by breeders due to its improved oil and protein quality, less pigments and lignin compared with the black-seeded counterpart.  This study compared the differences in flavonoid and fatty acid contents between yellow rapeseed from the progenies of BnapusSinapis alba somatic hybrids and the black-seeded counterpart using RNA-seq analysis.  Through HPLC-PDA-ESI(−)/MS2 analysis, it was found that phenylpropanoids and flavonoids (i.e., isorhamnetin, epicatechin, kaempferol, and other derivatives) in yellow seed were significantly lower than those in black seed.  The fatty acid (FA) content in yellow rapeseed was higher than that in black rapeseed due to the variation of C16:0, C18:0, C18:1, C18:2, and C18:3 contents.  RNA-seq analysis of seeds at four and five weeks after flowering (WAF) indicated that differentially expressed genes (DEGs) between black and yellow rapeseeds were enriched in flavonoid and FA biosynthesis, including BnTT3, BnTT4, BnTT18, and BnFAD2.  Also, genes related to FA biosynthesis, desaturation and elongation (FAD3, LEC1, FUS3, and LPAT2) in yellow seed were up-regulated compared to those in black seed, while genes involved in beta-oxidation cycle (AIM1 and KAT2) of yellow seed were down-regulated compared to those in black seed.  The DEGs related to the variation of flavonoids, phenylpropanoids, and FAs would help improve the knowledge of yellow seed character in Bnapus and promote rapeseed improvement.

Keywords:  rapeseed        gene expression analysis       fatty acid composition       phenolic content       yellow seed  
Received: 13 November 2020   Accepted: 22 February 2021
Fund: This research was funded by the National Natural Science Foundation of China (U20A2028 and 31972963), the Open Funds of the Key Laboratory of Plant Functional Genomics of the Ministry of Education, China (ML201804), the Project of Special Funding for Crop Science Discipline Development, China (yzuxk202006), the Priority Academic Program Development of Jiangsu Higher Education Institutions, China and the Yangzhou University for Excellent Talent Support Program, China.
About author:  Correspondence WANG You-ping, Tel: +86-514-87997303, E-mail:; JIANG Jin-jin, E-mail:

Cite this article: 

RONG Hao, YANG Wen-jing, XIE Tao, WANG Yue, WANG Xia-qin, JIANG Jin-jin, WANG You-ping. 2022. Transcriptional profiling between yellow- and black-seeded Brassica napus reveals molecular modulations on flavonoid and fatty acid content. Journal of Integrative Agriculture, 21(8): 2211-2226.

Adhikari N D, Bates P D, Browse J. 2016. WRINKLED1 rescues feedback inhibition of fatty acid synthesis in hydroxylase-expressing seeds. Plant Physiology, 171, 179–191. 
Ahmed N U, Park J I, Jung H J, Yang T J, Hur Y, Nou I S. 2014. Characterization of dihydroflavonol 4-reductase (DFR) genes and their association with cold and freezing stress in Brassica rapa. Gene, 550, 46–55.
Appelhagen I, Thiedig K, Nordholt N, Schmidt N, Huep G, Sagasser M, Weisshaar B. 2014. Update on transparent testa mutants from Arabidopsis thaliana characterization of new alleles from an isogenic collection. Planta, 240, 955–970.
Audic S, Claverie J M. 1997. The significance of digital gene expression profiles. Genome Research, 7, 986–995.
Auger B, Baron C, Lucas M O, Vautrin S, Berges H, Chalhoub B, Fautrel A, Renard M, Nesi N. 2009. Brassica orthologs from BANYULS belong to a small multigene family, which is involved in procyanidin accumulation in the seed. Planta, 230, 1167–1183.
Badani A G, Snowdon R J, Wittkop B, Lipsa F D, Baetzel R, Horn R, De Haro A, Font R, Luhs W, Friedt W. 2006. Colocalization of a partially dominant gene for yellow seed colour with a major QTL influencing acid detergent fibre (ADF) content in different crosses of oilseed rapa (Brassica napus). Genome, 49, 1499–1509.
Bao X, Ohlrogge J. 1999. Supply of fatty acid is one limiting factor in the accumulation of triacylglycerol in developing embryos. Plant Physiology, 120, 1057–1062.
Bates P D, Stymne S, Ohlrogge J. 2013. Biochemical pathways in seed oil synthesis. Current Opinion in Plant Biology, 16, 358–364.
Belide S, Petrie J R, Shrestha P, Singh S P. 2012. Modification of seed oil composition in Arabidopsis by artificial microRNA-mediated gene silencing. Frontiers in Plant Science, 3, 168–173.
Benjamini B Y, Yekutieli D. 2011. The control of the false discovery rate in multiple testing under dependency. Annals of Stats, 29, 1165–1188.
Borisjuk L, Neuberger T, Schwender J, Heinzel N, Sunderhaus S, Fuchs J, Hay J O, Tschiersch H, Braun H P, Denolf P, Lambert B, Jakob P M, Rolletschek H. 2013. Seed architecture shapes embryo metabolism in oilseed rape. The Plant Cell, 25, 1625–1640.
Cernac A, Benning C. 2004. WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. The Plant Journal, 40, 575–585.
Chai Y R, Lei B, Huang H L, Li J N, Yin J M, Tang Z L, Wang R, Chen L. 2009. TRANSPARENT TESTA 12 genes from Brassica napus and parental species cloning, evolution, and differential involvement in yellow seed trait. Molecular Genetics & Genomics, 281, 109–123.
Chapman K D, Ohlrogge J B. 2012. Compartmentation of triacylglycerol accumulation in plants. Journal of Biological Chemistry, 287, 2288–2294.
Conesa A, Gotz S, Garcia-Gomez J M, Terol J, Talon M, Robles M. 2005. Blast2GO: A universal tool for annotation visualization and analysis in functional genomics research. Bioinformatics, 21, 3674–3676.
Ding X Y, Xu J S, Huang H, Qiao X, Shen M Z, Cheng Y, Zhang X K. 2020. Unraveling waterlogging tolerance-related traits with QTL analysis in reciprocal intervarietal introgression lines using genotyping by sequencing in rapeseed (Brassica napus L.). Journal of Integrative Agriculture, 19, 1974–1983.
Dong Y, Wang Y, Jin F W, Xing L J, Fang Y, Zhang Z Y, Zou J J, Wang L, Xu M Y. 2020. Differentially expressed miRNAs in anthers may cotribute to the fertility of a novel Brassica napus genic male sterile line CN12A. Journal of Integrative Agriculture, 19, 1731–1742.
Demski K, Jeppson S, Lager I, Misztak A, Jasieniecka-Gazarkiewica K, Waleron M, Stymne S, Banas A. 2019. Isoforms of Acyl-CoA: Diacylglycerol acyltransferase-2 differ substantially in their specificities towards erucic acid. Plant Physiology, 181, 1468–1479.
Eisen M B, Spellman P T, Brown P O, Botstein D. 1998. Cluster analysis and display of genome-wide expression. Proceedings of the National Academy of Sciences of the United States of America, 95, 14863–14868.
Fan Y, Du K, Gao Y, Kong Y, Chu C, Sokolov V, Wang Y. 2013. Transformation of LTP gene into Brassica napus to enhance its resistance to Sclerotinia sclerotiorum. Genetika, 49, 439–447.
Fatima T, Snyder C L, Schroeder W R, Cram D, Datla R, Wishart D, Weselake R J, Krishna P. 2012. Fatty acid composition of developing sea buckthorn (Hippophae rhamnoides L.) berry and the transcriptome of the mature seed. PLoS ONE, 7, e34099.
Focks N, Benning C. 1998. Wrinkled1: A novel, low-seed-oil mutant of Arabidopsis with a deficiency in the seed-specific regulation of carbohydrate metabolism. Plant Physiology, 118, 91–101.
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. 2007. Localization of QTLs for seed color using recombinant inbred lines of Brassica napus in different environments. Genome, 50, 840–854.
Fulda M, Schnurr J, Abbadi A, Heinz E, Browse J. 2004. Peroxisomal Acyl-CoA synthetase activity is essential for seedling development in Arabidopsis thaliana. The Plant Cell, 16, 394–405.
Germain V, Rylott E L, Larson T R, Sherson S M, Bechtold N, Carde J P, Bryce J H, Graham I A, Smith S M. 2001. Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. The Plant Journal, 28, 1–12.
Hannoufa A, Pillai B V S, Chellamma S. 2014. Genetic enhancement of Brassica napus seed quality. Transgenic Research, 23, 39–52.
‘t Hoen P A C, Ariyurek Y, Thygesen H H, Vreugdenhil E, Vossen R H A M, de Menezes R X, Boer J M, van Ommen G J, den Dunnen J T. 2008. Deep sequencing-based expression analysis shows major advances in robustness resolution and inter-lab portability over five microarray platforms. Nucleic Acids Research, 36, 141–151.
Huo D A, Zhu B, Tian G F, Du X Y, Guo J, Cai M X. 2019. Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa–Brassica oleracea monosomic addition lines. Journal of Integrative Agriculture, 18, 1541–1546.
Hu Z Y, Wang X F, Zhang G M, Liu G H, Hua W, Wang H Z. 2009. Unusually large oilbodies are highly correlated with lower oil content in Brassica napus. Plant Cell Reports, 28, 541–549.
Hu Z Y, Hua W, Zhang L, Deng L B, Wang X F, Liu G H, Hao W J, Wang H Z. 2013. Seed structure characteristics to form ultrahigh oil content in rapeseed. PLoS ONE, 8, e62099.
Jiang J J, Shao Y L, Li A M, Lu C L, Zhang Y T, Wang Y P. 2013. Phenolic composition analysis and gene expression in developing seeds of yellow- and black-seeded Brassica napus. Journal of Integrative Plant Biology, 55, 537–551.
Jiang J J, Zhu S, Yuan Y, Wang Y, Zeng L, Batley J, Wang Y P. 2019. Transcriptomic comparison between developing seeds of yellow- and black-seeded Brassica napus reveals that genes influence seed quality. BMC Plant Biology, 19, 203–216.
Lepiniec L, Debeaujon I, Routaboul J M, Baudry A, Pourcel L, Nesi N, Caboche M. 2006. Genetics and biochemistry of seed flavonoids. Annual Review of Plant Biology, 57, 405–430.
Li A M, Jiang J J, Zhang Y T, Snowdon R J, Liang G H, Wang Y P. 2012. Molecular and cytological characterization of introgression lines in yellow seed derived from somatic hybrids between Brassica napus and Sinapis alba. Molecular Breeding, 29, 209–219.
Li A M, Wei C X, Jiang J J, Zhang Y T, Snowdon R J, Wang Y P. 2009. Phenotypic variation in progenies from somatic hybrids between Brassica napus and Sinapis alba. Euphytica, 170, 289–296.
Li C X, Gong X M, Zhang B, Liang Z, Wong C E, See B Y H, Yu H. 2020. TOP1α, UPF1, and TTG2 regulate seed size in a parental dosage-dependent manner. PLoS Biology, 18, e3000930.
Li R Q, Yu C, Li Y R, Lam T W, Yiu S M, Kristiansen K, Wang J. 2009. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966–1967. 
Lin P, Xia L X, Wong J H, Ng T B, Ye X Y, Wang S Y, Shi X Z. 2007. Lipid transfer proteins from Brassica campestris and mung bean surpass mung bean chitinase in exploitability. Journal of Peptide Science, 13, 642–648.
Liu L, Fan W Q, Liu F X, Tang T, Zhou Y, Tang Z W, Chen G M, Zhao X X. 2020. Increased BnaMFT-transcript level is associated with secondary dormancy in oilseed rape (Brassica napus L.). Journal of Integrative Agriculture, 19, 1565–1576.
Liu L Z, Stein A, Wittkop B, Sarvari P, Li J, Yan X, Dreyer F, Frauen M, Fredt W, Snowdon R J. 2012. A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds. Theoretical and Applied Genetics, 124, 1573–1586.
Liu Q, Siloto R M P, Lehner R, Stone S J, Weselake R J. 2012. Acyl-CoA: Diacylglycerol acyltransferase: Molecular biology, biochemistry and biotechnology. Progress in Lipid Research, 51, 350–377.
Ma N, Wan L, Zhao W, Liu H F, Li J, Zhang C L. 2020. Exogenous strigolactones promote lateral root growth by reducing the endogenous auxin level in rapeseed. Journal of Integrative Agriculture, 19, 465–482.
Mahmood T, Rahman M H, Sringam G R, Yeh F, Good A G. 2006. Identification of quantitative trait loci (QTL) for oil and protein contents and their relationships with other seed quality traits in Brasscia juncea. Theoretical and Applied Genetics, 113, 1211–1220.
Maisonneuve S, Bessoule J J, Lessire R, Delseny M, Roscoe T J. 2010. Expression of rapeseed microsomal lysophatidic acid acyltransferase isozymes enhances seed oil content in Arabidopsis. Plant Physiology, 152, 670–684.
Marinova K, Pourcel L, Weder B, Schwarz M, Barron D, Routaboul J M, Debeaujon I, Klein M. 2007. The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+-antipotpr active in proanthocyanidin-accumulating cells of the seed coat. The Plant Cell, 19, 2023–2038.
Mittasch J, Bottcher C, Frolov A, Strack D, Milkowski C. 2013. Reprogramming the phenylpropanoid metabolism in seeds of oilseed rape by suppressing the orthologs of RESUCED EPIERMAL FLUORESCENCE1. Plant Physiology, 161, 1656–1669.
Morrissy A S, Morin R D, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y J, Hirst M, Marra M A. 2009. Next-generation tag sequencing for cancer gene expression profiling. Genome Research, 19, 1825–1835.
Ni Y, Jiang H L, Lei B, Li J N, Chai Y R. 2008. Molecular cloning, characterization and expression of two rapeseed (Brassica napus L.) cDNAs orthologous to Arabidopsis thaliana phenylalanine ammonia-lyase 1. Euphytica, 159, 1–16.
Padmaja L K, Aqarwal P, Gupta V, Mukhopadhyay A, Sodhi Y S, Pental D, Pradhan A K. 2014. Natural mutations in two homoeologous TT8 genes control yellow seed trait in allotetraploid Brassica juncea (AABB). Theoretical and Applied Genetics, 127, 339–347.
Prakash S, Bhat S R. 2007. Contribution of wild crucifers in Brassica improvement: Past accomplishment and future perspectives. In: Proceedings of GCIRC 12th International Rapeseed Congress. Wuhan, China. pp. 213–215.
Qu C M, Fu F Y, Lu K, Zhang K, Wang R, Xu X F, Wang M, Lu J X, Wan H F, Tang Z L, Li J N. 2013. Differential accumulation of phenolic compounds and expression of related genes in black- and yellow-seeded Brassica napus. Journal of Experimental Botany, 64, 2885–2898.
Qu C M, Zhao H Y, Fu F Y, Wang Z, Zhang K, Zhou Y, Wang X, Wang R, Xu X F, Tang Z L, Lu K, Li J N. 2016. Genome-wide survey of flavonoid biosynthesis genes and gene expression analysis between black- and yellow-seeded Brassica napus. Frontiers in Plant Science, 7, 1755–1771.
Rylott E L, Eastmond P J, Gilday A D, Slocombe S P, Larson T R, Baker A, Graham I A. 2006. The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal beta-oxidation is essential for seedling establishment. The Plant Journal, 45, 930–941.
Saldanha A J. 2004. Java Treeview-extensible visualization of microarray data. Bioinformatics, 20, 3246–3248.
Shao Y L, Jiang J J, Ran L P, Lu C L, Wei C X, Wang Y P. 2014. Analysis of flavonoids and hydroxycinnamic acid derivatives in rapeseeds (Brassica napus L. var. napus) by HPLC-PDA–ESI(–)-MSn/HRMS. Journal of Agricultural & Food Chemistry, 62, 2935–2945.
Sharma A, Chauhan R S. 2012. In silico identification and comparative genomics of candidate genes involved in biosynthesis and accumulation of seed oil in plants. Comparative and Functional Genomics, 2012, 914843.
Sinlapadech T, Stout J, Ruegger M O, Deak M, Chapple C. 2007. The hyper-fluorescent trichome phenotype of the btr1 mutant of Arabidopsis is the result of a defect in a sinapic acid: UDPG glucosyltransferase. The Plant Journal, 49, 655–668.
Slominski B A, Jia W, Rogiewicz A, Nyachoti C M, Hickling D. 2012. Low-fiber canola. Part 1. Chemical and nutritive composition of the meal. Journal of Agricultural and Food Chemistry, 60, 12225–12230.
Sun M Y, Hua W, Liu J, Huang S M, Wang X F, Liu G H, Wang H Z. 2012. Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS ONE, 7, e47037.
Tan M L, Xue J F, Wang L, Huang J X, Fu C L, Yan X C. 2016. Transcriptomic analysis for different sex types of Ricinus communis L. during development from apical buds to inflorescences by digital gene expression profiling. Frontiers in Plant Science, 6, 1208.
Taylor D C, Barton D L, Giblin E M, MacKenzie S L, Van Den Berg C G J, McVetty P B E. 1995. Microsomal lyso-phosphatidic acid acyltransferase from a Brassica oleracea cultivar incorporates erucic acid into the sn-2 position of seed triacylglycerols. Plant Physiology, 109, 409–420.
Wang C, Lv Y D, Xu W T, Zhang T Z, Guo W Z. 2014. Aberrant phenotype and transcriptomeexpression during fiber cell wall thickeningcaused by the mutation of theImgene inimmature fiber (im) mutantin Gossypium hirsutum L. BMC Genomics, 15, 94.
Wang Y P, Zhao X X, Sonntag K, Wehling P, Snowdon R J. 2005. Behaviour of Sinapis alba chromosomes in a Brassica napus background revealed by genomic in-situ hybridization. Chromosome Research, 13, 819–826.
Wei Y L, Li J N, Lu J, Yang Z L, Pu D C, Chai Y R. 2007. Molecular cloning of Brassica napus TRANSPARENT TESTA2 gene family encoding potential MYB regulatory proteins of proanthocyanidin biosynthesis. Molecular Biology Reports, 34, 105–120.
Wen J, Zhu L X, Qi L P, Ke H M, Yi B, Shen J X, Tu J X, Ma C Z, Fu T D. 2012. Characterization of interploid hybrids from crosses between Brassica juncea and B. oleracea and the production of yellow-seeded B. napus. Theoretical and Applied Genetics, 125, 19–32.
Xie T, Chen X, Guo T L, Rong H, Chen Z Y, Sun Q F, Batley J, Jiang J J, Wang Y P. 2020. Targeted knockout of BnTT2 homologs for yellow-seeded Brassica napus with reduced flavonoids and improved fatty acid composition. Journal of Agricultural and Food Chemistry, 68, 5676–5690
Xu B B, Li J N, Zhang X K, Wang R, Xie L L, Chai Y R. 2007. Cloning and molecular characterization of a functional flavonoid 3’-hydroxylase gene from Brassica napus. Journal of Plant Physiology, 164, 350–363.
Yan L, Tariq S, Cheng Y, Lv Y, Zhang X K, Zou X L. 2019. Physiological and molecular responses to cold stress in rapsessed (Brassica napus L.). Journal of Integrative Agriculture, 18, 2742–2752.
Yang Q Y, Fan C C, Guo Z H, Qin J, Wu J Z, Li Q Y, Fu T D, Zhou Y M. 2012. Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents. Theoretical and Applied Genetics, 125, 715–729.
Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. 2006. WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 34, 293–297.
Yu C Y. 2013. Molecular mechanism of manipulating seed coat coloration in oilseed Brassica species. Journal of Applied Genetics, 54, 135–145.
Zhang J F, Lu Y, Yuan Y X, Zhang X W, Geng J F, Chen Y, Cloutier S, McVetty P B E, Li G Y. 2009. Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Molecular Biology, 69, 553–563.
Zhang K, Lu K, Qu C M, Liang Y, Wang R, Chai Y R, Li J N. 2013. Gene silencing of BnTT10 family genes causes retarded pigmentation and lignin reduction in the seed coat of Brassica napus. PLoS ONE, 8, e61247.
Zhang X L, Wang Y L, Yan Y Y, Peng H, Long Y, Zhang Y C, Jiang Z, Liu P, Zou C Y, Peng H W, Pan G T, Shen Y Q. 2019. Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation. BMC Genomics, 20, 159–180.
Zhang Y, Li X, Chen W, Yi B, Wen J, Shen J X, Ma C Z, Chen B Y, Tu J X, Fu T D. 2011. Identification of two major QTL for yellow seed color in two crosses of resynthesized Brassica napus line No. 2127–17. Molecular Breeding, 28, 335–342.
Zhou X R, Shrestha P, Yin F, Petrie J R, Singh S P. 2013. AtDGAT2 is a functional acyl-CoA: Diacylglycerol acyltransferase and displays different acyl-CoA substrate preferences than AtDGAT1. FEBS Letters, 587, 2371–2376.

No related articles found!
No Suggested Reading articles found!