Wittkop B, Snowdon RJ, Friedt W. New NIRS calibrations for fiber fractions reveal broad genetic variation in Brassica napus seed quality. J Agric Food Chem. 2012;60(9):2248–56.
Article
CAS
PubMed
Google Scholar
Abbadi A, Leckband G. Rapeseed breeding for oil content, quality, and sustainability. Eur J Lipid Sci Technol. 2011;113(10):1198–206.
Article
CAS
Google Scholar
Qu C, Zhao H, Fu F, Wang Z, Zhang K, Zhou Y, Wang X, Wang R, Xu X, Tang Z, et al. Genome-wide survey of flavonoid biosynthesis genes and gene expression analysis between black- and yellow-seeded Brassica napus. Front Plant Sci. 2016;7:1755.
PubMed
PubMed Central
Google Scholar
Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M. Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol. 2006;57:405–30.
Article
CAS
PubMed
Google Scholar
Liu Q, Luo L, Zheng L. Lignins: biosynthesis and biological functions in plants. Int J Mol Sci. 2018;19(2):335–50.
Article
PubMed Central
CAS
Google Scholar
Mittasch J, Bottcher C, Frolov A, Strack D, Milkowski C. Reprogramming the phenylpropanoid metabolism in seeds of oilseed rape by suppressing the orthologs of reduced epidermal fluorescence1. Plant Physiol. 2013;161(4):1656–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rahman MH, Joersbo M, Poulsen MH. Production of yellow-seeded Brassica napus of double low quality. Plant Breed. 2001;120:473–8.
Article
CAS
Google Scholar
Li A, Wei C, Jiang J, Zhang Y, Snowdon RJ, Wang Y. Phenotypic variation in progenies from somatic hybrids between Brassica napus and Sinapis alba. Euphytica. 2009;170(3):289–96.
Article
CAS
Google Scholar
Appelhagen I, Thiedig K, Nordholt N, Schmidt N, Huep G, Sagasser M, Weisshaar B. Update on transparent testa mutants from Arabidopsis thaliana: characterisation of new alleles from an isogenic collection. Planta. 2014;240(5):955–70.
Article
CAS
PubMed
Google Scholar
Xu W, Grain D, Bobet S, Le Gourrierec J, Thevenin J, Kelemen Z, Lepiniec L, Dubos C. Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB-bHLH-WDR complexes and their targets in Arabidopsis seed. New Phytol. 2014;202(1):132–44.
Article
CAS
PubMed
Google Scholar
Appelhagen I, Jahns O, Bartelniewoehner L, Sagasser M, Weisshaar B, Stracke R. Leucoanthocyanidin Dioxygenase in Arabidopsis thaliana: characterization of mutant alleles and regulation by MYB-BHLH-TTG1 transcription factor complexes. Gene. 2011;484(1–2):61–8.
Article
CAS
PubMed
Google Scholar
Xu BB, Li JN, Zhang XK, Wang R, Xie LL, Chai YR. Cloning and molecular characterization of a functional flavonoid 3′-hydroxylase gene from Brassica napus. J Plant Physiol. 2007;164(3):350–63.
Article
CAS
PubMed
Google Scholar
Wei YL, Li JN, Lu J, Tang ZL, Pu DC, Chai YR. Molecular cloning of Brassica napus TRANSPARENT TESTA 2 gene family encoding potential MYB regulatory proteins of proanthocyanidin biosynthesis. Mol Biol Rep. 2007;34(2):105–20.
Article
CAS
PubMed
Google Scholar
Ni Y, Jiang H-L, Lei B, Li J-N, Chai Y-R. Molecular cloning, characterization and expression of two rapeseed (Brassica napus L.) cDNAs orthologous to Arabidopsis thaliana phenylalanine ammonia-lyase 1. Euphytica. 2007;159(1–2):1–16.
Article
CAS
Google Scholar
Chai YR, Lei B, Huang HL, Li JN, Yin JM, Tang ZL, Wang R, Chen L. TRANSPARENT TESTA 12 genes from Brassica napus and parental species: cloning, evolution, and differential involvement in yellow seed trait. Mol Gen Genomics. 2009;281(1):109–23.
Article
CAS
Google Scholar
Auger B, Baron C, Lucas MO, Vautrin S, Berges H, Chalhoub B, Fautrel A, Renard M, Nesi N. Brassica orthologs from BANYULS belong to a small multigene family, which is involved in procyanidin accumulation in the seed. Planta. 2009;230(6):1167–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu J, Li JN, Lei B, Wang SG, Chai YR. Molecular cloning and characterization of two Brassica napus TTG1 genes reveal genus-specific nucleotide preference, extreme protein-level conservation and fast divergence of organ-specificity. Genes Genomics. 2009;31:129–42.
Article
CAS
Google Scholar
Zhang K, Lu K, Qu C, Liang Y, Wang R, Chai Y, Li J. Gene silencing of BnTT10 family genes causes retarded pigmentation and lignin reduction in the seed coat of Brassica napus. PLoS One. 2013;8(4):e61247.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lian J, Lu X, Yin N, Ma L, Lu J, Liu X, Li J, Lu J, Lei B, Wang R, et al. Silencing of BnTT1 family genes affects seed flavonoid biosynthesis and alters seed fatty acid composition in Brassica napus. Plant Sci. 2017;254:32–47.
Article
CAS
PubMed
Google Scholar
Yu CY. Molecular mechanism of manipulating seed coat coloration in oilseed Brassica species. J Appl Genet. 2013;54(2):135–45.
Article
PubMed
Google Scholar
Kebede B, Cheema K, Greenshields DL, Li C, Selvaraj G, Rahman H. Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa. Genome. 2012;55(12):813–23.
Article
PubMed
Google Scholar
Rahman M, McVetty PB, Li G. Development of SRAP, SNP and multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L. Theor Appl Genet. 2007;115(8):1101–7.
Article
CAS
PubMed
Google Scholar
Zhao H, Basu U, Kebede B, Qu C, Li J, Rahman H. Fine mapping of the major QTL for seed coat color in Brassica rapa var. yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes. PLoS One. 2019;14(2):e0209982.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mahmood T, Rahman MH, Stringam GR, Raney JP, Good AG. Molecular markers for seed colour in Brassica juncea. Genome. 2005;48(4):755–60.
Article
CAS
PubMed
Google Scholar
Mahmood T, Rahman MH, Stringam GR, Yeh F, Good AG. Identification of quantitative trait loci (QTL) for oil and protein contents and their relationships with other seed quality traits in Brassica juncea. Theor Appl Genet. 2006;113:1211–20.
Article
CAS
PubMed
Google Scholar
Liu L, Stein A, Wittkop B, Sarvari P, Li J, Yan X, Dreyer F, Frauen M, Friedt W, Snowdon RJ. A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds. Theor Appl Genet. 2012;124(8):1573–86.
Article
CAS
PubMed
Google Scholar
Stein A, Wittkop B, Liu L, Obermeier C, Friedt W, Snowdon RJ, Chevre AM. 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(4):382–9.
Article
CAS
Google Scholar
Wang J, Xian X, Xu X, Qu C, Lu K, Li J, Liu L. Genome-wide association mapping of seed coat color in Brassica napus. J Agric Food Chem. 2017;65(26):5229–37.
Article
CAS
PubMed
Google Scholar
Jaakola L. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends Plant Sci. 2013;18(9):477–83.
Article
CAS
PubMed
Google Scholar
Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345(6199):950–3.
Article
CAS
PubMed
Google Scholar
Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, et al. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. J Exp Bot. 2017;68(17):4791–801.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rashid A, Rakov G, Downey RK. Development of yellow seeded Brassica napus through interspecific crosses. Plant Breed. 1994;112:127–34.
Article
Google Scholar
Wen J, Zhu L, Qi L, Ke H, Yi B, Shen J, Tu J, Ma C, Fu T. Characterization of interploid hybrids from crosses between Brassica juncea and B. oleracea and the production of yellow-seeded B. napus. Theor Appl Genet. 2012;125:19–32.
Article
PubMed
Google Scholar
Wang YP, Zhao XX, Sonntag K, Wehling P, Snowdon RJ. Behaviour of Sinapis alba chromosomes in a Brassica napus background revealed by genomic in-situ hybridization. Chromosom Res. 2005;13(8):819–26.
Article
CAS
Google Scholar
Jiang JJ, Zhao XX, Tian W, Li TB, Wang YP. Intertribal somatic hybrids between Brassica napus and Camelina sativa with high linolenic acid content. Plant Cell, Tissue and Organ Culture (PCTOC). 2009;99(1):91–5.
Article
Google Scholar
Warwick SI, Simard MJ, Legere A, Beckie HJ, Braun L, Zhu B, Mason P, Seguin-Swartz G, Stewart CN, Jr.: Hybridization between transgenic Brassica napus L. and its wild relatives: Brassica rapa L., Raphanus raphanistrum L., Sinapis arvensis L., and Erucastrum gallicum (Willd.) O.E. Schulz. Theor Appl Genet 2003, 107(3):528–539.
Zhang L, Jiang S, Xin R, Zhang F, Wang J, Guan R. Obtaining of yellow-seeded rapeseed germplasm from intergeneric hybridization between Brassica napus and Descurainia sophia. Chinese Journal of Oil Crop Sciences. 2009;31:434–9.
Google Scholar
Wang Y, Sonntag K, Rudloff E, Chen J. Intergeneric somatic hybridization between Brassica napus L. and Sinapis alba L. J Integr Plant Biol. 2005;47(1):8.
Article
CAS
Google Scholar
Jiang J, Shao Y, Li A, Lu C, Zhang Y, Wang Y. Phenolic composition analysis and gene expression in developing seeds of yellow- and black-seeded Brassica napus. J Integr Plant Biol. 2013;55(6):537–51.
Article
CAS
PubMed
Google Scholar
Jiang J, Shao Y, Li A, Zhang Y, Wei C, Wang Y. FT-IR and NMR study of seed coat dissected from different colored progenies of Brassica napus-Sinapis alba hybrids. J Sci Food Agric. 2013;93(8):1898–902.
Article
CAS
PubMed
Google Scholar
Li S, Zachgo S. TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana. Plant J. 2013;76(6):901–13.
Article
CAS
PubMed
Google Scholar
Ayabe S, Akashi T. Cytochrome P450s in flavonoid metabolism. Phytochem Rev. 2006;5(2–3):271–82.
Article
CAS
Google Scholar
Wu G, Wu Y, Xiao L, Li X, Lu C. Zero erucic acid trait of rapeseed (Brassica napus L.) results from a deletion of four base pairs in the fatty acid elongase 1 gene. Theor Appl Genet. 2008;116(4):491–9.
Article
CAS
PubMed
Google Scholar
Schierholt A, Becker HC, Ecke W. Mapping a high oleic acid mutation in winter oilseed rape (Brassica napus L.). Theor Appl Genet. 2000;101(5–6):897–901.
Article
CAS
Google Scholar
Li A, Jiang J, Zhang Y, Snowdon RJ, Liang G, Wang Y. Molecular and cytological characterization of introgression lines in yellow seed derived from somatic hybrids between Brassica napus and Sinapis alba. Mol Breed. 2012;29:209–19.
Article
CAS
Google Scholar
Zhu J, Wang X, Xu Q, Zhao S, Tai Y, Wei C. Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis). BMC Plant Biol. 2018;18(1):266.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang G, Sun M, Wang J, Lei M, Li C, Zhao D, Huang J, Li W, Li S, Li J, et al. PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice. Plant J. 2019;97(2):296–305.
Article
CAS
PubMed
Google Scholar
Thakur O, Randhawa GS. Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonolobaL Taub) roots. BMC genomics. 2018;19(1):951.
Article
PubMed
PubMed Central
CAS
Google Scholar
Qu C, Fu F, Lu K, Zhang K, Wang R, Xu X, Wang M, Lu J, Wan H, Zhanglin T, et al. Differential accumulation of phenolic compounds and expression of related genes in black- and yellow-seeded Brassica napus. J Exp Bot. 2013;64(10):2885–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hong M, Hu K, Tian T, Li X, Chen L, Zhang Y, Yi B, Wen J, Ma C, Shen J, et al. Transcriptomic analysis of seed coats in yellow-seeded Brassica napus reveals novel genes that influence proanthocyanidin biosynthesis. Front Plant Sci. 2017;8:1674.
Article
PubMed
PubMed Central
Google Scholar
Liu X, Lu Y, Yuan Y, Liu S, Guan C, Chen S, Liu Z. De novo transcriptome of Brassica juncea seed coat and identification of genes for the biosynthesis of flavonoids. PLoS One. 2013;8(8):e71110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang H, Fan W, Li H, Yang J, Huang J, Zhang P. Functional characterization of Dihydroflavonol-4-reductase in anthocyanin biosynthesis of purple sweet potato underlies the direct evidence of anthocyanins function against abiotic stresses. PLoS One. 2013;8(11):e78484.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou B, Wang Y, Zhan Y, Li Y, Kawabata S. Chalcone synthase family genes have redundant roles in anthocyanin biosynthesis and in response to blue/UV-A light in turnip (Brassica rapa; Brassicaceae). Am J Bot. 2013;100(12):2458–67.
Article
CAS
PubMed
Google Scholar
Sasaki-Sekimoto Y, Saito H, Masuda S, Shirasu K, Ohta H. Comprehensive analysis of protein interactions between JAZ proteins and bHLH transcription factors that negatively regulate jasmonate signaling. Plant Signal Behav. 2014;9(1):e27639.
Article
CAS
PubMed
PubMed Central
Google Scholar
Min JH, Ju HW, Yoon D, Lee KH, Lee S, Kim CS. Arabidopsis basic helix-loop-helix 34 (bHLH34) is involved in glucose signaling through binding to a GAGA Cis-element. Front Plant Sci. 2017;8:2100.
Article
PubMed
PubMed Central
Google Scholar
Lam PY, Zhu FY, Chan WL, Liu H, Lo C. Cytochrome P450 93G1 is a flavone synthase II that channels flavanones to the biosynthesis of tricin O-linked conjugates in rice. Plant Physiol. 2014;165(3):1315–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam PY, Liu H, Lo C: Completion of Tricin biosynthesis pathway in Rice: cytochrome P450 75B4 is a unique Chrysoeriol 5′-hydroxylase. Plant Physiol 2015, 168(4):1527–1536.
Lei Z, Zhou C, Ji X, Wei G, Huang Y, Yu W, Luo Y, Qiu Y. Transcriptome analysis reveals genes involved in flavonoid biosynthesis and accumulation in Dendrobium catenatum from different locations. Sci Rep. 2018;8(1):6373.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ma B, Luo Y, Jia L, Qi X, Zeng Q, Xiang Z, He N. Genome-wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis). J Integr Plant Biol. 2014;56(9):887–901.
Article
CAS
PubMed
Google Scholar
Li S. Transcriptional control of flavonoid biosynthesis: fine-tuning of the MYB-bHLH-WD40 (MBW) complex. Plant Signal Behav. 2014;9(1):e27522.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang Y, Meng G, Chen S, Chen Y, Jiang J, Wang YP. Correlation analysis of phenolic contents and antioxidation in yellow- and black-seeded Brassica napus. Molecules. 2018;23:1815–29.
Article
PubMed Central
CAS
Google Scholar
Pourcel L, Routaboul JM, Cheynier V, Lepiniec L, Debeaujon I. Flavonoid oxidation in plants: from biochemical properties to physiological functions. Trends Plant Sci. 2007;12(1):29–36.
Article
CAS
PubMed
Google Scholar
Lonien J, Schwender J. Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol. 2009;151(3):1617–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keereetaweep J, Liu H, Zhai Z, Shanklin J. Biotin attachment domain-containing proteins irreversibly inhibit acetyl CoA carboxylase. Plant Physiol. 2018;177(1):208–15.
CAS
PubMed
PubMed Central
Google Scholar
Chivasa S, Tome DF, Slabas AR. UDP-glucose pyrophosphorylase is a novel plant cell death regulator. J Proteome Res. 2013;12(4):1743–53.
Article
CAS
PubMed
Google Scholar
Xu Z, Escamilla-Trevino L, Zeng L, Lalgondar M, Bevan D, Winkel B, Mohamed A, Cheng CL, Shih MC, Poulton J, et al. Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Mol Biol. 2004;55(3):343–67.
Article
CAS
PubMed
Google Scholar
Fukuchi-Mizutani M, Mizutani M, Tanaka Y, Kusumi T, Ohta D. Microsomal electron transfer in higher plants: cloning and heterologous expression of NADH-cytochrome b5 reductase from Arabidopsis. Plant Physiol. 1999;119(1):353–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen G, Kuppu S, Venkataramani S, Wang J, Yan J, Qiu X, Zhang H. ANKYRIN REPEAT-CONTAINING PROTEIN 2A is an essential molecular chaperone for peroxisomal membrane-bound ASCORBATE PEROXIDASE3 in Arabidopsis. Plant Cell. 2010;22(3):811–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang J, Wang Y, Xie T, Rong H, Li A, Fang Y, Wang Y. Metabolic characteristics in meal of black rapeseed and yellow-seeded progeny of Brassica napus-Sinapis alba hybrids. Molecules. 2015;20(12):21204–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Rong H, Xie T, Jiang J, Wu J, Wang Y. Comparison of DNA methylation in the developing seeds of yellow- and black-seeded Brassica napus through MSAP analysis. Euphytica. 2016;209:157–69.
Article
CAS
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011;21(9):1543–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghosh S, Chan CK. Analysis of RNA-Seq data using TopHat and cufflinks. Methods Mol Biol. 2016;1374:339–61.
Article
CAS
PubMed
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621–8.
Article
CAS
PubMed
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
Article
CAS
PubMed
PubMed Central
Google Scholar
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mao XCT, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics. 2005;21(19):3787–93.
Article
CAS
PubMed
Google Scholar
Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M. A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, maize. Plant Cell Environ. 2009;32(9):1211–29.
Article
PubMed
Google Scholar