161
Views
1
CrossRef citations to date
0
Altmetric
Articles

Comparative transcriptome analysis in three sorghum (Sorghum bicolor) cultivars reveal genomic basis of differential seed quality

ORCID Icon, , , , , , & show all
Pages 232-241 | Received 15 Dec 2019, Accepted 09 Nov 2020, Published online: 10 Dec 2020

References

  • Angelucci FB, Gourichon H, Mas Aparisi A, Witwer M. 2014. Monitoring and analysing food and agricultural policies in Africa. MAFAP Synthesis Report. p. 7–141.
  • Awika JM, Rooney LW, Wu X, Prior RL, Cisneros-Zevallos L. 2003. Screening methods to measure antioxidant activity of sorghum (sorghum bicolor) and sorghum products. J Agric Food Chem. 51(23):6657–6662.
  • Bar-Ya'akov I, Tian L, Amir R, Holland D. 2019. Primary metabolites, anthocyanins, and hydrolyzable tannins in the pomegranate fruit. Front Plant Sci. 10:620.
  • Calvino M, Messing J. 2012. Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol. 23(3):323–329.
  • Dai AG. 2011. Drought under global warming: a review. WIREs Clim Change. 2(1):45–65.
  • Dicko MH, Gruppen H, Traore AS, Van Berkel WJH, Voragen AGJ. 2005. Evaluation of the effect of germination on phenolic compounds and antioxidant activities in sorghum varieties. J Agric Food Chem. 53(7):2581–2588.
  • Dykes L, Rooney LW, Waniska RD, Rooney WL. 2005. Phenolic compounds and antioxidant activity of sorghum grains of varying genotypes. J Agric Food Chem. 53(17):6813–6818.
  • Ebadi MR, Sedghi M, Akbari Moghaddam Kakhki R. 2019. Accurate prediction of nutritional value of sorghum grain using image analysis. Br Poult Sci. 60(2):154–160.
  • Fernie AR, Stitt M. 2012. On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence. Plant Physiol. 158(3):1139–1145.
  • Hahn DH, Rooney LW, Earp CF. 1984. Tannins and phenols of sorghum. Cereal Food World. 29(12):776–779.
  • Han C, Li X, Fan Q, Liu G, Yin J. 2019. CCAT1 promotes triple-negative breast cancer progression by suppressing miR-218/ZFX signaling. Aging (Albany NY). 11(14):4858–4875.
  • Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC. 2003. The basic helix–loop–helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol. 20(5):735–747.
  • Hertog MGL, Feskens EJM, Hollman PCH, Katan MB, Kromhout D. 1993. Dietary antioxidant flavonoids and risk of coronary heart-disease − the Zutphen Elderly Study. Lancet. 342(8878):1007–1011.
  • Hou Y, Wang Y, Tang L, Tong X, Wang L, Liu L, Huang S, Zhang J. 2019. SAPK10-mediated phosphorylation on WRKY72 releases its suppression on jasmonic acid biosynthesis and bacterial blight resistance. iScience. 16:499–510.
  • Hu F, Min J, Cao X, Liu L, Ge Z, Hu J, Li X. 2016. MiR-363-3p inhibits the epithelial-to-mesenchymal transition and suppresses metastasis in colorectal cancer by targeting Sox4. Biochem Biophys Res Commun. 474(1):35–42.
  • Jiang SY, Ma ZG, Vanitha J, Ramachandran S. 2013. Genetic variation and expression diversity between grain and sweet sorghum lines. BMC Genomics. 14:18.
  • Jiang W, Liu T, Nan W, Jeewani DC, Niu Y, Li C, Wang Y, Shi X, Wang C, Wang J, et al. 2018. Two transcription factors TaPpm1 and TaPpb1 co-regulate anthocyanin biosynthesis in purple pericarps of wheat. J Exp Bot. 69(10):2555–2567.
  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36(Database issue):D480–D484.
  • Khoddami A, Truong HH, Liu SY, Roberts TH, Selle PH. 2015. Concentrations of specific phenolic compounds in six red sorghums influence nutrient utilisation in broiler chickens. Anim Feed Sci Technol. 210:190–199.
  • Kumar AA, Anuradha K, Ramaiah B, Grando S, Frederick H, Rattunde W, Virk P, Pfeiffer WH. 2015. Recent advances in Sorghum biofortification research. Plant Breed Rev. 39:89–124.
  • Liu Y, Lin-Wang K, Espley RV, Wang L, Yang H, Yu B, Dare A, Varkonyi-Gasic E, Wang J, Zhang J, et al. 2016. Functional diversification of the potato R2R3 MYB anthocyanin activators AN1, MYBA1, and MYB113 and their interaction with basic helix–loop–helix cofactors. J Exp Bot. 67(8):2159–2176.
  • Mace ES, Buhariwalla KK, Buhariwalla HK, Crouch JH. 2003. A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Rep. 21(4):459–460.
  • Mao XZ, Cai T, Olyarchuk JG, Wei LP. 2005. Automated genome annotation and pathway identification using the KEGG orthology (KO) as a controlled vocabulary. Bioinformatics. 21(19):3787–3793.
  • McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B, et al. 2018. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. Plant J. 93(2):338–354.
  • Mohammadi M, Kazemi H. 2002. Changes in peroxidase and polyphenol oxidase activities in susceptible and resistant wheat heads inoculated with Fusarium graminearum and induced resistance. Plant Sci. 162(4):491–498.
  • Montefiori M, Brendolise C, Dare AP, Lin-Wang K, Davies K, Hellens R, Allan A. 2015. In the Solanaceae, a hierarchy of bHLHs confer distinct target specificity to the anthocyanin regulatory complex. J Exp Bot . 66(5):1427–1436.
  • Mullet J, Morishige D, McCormick R, Truong S, Hilley J, McKinley B, Anderson R, Olson SN, Rooney W. 2014. Energy sorghum – a genetic model for the design of C4 grass bioenergy crops. J Exp Bot. 65(13):3479–3489.
  • Parr AJ, Bolwell GP. 2000. Phenols in the plant and in man. The potential for possible nutritional enhancement of the diet by modifying the phenols content or profile. J Sci Food Agric. 80(7):985–1012.
  • Paterson AH. 2008. Genomics of sorghum. Int J Plant Genomics. 2008:1–6.
  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457(7229):551–556.
  • Proteggente AR, Pannala AS, Paganga G, Van Buren L, Wagner E, Wiseman S, Van De Put F, Dacombe C, Rice-Evans CA. 2002. The antioxidant activity of regularly consumed fruit and vegetables reflects their phenolic and vitamin C composition. Free Radic Res. 36(2):217–233.
  • Schwender J, König C, Klapperstück M, Heinzel N, Munz E, Hebbelmann I, Hay JO, Denolf P, De Bodt S, Redestig H, et al. 2014. Transcript abundance on its own cannot be used to infer fluxes in central metabolism. Front Plant Sci. 5:668.
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498–2504.
  • Taylor SH, Ripley BS, Martin T, De-Wet LA, Woodward FI, Osborne CP. 2014. Physiological advantages of C4 grasses in the field: a comparative experiment demonstrating the importance of drought. Glob Chang Biol. 20(6):1992–2003.
  • Visioli F, De La Lastra CA, Andres-Lacueva C, Aviram M, Calhau C, Cassano A, D'Archivio M, Faria A, Favé G, Fogliano V, et al. 2011. Polyphenols and human health: a prospectus. Crit Rev Food Sci Nutr. 51(6):524–546.
  • Wang D, Bean S, McLaren J, Seib P, Madl R, Tuinstra M, Shi Y, Lenz M, Wu X, Zhao R. 2008. Grain sorghum is a viable feedstock for ethanol production. J Ind Microbiol Biotechnol. 35(5):313–320.
  • Weir TL, Park SW, Vivanco JM. 2004. Biochemical and physiological mechanisms mediated by allelochemicals. Curr Opin Plant Biol. 7(4):472–479.
  • Wu GC, Johnson SK, Bornman JF, Bennett SJ, Clarke MW, Singh V, Fang ZX. 2016. Growth temperature and genotype both play important roles in sorghum grain phenolic composition. Sci Rep. 6:21835.
  • Young MD, Wakefield MJ, Smyth GK, Oshlack A. 2010. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11(2):R14.
  • Yuan YW, Sagawa JM, Frost L, Vela JP, Bradshaw HD. 2014. Transcriptional control of floral anthocyanin pigmentation in monkeyflowers (Mimulus). New Phytol. 204(4):1013–1027.
  • Zhang Y, Fan J, Fu Y, Francis F, Chen J. 2019. Plant-mediated interactions between two cereal aphid species: promotion of aphid performance and attraction of more parasitoids by infestation of wheat with phytotoxic aphid Schizaphis graminum. J Agric Food Chem. 67(10):2763–2773.
  • Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, et al. 2011. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 12(11):R114.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.