Weighted gene co-expressed network analysis in barley and expression of hub genes involved at germination stage

Document Type : Research Paper

Authors

1 Ph.D. Student, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.

2 Professor, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.

3 Assistant Professor, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.

4 Associated Professor, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.

Abstract

Objective
Seed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules.
 
Materials and methods
Raw microarray data related to the germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h, and 71h after the germination stage. Then, weighted gene co-expression network analysis (WGCNA) was utilized for the detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression patterns after 9h, 18h, and 71h after the germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR.
 
Results
Most of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to a stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at the germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is a lack of information on the seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism of seed germination in barley.
 
Conclusions
The results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular-assisted selection and breeding of fast-germinating barley genotypes.

Keywords

References

 
Asakura T, Tamura T, Terauchi K et al. (2012) Global gene expression profiles in developing soybean seeds. PPB 52,147–153.
 Bakhtiarizadeh MR, Hosseinpour B, Shahhoseini M et al. (2018) Weighted gene co-expression network analysis of endometriosis and identification of functional modules associated with its main hallmarks. Front Genet 9, 453.
Bergler J, Hoth S (2011) Plant U‐box armadillo repeat proteins AtPUB18 and AtPUB19 are involved in salt inhibition of germination in Arabidopsis. Plant Biol 13(5), 725-30.
Bonas U, Lahaye T (2002) Plant disease resistance triggered by pathogen-derived molecules: refined models of specific recognition. Curr Opin Microbiol 5(1), 44–50.
Canonne J, Froidure-Nicolas S, Rivas S (2011) Phospholipases in action during plant defense signaling. Plant Signal Behav 6(1), 13–18. 
Carbonero P, Iglesias-Fernández R, Vicente-Carbajosa J (2017) The AFL subfamily of B3 transcription factors: evolution and function in angiosperm seeds. JXB 68(4), 871-80.
Chi W, He B, Mao J et al. (2012) The function of RH22, a DEAD RNA helicase, in the biogenesis of the 50S ribosomal subunits of Arabidopsis chloroplasts. Plant Physiol 158(2), 693–707.
Dangl JL, Jones DGJ (2001) Plant pathogens and integrated defence responses to infection. Nature 411(6839), 826–833.
Davière J-M, Achard P (2013) Gibberellin signaling in plants. Development 140(6), 1147–1151.
Durrant WE, Dong X (2004) Systemic acquired resistance. Annu Rev Phytopathol 42(1),185–209.
Finkelstein R, Gampala S, Rock C (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 141(1), S15–S45
Gershater MC, Edwards R (2007) Regulating biological activity in plants with carboxylesterases. Plant Sci 173(6), 579–588.
Hajibarat Z, Saidi A, Zeinalabedini M  et al. (2022) Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum. JGEB 20(1), 1-21.
Hsu YF, Chen YC, Hsiao YC et al. (2014) A t RH 57, a DEAD‐box RNA helicase, is involved in feedback inhibition of glucose‐mediated abscisic acid accumulation during seedling development and additively affects pre‐ribosomal RNA processing with high glucose. Plant J 77(1), 119-135.
Jing Y, Lin R (2020) Transcriptional regulatory network of the light signaling pathways. New Phytol 227(3), 683-97.
Jones SI, Gonzalez DO, Vodkin LO (2010) Flux of transcript patterns during soybean seed development. BMC Genomics 11(1),136. 
Jones SI, Vodkin LO (2013) Using RNA-Seq to profile soybean seed development from fertilization to maturity. PLoS One 8(3).e59270.
Kader JC (1996) Lipid-transfer proteins in plants. Ann Rev Plant Physiol Plant Mol Biol. 47, 627–654.
Kucera B, Cohn MA, Leubner-Metzger G (2005) Plant hormone interactions during seed dormancy release and germination. Seed Sci Res 15(4), 281–307.
Lee K, Kang H (2016) Emerging roles of RNA-binding proteins in plant growth, development, and stress responses. Mol Cells 39(3), 179–185. doi: 10.14348/molcells.2016.2359.
Li H, Li X, Wang G et al. (2022) Analysis of gene expression in early seed germination of rice: landscape and genetic regulation. BMC plant Boil 22(1), 1-14.
Liew LC, Narsai R, Wang Y et al. (2020) Temporal tissue‐specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. Plant J 101(3),700-715.
Ling TF, Xuan W, Fan YR et al. (2005) The effect of exogenous glucose, fructose and NO donor sodium nitroprusside (SNP) on rice seed germination under salt stress. Zhi wu Sheng li yu fen zi Sheng wu xue xue bao= Physiol Mol Biol Plants 31(2), 205-12.
Liu H, Stone SL (2011) E3 ubiquitin ligases and abscisic acid signaling. Plant Signal. Behav 6, 344-348.
Livak K.J, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25(4), 402-408.
Mindrebo JT, Nartey CM, Seto Y et al. (2016) Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. COSB 41, 233-246.
Nguyen HT, Silva JE, Podicheti R et al. (2013) Camelina seed transcriptome: a tool for meal and oil improvement and translational research. Plant Biotechnol J 11(6),759–769.
Nürnberger T, Brunner F, Kemmerling B, Piater L (2004) Innate immunity in plants and animals: striking similarities and obvious differences. Immunol Rev 198(1), 249–266.
Opassiri R, Pomthong B, Onkoksoong T et al. (2006) Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 β-glucosidase. BMC Plant Biol 6(1), 33–40.
Park J, Kim YS, Kim SG et al. (2011) Integration of auxin and salt signals by the NAC transcription factor NTM2 during seed germination in Arabidopsis. Plant Physiol 156(2), 537-549.
Qu C, Zuo Z, Cao L et al. (2019) Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar. BMC plant Boil 19(1), 1-5.
Rajjou L, Duval M, Gallardo K et al. (2012) Seed germination and vigor. Annu Rev Plant Biol 63(507), 2012
Ruan YL (2014) Sucrose metabolism: gateway to diverse carbon use and sugar signaling. Annual Review of Plant Biol 65(1), 33–67
Saeedipour S, Moradi F (2011) Comparison of the drought stress responses of tolerant and sensitive wheat cultivars during grain filling: impact of invertase activity on carbon metabolism during kernel development. J Agric Sci 3(2), 32.
Saidi A, Hajibarat Z, Hajibarat Z (2021) Phylogeny, gene structure and GATA genes expression in different tissues of solanaceae species. Biocatal Agric Biotechnol 35,102015.
Stein O, Granot D (2019) An overview of sucrose synthases in plants. Front Plant Sci. 8, 10:95.
Stotz HU, Thomson J, Wang Y (2009) Plant defensins. Plant Signal Behav 4(11), 1010–1012. https://doi.org/10.4161/psb.4.11.9755.
Thordal-Christensen H (2003) Fresh insights into processes of nonhost resistance. Curr Opin Plant Biol 6(4), 351–357.
Van Dam S, Vosa U, van der Graaf A et al. (2018) Gene co-expression analysis for functional classification and gene–disease predictions. Briefings in bioinformatics. 19(4), 575-592.
Wang J, Liu S, Li C et al. (2017) PnLRR-RLK27, a novel leucine-rich repeats receptor-like protein kinase from the Antarctic moss Pohlia nutans, positively regulates salinity and oxidation-stress tolerance. PLoS One 12(2), e0172869.
Wang J, Wang Y, Zhang J et al. (2021) The NAC transcription factor ClNAC68 positively regulates sugar content and seed development in watermelon by repressing ClINV and ClGH3. 6. Hortic Res 8(1), 1-1.
Yamaguchi S (2008) Gibberellin metabolism and its regulation. Ann Rev Plant Biol 59, 225-251.
Zhang X, Garreton V, Chua NH (2005) The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev 19(13), 1532–1543.
Agricultural Biotechnology Journal
Volume 14, Issue 4
December 2022
Pages 247-267

Files

Share

How to cite

Statistics