Research Article
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Year 2024, Volume: 41 Issue: 3, 101 - 105, 25.11.2024
https://doi.org/10.16882/hortis.1528220

Abstract

References

  • Akimoto, K., Katakami, H., Kim, H.J., Ogawa, E., Sano, C.M., Wada, Y., & Sano, H. (2007). Epigenetic inheritance in rice plants. Annals of Botany, 100(2): 205-217.
  • Allaire, J. (2011). RStudio: integrated development environment for R. Boston, MA, 770(394), 165-171.
  • Allis, C.D., & Jenuwein, T. (2016). The molecular hallmarks of epigenetic control. Nature Reviews Genetics, 17(8): 487-500.
  • Berger, S.L. (2007). The complex language of chromatin regulation during transcription. Nature, 447(7143): 407-412.
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10: 1-9.
  • Erdogan-Orhan, I., & Kartal, M. (2011). Insights into research on phytochemistry and biological activities of Prunus armeniaca L. (apricot). Food Research International, 44(5): 1238-1243.
  • FAOSTAT. (2024). FAOSTAT Online Database. Food and Agriculture Organization of the United Nations.
  • Gibson, U.E., Heid, C.A., & Williams, P.M. (1996). A novel method for real time quantitative RT-PCR. Genome Research, 6(10): 995-1001.
  • Gómez-Rubio, V. (2017). ggplot2-elegant graphics for data analysis. Journal of Statistical Software, 77: 1-3.
  • He, X., Wang, Q., Pan, J., Liu, B., Ruan, Y., & Huang, Y. (2021). Systematic analysis of JmjC gene family and stress-response expression of KDM5 subfamily genes in Brassica napus. PeerJ, 9: e11137.
  • Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., & Khurana, J.P. (2007). F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology, 143(4): 1467-1483.
  • Jeong, J.H., Song, H.R., Ko, J.H., Jeong, Y.M., Kwon, Y.E., Seol, J.H., & Noh, Y.S. (2009). Repression of Flowering Locus T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. Plos One, 4(11): e8033.
  • Jung, S., Lee, T., Cheng, C.H., Buble, K., Zheng, P., Yu, J., & Main, D. (2019). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 47(D1): D1137-D1145.
  • Karuppaiya, P., Yan, X.X., Liao, W., Wu, J., Chen, F., & Tang, L. (2017). Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas–A biodiesel plant. Plos One, 12(2): e0172460.
  • Keyzor, C., Mermaz, B., Trigazis, E., Jo, S., & Song, J. (2021). Histone demethylases ELF6 and JMJ13 antagonistically regulate self-fertility in Arabidopsis. Frontiers in Plant Science, 12: 640135.
  • Klose, R.J., & Zhang, Y. (2007). Regulation of histone methylation by demethylimination and demethylation. Nature Reviews Molecular Cell Biology, 8(4): 307-318.
  • Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., & Araki, T. (1999). A pair of related genes with antagonistic roles in mediating flowering signals. Science, 286(5446): 1960-1962.
  • Lan, F., Nottke, A.C., & Shi, Y. (2008). Mechanisms involved in the regulation of histone lysine demethylases. Current Opinion in Cell Biology, 20(3): 316-325.
  • Lee, M.G., Wynder, C., Cooch, N., & Shiekhattar, R. (2005). An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature, 437(7057): 432-435.
  • Li, G., Li, F., Zhang, S., Zhang, H., Zhang, S., & Sun, R. (2019). Cloning and function analysis of a novel flowering time regulatory gene BraELF6 in Brassica rapa. Scientia Horticulturae, 248: 126-131.
  • Liu, C., Lu, F., Cui, X., & Cao, X. (2010). Histone methylation in higher plants. Annual Review of Plant Biology, 61: 395-420.
  • Livak, K.J., & Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods, 25(4): 402-408.
  • Massa, A.N., Childs, K.L., Lin, H., Bryan, G.J., Giuliano, G., & Buell, C.R. (2011). The transcriptome of the reference potato genome Solanum tuberosum group phureja clone DM1-3 516R44. Plos One, 6(10): e26801.
  • Metzger, E., Wissmann, M., Yin, N., Müller, J.M., Schneider, R., Peters, A.H.F.M., Günther, T., Buettner, R., Schüle, R., 2005. LSD1 demethylates repressive histone marks to promote androgen-receptor- dependent transcription. Nature, 437. https://doi.org/10.1038/nature04020.
  • Niu, J., Zhu, B., Cai, J., Li, P., Wang, L., Dai, H., & Lin, S. (2014). Selection of reference genes for gene expression studies in Siberian Apricot (Prunus sibirica L.) Germplasm using quantitative real-time PCR. Plos One, 9(8): e103900.
  • Pfluger, J., & Wagner, D. (2007). Histone modifications and dynamic regulation of genome accessibility in plants. Current Opinion in Plant Biology, 10(6): 645-652.
  • Shi, X., Yu, W., Wang, L., Zhao, H., Hu, J., Wuyun, T., Liu, H., (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400): 635-641.
  • Shi, X., Yu, W., Wang, L., Zhao, H., Hu, J., Wuyun, T., & Liu, H. (2023). Genome-Wide Identification and Expression profiling of B3 transcription factor genes in Prunus armeniaca. Forests, 14(8): 1523.
  • Stricker, S.H., Köferle, A., & Beck, S. (2017). From profiles to function in epigenomics. Nature Reviews Genetics, 18(1): 51-66.
  • Tichopad, A., Dilger, M., Schwarz, G., & Pfaffl, M.W. (2003). Standardized determination of real‐time PCR efficiency from a single reaction set‐up. Nucleic Acids Research, 31(20): e122-e122.
  • Tong, Z., Gao, Z., Wang, F., Zhou, J., & Zhang, Z. (2009). Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Molecular Biology, 10: 1-13.
  • Wang, H., Liu, C., Cheng, J., Liu, J., Zhang, L., He, C. & Zhang, Y. (2016). Arabidopsis flower and embryo developmental genes are repressed in seedlings by different combinations of polycomb group proteins in association with distinct sets of cis-regulatory elements. Plos Genetics, 12(1): e1005771.
  • Ward, J.A., Ponnala, L., & Weber, C.A. (2012). Strategies for transcriptome analysis in nonmodel plants. American Journal of Botany, 99(2): 267-276.
  • Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G. V., & Provart, N.J. (2007). An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PloS One, 2(8): e718.
  • Yamaguchi, N., 2022. Editorial: Epigenetics in Plant Development. Frontiers in Plant Science, 13: 1–3.
  • Yan, W., Chen, D., Smaczniak, C., Engelhorn, J., Liu, H., Yang, W., & Kaufmann, K. (2018). Dynamic and spatial restriction of Polycomb activity by plant histone demethylases. Nature Plants, 4(9): 681-689.

Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages

Year 2024, Volume: 41 Issue: 3, 101 - 105, 25.11.2024
https://doi.org/10.16882/hortis.1528220

Abstract

In higher plants, regulation of gene expression and chromatin formation occurs by histone methylation and demethylation. Genes encoding JmjC-JmjN domains belong to the histone demethylase family and have an important role in the regulation of plant growth and development. Early Flowering 6 (AtELF6), which encodes the JmjC-JmjN domain in Arabidopsis thaliana, is a demethylase that regulates growth and development as well as the transition to flowering, but it has not been identified in apricot so far. In this study, two genes homologous to AtELF6 were identified for the first time in apricot. Gene expression analysis by RT-qPCR revealed that both ELF6 homologs were expressed in 12 different developmental stages of three different tissues. The fact that both homologues were expressed, especially in the flower bud, suggested that they play a role in the transition to flowering, similar to Arabidopsis thaliana. In summary, the information obtained from this study will provide a unique resource for understanding the role of ELF 6 in apricot growth and development, as well as for future functional characterization studies for the manipulation of the flowering transition.

References

  • Akimoto, K., Katakami, H., Kim, H.J., Ogawa, E., Sano, C.M., Wada, Y., & Sano, H. (2007). Epigenetic inheritance in rice plants. Annals of Botany, 100(2): 205-217.
  • Allaire, J. (2011). RStudio: integrated development environment for R. Boston, MA, 770(394), 165-171.
  • Allis, C.D., & Jenuwein, T. (2016). The molecular hallmarks of epigenetic control. Nature Reviews Genetics, 17(8): 487-500.
  • Berger, S.L. (2007). The complex language of chromatin regulation during transcription. Nature, 447(7143): 407-412.
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10: 1-9.
  • Erdogan-Orhan, I., & Kartal, M. (2011). Insights into research on phytochemistry and biological activities of Prunus armeniaca L. (apricot). Food Research International, 44(5): 1238-1243.
  • FAOSTAT. (2024). FAOSTAT Online Database. Food and Agriculture Organization of the United Nations.
  • Gibson, U.E., Heid, C.A., & Williams, P.M. (1996). A novel method for real time quantitative RT-PCR. Genome Research, 6(10): 995-1001.
  • Gómez-Rubio, V. (2017). ggplot2-elegant graphics for data analysis. Journal of Statistical Software, 77: 1-3.
  • He, X., Wang, Q., Pan, J., Liu, B., Ruan, Y., & Huang, Y. (2021). Systematic analysis of JmjC gene family and stress-response expression of KDM5 subfamily genes in Brassica napus. PeerJ, 9: e11137.
  • Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., & Khurana, J.P. (2007). F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology, 143(4): 1467-1483.
  • Jeong, J.H., Song, H.R., Ko, J.H., Jeong, Y.M., Kwon, Y.E., Seol, J.H., & Noh, Y.S. (2009). Repression of Flowering Locus T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. Plos One, 4(11): e8033.
  • Jung, S., Lee, T., Cheng, C.H., Buble, K., Zheng, P., Yu, J., & Main, D. (2019). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 47(D1): D1137-D1145.
  • Karuppaiya, P., Yan, X.X., Liao, W., Wu, J., Chen, F., & Tang, L. (2017). Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas–A biodiesel plant. Plos One, 12(2): e0172460.
  • Keyzor, C., Mermaz, B., Trigazis, E., Jo, S., & Song, J. (2021). Histone demethylases ELF6 and JMJ13 antagonistically regulate self-fertility in Arabidopsis. Frontiers in Plant Science, 12: 640135.
  • Klose, R.J., & Zhang, Y. (2007). Regulation of histone methylation by demethylimination and demethylation. Nature Reviews Molecular Cell Biology, 8(4): 307-318.
  • Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., & Araki, T. (1999). A pair of related genes with antagonistic roles in mediating flowering signals. Science, 286(5446): 1960-1962.
  • Lan, F., Nottke, A.C., & Shi, Y. (2008). Mechanisms involved in the regulation of histone lysine demethylases. Current Opinion in Cell Biology, 20(3): 316-325.
  • Lee, M.G., Wynder, C., Cooch, N., & Shiekhattar, R. (2005). An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature, 437(7057): 432-435.
  • Li, G., Li, F., Zhang, S., Zhang, H., Zhang, S., & Sun, R. (2019). Cloning and function analysis of a novel flowering time regulatory gene BraELF6 in Brassica rapa. Scientia Horticulturae, 248: 126-131.
  • Liu, C., Lu, F., Cui, X., & Cao, X. (2010). Histone methylation in higher plants. Annual Review of Plant Biology, 61: 395-420.
  • Livak, K.J., & Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods, 25(4): 402-408.
  • Massa, A.N., Childs, K.L., Lin, H., Bryan, G.J., Giuliano, G., & Buell, C.R. (2011). The transcriptome of the reference potato genome Solanum tuberosum group phureja clone DM1-3 516R44. Plos One, 6(10): e26801.
  • Metzger, E., Wissmann, M., Yin, N., Müller, J.M., Schneider, R., Peters, A.H.F.M., Günther, T., Buettner, R., Schüle, R., 2005. LSD1 demethylates repressive histone marks to promote androgen-receptor- dependent transcription. Nature, 437. https://doi.org/10.1038/nature04020.
  • Niu, J., Zhu, B., Cai, J., Li, P., Wang, L., Dai, H., & Lin, S. (2014). Selection of reference genes for gene expression studies in Siberian Apricot (Prunus sibirica L.) Germplasm using quantitative real-time PCR. Plos One, 9(8): e103900.
  • Pfluger, J., & Wagner, D. (2007). Histone modifications and dynamic regulation of genome accessibility in plants. Current Opinion in Plant Biology, 10(6): 645-652.
  • Shi, X., Yu, W., Wang, L., Zhao, H., Hu, J., Wuyun, T., Liu, H., (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400): 635-641.
  • Shi, X., Yu, W., Wang, L., Zhao, H., Hu, J., Wuyun, T., & Liu, H. (2023). Genome-Wide Identification and Expression profiling of B3 transcription factor genes in Prunus armeniaca. Forests, 14(8): 1523.
  • Stricker, S.H., Köferle, A., & Beck, S. (2017). From profiles to function in epigenomics. Nature Reviews Genetics, 18(1): 51-66.
  • Tichopad, A., Dilger, M., Schwarz, G., & Pfaffl, M.W. (2003). Standardized determination of real‐time PCR efficiency from a single reaction set‐up. Nucleic Acids Research, 31(20): e122-e122.
  • Tong, Z., Gao, Z., Wang, F., Zhou, J., & Zhang, Z. (2009). Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Molecular Biology, 10: 1-13.
  • Wang, H., Liu, C., Cheng, J., Liu, J., Zhang, L., He, C. & Zhang, Y. (2016). Arabidopsis flower and embryo developmental genes are repressed in seedlings by different combinations of polycomb group proteins in association with distinct sets of cis-regulatory elements. Plos Genetics, 12(1): e1005771.
  • Ward, J.A., Ponnala, L., & Weber, C.A. (2012). Strategies for transcriptome analysis in nonmodel plants. American Journal of Botany, 99(2): 267-276.
  • Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G. V., & Provart, N.J. (2007). An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PloS One, 2(8): e718.
  • Yamaguchi, N., 2022. Editorial: Epigenetics in Plant Development. Frontiers in Plant Science, 13: 1–3.
  • Yan, W., Chen, D., Smaczniak, C., Engelhorn, J., Liu, H., Yang, W., & Kaufmann, K. (2018). Dynamic and spatial restriction of Polycomb activity by plant histone demethylases. Nature Plants, 4(9): 681-689.
There are 36 citations in total.

Details

Primary Language English
Subjects Agricultural Engineering (Other)
Journal Section Araştırma Makalesi
Authors

Ali Kıyak 0000-0002-6631-7778

Early Pub Date August 27, 2024
Publication Date November 25, 2024
Submission Date May 23, 2024
Acceptance Date August 22, 2024
Published in Issue Year 2024 Volume: 41 Issue: 3

Cite

APA Kıyak, A. (2024). Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages. Horticultural Studies, 41(3), 101-105. https://doi.org/10.16882/hortis.1528220
AMA Kıyak A. Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages. HortiS. November 2024;41(3):101-105. doi:10.16882/hortis.1528220
Chicago Kıyak, Ali. “Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages”. Horticultural Studies 41, no. 3 (November 2024): 101-5. https://doi.org/10.16882/hortis.1528220.
EndNote Kıyak A (November 1, 2024) Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages. Horticultural Studies 41 3 101–105.
IEEE A. Kıyak, “Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages”, HortiS, vol. 41, no. 3, pp. 101–105, 2024, doi: 10.16882/hortis.1528220.
ISNAD Kıyak, Ali. “Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages”. Horticultural Studies 41/3 (November 2024), 101-105. https://doi.org/10.16882/hortis.1528220.
JAMA Kıyak A. Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages. HortiS. 2024;41:101–105.
MLA Kıyak, Ali. “Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages”. Horticultural Studies, vol. 41, no. 3, 2024, pp. 101-5, doi:10.16882/hortis.1528220.
Vancouver Kıyak A. Gene Expression Analysis of the Early Flowering 6 Homologues in Apricot Reveals Their Potential Role in Developmental Stages. HortiS. 2024;41(3):101-5.