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Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening.
BMC Genomics. 2016 Jan 07; 17:36.BG

Abstract

BACKGROUND

Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses.

RESULTS

In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm.

CONCLUSIONS

In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions.

Authors+Show Affiliations

The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. lishan@cau.edu.cn.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. 1280331905@qq.com.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. 469095437@qq.com.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. 1019075246@qq.com.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. daqifu@126.com.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. hlzhu@cau.edu.cn.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. zbz@cau.edu.cn.The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China. lyb@cau.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26742635

Citation

Li, Shan, et al. "Genome-wide Analysis of Tomato NF-Y Factors and Their Role in Fruit Ripening." BMC Genomics, vol. 17, 2016, p. 36.
Li S, Li K, Ju Z, et al. Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. BMC Genomics. 2016;17:36.
Li, S., Li, K., Ju, Z., Cao, D., Fu, D., Zhu, H., Zhu, B., & Luo, Y. (2016). Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. BMC Genomics, 17, 36. https://doi.org/10.1186/s12864-015-2334-2
Li S, et al. Genome-wide Analysis of Tomato NF-Y Factors and Their Role in Fruit Ripening. BMC Genomics. 2016 Jan 7;17:36. PubMed PMID: 26742635.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. AU - Li,Shan, AU - Li,Ka, AU - Ju,Zheng, AU - Cao,Dongyan, AU - Fu,Daqi, AU - Zhu,Hongliang, AU - Zhu,Benzhong, AU - Luo,Yunbo, Y1 - 2016/01/07/ PY - 2015/10/07/received PY - 2015/12/18/accepted PY - 2016/1/9/entrez PY - 2016/1/9/pubmed PY - 2016/9/30/medline SP - 36 EP - 36 JF - BMC genomics JO - BMC Genomics VL - 17 N2 - BACKGROUND: Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses. RESULTS: In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm. CONCLUSIONS: In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26742635/Genome_wide_analysis_of_tomato_NF_Y_factors_and_their_role_in_fruit_ripening_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2334-2 DB - PRIME DP - Unbound Medicine ER -