title: Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening.
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.affiliation: 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.
authors.forename: Shan
authors.initials: S
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Ka
authors.initials: K
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Ju
authors.affiliation: 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.
authors.forename: Dongyan
authors.initials: D
authors.lastname: Cao
authors.affiliation: 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.
authors.forename: Daqi
authors.initials: D
authors.lastname: Fu
authors.affiliation: 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.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Zhu
authors.affiliation: 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.
authors.forename: Benzhong
authors.initials: B
authors.lastname: Zhu
authors.affiliation: 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.
authors.forename: Yunbo
authors.initials: Y
authors.lastname: Luo
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D023081:CCAAT-Binding Factor / Q000235:genetics*; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny
chemical_list: D023081:CCAAT-Binding Factor