title: The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.
abstract: BACKGROUND
  Reciprocal hybrids showing different phenotypes have been well documented in previous studies, and many factors accounting for different phenotypes have been extensively investigated. However, less is known about whether the profiles of small RNAs differ between reciprocal hybrids and how these small RNAs affect gene expression and phenotypes. To better understand this mechanism, the role of small RNAs on phenotypes in reciprocal hybrids was analysed.
  
  
  RESULTS
  Reciprocal hybrids between Solanum lycopersicum cv. Micro-Tom and S. pimpinellifolium line WVa700 were generated. Significantly different phenotypes between the reciprocal hybrids were observed, including fruit shape index, single fruit weight and plant height. Then, through the high-throughput sequencing of small RNAs, we found that the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids. Subsequently, a total of 410 target genes were predicted to correspond with these differentially expressed miRNAs. Furthermore, gene ontology (GO) annotation indicated that those target genes are primarily involved in metabolic processes. Finally, differentially expressed miRNAs, such as miR156f and 171a, and their target genes were analysed by qRT-PCR, and their expression levels were well correlated with the different phenotypes.
  
  
  CONCLUSIONS
  This study showed that the profiles of small RNAs differed between the reciprocal hybrids, and differentially expressed genes were also observed based on the different phenotypes. The qRT-PCR results of target genes showed that differentially expressed miRNAs negatively regulated their target genes. Moreover, the expression of target genes was well correlated with the observations of different phenotypes. These findings may aid in elucidating small RNAs contribute significantly to different phenotypes through epigenetic modification during reciprocal crossing.
authors.forename: Junxing
authors.initials: J
authors.lastname: Li
authors.forename: Qian
authors.initials: Q
authors.lastname: Sun
authors.forename: Ningning
authors.initials: N
authors.lastname: Yu
authors.forename: Jiajin
authors.initials: J
authors.lastname: Zhu
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Zou
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Qi
authors.forename: Muhammad Awais
authors.initials: MA
authors.lastname: Ghani
authors.forename: Liping
authors.initials: L
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D002678:Chimera; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010641:Phenotype; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering