Working group session:
Breeding and Applied Genomics
Presentation type:
oral
Authors:
Mansoor, Shahid ; Guo, Hui; Paterson, Andrew
Presenter:
Mansoor, Shahid ; Guo, Hui
Correspondent:
Mansoor, Shahid ; Guo, Hui
Abstract:
MicroRNAs are 18-24 nucleotide elements that regulate developmental processes and are a subject of great interest in recent years. The deep sequencing of short RNAs has revolutionized their cloning and millions of short RNA sequences are available in public databases from various tissues of G. arboreum and G. hirsutum. In the present study, short RNA data from G. hirsutum and G. arboreum were compared in silico. The comparison of miRNAs from G. arboreum with validated miRNAs in miRBase identified 256 families of conserved miRNAs. These miRNAs were validated by homology search with ESTs derived from G. hirsutum, G. arboreum and G. raimondii. Additionally, sRNA data was compared with cotton ESTs and the miRDeep program was used to identify novel miRNAs that have not been deposited in miRBase from any species. Five novel miRNA were identified in cotton by using this approach. All identified miRNA families from G. arboreum and G. hirsutum were annotated in miRBase. Each miRNA family has several isoforms that differ in the sequence or length of miRNAs. We also identified a substantial number of miRNAs homologous to animal miRNAs. There were major differences in the relative abundance of miRNA species from leaf, flower and developing boll in the two species. Interestingly, we also identified longer miRNAs (26-34 nucleotides) in both cotton species that differed in abundance in different tissues. The miRNAs involved in biotic and abiotic stress response and fiber development were compared between the two cotton species. The implications of these findings for abiotic/biotic stress tolerance and fiber quality between G. arboreum and G. hirsutum will be discussed.