Abstract
Common wild rice (Oryza rufipogon Griff.) is the most closely related ancestral species to Asian cultivated rice (Oryza sativa L.). It contains various valuable traits with regard to tolerance to cold, drought and salinity, flowering diversity and many quantitative trait loci with agronomic important traits. Flowering is one of the most important agronomic traits. However, flowering-related transcriptome and how to be regulated by miRNAs have not been estimated in O.rufipogon. To identify how the genes and miRNAs regulating flowering in O.rufipogon. Three O.rufipogon RNA libraries, two vegetative stages (CWRT-V1 and CWRT-V2) and one flowering stage (CWRT-F2) were constructed using leaves tissue and sequenced using Illumina deep sequencing. 27,405, 27,333, 28,979 unique genes were obtained after mapping to the reference genome from CWRT-V1, CWRT-V2 and CWRT-F2, respectively. Then differentially expressed genes (DEGs) were screened and got 1419 unique genes are likely to involve in flower development. Detailed information showed that MADS box and floral meristem identity genes, such as MADS 1, MADS14, Hd1 are involved in common wild rice. Then, combined analysis of miRNA and mRNA expression profiles was performed. Twenty three known miRNA-mRNA pairs and five new candidates were presented an anti-correlationship. Interestingly, 12 miRNAs were negatively correlated with 20 mRNAs encoding flowering-related proteins, indicating that miRNAs regulated target genes to promote flowering in CWRT-F2 group. The results provided here genomic resources for flowering related genes and how these flowering genes were regulated by miRNAs in common wild rice.
Highlights
Flowering is an important transition stage between the vegetative to reproductive stage
In addition to the core regulators, several other genes have been identified by using classical genetic methods as flowering time regulatory factors, for example, OsGI (Hayama et al 2003), OsMADS14,15 (Kyozuka et al 2000), OsMADS50 (Lee et al 2004; Yoshida and Nagato 2011), Days to heading 7 (DTH7) (Gao et al 2014), Heading Date Repressor1 (HDR1) (Sun et al 2016), Heading date 18 (Hd18) (Shibaya et al 2016)
We identified common wild rice plants which collected from the same population but with different flowering time
Summary
Flowering is an important transition stage between the vegetative to reproductive stage. Appropriate flowering time is necessary for crop reproduction (Jarillo and Pineiro 2011). The biological phenomenon and genetic mechanism that govern flowering in plants have been investigated for more than 100 years (Kovach et al 2007). There are two pathways to regulate photoperiodic flowering: the Hd1-Hd3a and Ghd7Ehd1-Hd3a/RFT1 module (Izawa 2007). In addition to the core regulators, several other genes have been identified by using classical genetic methods as flowering time regulatory factors, for example, OsGI (Hayama et al 2003), OsMADS14,15 (Kyozuka et al 2000), OsMADS50 (Lee et al 2004; Yoshida and Nagato 2011), Days to heading 7 (DTH7) (Gao et al 2014), Heading Date Repressor (HDR1) (Sun et al 2016), Heading date 18 (Hd18) (Shibaya et al 2016)
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