Abstract
Key messagencRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes.Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30–60 members, of which at least eight are expressed at moderate levels in florets. The sequences of these genes show no functional ORFs, but include segments of different protein coding genes. Particularly, N13 shows partial identity to maize gene BT068773 (RESPONSE REGULATOR 6). Secondary structure predictions as well as mature miRNA and target cleavage detection suggested that N13 is not a miRNA precursor. Moreover, N13 family members produce abundant 24-nucleotide small RNAs along extensive parts of their sequences. Surveys in the GREENC and CANTATA databases indicated similarity with plant long non-coding RNAs (lncRNAs) involved in splicing regulation; consequently, N13 was renamed as PN_LNC_N13. The Paspalum BT068773 predicted ortholog (N13TAR) originates floral transcript variants shorter than the canonical maize isoform and with possible structural differences between the apomictic and sexual types. PN_LNC_N13 is expressed only in apomictic plants and displays quantitative representation variation across reproductive developmental stages. However, PN_LNC_N13-like homologs and/or its derived sRNAs showed overall a higher representation in ovules of sexual plants at late premeiosis. Our results suggest the existence of a whole family of N13-like lncRNAs possibly involved in splicing regulation, with some members characterized by differential activity across reproductive types.
Highlights
Apomictic plants form true seeds originating clonal offspring genetically identical to the mother (Nogler 1984)
Our results suggest the existence of a whole family of N13like long non-coding RNAs (lncRNAs) possibly involved in splicing regulation, with some members characterized by differential activity across reproductive types
These results indicate that N13 is a Paspalum genomic non-coding sequence and belongs to a gene family including from 30 to 60 members
Summary
Apomictic plants form true seeds originating clonal offspring genetically identical to the mother (Nogler 1984). Plant Mol Biol (2018) 96:53–67 and Koltunow 2014) This trait is considered a deviation of sexuality, caused by genetic and/or epigenetic alterations affecting one or a few genes (Ozias-Akins 2006). It is often associated with polyploidy and/or hybridity, and displays a variety of mechanisms that evolved following a recurrent distribution pattern, suggesting a polyphyletic origin. Harnessing apomixis in agriculture would allow immediate fixation of any hybrid combination through an indefinite number of generations (Hand and Koltunow 2014) This capacity would dramatically reduce the efforts and costs inherent to plant breeding programs, as it was already shown for natural apomictic forage grasses (Ortiz et al 2013). The elucidation of the underlying molecular mechanisms of apomictic reproduction is essential for its effective use in breeding (Ortiz et al 2013)
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