Short, direct repeats (SDRs)-mediated post-transcriptional processing of a transcription factor gene OsVP1 in rice (Oryza sativa)

Abstract

The various degrees of preharvest sprouting occurring in hybrid rice is a limiting factor in the propagation and production of hybrid rice seeds. The phenotype of sprouted rice is very similar to that of the maize (Zea mays) seed-specific mutation viviparous 1. VP1 has been shown to be a transcription factor essential for seed maturation and dormancy induction. In this study, numerous truncated transcripts of OsVP1 resulting from an unusual post-transcriptional processing, were detected in four rice (Oryza sativa) cultivars. The observed events took place at a region spanning exons 1 to 5, and led to a variety of deletions that resulted in the loss of functional domain and frame-shifts with premature termination by introducing a stop codon. Various proportions of the transcripts expressed in both immature and mature embryos were observed to be incorrectly processed and associated with the genetic variation of preharvest sprouting rates among various rice varieties. In sprouting-susceptible rice cultivars, G46B and HeiB, many more incorrectly processed OsVP1 transcripts were expressed in immature than in mature embryos, indicating that the unusual post-transcriptional processing of the OsVP1 gene was developmentally regulated. In addition, comprehensive sequence analyses demonstrated the presence of paired short direct repeats (SDRs) at the junctions of the unusual excision sites in exons of OsVP1 gene. Site selection for the deletion of exon materials was altered along with the genotypes and developmental stages.

The Conserved Splicing Factor SUA Controls Alternative Splicing of the Developmental Regulator ABI3 in Arabidopsis

“…et al, 2002;Fan et al, 2007;Gagete et al, 2009) generates multiple mis-spliced transcripts that often code for truncated polypeptides. This has been linked to reduced grain quality in rice and wheat (McKibbin et al, 2002;Fan et al, 2007). Here, we show that the ABI3 gene of Arabidopsis is also regulated by alternative splicing.…”

“…During germination, ABI3 is repressed by the chromatin remodeling factor PICKLE (Perruc et al, 2007) and the ABI3 protein is targeted to 26S proteasome degradation by the ABI3-INTERACTING PRO-TEIN2 (Zhang et al, 2005). The identification of several splice variants of ABI3 homologs in monocotyledon and dicotyledon species (McKibbin et al, 2002;Fan et al, 2007;Gagete et al, 2009) implies that alternative splicing also has an important role in controlling ABI3 expression. However, splicing variants of ABI3 were not observed in Arabidopsis.…”

Dormancy in cereals (not too much, not so little): about the mechanisms behind this trait

“…In two grain sorghum inbred lines with contrasting dormancy, expression of VP1 in embryos of developing grains did not differ substantially (Carrari et al, 2001). However, in wheat and rice, evidence of missplicing was obtained for genotypes displaying early dormancy release (Fan et al, 2007). Another protein, Sdr4, is involved in the natural variability of dormancy in rice.…”

Vp1 expression profiles during kernel development in six genotypes of wheat, triticale and rye

“…The incidence of alternative splicing appears to be dependent on the developmental stage of the seed. In wheat and rice, the relative proportion of alternatively spliced transcripts decreases as the seed develops and reaches maturity (Fan et al 2007;Utsugi et al 2008;Yang et al 2007a). Although alternative splicing has been observed in triticale (De Laethauwer et al 2006), we did not explicitly differentiate between the splicing forms when choosing the primers for the RTqPCR assay.…”