Abstract
Root restriction cultivation leads to early maturation and quality improvement, especially in the anthocyanin content in grapevine. However, the molecular mechanisms that underlie these changes have not been thoroughly elucidated. In this study, four small RNA libraries were constructed, which included the green soft stage (GS) and ripe stage (RS) of ‘Muscat’ (Vitis vinifera L.) grape berries that were grown under root restriction (RR) and in traditional cultivation (no root restriction, CK). A total of 162 known miRNAs and 14 putative novel miRNAs were detected from the four small RNA libraries by high-throughput sequencing. An analysis of differentially expressed miRNAs (DEMs) revealed that 13 miRNAs exhibited significant differences in expression between RR and CK at the GS and RS stages, respectively. For different developmental stages of fruit, 23 and 34 miRNAs showed expression differences between the GS and RS stages in RR and CK, respectively. The expression patterns of the eight DEMs and their targets were verified by qRT-PCR, and the expression profiles of target genes were confirmed to be complementary to the corresponding miRNAs in RR and CK. The function of Vvi-miR828, which showed the down regulated expression in the RS stage under root restriction, was identified by gene transformation in Arabidopsis. The anthocyanin content significantly decreased in transgenic lines, which indicates the regulatory capacity of Vvi-miR828 in fruit coloration. The miRNA expression pattern comparison between RR and CK might provide a means of unraveling the miRNA-mediated molecular process regulating grape berry development under root restricted cultivation.
Highlights
In recent years, with the development of dense and dwarf culture, root-limited cultivation, which is called root restriction, rooting zone restriction, or root confinement, has been widely applied in fruit production
The growth and development of roots are restrained by limited space under root restriction cultivation, which makes the growth of ground part more likely to transform toward reproductive development
The results revealed that root restriction cultivation could increase the fruit quality of grapevines
Summary
With the development of dense and dwarf culture, root-limited cultivation, which is called root restriction, rooting zone restriction, or root confinement, has been widely applied in fruit production. Studies on some key coding RNAs that affect grape fruit quality under root restriction have been performed [48], but as a regulator in plant growth and development, how miRNA affects grape fruit development and quality under root restriction has not been reported to date. MiRNAs from two developmental stages grape berries under root restriction and traditional cultivations were analyzed by high-throughput sequencing. Our study analyzed how root restriction cultivation affected the quality and development of grape berries at the miRNA level, which further provides a theoretical basis for the application of root restriction cultivation in fruit trees. These findings are consistent with previous reports [19,20,49] that most of the miRNAs start with a 5 U, which is one of the classic features of miRNAs, it is not the case for other miRNAs, for example, 24 nt long miRNAs (lmiRNAs) are loaded into AGO4 proteins and mainly start with a 5 A [50]
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