In silico and in vivo analysis of ABI3 and VAL2 genes during somatic embryogenesis of Coffea arabica: competence acquisition and developmental marker genes

Abstract

The employment of biotechnology-based approaches such as somatic embryogenesis has been applied to several plants including Coffea sp. Despite the economic importance of this genus, few information about the role of key regulatory genes in somatic embryogenesis in coffee is available. This work provides information about ABI3 and VAL2 genes performance by RT-qPCR during indirect somatic embryogenesis of Coffea arabica. To achieve this, bioinformatics analysis was performed to identify the genes of the B3 superfamily in the coffee genome. The cell suspensions lines presented similar histological and regeneration patterns, yielding of up to 6.6 embryos per 1 mg of embryogenic aggregates at 7 months. We have identified possible orthologs for VAL2 (Cc06g00410) and ABI3 (Cc01g17380) as well as the other members belonging to superfamily B3. The CaABI3 expression was higher in dedifferentiated competent cells for somatic embryogenesis as compared with non-embryogenic calli. Whereas the expression of VAL2 gene is more active in cotyledonary embryos and plantlets, showing its clear performance in the embryogenesis late stages. The present study suggests that CaABI3 gene could be potentially used as a biomarker for embryogenic process improvement. The good plantlets development obtained from the protocol used may be a reflection of the high expression of CaVAL2 in cotyledonary embryos and plantlets. Key message The activity of CaABI3 is correlated to embryogenic potential with highly expressed in embryogenic masses and expression of the VAL2 gene is increased at the end of the embryogenic process.

Osmotic stress-induced somatic embryo maturation of coffee Coffea arabica L., shoot and root apical meristems development and robustness

“…It is important to notice that shoot and root apical meristems were developed compared to untreated SE. Failure in forming proper SAM and RAM in SEs was published elsewhere 1 , 3 , 7 , 9 , 13 , 50 . The importance of the apical meristems in plant growth and development has long been recognized 51 , but in woody plants, little is known about meristems formation during SE 11 .…”

Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

“…Taking into account the differences in regulation profile of each CcGH3 proposed by the network, we performed an RT-qPCR experiment to analyze the expression pattern of these genes in C. arabica cell types contrasting in its embryogenic potential. The cell types used are clearly different; those with embryogenic potential are isodiametric, have larger nucleus and high cytoplasmic density, which are the expected characteristics for embryogenic coffee cells [19, 38, 39]; whereas the non-embryogenic ones are larger, with undefined shape and low cytoplasmic density [40]. The embryogenic cell suspension is composed by these two cell types, an interesting material for correlating embryogenic potential to gene expression pattern.…”

“…The auxin content decreases during the induction phase, what may also be due to its transport to explant extremities, where the embryos need this phytohormone supply to develop [48]. The process in C. arabica is through indirect embryogenesis, with the need of embryogenic calli induction before somatic embryo regeneration, and two types of auxins were included in the medium [40]. Embryogenic and non-embryogenic calli derive from the same explant (leaf cuts, Fig.…”

Genomic Analysis and Expression Investigation of Steroleosin Gene Family in Arabidopsis Thaliana

“…RY element is known to be bound by the transcription factors with B3 domain (Ezcurra et al, 2000;Jing et al, 2019). Numerous transcription factors such as LEC2, FUS3 and ABI3 exhibit B3 domain (Freitas et al, 2019), which are known to regulate lipid metabolism (McGlew et al, 2015). The SKn-1 motif , which is also known to have roles in lipid metabolism (Pang et al, 2014;Dowen, 2019), exists on promoters of most steroleosin genes.…”