Abstract
BackgroundCoffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants.ResultsWe have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator.ConclusionTherefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.
Highlights
Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species
Identification and distribution of Gretchen Hagen 3 (GH3) members in C. canephora The blastp analysis against C. canephora proteome resulted in 20 amino acid sequences, but three of them (Additional file 1: Data S1) lacked the domains commonly shared by GH3 proteins (PLN02247 and pfam03321)
We suggest that the CaGH3.15, one of the members of GH3 gene family in C. arabica, could be regulated by CaBBM, and it possibly influences auxin homeostasis during somatic embryogenesis in coffee
Summary
Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. An efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. The GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants. In vitro somatic embryogenesis (SE) followed by development and acclimatization of the plantlets is an interesting option for achieving efficient clonal propagation, as in 2016 around 7 million coffee plants were produced through this process in Central America [5]. One of the challenges is to understand what differentiates cells with embryogenic competence from the others, and possibly confirm or establish new molecular markers, as morphological characteristics alone are not enough to predict embryogenic capacity [6]
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