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Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp.
Pinto, Renan Terassi; Freitas, Natália Chagas; Máximo, Wesley Pires Flausino; Cardoso, Thiago Bergamo; Prudente, Débora de Oliveira; Paiva, Luciano Vilela.
Afiliação
  • Pinto RT; Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil.
  • Freitas NC; Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil.
  • Máximo WPF; Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil. wesleypfm@hotmail.com.
  • Cardoso TB; Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil.
  • Prudente DO; Sugarcane Technology Center, Piracicaba, SP, 13400970, Brazil.
  • Paiva LV; Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil. luciano@ufla.br.
BMC Genomics ; 20(1): 812, 2019 Nov 06.
Article em En | MEDLINE | ID: mdl-31694532
BACKGROUND: Coffee 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. RESULTS: We 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. CONCLUSION: Therefore, 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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteínas de Plantas / Sementes / Fatores de Transcrição / Perfilação da Expressão Gênica / Coffea / Redes Reguladoras de Genes / Estudo de Associação Genômica Ampla Tipo de estudo: Prognostic_studies Idioma: En Revista: BMC Genomics Assunto da revista: GENETICA Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteínas de Plantas / Sementes / Fatores de Transcrição / Perfilação da Expressão Gênica / Coffea / Redes Reguladoras de Genes / Estudo de Associação Genômica Ampla Tipo de estudo: Prognostic_studies Idioma: En Revista: BMC Genomics Assunto da revista: GENETICA Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido