Gene expression profile during coffee fruit development and identification of candidate markers for phenological stages

Abstract

-The objective of this work was to identify genes that could be used as suitable markers for molecular recognition of phenological stages during coffee (Coffea arabica) fruit development. Four cultivars were evaluated as to their differential expression of genes associated to fruit development and maturation processes. Gene expression was characterized by both semi-quantitative and quantitative RT-PCR, in fruit harvested at seven different developmental stages, during three different seasons. No size polymorphisms or differential expression were observed among the cultivars for the evaluated genes; however, distinct expression profiles along fruit development were determined for each gene. Four out of the 28 evaluated genes exhibited a regular expression profile in all cultivars and harvest seasons, and, therefore, they were validated as candidate phenological markers of coffee fruit. The gene α-galactosidase can be used as a marker of green stage, caffeine synthase as a marker of transition to green and yellowish-green stages, and isocitrate lyase and ethylene receptor 3 as markers of late maturation.Index terms: Coffea arabica, cup quality, differential expression, fruit phenology, ripening, qRT-PCR. Perfil da expressão gênica durante o desenvolvimento de frutos de café e identificação de genes marcadores para fases fenológicasResumo -O objetivo deste trabalho foi identificar genes que possam ser utilizados como marcadores moleculares para reconhecimento de fases fenológicas, durante o desenvolvimento de frutos do cafeeiro (Coffea arabica). Quatro cultivares foram avaliadas quanto à expressão diferencial de genes associados a processos de desenvolvimento e maturação de frutos. A caracterização da expressão gênica foi realizada pelas técnicas de RT-PCR semi-quantitativa e quantitativa, em frutos coletados em sete estádios de desenvolvimento, durante três safras. Não foi observado nenhum polimorfismo de tamanho ou expressão diferencial entre as cultivares, para os genes avaliados; porém, perfis de expressão distintos durante o desenvolvimento dos frutos foram determinados para cada gene. Quatro entre os 28 genes avaliados apresentaram perfil de expressão constante, em todas as cultivares e safras e, portanto, foram validados como genes candidatos a marcadores fenológicos de frutos de cafeeiro. O gene α-galactosidase pode ser usado como marcador do estágio de fruto verde, o gene de cafeína sintase como marcador do estádio de transição entre fruto verde e fruto verde-cana, e o isocitrato liase e o etileno-receptor 3 como marcadores das fases finais de maturação.Termos para indexação: Coffea arabica, qualidade de bebida, expressão diferencial, fenologia do fruto, amadurecimento, qRT-PCR.

Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size

“…13 Transcriptional studies with fruits at the initial stages of development reported 11S transcripts at the early stages of fruit development, when the main fruit tissue is the perisperm. 26,27 Here, we provide the first evidence of the presence of the 11S protein in the isolated perisperm of coffee seeds. As perisperm was isolated, there was no pericarp or endosperm contamination that could be the sources of 11S at 90 DAF.…”

“…30 Interestingly, methionine synthase genes are highly expressed in early fruit stage, 27 and the transcriptional profile of the caffeine synthase gene in coffee fruits showed a pattern of accumulation according to the perisperm development. 26 Another possible explanation for the higher expression of MeSe in the initial stages of seed development is related with ethylene synthesis. Methionine is the ethylene precursor, being converted to SAM by SAM-synthase.…”

“…10 The expression of genes involved in ethylene biosynthesis also has been reported in early stages of coffee fruit development. 26,27 Understanding the accumulation dynamics of proteins related to ethylene biosynthesis can be of interest for further studies not only on the mechanisms controlling grain size but also on ripening uniformity, two characteristics related to coffee quality and, consequently, higher commercial coffee value.…”

Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato

“…4). It should be emphasized that Obatã and Catuaí Vermelho are late and intermediate maturation cultivars, respectively, a feature that, associated with punctual environmental effects, could explain the observed differences in gene expression timing of CaSMP (Gaspari- Pezzopane et al 2012). Nevertheless, taken together, these results indicate that CaSMP is preferentially expressed in the endosperm.…”

Endo-β-mannanase and β-tubulin gene expression during the final phases of coffee seed maturation

“…Genes have recently been identified as having differential levels of expression associated with the five maturation stages. For example, α-galactosidase can be used as a marker of the green stage, caffeine synthase can be used as a marker of the transition from the green to the yellow-green stage, and isocitrate lyase and ethylene receptor 3 can be used as markers of the final stages of seed maturation (Gaspari-Pezzopane et al, 2012).…”