Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

Background: Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress.Results: The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), beta-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions.Conclusion: Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/ organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant.

Identificação e caracterização de promotores de genes de café (coffea arabica)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análise por sequências multilocus de Xanthomonas fuscans subsp. aurantifolii

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular Evaluation of Developmental Competence of Oocytes Collected In Vivo from Buffalo and Bovine Heifers during Winter and Summer

Buffaloes and bovines are polyestrous and seasonal or annual livestock, respectively, that show reduced fertility during heat stress. To investigate whether reduced fertility is related to oocyte competence in both species, immature oocytes from buffalo and bovine heifers were collected during winter and summer and subjected to molecular analyses. In each season, heifers of both species had their follicular wave emergence synchronized with a standard protocol (Ferreira et al., 2011). Before being subjected to ovum pick up (OPU), cutaneous (CT; degrees C) and rectal (RT; degrees C) temperatures and respiratory rate (RR; breaths/min) were measured. Oocytes' RNA was extracted to evaluate the expression of target genes related to mtDNA replication/transcription (PPARGC1A, TFAM and MT-CO1), apoptosis (BAX and BCL2) and HS (HSP90AA1 and HSPA1AB). ACTB, HIST1H2AG and GAPDH were initially chosen as housekeeping genes. In buffaloes, CT (35.0 +/- 0.4 vs 23.8 +/- 0.5), RT (38.7 +/- 0.1 vs 38.0 +/- 0) and RR (21.3 +/- 1.2 vs 15.4 +/- 1.1) were higher during summer than winter. However, in bovine heifers, RT (38.7 +/- 0.1 vs 38.6 +/- 0.1) and RR (44.8 +/- 1.5 vs 40.6 +/- 1.5) were similar in both seasons, while CT (31.6 +/- 0.3 vs 30.2 +/- 0.3) was increased during summer. Reduced expression of ACTB, HIST1H2AG and GAPDH was evidenced during summer, disqualifying them as housekeeping genes. Similarly, the expression of all target genes was reduced during summer in oocytes of both species. In summary, physiological responses to heat stress seem to be more intense in buffalo than bovine heifers. However, in both species, negative effects of heat stress upon oocyte quality occur at the molecular level and affects genes related to several biological functions.

Curtobacterium flaccumfaciens PV. flaccumfaciens: aspectos epidemiológicos e variabilidade genética

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Epigenética do desenvolvimento em bovinos: DNA metiltransferases e genes imprinted em embriões, fetos e placentas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)