Assessment of candidate reference genes for expression studies in <Emphasis Type="Italic">Vicia faba</Emphasis> L. by real-time quantitative PCR

Faba bean (Vicia faba L.) cultivation has declined in recent years due to several factors, including diseases and anti-nutritional compounds in the seeds. The introduction of disease resistance and the elimination of anti-nutritional factors in new varieties are important objectives in any breeding program for the species. Because of the faba bean’s huge genome, it is necessary to rely on synteny with related species in order to identify candidate genes responsible for the character under study. Quantification of expression level of candidate genes could help to validate them. Appropriate normalization is an essential prerequisite for obtaining accurate and reproducible quantification of gene expression level. Real-time quantitative PCR was used for evaluate the expression stability of 11 candidate reference genes. A wide set of samples, including different tissues, genotypes and several inoculations for the most important pathogens were employed. The expression stability of the candidate genes was analyzed using two different algorithms, geNorm and NormFinder, and results obtained from both algorithms were highly correlated for each experimental set. In all cases, either ACT1, CYP2 or ELF1A genes performed as the most stable genes in our experimental sets. They also represent part of the best combination of genes according to the geNorm and NormFinder algorithms. Our data showed the wide expression range of the selected genes, confirming that no single reference gene had a stable expression under these conditions in the faba bean. We recommend the use of ACT1, CYP2 and ELF1A as the most suitable reference genes to normalize gene expression for future studies in V. faba.     

The validation of housekeeping genes as a reference in quantitative Real Time PCR analysis : Application in the milk somatic cells and frozen whole blood of goats infected with caprine arthritis encephalitis virus

The validation of housekeeping genes (HKGs) for normalization of RNA expression in Real-Time PCR is crucial to obtain the most reliable results. There is limited information on reference genes used in the study of gene expression in milk somatic cells and the frozen whole blood of goats. Thus, the aim of this study was to propose the most stable housekeeping genes that can be used as a reference in Real-Time PCR analysis of milk somatic cells and whole blood of goats infected with caprine arthritis encephalitis virus (CAEV). Animals were divided into two groups: non-infected (N = 13) and infected with CAEV (N = 13). Biological material (milk somatic cells and whole blood) was collected 4 times during the lactation period (7, 30, 100 and 240 days post-partum). The expression levels of candidate reference genes were analyzed using geNorm and NormFinder software. The stability of candidates for reference gene expression was analyzed for CAEV-free (control) and CAEV-infected groups, and also for both groups together (combined group). The stability of expression of β-actin (ACTB), glyceraldehyde-3P-dehydrogenase (GAPDH), cyclophilin A (PPIA), RNA18S1, ubiquilin (UBQLN1) and ribosomal protein large subunit P0 (RPLP0) was determined in milk somatic cells, while ACTB, PPIA, RPLP0, succinate dehydrogenase complex subunit A (SDHA), zeta polypeptide (YWHAZ), battenin (CLN3), eukaryotic translation initiation factor 3K (EIF3K) and TATA box-binding protein (TBP) were measured in frozen whole blood of goats. PPIA and RPLP0 were considered as the most suitable internal controls as they were stably expressed in milk somatic cells regardless of disease status, according to NormFinder software. Furthermore, geNorm results indicated the expression of PPIA/RPLP0 genes as the best combination under these experimental conditions. The results of frozen whole blood analysis using NormFinder software revealed that the most stable reference gene in control, CAEV-infected and combined groups is YWHAZ, and – according to the geNorm results – the combined expression of PPM/YWHAZ genes is the best reference in the presented experiment. The usefulness in gene expression analysis of whole blood samples frozen immediately in liquid nitrogen and stored at -80 °C was also proved.     

Identification and Evaluation of Reference Genes for Accurate Transcription Normalization in Safflower under Different Experimental Conditions

Safflower (Carthamus tinctorius L.) has received a significant amount of attention as a medicinal plant and oilseed crop. Gene expression studies provide a theoretical molecular biology foundation for improving new traits and developing new cultivars. Real-time quantitative PCR (RT-qPCR) has become a crucial approach for gene expression analysis. In addition, appropriate reference genes (RGs) are essential for accurate and rapid relative quantification analysis of gene expression. In this study, fifteen candidate RGs involved in multiple metabolic pathways of plants were finally selected and validated under different experimental treatments, at different seed development stages and in different cultivars and tissues for real-time PCR experiments. These genes were ABCS, 60SRPL10, RANBP1, UBCL, MFC, UBCE2, EIF5A, COA, EF1-β, EF1, GAPDH, ATPS, MBF1, GTPB and GST. The suitability evaluation was executed by the geNorm and NormFinder programs. Overall, EF1, UBCE2, EIF5A, ATPS and 60SRPL10 were the most stable genes, and MBF1, as well as MFC, were the most unstable genes by geNorm and NormFinder software in all experimental samples. To verify the validation of RGs selected by the two programs, the expression analysis of 7 CtFAD2 genes in safflower seeds at different developmental stages under cold stress was executed using different RGs in RT-qPCR experiments for normalization. The results showed similar expression patterns when the most stable RGs selected by geNorm or NormFinder software were used. However, the differences were detected using the most unstable reference genes. The most stable combination of genes selected in this study will help to achieve more accurate and reliable results in a wide variety of samples in safflower.     

Nitric oxide and hydrogen cyanide as regulating factors of enzymatic antioxidant system in germinating apple embryos

Short-term (3 or 6 h) pre-treatment of apple (Malus domestica Borkh.) embryos with nitric oxide (NO) or hydrogen cyanide (HCN) induces transient accumulation of reactive oxygen species (ROS) leading to dormancy removal and germination. We demonstrated that enhanced NO emission by apple embryos during early phase of germination “sensu stricto” is required for seed transition from dormant into non-dormant state, and may be described by the model of “nitrosative door”, analogous to “oxidative window”. Cellular ROS concentration, resulting from NO or HCN embryo pre-treatment, seems to be under severe control of antioxidant system. Activity of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPX) and total peroxidases (Prxs) was determined during NO and HCN-mediated germination “sensu stricto” of embryos. CAT and SOD activity increased transiently 24 h after embryos pre-treatment, while GR and Prx activity was stimulated mainly after 96 h. The most evident alterations were detected in GPX activity, being more than threefold stimulated by NO or HCN. Based on this results, we conclude that these reactive molecules act simultaneously crossing their signaling pathways and we propose that ROS, reactive nitrogen species, HCN at accurate level are essential during seed germination as signaling factors.     

The expression of floral organ identity genes in contrasting water lily cultivars

The floral organs of typical eudicots such as Arabidopsis thaliana are arranged in four characteristic whorls, namely the sepal, petal, stamen and carpel, and the “ABC” floral organ identity model has been based on this arrangement. However, the floral organs in most basal angiosperms are spirally arranged with a gradual transition from the inside to outside, and an alternative model referred to as “fading borders” was developed to take account of this. The flower morphology of the water lily was tested against the “fading borders” model by determining the expression profile of the six primary floral organ identity genes AP2, AGL6, AP3, PI, AG and SEP1 in two cultivars showing contrasting floral morphology. In addition, to get accurate floatation of the genes expression level from outer to inner, we divided the floral organs into eight whorls according to morphological features. All these genes were expressed throughout all whorls of the flower, but their expression level changed gradually from the outside of the flower to its inside. This pattern was consistent with the “fading borders” model.     

Reproductive biology of Abies cephalonica Loudon in Mount Aenos National Park, Cephalonia, Greece

The reproductive biology of the endemic to Greece Abies cephalonica Loudon, including the phenology of the reproductive life cycle, cone production in relation to plant age and the required seed germination conditions, was studied. All individuals growing within 20 permanent plots of 100 m² each established in 11 different locations covering the entire strictly protected area of Mount Aenos National Park (Cephalonia) were monitored over a period of 4 years. The cones are formed on the upper part of the previous year’s branches, mostly at the upper crown half of the reproductive individuals (over 53 years old). Female flowers are pollinated in spring and cone maturation lasts until the beginning of autumn, when seed dispersal occurs. The annual production of cones per individual varied significantly, revealing masting behavior for this tree. This behavior was also expressed in the number of trees producing cones, as well as the percentage of sound seeds per cone. A significant difference in the mass and the length of the cones between the years of low and high cone production was observed, being higher in the years of massive cone production. Similar germination percentages were observed in full darkness or under “canopy light” and “sun light”, provided that the seeds were previously stratified for 6 weeks. It is concluded that A. cephalonica exhibits plasticity expressed in its reproductive behavior for alternating years of high to low cone production and in its seed germination for an array of habitat light conditions.     

Selection of optimal reference genes for expression analysis in the entomopathogenic fungus <Emphasis Type="Italic">Beauveria bassiana</Emphasis> during development,under changing nutrient conditions,and after exposure to abiotic stresses

The selection of suitable reference genes is crucial for accurate quantification of gene expression. To identify suitable reference genes in Beauveria bassiana, the expression of 14 candidates (18S, 28S, β-Tub, GAPD, γ-Act, TEF, HGPT, His3, His2A, TBP, CypA, CypB, PP1, and CrzA) was measured by quantitative polymerase chain reaction at different development stages and under various nutritional and stress conditions. Expression stability, as evaluated by the geNorm and NormFinder programs, revealed that His2A/γ-Act/CrzA was the most stably expressed set of genes throughout development, while 28S/PP1/CypA and His2A/γ-Act/CypA were the most stably expressed gene sets under a variety of nutritional and stress conditions, respectively. Overall, the most stably expressed genes under all conditions examined were PP1, γ-Act, and CypA.     

Validation of Reference Genes for Real-Time PCR of Reproductive System in the Black Tiger Shrimp

Gene expression of reproductive system of the black tiger shrimp (Peneaus monodon) has been widely studied to address poor maturation problem in captivity. However, a systematic evaluation of reference genes in quantitative real-time PCR (qPCR) for P. monodon reproductive organs is lacking. In this study, the stability of four potential reference genes (18s rRNA, GAPDH, β-actin, and EF1-α) was examined in the reproductive tissues in various conditions using bioinformatic tools: NormFinder and geNorm. For NormFinder, EF1-α and GAPDH ranked first and second as the most stable genes in testis groups whereas GAPDH and EF1-α were for ovaries from wild-caught broodstock and domesticated groups. EF1-α and β-actin ranked first and second for the eyestalk ablated ovaries. For geNorm, EF1-α and GAPDH had the best stability in all testis and ovaries from domesticated groups whereas EF1-α and β-actin were the best for ovaries from wild-caught and eyestalk ablated groups. Moreover, the expression levels of two well-known reproductive genes, Dmc1 and Vitellogenin, were used to validate these reference genes. When normalized to EF1-α, the expected expression patterns were obtained in all cases. Therefore, this work suggests that EF1-α is more versatile as reference genes in qPCR analysis for reproductive system in P. monodon.     

Identification of S-genotypes in Chinese cherry cultivars (Prunus pseudocerasus Lindl.)

Self-incompatibility has been studied extensively at the molecular level in Solanaceae, Rosaceae, and Scrophulariaceae, all of which exhibit gametophytic self-incompatibility. In the present study, we successfully isolated nine S-RNase alleles from cultivars of Chinese cherry by PCR amplification from genomic DNA and stylar cDNA combining with cleaved amplified polymorphic sequence marker. Analysis of amino acid sequences revealed five novel S-alleles, S ₂ , S ₄ , S ₆ , S ₈ , and S ₉ , with respective accession numbers in the NCBI database of EF541168, EF541173, EF541172, FJ628598, and FJ628599. Results showed that “Dongtang” and “Yinzhu” contained six S-alleles (S ₁ , S ₃ , S ₅ , S ₇ , S ₈ , and S ₉ ); “Taishanganying” contained four S-alleles (S ₁ , S ₂ , S ₄ , and S ₆ ); “Daiba”, “Dayingzui”, and “Xiaomizi” contained four S-alleles (S ₁ , S ₂ , S ₅ , and S ₈ ); “Laiyangduanzhi”, “Shuangquanchangba”, and “Daqingye” contained three S-alleles (S ₁ , S ₂ , and S ₈ ). It is interesting that different cultivars collected from the same place hold the same S-genotypes. Moreover, pollination tests and pollen tube growth assays showed that nine cultivars were self-compatible. Chinese cherry presented in this article are naturally polyploidy, which is a very useful material for the study of self-compatibility, and much of this information will be valuable for further work on self-(in)compatibility of fruit tree in Rosaceae.     

Lectin fromCanavalia brasiliensis (MART.). isolation,characterization and behavior during germination

A lectin was isolated fromCanavalia brasiliensis Mart. seeds by combining solubility fractionation with affinity chromatography on Sephadex G-50. The lectin showed a carbohydrate specificity for D-mannose (D-glucose) binding and a requirement for Ca²⁺ and Mn²⁺. All the hemagglutinating activity was found in the cotyledons and the presence of the lectin was followed during the first 15 days of plant germination, through the activity against rabbit erythrocytes, the presence of the “lectin peak” in Sephadex G-50 affinity chromatography, presence of the “lectin bands” in SDS-polyacrylamide gel electrophoresis and the “lectin arcs and rockets” in immunoelectrophoresis in agarose gel. On application of all these methods the lectin showed a differentiated metabolism, disappearing more slowly than the other high molecular weight proteins of the seed.     

Induction of free radicals in seeds by high intensive flashes and the relevant phosphorus metabolism in the seedling

Influence of high intensive flashes on the yield of free radicals in intact seeds and excised embryonic axis, endosperm, and seed coat, and its resulting effect on seedling growth, total biomass production and phosphorus metabolism in wheat (Triticum aeativum), vetch (Vicia sativa L.) and onion (Allium cepa L.) was studied. Free radicals (f.r.) were formed mainly in seed coat and not in the endosperm. Vetch seeds after irradiation had 20.76 X 10¹³ f.r. g^-1 dry intact seed and 17.30 X 10¹³ f.r. g^-1 dry seed coat. Excised seed coats exposed to irradiation also yielded 17.28 × 10¹³ f.r. g^-1 dry matter. High irradiance “white light” flashes induced more f.r. than a monochromatic one of the same photon content. Red (650 nm), farred (750 nm) and even infra-red (1100 nm) radiation did not initiated f.r. formation but resulted in their decay in samples irradiated earlier by “white”, blue and green parts of the spectrum. Blue irradiation of seeds led to the decrease in the length of shoots and roots in comparison to “white”, green and red irradiation but their biomass increased faster than in the seedlings obtained from non-irradiated or irradiated with “white” and green radiation. The quantity of total acid soluble phosphorus followed a sequence with respect to wavelength of radiation: 436 nm > 650 nm> > 540 nm > non-irradiated > 300–800 nm. Quantity of inorganic phosphorus remained unaffected by different spectral character of radiation. The quantity of organic acid soluble nucleic phosphorus and acid insoluble polyphosphates was higher in samples irradiated with red beams (650 ± 6 nm).     

Seeds and seedlings of two neotropical montane understory shrubs respond differently to anthropogenic edges and treefall gaps

Edges resulting from forest clear-cutting and treefall gaps can affect plant populations and consequently the distribution of species across landscapes. These two types of disturbance might interact to exacerbate or ameliorate “edge effects”, a rarely tested possibility. We focused on the effects of distance from forest edge (0–10, 30–40, 60–70, and 190–200 m) and habitat within forest fragments (treefall gaps and intact forest) on the early stages of development of Palicourea gibbosa and Faramea affinis, two common shrubs of montane forests in southwest Colombia. Seed germination and seedling growth did not change with distance from forest edge. Within forest fragments, however, seed germination and seedling growth were higher in treefall gaps than in intact forest understory for both species. In contrast, seed predation was influenced by distance from forest edge and in P gibbosa it depended on habitat. Seed predation was highest in the forest interior (190–200 m from forest edge) and in P. gibbosa this was true only in treefall gap habitats. These results suggest that animal mediated processes such as post-dispersal seed predation are more likely than physiological processes to be affected by anthropogenic edges. Our results provide some evidence that treefall gaps may interact with “edge effects”, however, they are inconclusive as to whether they exacerbate or ameliorate them. Received: 31 August 1998 / Accepted: 18 February 1999     

A smoke-derived butenolide improves early growth of tomato seedlings

3-Methyl-2H-furo[2,3-c]pyran-2-one is an active compound isolated from plant-derived smoke water. It has a stimulatory role during seed germination similar to that of smoke or aqueous extracts of smoke. The present study was undertaken to gain insight into the physiological events involved in seed germination and seedling development and which are affected by butenolide using tomato (Lycopersicon esculentum Mill.) cultivar “Heinz 1370” seeds. No stimulatory role on the seed germination of tomato was recorded following the use of the butenolide, however, post-germinative growth of tomato seedlings was significantly improved over the control (P ≤ 0.05). The emergence of the radicle and elongation of the hypocotyls and radicles were accelerated in seeds imbibed with butenolide at 10⁻⁷ M. Flow cytometry studies showed that in butenolide-treated seeds the ratio of cells with replicated DNA was increased. Seedling vigour and weight were significantly increased by the butenolide (P ≤ 0.05). An inverse correlation was observed between the weight of cotyledons and the weight of the hypocotyls and radicle during seedling development. This is an indication that the butenolide is implicated in mobilization and utilization of stored reserve materials in developing tomato seedlings.     

Selection and Validation of Reference Genes for Normalization of RT-qPCR Analysis in Developing or Abiotic-Stressed Tissues of Loquat (<i>Eriobotrya japonica</i>)

Loquat (Eriobotrya japonica Lindl.) is a subtropical evergreen fruit tree that produces fruits with abundant nutrients and medicinal components. Confirming suitable reference genes for a set of loquat samples before qRT-PCR experiments is essential for the accurate quantification of gene expression. In this study, eight candidate reference genes were selected from our previously published RNA-seq data, and primers for each candidate reference gene were designed and evaluated. The Cq values of the candidate reference genes were calculated by RT-qPCR in 31 different loquat samples, including 12 subgroups of developing or abiotic-stressed tissues. Different combinations of stable reference genes were screened according to a comprehensive rank, which was synthesized from the results of four algorithms, including the geNorm, NormFinder, BestKeeper and ΔCt methods. The screened reference genes were verified by normalizing EjLGA1 in each subgroup. The obtained suitable combinations of reference genes for accurate normalization were GAPDH, EF1α and ACT for floral development; GAPDH, UBCE and ACT for fruit setting; EF1α, GAPDH and eIF2B for fruit ripening; ACT, EF1α and UBCE for leaves under heat stress; eIF2B, UBCE and EF1α for leaves under freezing stress; EF1α, TUA and UBCE for leaves under salt stress; ACT, EF1α and eIF2B for immature pulp under freezing stress; ACT, UBCE and eIF2B for immature seeds under freezing stress; EF1α, eIF2B and UBCE for both immature pulp and seeds under freezing stress; UBCE, TUB and TUA for red-fleshed fruits under cold-storage stress; eIF2B, RPS3 and TUB for white-fleshed fruits under cold-storage stress; and eIF2B, UBCE and RPS3 for both red- and white-fleshed fruits under cold-storage stress. This study obtained different combinations of stable reference genes for accurate normalization in twelve subgroups of developing or abiotic-stressed tissues in loquat. To our knowledge, this is the first report to obtain stable reference genes for normalizing gene expression of abiotic-stressed tissues in E. japonica. The use of the three most stable reference genes could increase the reliability of future quantification experiments.     

Fruits foraging patterns and seed dispersal effect of frugivorous birds on Hippophae rhamnoides sinensis

Behaviors of 18 species of birds eating fruits of Hippophae rhamnoides spp. sinensis were observed from September 2003 to March 2004. Their foraging patterns were found to be very different and can be divided into five classes: (1) direct swallowing the fruits on crown of the shrubs and sometimes regurgitating seeds soon after; (2) carrying the fruits to their perching sites and swallowing; (3) pecking the fruits from the shrubs to the ground, eating pulp and seeds but leaving pericarp; (4) pecking through the pericarp, eating pulp and leaving pericarp and seeds; (5) pecking through the pericarp on the top of fruits, and only eating seeds. These foraging patterns have different effects on seed dispersal of H. rhamnoides spp. sinensis. The germination experiment of three groups of seeds (seeds from feces, dry fruits and extracted seeds from dry fruits) was carried out. Although ingestion processes of birds had some adverse effects on the seed germination of H. rhamnoides spp. sinensis, the seeds from feces still have a relatively higher germination ratio. H. rhamnoides spp. sinensis provides food to a variety of frugivorous birds, and the birds disperse its seeds. Thus, a mutually beneficial relationship between the bird and the seed is formed. __________ Translated from Chinese Journal of Ecology, 2005, 24(6): 635–638 [译自: 生态学杂志, 2005, 24(6): 635–638]     

Hydrogen sulfide promotes wheat seed germination under osmotic stress

Effects of NaHS, H₂S donor, on germination and antioxidant metabolism in wheat (Triticum aestivum L.) seeds under osmotic stress were investigated. With the enhancement of osmotic stress, which was mimicked by PEG-6000, the seed germination dropped gradually. NaHS treatment could promote wheat seed germination against osmotic stress in a dose-dependent manner; while Na⁺ and other sulfur-containing components, such as S²⁻, SO₄²⁻, SO₃²⁻, HSO₄⁻ and HSO₃⁻, were not able to improve seed germination as NaHS did, confirming H₂S or HS⁻ derived from NaHS contribute to the protective roles. Further experiments showed that NaHS treatment combined with PEG enhanced the activities of amylase and esterase in comparison to PEG treatment alone. Alternatively, NaHS treatment significantly reduced malondialdehyde and hydrogen peroxide accumulation in seeds. Significant enhancement of catalase and ascorbate peroxidase activities and decrease in lipoxygenase activity were observed in NaHS treated seeds, while peroxidase and superoxide dismutase activities were not affected as compared with the control. Furthermore, the H₂S donor treatment could retain higher levels of endogenous H₂S in wheat seeds under osmotic stress. These data indicated that H₂S played a protective role in wheat seed against osmotic stress.