IntroductionTomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated wor... more IntroductionTomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated worldwide and is characteristic of the Mediterranean agricultural system. It represents a key component of the diet of billion people and an important source of vitamins and carotenoids. Tomato cultivation in open field often experiences drought episodes, leading to severe yield losses, since most modern cultivars are sensitive to water deficit. Water stress leads to changes in the expression of stress-responsive genes in different plant tissues, and transcriptomics can support the identification of genes and pathways regulating this response. MethodsHere, we performed a transcriptomic analysis of two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs. ResultsA total of 6,267 differentially expressed transcripts related to stress response was det...
Comparisons of RNA-Seq and qRT-PCR data. Comparisons of transcript fold changes as detected by RN... more Comparisons of RNA-Seq and qRT-PCR data. Comparisons of transcript fold changes as detected by RNA-Seq and qRT-PCR expression analyses for 10 selected genes in all of the experimental conditions. Comparisons of the differences between the means of treated and untreated samples of qRT-PCR data were performed using Student's t-tests (p-value ≤ 0.05 except for the data marked with ns). OsCAT-A: Catalase isozyme A; OsZCO: Zeaxanthin cleavage oxygenase. (PDF 291 kb)
List of common GO terms. List of GO terms common in all of the tissues and treatments, in all of ... more List of common GO terms. List of GO terms common in all of the tissues and treatments, in all of the root samples or in all of the leaf samples. (XLSX 21 kb)
List of enriched GO terms for the contrasts with accompanying enrichment p-values as resulting fr... more List of enriched GO terms for the contrasts with accompanying enrichment p-values as resulting from goseq analysis. (XLSX 62 kb)
The temperature-sensitive carrot cell variant ts11c, arrested in somatic embryogenesis after the ... more The temperature-sensitive carrot cell variant ts11c, arrested in somatic embryogenesis after the globular stage, was characterized. The sensitivity to a shift from 24 degrees C (permissive temperature) to 32 degrees C (non-permissive temperature) is greatest at the globular stage of embryogenesis, while cells proliferating in unorganized fashion and plantlets are not affected. Embryogenesis in ts11c is also arrested at the permissive temperature by replacement of conditioned culture medium with fresh medium. The timing of sensitivity of ts11c to medium replacement coincides with the sensitivity to temperature shift. Both sensitivities are recessive in somatic hybrids between ts11c and wild-type cells. Extracellular glycoproteins synthesized by ts11c at the non-permissive temperature contain much less fucose than those synthesized by the wild type. The glycoproteins synthesized by the variant under non-permissive conditions do not accumulate at the periphery of the embryo, as their wild-type counterparts do, but instead show a diffuse distribution throughout the embryo. The defect in ts11c can be fully complemented by the addition of extracellular wild-type proteins. A revertant of ts11c was isolated that simultaneously reacquired temperature insensitivity and normal glycosylation ability. Collectively, these observations indicate that ts11c is not able to perform proper glycosylation at the non-permissive temperature and suggest that the activity of certain extracellular proteins, essential for the transition of globular to heart stage somatic embryos, depends on the correct modification of their oligosaccharide side-chains.
Several environmental factors, such as drought, salinity, and extreme temperatures, negatively af... more Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesi...
IntroductionTomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated wor... more IntroductionTomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated worldwide and is characteristic of the Mediterranean agricultural system. It represents a key component of the diet of billion people and an important source of vitamins and carotenoids. Tomato cultivation in open field often experiences drought episodes, leading to severe yield losses, since most modern cultivars are sensitive to water deficit. Water stress leads to changes in the expression of stress-responsive genes in different plant tissues, and transcriptomics can support the identification of genes and pathways regulating this response. MethodsHere, we performed a transcriptomic analysis of two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs. ResultsA total of 6,267 differentially expressed transcripts related to stress response was det...
Comparisons of RNA-Seq and qRT-PCR data. Comparisons of transcript fold changes as detected by RN... more Comparisons of RNA-Seq and qRT-PCR data. Comparisons of transcript fold changes as detected by RNA-Seq and qRT-PCR expression analyses for 10 selected genes in all of the experimental conditions. Comparisons of the differences between the means of treated and untreated samples of qRT-PCR data were performed using Student's t-tests (p-value ≤ 0.05 except for the data marked with ns). OsCAT-A: Catalase isozyme A; OsZCO: Zeaxanthin cleavage oxygenase. (PDF 291 kb)
List of common GO terms. List of GO terms common in all of the tissues and treatments, in all of ... more List of common GO terms. List of GO terms common in all of the tissues and treatments, in all of the root samples or in all of the leaf samples. (XLSX 21 kb)
List of enriched GO terms for the contrasts with accompanying enrichment p-values as resulting fr... more List of enriched GO terms for the contrasts with accompanying enrichment p-values as resulting from goseq analysis. (XLSX 62 kb)
The temperature-sensitive carrot cell variant ts11c, arrested in somatic embryogenesis after the ... more The temperature-sensitive carrot cell variant ts11c, arrested in somatic embryogenesis after the globular stage, was characterized. The sensitivity to a shift from 24 degrees C (permissive temperature) to 32 degrees C (non-permissive temperature) is greatest at the globular stage of embryogenesis, while cells proliferating in unorganized fashion and plantlets are not affected. Embryogenesis in ts11c is also arrested at the permissive temperature by replacement of conditioned culture medium with fresh medium. The timing of sensitivity of ts11c to medium replacement coincides with the sensitivity to temperature shift. Both sensitivities are recessive in somatic hybrids between ts11c and wild-type cells. Extracellular glycoproteins synthesized by ts11c at the non-permissive temperature contain much less fucose than those synthesized by the wild type. The glycoproteins synthesized by the variant under non-permissive conditions do not accumulate at the periphery of the embryo, as their wild-type counterparts do, but instead show a diffuse distribution throughout the embryo. The defect in ts11c can be fully complemented by the addition of extracellular wild-type proteins. A revertant of ts11c was isolated that simultaneously reacquired temperature insensitivity and normal glycosylation ability. Collectively, these observations indicate that ts11c is not able to perform proper glycosylation at the non-permissive temperature and suggest that the activity of certain extracellular proteins, essential for the transition of globular to heart stage somatic embryos, depends on the correct modification of their oligosaccharide side-chains.
Several environmental factors, such as drought, salinity, and extreme temperatures, negatively af... more Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesi...
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Papers by Annamaria Genga