Poplar interspecific hybrids are largely cultivated because of their heterotic behaviour. To contribute new data on molecular basis of heterosis, Illumina next generation sequencing technology was used to compare gene and allelic expression in two Populus deltoides x P. nigra hybrids, showing or not heterosis concerning stem circumference and height. Such an approach allows the identification of genes and gene networks that contribute to poplar tolerance to waterlimiting environments, with a long-term aim of developing strategies to improve plant productivity under drought. Analyses were performed on RNAs isolated from leaves of plants grown in normal conditions or exposed to moderate (85% leaf RWC) or severe (57% leaf RWC) drought. We generated 76,635,449 sequence reads, each 51 nt in length, encompassing 3.9 Gb of sequence data from 12 cDNA libraries obtained from leaves of plants of Populus deltoides x P. nigra subjected or not to moderate or severe drought stress. The expression of 45,033 poplar genes included in P. trichocarpa Phytozome database was studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were characterized by gene ontology and by determining the metabolic pathway to which they belong. Most genes resulted expressed in control and drought stressed plants, however a number of genes were significantly induced or repressed by drought. Analysis of expression profiles revealed that only genes involved in the biological process of stress response showed, in the majority, a precocious induction at moderate drought stress. On the contrary, induction or repression of most of other genes was more common after severe stress, even for genes that usually respond promptly to changes in environmental conditions, as those encoding transcription factors. On the whole, 1.80, 5.87, and 4.80% of genes resulted differentially expressed in the two hybrids in control, moderate, and severe stress, respectively. Moreover, the number of genes differentially expressed between the two hybrids increase in response to drought, suggesting that genetic differences can have an important role in stress tolerance. The occurrence of differential allelic expression in the same samples was also analysed in 200 randomly chosen genes. Fifty to sixty percent of these genes, depending on the hybrid and on the treatment, showed equal allelic expression but in the other genes the proportion between two alleles ranged from 60:40 to 90:10, i.e. they showed significant differential allelic expression. These resultsare comparable to those obtained in similar studies in the literature and point out the importance of such phenomena in generating heterosis.

NGS Analysis of Gene and Allelic Expression in Poplar Hybrids Subjected to Water Stress

GIORDANI, TOMMASO;CAVALLINI, ANDREA;NATALI, LUCIA
2012

Abstract

Poplar interspecific hybrids are largely cultivated because of their heterotic behaviour. To contribute new data on molecular basis of heterosis, Illumina next generation sequencing technology was used to compare gene and allelic expression in two Populus deltoides x P. nigra hybrids, showing or not heterosis concerning stem circumference and height. Such an approach allows the identification of genes and gene networks that contribute to poplar tolerance to waterlimiting environments, with a long-term aim of developing strategies to improve plant productivity under drought. Analyses were performed on RNAs isolated from leaves of plants grown in normal conditions or exposed to moderate (85% leaf RWC) or severe (57% leaf RWC) drought. We generated 76,635,449 sequence reads, each 51 nt in length, encompassing 3.9 Gb of sequence data from 12 cDNA libraries obtained from leaves of plants of Populus deltoides x P. nigra subjected or not to moderate or severe drought stress. The expression of 45,033 poplar genes included in P. trichocarpa Phytozome database was studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were characterized by gene ontology and by determining the metabolic pathway to which they belong. Most genes resulted expressed in control and drought stressed plants, however a number of genes were significantly induced or repressed by drought. Analysis of expression profiles revealed that only genes involved in the biological process of stress response showed, in the majority, a precocious induction at moderate drought stress. On the contrary, induction or repression of most of other genes was more common after severe stress, even for genes that usually respond promptly to changes in environmental conditions, as those encoding transcription factors. On the whole, 1.80, 5.87, and 4.80% of genes resulted differentially expressed in the two hybrids in control, moderate, and severe stress, respectively. Moreover, the number of genes differentially expressed between the two hybrids increase in response to drought, suggesting that genetic differences can have an important role in stress tolerance. The occurrence of differential allelic expression in the same samples was also analysed in 200 randomly chosen genes. Fifty to sixty percent of these genes, depending on the hybrid and on the treatment, showed equal allelic expression but in the other genes the proportion between two alleles ranged from 60:40 to 90:10, i.e. they showed significant differential allelic expression. These resultsare comparable to those obtained in similar studies in the literature and point out the importance of such phenomena in generating heterosis.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/203340
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