Abstract:The response and adaption to salt remains poorly understood for beach morning glory [Ipomoea imperati (Vahl) Griseb], one of a few relatives of sweetpotato, known to thrive under salty and extreme drought conditions. In order to understand the genetic mechanisms underlying salt tolerance of a Convolvulaceae member, a genome-wide transcriptome study was carried out in beach morning glory by 454 pyrosequencing. A total of 286,584 filtered reads from both salt stressed and unstressed (control) root and shoot tiss… Show more
“…FAD2 genes exhibited higher expression in the qRT-PCR validation experiment at 140 DAF. Such inconsistency in the expression level of FATB and FAD2 genes could be due to primers’ specificity and qRT-PCR reaction conditions during the experimental validation analysis [75]. Fig.…”
Background
Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages.ResultsThe transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data.ConclusionsThe transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users.
“…FAD2 genes exhibited higher expression in the qRT-PCR validation experiment at 140 DAF. Such inconsistency in the expression level of FATB and FAD2 genes could be due to primers’ specificity and qRT-PCR reaction conditions during the experimental validation analysis [75]. Fig.…”
Background
Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages.ResultsThe transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data.ConclusionsThe transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users.
“…14) and a somatic hybrid between the two species, finding genes that are differentially regulated in the I. batatas parent compared to either I. triloba or the hybrid, which are more drought tolerant. Other de novo transcriptome approaches have been reported for hexaploid Ipomoea trifida and Ipomoea imperati for drought and salt stress, respectively (Peng et al., ; Solis, Baisakh, Brandt, Villordon, & Bonte, ). In this study, global gene expression patterns in leaf tissue of two varieties of I. batatas , Beauregard, and Tanzania, during PEG‐simulated drought stress were characterized with RNA‐Sequencing (RNA‐Seq); diploid I. trifida , which is closely related to I. batatas and is a putative progenitor species (Austin, ; Kobayashi, ), was used as the reference genome sequence (http://sweetpotato.plantbiology.msu.edu/gt4sp_download.shtml).…”
Sweet potato (Ipomoea batatas [L.] Lam.) is an important subsistence crop in Sub‐Saharan Africa, yet as for many crops, yield can be severely impacted by drought stress. Understanding the genetic mechanisms that control drought tolerance can facilitate the development of drought‐tolerant sweet potato cultivars. Here, we report an expression profiling study using the US‐bred cultivar, Beauregard, and a Ugandan landrace, Tanzania, treated with polyethylene glycol (PEG) to simulate drought and sampled at 24 and 48 hr after stress. At each time‐point, between 4,000 to 6,000 genes in leaf tissue were differentially expressed in each cultivar. Approximately half of these differentially expressed genes were common between the two cultivars and were enriched for Gene Ontology terms associated with drought response. Three hundred orthologs of drought tolerance genes reported in model species were identified in the Ipomoea trifida reference genome, of which 122 were differentially expressed under at least one experimental condition, constituting a list of drought tolerance candidate genes. A subset of genes was differentially regulated between Beauregard and Tanzania, representing genotype‐specific responses to drought stress. The data analyzed and reported here provide a resource for geneticists and breeders toward identifying and utilizing drought tolerance genes in sweet potato.
“…Although salt‐tolerant plants usually have a better ability to exclude sodium to avoid toxic sodium concentrations in the cell (Bose, Rodrigo‐Moreno, & Shabala, ; Kosová, Prášil, & Vítámvás, ), Ca 2+ elevation and proper ROS regulation with higher antioxidant capacity are believed to be key components in the salinity tolerance response in plants (Bose et al, ; Kader & Lindberg, ). Recently Solis, Baisakh, Brandt, Villordon, and La Bonte () found that genes encoding calcineurin B‐like (CBL)‐interacting protein kinases (CIPKs) were induced in a halophyte relative of sweet potato, suggesting a role of a Ca 2+ signalling pathway in salinity tolerance. The crosstalk of ROS production with other signalling molecules, such as ABA, JA, and their downstream signalling components, has been shown to play an essential role in salinity tolerance response (Fahad et al, ; Kurusu et al, ; Zhang, Smith, Harberd, & Jiang, ).…”
Section: Adaptive Mechanisms and Signalling During Salt Exposurementioning
Salinity exerts a severe detrimental effect on crop yields globally. Growth of plants in saline soils results in physiological stress, which disrupts the essential biochemical processes of respiration, photosynthesis, and transpiration. Understanding the molecular responses of plants exposed to salinity stress can inform future strategies to reduce agricultural losses due to salinity; however, it is imperative that signalling and functional response processes are connected to tailor these strategies. Previous research has revealed the important role that plant mitochondria play in the salinity response of plants. Review of this literature shows that 2 biochemical processes required for respiratory function are affected under salinity stress: the tricarboxylic acid cycle and the transport of metabolites across the inner mitochondrial membrane. However, the mechanisms by which components of these processes are affected or react to salinity stress are still far from understood. Here, we examine recent findings on the signal transduction pathways that lead to adaptive responses of plants to salinity and discuss how they can be involved in and be affected by modulation of the machinery of energy metabolism with attention to the role of the tricarboxylic acid cycle enzymes and mitochondrial membrane transporters in this process. Saline landscapes occur naturally, and many halophytes (salt tolerant plants) survive and complete their life cycle in these environments (Flowers & Colmer, 2015). Human activity including intense irrigation and land clearing can also cause soil salinity, as these activities lead to changes in the soil water table, which can contain high salt concentrations (Rengasamy, 2006). These agricultural practices result in a rising water table, which liberates soil solutes bringing them to the surface, creating salinized areas in previously productive land (Rengasamy, 2006). This severely limits crop production in these areas as typically elite high yielding crop varieties cannot tolerate these high salt concentrations (Roy, Negrão, & Tester, 2014).Although the salinization of soils has and is increasingly limiting crop production in many areas of the world (Sha Valli Khan, Nagamallaiah, Dhanunjay, Sergeant, & Hausman, 2014), reliable measures of salt-affected land are very difficult to obtain because salinity varies both spatially and temporally. Nevertheless, a number of studies have attempted to estimate the extent of soil salinity.According to the Food and Agriculture Organisation of the United Nations, it is estimated that approximately 20% of all global irrigated land has become salt-affected and this percentage is expected to continue to increase over time (FAO, 2009;Parihar, Singh, Singh, Singh, & Prasad, 2014). It was further estimated that this salinization of irrigated
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