Dataset Information

Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage.

ABSTRACT: Canola (Brassica napus) is one of the most important oil crops in the world. However, its yield has been constrained by salt stress. In this study, transcriptome profiles were explored using Digital Gene Expression (DGE) at 0, 3, 12 and 24 hours after H2O (control) and NaCl treatments on B. napus roots at the germination stage. Comparisons of gene-expression between the control and the treatment were conducted after tag-mapping to the sequenced Brassica rapa genome. The differentially expressed genes during the time course of salt stress were focused on, and 163 genes were identified to be differentially expressed at all the time points. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of the genes were involved in proline metabolism, inositol metabolism, carbohydrate metabolic processes and oxidation-reduction processes and may play vital roles in the salt-stress response at the germination stage. Thus, this study provides new candidate salt stress responding genes, which may function in novel putative nodes in the molecular pathways of salt stress resistance.

SUBMITTER: Long W

PROVIDER: S-EPMC4332669 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage.

Long Weihua W Zou Xiling X Zhang Xuekun X

PloS one 20150213 2

Canola (Brassica napus) is one of the most important oil crops in the world. However, its yield has been constrained by salt stress. In this study, transcriptome profiles were explored using Digital Gene Expression (DGE) at 0, 3, 12 and 24 hours after H2O (control) and NaCl treatments on B. napus roots at the germination stage. Comparisons of gene-expression between the control and the treatment were conducted after tag-mapping to the sequenced Brassica rapa genome. The differentially expressed ...[more]

PMID: 25679513

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Project description:Lipoic acid (LA) and melatonin (MT) are pleiotropic molecules participating in plant stress resistance by modulating cellular biochemical changes, ion homeostasis, and antioxidant enzyme activities. However, the combined role of these two molecules in counteracting the detrimental impacts of salinity stress is still unknown. In the present study, we determined the effects of exogenous LA (0.5 µM), MT (1 µM) and their combination (LA + MT) on growth performance and biomass accumulation, photosynthetic pigments, enzymatic and non-enzymatic antioxidant activities, and ions homeostatic in canola (Brassica napus L.) seedlings under salinity stress (0, 100 mM) for 40 days. The results indicate that exogenous application of LA + MT improved the phenotypic growth (by 25 to 45%), root thickness (by 68%), number of later lateral roots (by 52%), root viability (by 44%), and root length (by 50%) under salinity stress. Moreover, total soluble protein, chlorophyll pigments, the concentration of superoxide dismutase (SOD), catalase peroxidase (CAT), and ascorbic peroxidase (ASA) increased with the presence of salt concentration into the growth media and then decreased with the addition of LA + MT to saline solution. Leaf protein contents and the degradation of photosynthetic pigments were lower when LA + MT treatments were added into NaCl media. The proline and phenol contents decreased in the exogenous application of LA + MT treatments more than individual LA or MT treatments under the salinity stress. The incorporation of LA or MT or a combination of LA + MT to saline solution decreased salinity-induced malondialdehyde and electrolyte leakage. In conclusion, the alteration of metabolic pathways, redox modulation, and ions homeostasis in plant tissues by the combined LA and MT application are helpful towards the adaptation of Brassica napus L. seedlings in a saline environment. The results of this study provide, for the first time, conclusive evidence about the protective role of exogenous LA + MT in canola seedlings under salinity stress.

Project description:Salinity is one of the major abiotic stresses prevailing throughout the world that severely limits crop establishment and production. Every crop has an intra-specific genetic variation that enables it to cope with variable environmental conditions. Hence, this genetic variability is a good tool to exploit germplasms in salt-affected areas. Further, the selected cultivars can be effectively used by plant breeders and molecular biologists for the improvement of salinity tolerance. In the present study, it was planned to identify differential expression of genes associated with selective uptake of different ions under salt stress in selected salt-tolerant canola (Brassica napus L.) cultivar. For the purpose, an experiment was carried out to evaluate the growth response of different salt-sensitive and salt-tolerant canola cultivars. Plants were subjected to 200 mM NaCl stress. Canola cultivars-Faisal Canola, DGL, Dunkled, and CON-II-had higher growth than in cvs Cyclone, Ac-EXcel, Legend, and Oscar. Salt-tolerant cultivars were better able to maintain plant water status probably through osmotic adjustment as compared to salt-sensitive cultivars. Although salt stress increased shoot Na+ and shoot Cl- contents in all canola cultivars, salt-tolerant cultivars had a lower accumulation of these toxic nutrients. Similarly, salt stress reduced shoot K+ and Ca2+ contents in all canola cultivars, while salt-tolerant cultivars had a higher accumulation of K+ and Ca2+ in leaves, thereby having greater shoot K+/Na+ and Ca2+/Na+ ratios. Nutrient utilization efficiency decreased significantly in all canola cultivars due to the imposition of salt stress; however, it was greater in salt-tolerant cultivars-Faisal Canola, DGL, and Dunkled. Among four salt-tolerant canola cultivars, cv Dunkled was maximal in physiological attributes, and thus differentially expressed genes (DEGs) were assessed in it by RNA-seq analysis using next-generation sequencing (NGS) techniques. The differentially expressed genes (DEG) in cv Dunkled under salt stress were found to be involved in the regulation of ionic concentration, photosynthesis, antioxidants, and hormonal metabolism. However, the most prominent upregulated DEGs included Na/K transporter, HKT1, potassium transporter, potassium channel, chloride channel, cation exchanger, Ca channel. The RNA-seq data were validated through qRT-PCR. It was thus concluded that genes related to the regulation of ionic concentrate are significantly upregulated and expressed under salt stress, in the cultivar Dunkled.

Project description:Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorphism (SNP) marker profiles are simultaneously used to estimate performance of untested genotypes. In this study, the potential of genomic selection methods to predict testcross performance for hybrid canola breeding was applied for various agronomic traits based on genome-wide marker profiles. A total of 475 genetically diverse spring-type canola pollinator lines were genotyped at 24,403 single-copy, genome-wide SNP loci. In parallel, the 950 F1 testcross combinations between the pollinators and two representative testers were evaluated for a number of important agronomic traits including seedling emergence, days to flowering, lodging, oil yield and seed yield along with essential seed quality characters including seed oil content and seed glucosinolate content. A ridge-regression best linear unbiased prediction (RR-BLUP) model was applied in combination with 500 cross-validations for each trait to predict testcross performance, both across the whole population as well as within individual subpopulations or clusters, based solely on SNP profiles. Subpopulations were determined using multidimensional scaling and K-means clustering. Genomic prediction accuracy across the whole population was highest for seed oil content (0.81) followed by oil yield (0.75) and lowest for seedling emergence (0.29). For seed yieId, seed glucosinolate, lodging resistance and days to onset of flowering (DTF), prediction accuracies were 0.45, 0.61, 0.39 and 0.56, respectively. Prediction accuracies could be increased for some traits by treating subpopulations separately; a strategy which only led to moderate improvements for some traits with low heritability, like seedling emergence. No useful or consistent increase in accuracy was obtained by inclusion of a population substructure covariate in the model. Testcross performance prediction using genome-wide SNP markers shows considerable potential for pre-selection of promising hybrid combinations prior to resource-intensive field testing over multiple locations and years.

Dataset Information

Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage.

Publications

Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage.

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