scholarly journals Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaojuan Wang ◽  
Hua Rao ◽  
Jianxiang Ma ◽  
Xiaodan Chen ◽  
Guanglin Li ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Local Adaptation ◽  
Molecular Mechanisms ◽  
Natural Populations ◽  
Northern China ◽  
Genomic Variation ◽  
Forward Genetics ◽  
Local Adaptations ◽  
Salt Cress ◽  
Eutrema Salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

scholarly journals Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

2021 ◽  
Author(s):  
Aglaia Antoniou ◽  
Tereza Manousaki ◽  
Francisco Ramírez ◽  
Alessia Cariani ◽  
Rita Cannas ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Dynamic Equilibrium ◽  
Natural Populations ◽  
Spatial Dimension ◽  
Western Mediterranean ◽  
Genomic Variation ◽  
Entire Genome ◽  
Outlier Loci ◽  
Genomic Approach ◽  
Nw Mediterranean

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.

Molecular mechanisms of local adaptation for salt‐tolerance in a treefrog

2021 ◽  
Author(s):  
Molly A. Albecker ◽  
Adam M.M. Stuckert ◽  
Christopher N. Balakrishnan ◽  
Michael W. McCoy
Keyword(s):  
Salt Tolerance ◽  
Local Adaptation ◽  
Molecular Mechanisms

scholarly journals sxtA4+ and sxtA4- Genotypes Occur Together within Natural Pyrodinium bahamense Sub-Populations from the Western Atlantic

2021 ◽  
Vol 9 (6) ◽  
pp. 1128
Author(s):  
Kathleen Cusick ◽  
Gabriel Duran
Keyword(s):  
Molecular Mechanisms ◽  
Harmful Algal Bloom ◽  
Single Cells ◽  
Natural Populations ◽  
Indian River Lagoon ◽  
Toxin Production ◽  
Genotype Frequency ◽  
Rrna Gene ◽  
Western Atlantic ◽  
Pyrodinium Bahamense

Saxitoxin (STX) is a secondary metabolite and potent neurotoxin produced by several genera of harmful algal bloom (HAB) marine dinoflagellates. The basis for variability in STX production within natural bloom populations is undefined as both toxic and non-toxic strains (of the same species) have been isolated from the same geographic locations. Pyrodinium bahamense is a STX-producing bioluminescent dinoflagellate that blooms along the east coast of Florida as well as the bioluminescent bays in Puerto Rico (PR), though no toxicity reports exist for PR populations. The core genes in the dinoflagellate STX biosynthetic pathway have been identified, and the sxtA4 gene is essential for toxin production. Using sxtA4 as a molecular proxy for the genetic capacity of STX production, we examined sxtA4+ and sxtA4- genotype frequency at the single cell level in P. bahamense populations from different locations in the Indian River Lagoon (IRL), FL, and Mosquito Bay (MB), a bioluminescent bay in PR. Multiplex PCR was performed on individual cells with Pyrodinium-specific primers targeting the 18S rRNA gene and sxtA4. The results reveal that within discrete natural populations of P. bahamense, both sxtA4+ and sxtA4- genotypes occur, and the sxtA4+ genotype dominates. In the IRL, the frequency of the sxtA4+ genotype ranged from ca. 80–100%. In MB, sxtA4+ genotype frequency ranged from ca 40–66%. To assess the extent of sxtA4 variation within individual cells, sxtA4 amplicons from single cells representative of the different sampling sites were cloned and sequenced. Overall, two variants were consistently obtained, one of which is likely a pseudogene based on alignment with cDNA sequences. These are the first data demonstrating the existence of both genotypes in natural P. bahamense sub-populations, as well as sxtA4 presence in P. bahamense from PR. These results provide insights on underlying genetic factors influencing the potential for toxin variability among natural sub-populations of HAB species and highlight the need to study the genetic diversity within HAB sub-populations at a fine level in order to identify the molecular mechanisms driving HAB evolution.

scholarly journals Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 782
Author(s):  
Joon-Yung Cha ◽  
Sang-Ho Kang ◽  
Myung Geun Ji ◽  
Gyeong-Im Shin ◽  
Song Yi Jeong ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Humic Acid ◽  
Stress Tolerance ◽  
Plant Development ◽  
Molecular Mechanisms ◽  
Abiotic Stress Tolerance ◽  
Principal Component ◽  
Salt Stress Tolerance ◽  
Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

scholarly journals Potassium: A Vital Regulator of Plant Responses and Tolerance to Abiotic Stresses

Agronomy ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 31 ◽  
Author(s):  
Mirza Hasanuzzaman ◽  
M. Bhuyan ◽  
Kamrun Nahar ◽  
Md. Hossain ◽  
Jubayer Mahmud ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
Abiotic Stress Tolerance ◽  
Ion Homeostasis ◽  
Enzyme Activation ◽  
Regulatory Function ◽  
Plant Responses ◽  
Plant Structure ◽  
Physiological Processes

Among the plant nutrients, potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of the plant structure but it also has a regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, and enzyme activation. Several physiological processes depend on K, such as stomatal regulation and photosynthesis. In recent decades, K was found to provide abiotic stress tolerance. Under salt stress, K helps to maintain ion homeostasis and to regulate the osmotic balance. Under drought stress conditions, K regulates stomatal opening and helps plants adapt to water deficits. Many reports support the notion that K enhances antioxidant defense in plants and therefore protects them from oxidative stress under various environmental adversities. In addition, this element provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although considerable progress has been made in understanding K-induced abiotic stress tolerance in plants, the exact molecular mechanisms of these protections are still under investigation. In this review, we summarized the recent literature on the biological functions of K, its uptake, its translocation, and its role in plant abiotic stress tolerance.

scholarly journals Advances in 5-Aminolevulinic Acid Priming to Enhance Plant Tolerance to Abiotic Stress

2022 ◽  
Vol 23 (2) ◽  
pp. 702
Author(s):  
Shuya Tan ◽  
Jie Cao ◽  
Xinli Xia ◽  
Zhonghai Li
Keyword(s):  
Abiotic Stresses ◽  
Nitrogen Assimilation ◽  
Molecular Mechanisms ◽  
Aminolevulinic Acid ◽  
Adaptive Strategy ◽  
Forward Genetics ◽  
Plant Tolerance ◽  
Biotic And Abiotic Stresses ◽  
Defense Priming ◽  
Made In

Priming is an adaptive strategy that improves plant defenses against biotic and abiotic stresses. Stimuli from chemicals, abiotic cues, and pathogens can trigger the establishment of priming state. Priming with 5-aminolevulinic acid (ALA), a potential plant growth regulator, can enhance plant tolerance to the subsequent abiotic stresses, including salinity, drought, heat, cold, and UV-B. However, the molecular mechanisms underlying the remarkable effects of ALA priming on plant physiology remain to be elucidated. Here, we summarize recent progress made in the stress tolerance conferred by ALA priming in plants and provide the underlying molecular and physiology mechanisms of this phenomenon. Priming with ALA results in changes at the physiological, transcriptional, metabolic, and epigenetic levels, and enhances photosynthesis and antioxidant capacity, as well as nitrogen assimilation, which in turn increases the resistance of abiotic stresses. However, the signaling pathway of ALA, including receptors as well as key components, is currently unknown, which hinders the deeper understanding of the defense priming caused by ALA. In the future, there is an urgent need to reveal the molecular mechanisms by which ALA regulates plant development and enhances plant defense with the help of forward genetics, multi-omics technologies, as well as genome editing technology.

scholarly journals De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

2021 ◽  
Vol 22 (18) ◽  
pp. 9874
Author(s):  
Matin Miryeganeh ◽  
Hidetoshi Saze
Keyword(s):  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
High Salinity ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Natural Habitats ◽  
Mangrove Species ◽  
Mangrove Tree ◽  
Bruguiera Gymnorhiza

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

scholarly journals Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants

2018 ◽  
Author(s):  
Sara Marin ◽  
Juliette Archambeau ◽  
Vincent Bonhomme ◽  
Mylène Lascoste ◽  
Benoit Pujol
Keyword(s):  
Local Adaptation ◽  
Natural Populations ◽  
Common Garden ◽  
Global Scale ◽  
Structured Populations ◽  
Adaptive Divergence ◽  
Adaptation To Climate Change ◽  
Phenotypic Differentiation ◽  
Multiple Populations ◽  
Environmental Demand

ABSTRACTPhenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.

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