scholarly journals Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

2020 ◽  
Vol 21 (17) ◽  
pp. 6017 ◽  
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Heat Stress ◽  
Durum Wheat ◽  
Water Deficit ◽  
Crop Production ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Multiple Time ◽  
Altered Expression ◽  
Heat Stress Response ◽  
Omics Analysis

Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.

scholarly journals Multi-Omics Analysis of Small RNA, Transcriptome, and Degradome in T. turgidum—Regulatory Networks of Grain Development and Abiotic Stress Response

2020 ◽  
Vol 21 (20) ◽  
pp. 7772
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Heat Stress ◽  
Water Deficit ◽  
Regulatory Networks ◽  
Starch Synthesis ◽  
Differentially Expressed ◽  
Molecular Networks ◽  
Integrated Analysis ◽  
Transcriptional Networks ◽  
Grain Development ◽  
Omics Analysis

Crop reproduction is highly sensitive to water deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (Triticum turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome, and degradome in T. turgidum developing grains, under single and combined water deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNAs (DEMs) specific to genotypes, stress types, and different reproductive time-points are provided. The first degradome sequencing report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome sequencing profiled 53,146 T. turgidum genes, swith differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development, and hormone transduction pathways. miRNA–mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed on the basis of integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.

scholarly journals Transgenerational Effects of Water-Deficit and Heat Stress on Germination and Seedling Vigour—New Insights from Durum Wheat microRNAs

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 189 ◽  
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Heat Stress ◽  
Durum Wheat ◽  
Water Deficit ◽  
Seedling Establishment ◽  
Crop Production ◽  
Small Rna Sequencing ◽  
Transgenerational Effects ◽  
Seedling Vigour ◽  
Seed Vigour ◽  
Phenotypic Differences

Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in their germination and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally, stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provide the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for breeding superior germplasm and/or varieties.

scholarly journals Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Durum Wheat ◽  
Water Deficit ◽  
Small Rna ◽  
Wheat Yield ◽  
Water Deficit Stress ◽  
Integrated Analysis ◽  
Sequencing Analysis ◽  
Biological Interactions ◽  
Transgenerational Effects ◽  
Nutrient Metabolism

AbstractWater-deficit stress negatively affects wheat yield and quality. Abiotic stress on parental plants during reproduction may have transgenerational effects on progeny. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in first generation progeny. Parental water-deficit stress had positive impacts on the progeny for traits including harvest index and protein content in the less stress-tolerant variety. Small RNA-seq identified 1739 conserved and 774 novel microRNAs (miRNAs). Transcriptome-seq characterised the expression of 66,559 genes while degradome-seq profiled the miRNA-guided mRNA cleavage dynamics. Differentially expressed miRNAs and genes were identified, with significant regulatory patterns subject to trans- and inter-generational stress. Integrated analysis using three omics platforms revealed significant biological interactions between stress-responsive miRNA and targets, with transgenerational stress tolerance potentially contributed via pathways such as hormone signalling and nutrient metabolism. Our study provides the first confirmation of the transgenerational effects of water-deficit stress in durum wheat. New insights gained at the molecular level indicate that key miRNA-mRNA modules are candidates for transgenerational stress improvement.

scholarly journals The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa During Heat Stress

2019 ◽  
Vol 7 (8) ◽  
pp. 256 ◽  
Author(s):  
Dalit ◽  
Keren ◽  
Eviatar ◽  
Hiba ◽  
Gal ◽  
...  
Keyword(s):  
Heat Stress ◽  
Differentially Expressed Genes ◽  
Elevated Temperatures ◽  
Negative Impact ◽  
Global Climate ◽  
Differentially Expressed ◽  
Heat Stress Response ◽  
Stress Genes ◽  
Mutualistic Symbiosis ◽  
Algal Symbiont

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of “symbiosis differentially expressed genes” and “coral heat-stress genes” in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

2020 ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
The Philippines ◽  
Differentially Expressed ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab ◽  
Heat Response

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals Variation in the sugar yield in response to drying-off of sugarcane before harvest and the occurrence of low air temperatures

Bragantia ◽  
2016 ◽  
Vol 75 (1) ◽  
pp. 118-127 ◽  
Author(s):  
Renato Araújo ◽  
José Alves Junior ◽  
Derblai Casaroli ◽  
Adão Wagner Pêgo Evangelista
Keyword(s):  
Heat Stress ◽  
Water Deficit ◽  
Crop Production ◽  
Block Design ◽  
Sugar Yield ◽  
Raw Material ◽  
Sugar Accumulation ◽  
Maturation Stage ◽  
Air Temperatures ◽  
Sugarcane Yield

ABSTRACT The need to irrigate sugarcane in the Brazilian Savanna is due to the lack of rain from April to September. For efficient sugar accumulation, the crop needs water stress or heat stress at the maturation stage. However, when the water deficit is intense at this stage, it occurs the reduction in crop production. The objective of this study was: (i) to assess the quality of the raw material of sugarcane in different drying-off seasons before harvest; (ii) to evaluate the influence of heat stress on the culture. The experiment was conducted in Santo Antônio de Goiás (GO), Brazil, in Oxisol, with CTC4 variety in cane-plant cycle. A randomized block design in a split-plot array in time was used. The treatments of the plots were five drying-off times (90, 60, 30, 15 and 0 days before harvest) and, in the subplots, five seasons of the yield evaluation. Irrigation was carried out by surface drip method, which provided 50% of crop water requirement. The best results for sugar yield occurred 30 days before harvest, period in which the crop irrigation could be interrupted. The water deficit of 37.76 mm appears to be the critical limit of water shortage in the soil, from which the sugarcane yield starts to be reduced. The sugar concentration in the stalk was more influenced by low air temperatures than sugarcane yield.

scholarly journals Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 395 ◽  
Author(s):  
Yaokun Li ◽  
Lingxuan Kong ◽  
Ming Deng ◽  
Zhiquan Lian ◽  
Yinru Han ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanism ◽  
Stress Responses ◽  
Animal Health ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Ppar Signaling ◽  
Hu Sheep

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses.

scholarly journals Genotypic performance of Australian durum under single and combined water-deficit and heat stress during reproduction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Heat Stress ◽  
Water Deficit ◽  
Crop Production ◽  
Expression Patterns ◽  
Physiological Traits ◽  
Molecular Networks ◽  
Systematic Evaluation ◽  
Water Deficit Stress ◽  
Response Factors ◽  
Auxin Response Factors

Abstract In Mediterranean environments, water deficiency and heat during reproduction severely limit cereal crop production. Our research investigated the effects of single and combined pre-anthesis water-deficit stress and post-anthesis heat stress in ten Australian durum genotypes, providing a systematic evaluation of stress response at the molecular, physiological, grain quality and yield level. We studied leaf physiological traits at different reproductive stages, evaluated the grain yield and quality, and the associations among them. We profiled the expression dynamics of two durum microRNAs and their protein-coding targets (auxin response factors and heat shock proteins) involved in stress adaptation. Chlorophyll content, stomatal conductance and leaf relative water content were mostly reduced under stress, however, subject to the time-point and genotype. The influence of stress on grain traits (e.g., protein content) also varied considerably among the genotypes. Significant positive correlations between the physiological traits and the yield components could be used to develop screening strategies for stress improvement in breeding. Different expression patterns of stress-responsive microRNAs and their targets in the most stress-tolerant and most stress-sensitive genotype provided some insight into the complex defense molecular networks in durum. Overall, genotypic performance observed indicates that different stress-coping strategies are deployed by varieties under various stresses.

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