Genome-wide identification of late embryogenesis abundant protein family and their key regulatory network in Pinus tabuliformis cold acclimation

Cold acclimation is a crucial biological process that enables conifers to overwinter safely. The late embryogenesis abundant (LEA) protein family plays a pivotal role in enhancing freezing tolerance during this process. Despite its importance, the identification, molecular functions and regulatory networks of the LEA protein family have not been extensively studied in conifers or gymnosperms. Pinus tabuliformis, a conifer with high ecological and economic values and with high-quality genome sequence, is an ideal candidate for such studies. Here, a total of 104 LEA genes were identified from P. tabuliformis, and we renamed them according to their subfamily group: PtLEA1-PtLEA92 (group LEA1-LEA6), PtSMP1-PtSMP6 (group seed maturation protein) and PtDHN1-PtDHN6 (group Dehydrin). While the sequence structure of P. tabuliformis  LEA genes are conserved, their physicochemical properties exhibit unique characteristics within different subfamily groupings. Notably, the abundance of low-temperature responsive elements in PtLEA genes was observed. Using annual rhythm and temperature gradient transcriptome data, PtLEA22 was identified as a key gene that responds to low-temperature induction while conforming to the annual cycle of cold acclimation. Overexpression of PtLEA22 enhanced Arabidopsis freezing tolerance. Furthermore, several transcription factors potentially co-expressed with PtLEA22 were validated using yeast one-hybrid and dual-luciferase assays, revealing that PtDREB1 could directly bind PtLEA22 promoter to positively regulate its expression. These findings reveal the genome-wide characterization of P. tabuliformis  LEA genes and their importance in the cold acclimation, while providing a theoretical basis for studying the molecular mechanisms of cold acclimation in conifers.

Integrative analysis of physiology and genomics provides insights into freeze tolerance adaptations of Acacia koa along an elevational cline

Natural selection for plant species in heterogeneous environments creates genetic variation for traits such as cold tolerance. While physiological or molecular analyses have been used to evaluate stress tolerance adaptations, combining these approaches may provide deeper insight. Acacia koa (koa) occurs from sea level to 2300 m in Hawai'i, USA. At high elevations, natural koa populations have declined due to deforestation, and freeze tolerance is a limiting factor for tree regeneration. We used physiology and molecular analyses to evaluate cold tolerance of koa populations from low (300-750 m), middle (750-1500 m), and high elevations (1500-2100 m). Half of the seedlings were cold acclimated by exposure to progressively lowered air temperatures for eight weeks (from 25.6/22.2°C to 8/4°C, day/night). Using the whole plant physiology-freezing test and koa C-repeat Binding Factor CBF genes, our results indicated that koa can be cold-acclimated when exposed to low, non-freezing temperatures. Seedlings from high elevations had consistently higher expression of Koa CBF genes associated with cold tolerance, helping to explain variation in cold-hardy phenotypes. Evaluation of the genetic background of 22 koa families across the elevations with low coverage RNA sequencing indicated that high elevation koa had relatively low values of heterozygosity, suggesting that adaptation is more likely to arise in the middle and low elevation sources. This physiology and molecular data for cold tolerance of koa across the elevation gradient of the Hawaiian Islands provides insights into natural selection processes and may help to support guidelines for conservation and seed transfer in forest restoration efforts.

Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation

Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light (HL) acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under HL conditions at a locus in chromosome 2. Ascorbate levels under HL and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7-fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3-fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of HL acclimation. The results strongly suggest that this is achieved via the release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during HL acclimation.

Molecular determinants for cold adaptation in an Antarctic Na+/K+-ATPase

Enzymes from ectotherms living in chronically cold environments have evolved structural innovations to overcome the effects of temperature on catalysis. Cold adaptation of soluble enzymes is driven by changes within their primary structure or the aqueous milieu. For membrane-embedded enzymes, like the Na+/K+-ATPase, the situation is different because changes to the lipid bilayer in which they operate may also be relevant. Although much attention has been focused on thermal adaptation within lipid bilayers, relatively little is known about the contribution of structural changes within membrane-bound enzymes themselves. The identification of specific mutations that confer temperature compensation is complicated by the presence of neutral mutations, which can be more numerous. In the present study, we identified specific amino acids in a Na+/K+-ATPase from an Antarctic octopus that underlie cold resistance. Our approach was to generate chimeras between an Antarctic clone and a temperate ortholog and then study their temperature sensitivities in Xenopus oocytes using an electrophysiological approach. We identified 12 positions in the Antarctic Na+/K+-ATPase that, when transferred to the temperate ortholog, were sufficient to confer cold tolerance. Furthermore, although all 12 Antarctic mutations were required for the full phenotype, a single leucine in the third transmembrane segment (M3) imparted most of it. Mutations that confer cold resistance are mostly in transmembrane segments, at positions that face the lipid bilayer. We propose that the interface between a transmembrane enzyme and the lipid bilayer is a critical determinant of temperature sensitivity and, accordingly, has been a prime evolutionary target for thermal adaptation.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees

A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.

Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods

In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.

Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress

Bacterial adaptation to cold stress requires wide transcriptional reprogramming. However, the knowledge of molecular mechanisms underlying the cold stress response of mycobacteria is limited. We conducted comparative transcriptomic analysis of Mycobacterium smegmatis subjected to cold shock. The growth of M. smegmatis cultivated at 37 °C was arrested just after exposure to cold (acclimation phase) but later (by 24 h) was resumed at a much slower rate (adaptation phase). Transcriptomic analyses revealed distinct gene expression patterns corresponding to the two phases. During the acclimation phase, differential expression was observed for genes associated with cell wall remodeling, starvation response, and osmotic pressure stress, in parallel with global changes in the expression of transcription factors and the downregulation of ribosomal genes, suggesting an energy-saving strategy to support survival. At the adaptation phase, the expression profiles were recovered, indicating restoration of the processes repressed earlier. Comparison of transcriptional responses in M. smegmatis with those in other bacteria revealed unique adaptation strategies developed by mycobacteria. Our findings shed light on the molecular mechanisms underlying M. smegmatis survival under cold stress. Further research should clarify whether the discovered transcriptional mechanisms exist in other mycobacterial species, including pathogenic Mycobacterium tuberculosis, which could be important for transmission control.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

The role and risks of selective adaptation in extreme coral habitats

The alarming rate of climate change demands new management strategies to protect coral reefs. Environments such as mangrove lagoons, characterized by extreme variations in multiple abiotic factors, are viewed as potential sources of stress-tolerant corals for strategies such as assisted evolution and coral propagation. However, biological trade-offs for adaptation to such extremes are poorly known. Here, we investigate the reef-building coral Porites lutea thriving in both mangrove and reef sites and show that stress-tolerance comes with compromises in genetic and energetic mechanisms and skeletal characteristics. We observe reduced genetic diversity and gene expression variability in mangrove corals, a disadvantage under future harsher selective pressure. We find reduced density, thickness and higher porosity in coral skeletons from mangroves, symptoms of metabolic energy redirection to stress response functions. These findings demonstrate the need for caution when utilizing stress-tolerant corals in human interventions, as current survival in extremes may compromise future competitive fitness.

Response of seed yield and biochemical traits of Eruca sativa Mill. to drought stress in a collection study

Drought tolerance is a complex trait in plants that involves different biochemical mechanisms. During two years of study (2019-2020), the responses of 64 arugula genotypes to drought stress were evaluated in a randomized complete block design with three replications under field conditions. Several metabolic traits were evaluated, i.e. relative water content, photosynthetic pigments (chlorophyll and carotenoids), proline, malondialdehyde, enzymatic antioxidants (catalase, ascorbate peroxidase, and peroxidase), total phenolic and flavonoid contents and seed yield. On average, the drought stress significantly increased the proline content (24%), catalase (42%), peroxidase (60%) and malondialdehyde activities (116%) over the two years of study. As a result of the drought stress, the seed yield (18%), relative water content (19.5%) and amount of photosynthetic pigments (chlorophyll and carotenoids) dropped significantly. However, the total phenolic and flavonoid contents showed no significant changes. Under drought stress, the highest seed yields were seen in the G50, G57, G54, G55 and G60 genotypes, while the lowest value was observed in the G16 genotype (94 g plant-1). According to the findings, when compared to the drought-sensitive genotypes, the drought-tolerant arugula genotypes were marked with higher levels of proline accumulation and antioxidant enzyme activity. Correlation analysis indicated the positive effects of peroxidase, catalase and proline on seed yield under drought conditions. These traits can be considered for the selection of drought-tolerant genotypes in breeding programs.

Divergent contributions of coding and noncoding sequences to initial high-altitude adaptation in passerine birds endemic to the Qinghai-Tibet Plateau

Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high-altitude snowfinch species endemic to the Qinghai-Tibet Plateau. Our genome-wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development-related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high-altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.

Rapid evolution during climate change: demographic and genetic constraints on adaptation to severe drought

Populations often vary in their evolutionary responses to a shared environmental perturbation. A key hurdle in building more predictive models of rapid evolution is understanding this variation-why do some populations and traits evolve while others do not? We combined long-term demographic and environmental data, estimates of quantitative genetic variance components, a resurrection experiment and individual-based evolutionary simulations to gain mechanistic insights into contrasting evolutionary responses to a severe multi-year drought. We examined five traits in two populations of a native California plant, Clarkia xantiana, at three time points over 7 years. Earlier flowering phenology evolved in only one of the two populations, though both populations experienced similar drought severity and demographic declines and were estimated to have considerable additive genetic variance for flowering phenology. Pairing demographic and experimental data with evolutionary simulations suggested that while seed banks in both populations probably constrained evolutionary responses, a stronger seed bank in the non-evolving population resulted in evolutionary stasis. Gene flow through time via germ banks may be an important, underappreciated control on rapid evolution in response to extreme environmental perturbations.

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.

"What We Know and What We Do Not Know about Evolutionary Genetic Adaptation to High Altitude Hypoxia in Andean Aymaras"

Three well-studied populations living at high altitudes are Tibetans, Andeans (Aymaras and Quechuas), and Ethiopians. Unlike Tibetans and Ethiopians who have similar hemoglobin (Hb) levels as individuals living at sea level, Aymara Hb levels increase when living at higher altitudes. Our previous whole genome study of Aymara people revealed several selected genes that are involved in cardiovascular functions, but their relationship with Hb levels was not elucidated. Here, we studied the frequencies of known evolutionary-selected variants in Tibetan and Aymara populations and their correlation with high Hb levels in Aymara. We genotyped 177 Aymaras at three different altitudes: 400 m (Santa Cruz), 4000 m (La Paz), and 5000 m (Chorolque), and correlated the results with the elevation of residence. Some of the Tibetan-selected variants also exist in Aymaras, but at a lower prevalence. Two of 10 Tibetan selected variants of EPAS1 were found (rs13005507 and rs142764723) and these variants did not correlate with Hb levels. Allele frequencies of 5 Aymara selected SNPs (heterozygous and homozygous) at 4000 m (rs11578671_BRINP3, rs34913965_NOS2, rs12448902_SH2B1, rs10744822_TBX5, and rs487105_PYGM) were higher compared to Europeans. The allelic frequencies of rs11578671_BRINP3, rs34913965_NOS2, and rs10744822_SH2B1 were significantly higher for Aymaras living at 5000 m than those at 400 m elevation. Variant rs11578671, close to the BRINP3 coding region, correlated with Hb levels in females. Variant rs34913965 (NOS2) correlated with leukocyte counts. Variants rs12448902 (SH2B1) and rs34913965 (NOS2) associated with higher platelet levels. The correlation of these SNPs with blood cell counts demonstrates that the selected genetic variants in Aymara influence hematopoiesis and cardiovascular effects.

From common gardens to candidate genes: exploring local adaptation to climate in red spruce

Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.

FER and LecRK show haplotype-dependent cold-responsiveness and mediate freezing tolerance in Lotus japonicus

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, FERONIA-receptor like kinase (LjFER) and a S-receptor-like kinase gene (LjLecRK), are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work suggests that recruiting a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering functional genetic insight into perennial herb evolution.

The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica

Saccharina japonica is an ecologically and economically important kelp in cold-temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non-coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome-ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.

DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors

DNA methylation (DNAm) has been intensively studied in terrestrial plants in response to environmental changes, but its dynamic changes in a temporal scale remain unexplored in marine plants. The seagrass Posidonia oceanica ranks among the slowest-growing and longest-living plants on Earth, and is particularly vulnerable to sea warming and local anthropogenic pressures. Here, we analysed the dynamics of DNAm changes in plants collected from coastal areas differentially impacted by eutrophication (i.e. oligotrophic, Ol; eutrophic, Eu) and exposed to abiotic stressors (nutrients, temperature increase and their combination). Levels of global DNAm (% 5-mC) and the expression of key genes involved in DNAm were assessed after one, two and five weeks of exposure. Results revealed a clear differentiation between plants, depending on environmental stimuli, time of exposure and plants' origin. % 5-mC levels were higher during the initial stress exposure especially in Ol plants, which upregulated almost all genes involved in DNAm. Contrarily, Eu plants showed lower expression levels, which increased under chronic exposure to stressors, particularly to temperature. These findings show that DNAm is dynamic in P. oceanica during stress exposure and underlined that environmental epigenetic variations could be implicated in the regulation of acclimation and phenotypic differences depending on local conditions.

Psychrophilic Yeasts: Insights into Their Adaptability to Extremely Cold Environments

Psychrophilic yeasts are distributed widely on Earth and have developed adaptation strategies to overcome the effect of low temperatures. They can adapt to low temperatures better than bacteriophyta. However, to date, their whole-genome sequences have been limited to the analysis of single strains of psychrophilic yeasts, which cannot be used to reveal their possible psychrophilic mechanisms to adapt to low temperatures accurately and comprehensively. This study aimed to compare different sources of psychrophilic yeasts at the genomic level and investigate their cold-adaptability mechanisms in a comprehensive manner. Nine genomes of known psychrophilic yeasts and three representative genomes of mesophilic yeasts were collected and annotated. Comparative genomic analysis was performed to compare the differences in their signaling pathways, metabolic regulations, evolution, and psychrophilic genes. The results showed that fatty acid desaturase coding genes are universal and diverse in psychophilic yeasts, and different numbers of these genes exist (delta 6, delta 9, delta 12, and delta 15) in the genomes of various psychrophilic yeasts. Therefore, they can synthesize polyunsaturated fatty acids (PUFAs) in a variety of ways and may be able to enhance the fluidity of cell membranes at low temperatures by synthesizing C18:3 or C18:4 PUFAs, thereby ensuring their ability to adapt to low-temperature environments. However, mesophilic yeasts have lost most of these genes. In this study, psychrophilic yeasts could adapt to low temperatures primarily by synthesizing PUFAs and diverse antifreeze proteins. A comparison of more psychrophilic yeasts' genomes will be useful for the study of their psychrophilic mechanisms, given the presence of additional potential psychrophilic-related genes in the genomes of psychrophilic yeasts. This study provides a reference for the study of the psychrophilic mechanisms of psychrophilic yeasts.

The evening complex promotes maize flowering and adaptation to temperate regions

Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.

Population genetic analysis and scans for adaptation and contemporary selection footprints provide genomic insight into aus, indica and japonica rice cultivars diversification

Following domestication, rice cultivars have been spread worldwide to different climates and have experienced selection pressures to improve desirable traits. This has resulted in diverse cultivars that display variations in phenotypic traits, such as stress tolerance, grain size, and yield. To better understand the genomic composition arising from cultivar's development and local adaptation, high-density genotypes (containing 286,183 single-nucleotide polymorphisms after the quality control) of 1284 rice cultivars of aus, indica, and temperate and tropical japonica were scanned for diversifying signatures by applying a pairwise comparison of fixation index (Fst) test. Each cultivar's population was investigated for contemporary selection using the integrated haplotype score test. Signatures of diversifying selection among the pairwise comparisons were found in genomic regions mainly involved in response to stress (pathogens, drought, heat, cold) and development and morphology of various structures, such as root, pollen, spikelet, and grain. The most significant diversification signal between indica and japonica cultivars was detected at the location of ROX2 gene. Aus with indica comparison detected the most divergent signal at important candidate genes of OsEXPA8 and OsEXPA9, whereas temperate with tropical japonica comparison resulted in two well-known candidate genes OsHCT4 and OsGpx4. Recent selection analysis detected different patterns of contemporary selection in genomic regions related to rice breeding standard criteria such as stress tolerance, seed germination, starch content, and flowering time. Our findings highlight the underlying molecular basis of adaptive divergence and propose that modern rice breeding may provide additional diversification among rice cultivars.

Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod

Plants can cold acclimate to enhance their freezing tolerance by sensing declining temperature and photoperiod cues. However, the factors influencing genotypic variation in the induction of cold acclimation are poorly understood among perennial grasses. We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod. Next, we identified the temperature required to induce cold acclimation by exposing the 16 genotypes for 7 days at 20-6°C constant temperatures under a 10 or 16 h photoperiod. Cold acclimation initiated at temperatures 5 and 7°C higher in upland than in coastal and lowland genotypes. Among upland genotypes the shorter photoperiod induced cold acclimation at a 1°C higher temperature. Genotypes originating from a more northern latitude initiate cold acclimation at higher temperatures and develop higher maximum freezing tolerances. An earlier response to declining temperatures may provide the upland ecotype with additional time to prepare for winter and provide an advantage when plants are subjected to the rapid changes in fall temperature associated with injurious frosts.

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.