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Background: Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker – trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS). Results: Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length. Conclusion: FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security. [ABSTRACT FROM AUTHOR]

Abstract Background Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker – trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS). Results Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length. Conclusion FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security.

Most of the attention given to intraspecific crop, livestock, and aquaculture diversity in agricultural production systems has been targeted at their roles in providing provisioning services, such as food and fibre or their cultural services, providing non-material benefits, such as places for recreation and inspiration. The additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services for agricultural productivity and ecosystem resilience has been largely neglected. A literature review was carried out across sectors (crop, livestock, aquaculture), both on the counterfactual, i.e., the lack of intraspecific diversity in the production system and on the direct and indirect roles that intraspecific diversity plays in maintaining seven of the regulating and supporting ecosystem services: (i) regulating pest and diseases; (ii) maintaining and regulating water and soil quality; (iii) regulating and improving the flow of reproductive diversity; (iv) buffering excess or lack of water; (v) regulating soil erosion; (vi) nutrient cycling in water and soil; and (vii) supporting habitat maintenance. Benefits from the use of intraspecific diversity, diversity per se, and adaptive traits include a limited use of chemical inputs and unsustainable practices and their negative impact on livelihoods, ecosystem functioning, and productivity. All sectors (crop, livestock, and aquaculture) should be examined in the agricultural production system to understand the provision of the different ecosystem services by intraspecific diversity. Differences in structure, functioning, and temporal and spatial scales of these sectors should also be considered. Supporting and regulating ecosystem services often have relatively longer-term processes than food provisioning and rely not only on the current diversity but also on its presence over time. The presented regulating and supporting ecosystem services rely on the presence of the diversity from the farm to the landscape and to agroecological zone. Neglecting the additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services is shown in this review to be detrimental to agricultural productivity and landscape resilience. [ABSTRACT FROM AUTHOR]

The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3–18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9–297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5–471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding. [ABSTRACT FROM AUTHOR]

The contribution of genetic adaptation and plasticity to intraspecific phenotypic variability remains insufficiently studied in long‐lived plants, as well as the relevance of neutral versus adaptive processes determining such divergence. We examined the importance of phylogeographic structure and climate in modulating genetic and plastic changes and their interdependence in fitness‐related traits of a widespread Mediterranean conifer (Pinus pinaster). Four marker‐based, previously defined neutral classifications along with two ad hoc climate‐based categorizations of 123 range‐wide populations were analyzed for their capacity to summarize genetic and plastic effects of height growth and survival (age 20) in 15 common gardens. The plasticity of tree height and differential survival were interpreted through mixed modeling accounting for heteroscedasticity in the genotype‐by‐environment dataset. The analysis revealed a slight superiority of phylogeographic classifications over climate categorizations on the explanation of genetic and plastic effects, which suggests that neutral processes can be at least as important as isolation by climate as a driving factor of evolutionary divergence in a prevalent pine. The best phylogeographic classification involved eight geographically discrete genetic groups, which explained 92% (height) and 52% (survival) of phenotypic variability, including between‐group mean differentiation and differential expression across trials. For height growth, there was high predictability of plastic group responses described by different reaction norm slopes, which were unrelated to between‐group mean differentiation. The latter differences (amounting to ca. 40% among groups) dominated intraspecific performance across trials. Local adaptation was evident for genetic groups tested in their native environments in terms of tree height and, especially, survival. This finding was supported by QST > FST estimates. Additionally, our range‐wide evaluation did not support a general adaptive syndrome by which less reactive groups to ameliorated conditions would be associated with high survival and low growth. In fact, a lack of relationship between mean group differentiation, indicative of genetic adaptation, and predictable group plasticity for height growth suggests different evolutionary trajectories of these mechanisms of phenotypic divergence. Altogether, the existence of predictable adaptive‐trait phenotypic variation for the species, involving both genetic differentiation and plastic effects, should facilitate integrating genomics and environment into decision‐making tools to assist forests in coping with climate change. [ABSTRACT FROM AUTHOR]

Most of the attention given to intraspecific crop, livestock, and aquaculture diversity in agricultural production systems has been targeted at their roles in providing provisioning services, such as food and fibre or their cultural services, providing non-material benefits, such as places for recreation and inspiration. The additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services for agricultural productivity and ecosystem resilience has been largely neglected. A literature review was carried out across sectors (crop, livestock, aquaculture), both on the counterfactual, i.e., the lack of intraspecific diversity in the production system and on the direct and indirect roles that intraspecific diversity plays in maintaining seven of the regulating and supporting ecosystem services: (i) regulating pest and diseases; (ii) maintaining and regulating water and soil quality; (iii) regulating and improving the flow of reproductive diversity; (iv) buffering excess or lack of water; (v) regulating soil erosion; (vi) nutrient cycling in water and soil; and (vii) supporting habitat maintenance. Benefits from the use of intraspecific diversity, diversity per se, and adaptive traits include a limited use of chemical inputs and unsustainable practices and their negative impact on livelihoods, ecosystem functioning, and productivity. All sectors (crop, livestock, and aquaculture) should be examined in the agricultural production system to understand the provision of the different ecosystem services by intraspecific diversity. Differences in structure, functioning, and temporal and spatial scales of these sectors should also be considered. Supporting and regulating ecosystem services often have relatively longer-term processes than food provisioning and rely not only on the current diversity but also on its presence over time. The presented regulating and supporting ecosystem services rely on the presence of the diversity from the farm to the landscape and to agroecological zone. Neglecting the additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services is shown in this review to be detrimental to agricultural productivity and landscape resilience.

Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries’ adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima’s D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries’ adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.

Abstract Background Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. Results We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. Conclusions This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems.

Background: Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. Results: We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. Conclusions: This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems. [ABSTRACT FROM AUTHOR]

The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3–18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9–297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5–471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding.

Societal Impact Statement The productivity of sorghum in Ethiopia has been largely limited by rain‐fed conditions because farmers tend to use local drought‐tolerant but low‐yielding landraces, as high‐yielding and late‐maturing landrace cultivars risk failure due to drought. Addressing such issues often requires a far‐reaching approach to identify and incorporate new traits into a gene pool, followed by a period of selection to re‐establish an overall adaptive phenotype. The sorghum backcross nested association mapping (BC‐NAM) population developed in this study increases the genetic diversity available in Ethiopian elite adapted sorghum germplasm, providing new scope to improve food security in a region known for periodic devastating droughts. Summary As the center of diversity for sorghum, Sorghum bicolor (L.) Moench, elite cultivars selected in Ethiopia are of central importance to sub‐Saharan food security. Despite being presumably well adapted to their center of diversity, elite Ethiopian sorghums nonetheless experience constraints to productivity, for example, associated with shifting rainfall patterns associated with climate change. A sorghum backcross nested association mapping (BC‐NAM) population developed by crossing 13 diverse lines pre‐identified to have various drought resilience mechanisms with an Ethiopian elite cultivar, Teshale, was tested under three rain‐fed environments in Ethiopia. Twenty‐seven, 15, and 15 quantitative trait loci (QTLs) with predominantly small additive effects were identified for days to flowering, days to maturity, and plant height, respectively. Many associations detected in this study corresponded closely to known or candidate genes or previously mapped QTLs, supporting their validity. The expectation that genotypes such as Teshale from the center of diversity tend to have a history of strong balancing selection, with novel variations more likely to persist in small marginal populations, was strongly supported in that for these three traits, nearly equal numbers of alleles from the donor lines conferred increases and decreases in phenotype relative to the Teshale allele. Such rich variation provides a foundation for selection to arrive at a new “adaptive peak,” exemplifying the nature of efforts that may be necessary to adapt many crops to new climate extremes.

Simple Summary: In this study, we investigated whether predation pressures in the early life history of frogs can result in an anuran-affect behavior response in the later stages of their life history. Tadpoles that undergo predation pressure possess smaller body sizes, slower development rates, and broader caudal fins. In particular, juvenile frogs that undergo predation pressure from the tadpole stage also metamorphosize later, develop longer limbs, narrower skulls, and demonstrate other finer changes in the skeleton of the lower body. On this note, we predicted that this would change the locomotory performance of such juvenile frogs in terms of their swimming and jumping speed, but such an eventuality did not take place. It appears, then, that predation pressure in the early life history of frogs does not alter their jumping and swimming speed abilities. Moreover, such a fact suggests that this morphological change may not be a predator-adaptive response. Anuran species can respond to environmental changes via phenotypic plasticity, which can also result in ecological impacts across the life history of such species. We investigated the effects of predation pressure (i.e., the non-consumption effect) from the dragonfly larva (Anax parthenope) on the phenotypical change of tadpoles into juvenile frogs (specifically the black-spotted pond frog, Pelophylax nigromaculatus), and also analyzed the impact of morphological changes on locomotory performance after metamorphosis. The experiments on predator impact were conducted in the laboratory. Body length, weight, development timing, and metamorphosis timing in the presence of dragonfly nymphs were measured in both tadpoles and juvenile frogs. The body and tail shapes of the tadpoles, as well as the skeletal shape of the juvenile frogs, were analyzed using landmark-based geometric morphometrics. Furthermore, the locomotory performance of the juvenile frogs was tested by measuring their jumping and swimming speeds. Tadpoles that had grown with predators possessed smaller bodies, deeper tail fins, and slower development rates, and they waited longer periods of time before commencing metamorphosis. Having said this, however, the effect of predator cues on the body length and weight of juvenile frogs was not found to be significant. These juvenile frogs possessed longer limbs and narrower skulls, with subtle morphological changes in the pelvis and ilium, but there was no subsequent difference in their swimming and jumping speeds. Our results showed that the changes in anatomical traits that can affect locomotor performance are so subtle that they do not affect the jumping or swimming speeds. Therefore, we support the view that these morphological changes are thus by-products of an altered tadpole period, rather than an adaptive response to predator-escape ability or to post-metamorphosis life history. On the other hand, delayed metamorphosis, without an increase in body size, may still be disadvantageous to the reproduction, growth, and survival of frogs in their life history following metamorphosis. [ABSTRACT FROM AUTHOR]

Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is an invasive pest species that uses a wide variety of commercial fruit as a breeding and feeding resource. The damage to the fruit generated by D. suzukii´ oviposition causes considerable economic losses. Therefore, the maintenance of D. suzukii in the lab conditions constitutes a fundamental tool for research proposal. Two of the determining factors affecting the lab rearing conditions are the culture medium and density. In this study, we evaluated the impact of these factors on three components associated with fitness: development time, larval-adult viability and body size, comparing the effects of three culture media: cornmeal (polenta), mashed potato and plum when the flies were reared at three densities: 10, 30 and 50 larvae per 5ml of culture medium. Our results revealed that the flies reared the cornmeal culture medium and at lower densities provide the better conditions for the maintenance of D. suzukii under lab conditions. [ABSTRACT FROM AUTHOR]

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

Abstract Background Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

Drought challenges crop production worldwide. The issue is aggravated by frequent drought episodes and unpredictable rainfall patterns associated with global climate change. While the efforts to breed drought-resistant crop varieties are progressing, the need of the hour is immediate strategies to sustain the yields of existing ones. As per recent studies, stress adaptive traits can be activated using specific elicitors. Endophytes that inhabit host plants asymptomatically are natural elicitors/bio-stimulators capable of activating host gene expression, conferring several benefits to the hosts. This review discusses the scope of using trait-specific endophytes in activating drought adaptive traits in crop varieties.

Societal Impact Statement: The productivity of sorghum in Ethiopia has been largely limited by rain‐fed conditions because farmers tend to use local drought‐tolerant but low‐yielding landraces, as high‐yielding and late‐maturing landrace cultivars risk failure due to drought. Addressing such issues often requires a far‐reaching approach to identify and incorporate new traits into a gene pool, followed by a period of selection to re‐establish an overall adaptive phenotype. The sorghum backcross nested association mapping (BC‐NAM) population developed in this study increases the genetic diversity available in Ethiopian elite adapted sorghum germplasm, providing new scope to improve food security in a region known for periodic devastating droughts. Summary: As the center of diversity for sorghum, Sorghum bicolor (L.) Moench, elite cultivars selected in Ethiopia are of central importance to sub‐Saharan food security. Despite being presumably well adapted to their center of diversity, elite Ethiopian sorghums nonetheless experience constraints to productivity, for example, associated with shifting rainfall patterns associated with climate change.A sorghum backcross nested association mapping (BC‐NAM) population developed by crossing 13 diverse lines pre‐identified to have various drought resilience mechanisms with an Ethiopian elite cultivar, Teshale, was tested under three rain‐fed environments in Ethiopia.Twenty‐seven, 15, and 15 quantitative trait loci (QTLs) with predominantly small additive effects were identified for days to flowering, days to maturity, and plant height, respectively. Many associations detected in this study corresponded closely to known or candidate genes or previously mapped QTLs, supporting their validity.The expectation that genotypes such as Teshale from the center of diversity tend to have a history of strong balancing selection, with novel variations more likely to persist in small marginal populations, was strongly supported in that for these three traits, nearly equal numbers of alleles from the donor lines conferred increases and decreases in phenotype relative to the Teshale allele. Such rich variation provides a foundation for selection to arrive at a new "adaptive peak," exemplifying the nature of efforts that may be necessary to adapt many crops to new climate extremes. [ABSTRACT FROM AUTHOR]

BackgroundModern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.ResultsWe sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.ConclusionsWe uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

'Caviano' is a black bean cultivar recommended for Santa Catarina, for being highly adaptable to the main grain-producing regions of the state (mean grain yield 2315 kg ha-1). Compared to previously released cultivars, Caviano has a larger root system and desirable characteristics for mechanical harvesting. [ABSTRACT FROM AUTHOR]

Promiscuous plasmids like IncP-1 plasmids play an important role in the bacterial adaptation to pollution by acquiring and distributing xenobiotic catabolic genes. However, most information comes from isolates and the role of plasmids in governing community-wide bacterial adaptation to xenobiotics and other adaptive forces is not fully understood. Current information on the contribution of IncP-1 plasmids in community adaptation is limited because methods are lacking that directly isolate and identify the plasmid borne adaptive functions in whole-community DNA. In this study, we optimized long-range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA. The DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, is amplified and its content analyzed by high-throughput sequencing. The method was applied to DNA of an onfarm biopurification system (BPS), treating pesticide contaminated wastewater, to examine whether horizontal gene exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. The cargo recovered from BPS community DNA encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, genes with catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be remnants of random gene recruitment, or confer other crucial functions for proliferation in the BPS environment. IMPORTANCE This study presents a long-range PCR for direct and cultivation-independent access to the identity of the cargo of a major insertion hot spot of adaptive genes in IncP-1 plasmids and hence a new mobilome tool for understanding the role of IncP-1 plasmids in complex communities. The method was applied to DNA of an on-farm biopurification system (BPS) treating pesticide-contaminated wastewater, aiming at new insights on whether horizontal exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. Unexpectedly, catabolic functions represented a small fraction of the cargo genes while multiple other gene functions were recovered. These results show that the cargo of the target insertion hot spot in IncP-1 plasmids in a community, not necessarily relates to the main obvious selective trait imposed on that community. Instead, these functions might contribute to adaptation to unknown selective forces or represent remnants of random gene recruitment. [ABSTRACT FROM AUTHOR]

Anuran species can respond to environmental changes via phenotypic plasticity, which can also result in ecological impacts across the life history of such species. We investigated the effects of predation pressure (i.e., the non-consumption effect) from the dragonfly larva (Anax parthenope) on the phenotypical change of tadpoles into juvenile frogs (specifically the black-spotted pond frog, Pelophylax nigromaculatus), and also analyzed the impact of morphological changes on locomotory performance after metamorphosis. The experiments on predator impact were conducted in the laboratory. Body length, weight, development timing, and metamorphosis timing in the presence of dragonfly nymphs were measured in both tadpoles and juvenile frogs. The body and tail shapes of the tadpoles, as well as the skeletal shape of the juvenile frogs, were analyzed using landmark-based geometric morphometrics. Furthermore, the locomotory performance of the juvenile frogs was tested by measuring their jumping and swimming speeds. Tadpoles that had grown with predators possessed smaller bodies, deeper tail fins, and slower development rates, and they waited longer periods of time before commencing metamorphosis. Having said this, however, the effect of predator cues on the body length and weight of juvenile frogs was not found to be significant. These juvenile frogs possessed longer limbs and narrower skulls, with subtle morphological changes in the pelvis and ilium, but there was no subsequent difference in their swimming and jumping speeds. Our results showed that the changes in anatomical traits that can affect locomotor performance are so subtle that they do not affect the jumping or swimming speeds. Therefore, we support the view that these morphological changes are thus by-products of an altered tadpole period, rather than an adaptive response to predator-escape ability or to post-metamorphosis life history. On the other hand, delayed metamorphosis, without an increase in body size, may still be disadvantageous to the reproduction, growth, and survival of frogs in their life history following metamorphosis.

Background: Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results: A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions: The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change. [ABSTRACT FROM AUTHOR]

Seasonality, rather than annual precipitation levels, is expected to affect the adaptive responses of plant populations under future climate change. To estimate adaptive traits’ variation, we conducted a common garden experiment with two beech populations from contrasting climatic origins (Evros with longer drought intervals during summer and higher precipitation seasonality, and Drama representing a more temperate ecosystem). We simulated two different watering treatments (frequent vs. non-frequent) on beech seedlings, according to predicted monthly precipitation levels expected to prevail in 2050 by the CSIRO MK3.6 SRESA1B model, considering as reference area a natural beech stand in Mt. Rodopi, Greece. A series of morphological and stem anatomical traits were measured. Seedling survival was greater for the Evros population compared to that of Drama under non-frequent watering, while no difference in survival was detected under frequent watering. Leaf morphological traits were not generally affected by watering frequency except for leaf circularity, which was found to be lower under non-frequent watering for both populations. Stomata density in leaves was found to be higher in the Evros population and lower in the Drama population under non-frequent watering than frequent. Stem anatomical traits were higher under non-frequent watering for Evros but lower for the Drama population. Multivariate analyses clearly discriminated populations under non-frequent rather than frequent watering, indicating genetic adaptation to the population’s environment of origin.

Abstract Background The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture of these traits remains poorly understood. Results We integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations. Conclusions Our results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties. [ABSTRACT FROM AUTHOR]

Ants are a widespread group of ecologically important insects. Therefore, ants that are important predators of other ants are likely to play key roles by changing the abundance and impacts of their prey. Familiar arthropod predators, like army ants, are known for their overwhelming raids on invertebrate prey but are limited to mostly tropical systems. Thief ants (Genus: Solenopsis Westwood) are a cosmopolitan group of mostly subterranean ants found in a wide variety of ecosystem types. They are known for their extremely small sizes and their specialized predation where they stealthily tunnel into the nests of other larger ant species to capture and consume only immature ants (larvae and pupae). Predation of ant colonies by other ants, and specialized predatory behaviors of presumed top ant predators (e.g., army ants) are well known. However long‐term predation effects, such as across several seasons, are still poorly understood because of a lack of experimental studies. Here we report results of a ~1.5‐year press field experiment where thief ants were reduced in natural ant communities. Potential impacts, such as predator‐release, were quantified by sampling the co‐occurring ant community. Compared to control plots, overall worker abundance and biomass increased where thief ants were reduced, and effects varied among ant species. Results suggest predator release as select aboveground foraging ant species increased in abundance and that thief ants may act as significant predators. Because thief ants are abundant and widespread, similar predatory effects may occur in many ant communities, and our understanding of important predators may need to adjust to include thieving species as well as army ants. Thief ants are very abundant, tiny, specialized to consume immature life stages, equipped with powerful venom, eusocial, and subterranean. This suite of adaptive traits seems unique to eusocial predators compared to animals, where "thieving" predators are usually larger in size compared to their adult‐sized prey. Future work quantifying top‐down regulation of prey and cascading consumptive and non‐consumptive effects will help to understand thief ant predation and potential effects on ecosystem processes. [ABSTRACT FROM AUTHOR]

• Geographical-wise genetic distinction among the dromedary populations was revealed. • Regions under selection were defined on the autosomes of dromedary camels. • Genes related to adaptive physiologies were found within the defined regions. • Haplotype blocks overlapping the candidate regions were defined. • Dromedary genetic diversity and haplotypes under selection need to be conserved. Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome. [ABSTRACT FROM AUTHOR]

Abstract Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here. [ABSTRACT FROM AUTHOR]

The garden chrysanthemum (Chrysanthemum morifolium Ramat.) is a highly demanded autumn flowering culture for parks and gardens and as cut flowers and has long, abundant and colorful flowering. The lack of winter-hardy and season-adequate flowering cultivars and poor resistance to diseases limit its distribution in most regions of Russia. The development of new plant-breeding material by artificial interspecific hybridization able to combine valuable traits of different Chrysanthemum species in a single organism is therefore of importance. Reciprocal crossing has been conducted between the species of the Manchurian (C. chanetii H. Lév., C. coreanum (H. Lév. et Vaniot) Nakai, C. maximoviczii Kom., C. naktongense Nakai, C. zawadskii subsp. acutilobum (DC.) Kitag., C. tenuisectum Kitag., C. zawadskii subsp. latilobum (Maxim.) Kitag., C. leiophyllum Nakai), Mongolian-Siberian (C. mongolicum Y. Ling, C. zawadskii Herbich) flora and interspecific hybrid forms with the involvement of subtropical Chrysanthemum species. Crossing and backcrossing of species with identical numbers of chromosomes (hexaploid × hexaploid, 2n = 54 and tetraploid × tetraploid, 2n = 36) were easy. Tetraploids × hexaploids showed good compatibility. Diploids (2n = 18) are not always compatible between themselves and are partly compatible with hexaploids. Interspecific hybrids in the first generation (F1) were characterized by phenotypic uniformity with intermediate inheritance or predominance of traits of the highploidy parent and differed in hybrid power, intensity of emergent rhizomes and complex of adaptive qualities. Multicomponent interspecific hybrids have been obtained from combinations of crossing, consisting of three different components. The selected highly decorative interspecific and multicomponent forms have promise for planting of greenery and serve as complex sources of adaptiveness for the development of garden chrysanthemum native to Russia.

Seven species are recorded and ten new species are described from Oriental, Afrotropical and Neotropical Fauna Regions: Abacaria dufforum sp. nov., Cyrnellus kesken sp. nov., C. kozepes sp. nov., Orthotrichia palama sp. nov., Marilia annae sp. nov., Phylloicus kinovos sp. nov., Atanatolica homora sp. nov., Oecetis fura sp. nov., O. siska sp. nov., Contulma duffi sp. nov. Based on theoretical outline of how to delineate young incipient sibling species with more phenomics and less genomics, the new species complex of Oecetis amazonica is erected as well as an instantiated failure of neutral DNA markers are presented on Allogamus auricollis and A. alpinus siblings.

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

Persistence of Aeromonas hydrophila in aquatic environments is the principle cause of fish hemorrhagic septicemia. Protistan predation has been considered to be a strong driving force for the evolution of bacterial defense strategies. In this study, we investigated the adaptive traits of A. hydrophila NJ-35, a carp pathogenic strain, in response to Tetrahymena thermophila predation. After subculturing with Tetrahymena, over 70% of A. hydrophila colonies were small colony variants (SCVs). The SCVs displayed enhanced biofilm formation, adhesion, fitness, and resistance to bacteriophage infection and oxidative stress as compared to the non-Tetrahymena-exposed strains. In contrast, the SCVs exhibited decreased intracellular bacterial number in RAW264.7 macrophages and were highly attenuated for virulence in zebrafish. Considering the outer membrane proteins (OMPs) are directly involved in bacterial interaction with the external surroundings, we investigated the roles of OMPs in the antipredator fitness behaviors of A. hydrophila. A total of 38 differentially expressed proteins were identified in the SCVs by quantitative proteomics. Among them, three lipoproteins including SurA, Slp, and LpoB, and a serine/threonine protein kinase (Stpk) were evidenced to be associated with environmental adaptation of the SCVs. Also, the three lipoproteins were involved in attenuated virulence of SCVs through the proinflammatory immune response mediated by TLR2. This study provides an important contribution to the understanding of the defensive traits of A. hydrophila against protistan predators.

The differential exploration of natural resources by Drosophila species has effects on fitness, with changes in life history and metabolic traits. There is a lack of research on the variation in these characters in different environments in Neotropical species of Drosophila . The purpose of this study was to evaluate the profile of life history traits, including viability, development time, and dry weight (as a measure of size), as well as the metabolic pools of triglyceride, glycogen, and protein, in populations from the southern and southeastern regions of Brazil of four Neotropical Drosophila species: D. willistoni , of the Sophophora subgenus, and D. mercatorum , D. maculifrons , and D. ornatifrons , which belong to the Drosophila subgenus. Life history and metabolic traits showed interpopulational variation in at least one species. When significant differences in life history parameters occurred, species of the same subgenus presented similar profiles, i.e. , southern populations were larger, less viable, and showed longer development time. This was also observed for triglyceride. However, for the other two metabolic pools (glycogen and total proteins), D. maculifrons and D. ornatifrons presented inverse patterns to the other two species, with the highest values in southeastern populations and the lowest in southern populations. These populational variations indicate plasticity of the examined life history traits, which allows distinctive responses to different environmental conditions shared by speciesof the same subgenus. Nevertheless, interspecific comparisons did not reflect phylogenetic relationships, with the highest viability being found for D. willistoni and D. mercatorum , which is probably correlated to the ability of these species to explore a broader variety of habitats. On the other hand, the storage capability of metabolic pools seems to be species specific, determined by the adaptive history to the quality and availability of resources, with D. mercatorum (low) and D. ornatifrons (high) having opposing capacities to store metabolites from their diets.

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus , references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan. [ABSTRACT FROM AUTHOR]

Genetic resources have to be managed appropriately to mitigate the impact of climate change. For many wildland plants, conservation will require knowledge of the climatic factors affecting intraspecific genetic variation to minimize maladaptation. Knowledge of the interaction between traits and climate can focus management resources on vulnerable populations, provide guidance for seed transfer, and enhance fitness and resilience under changing climates. In this study, traits of big sagebrush (Artemisia tridentata) were examined among common gardens located in different climates. We focus on two subspecies, wyomingensis and tridentata, that occupy the most imperiled warm‐dry spectrum of the sagebrush biome. Populations collected across the sagebrush biome were recorded for flower phenology and survival. Mixed‐effects models examined each trait to evaluate genetic variation, environmental effects, and adaptive breadth of populations. Climate variables derived from population‐source locations were significantly associated with these traits (P < 0.0001), explaining 31% and 11% of the flower phenology and survival variation, respectively. To illustrate our model and assess variability in prediction, we examine fixed and focal point seed transfer approaches to map contemporary and climate model ensemble projections in two different regions of the sagebrush biome. A comparison of seed transfer areas predicts that populations from warmer climates become more prevalent, replacing colder‐adapted populations by mid‐century. However, these warm‐adapted populations are often located along the trailing edge, margins of the species range predicted to be lost due to a contraction of the climatic niche. Management efforts should focus on the collection and conservation of vulnerable populations and prudent seed transfer to colder regions where these populations are projected to occur by mid‐century. Our models provide the foundation to develop an empirical, climate‐based seed transfer system for current and future restoration of big sagebrush. [ABSTRACT FROM AUTHOR]

Persistence of Aeromonas hydrophila in aquatic environments is the principle cause of fish hemorrhagic septicemia. Protistan predation has been considered to be a strong driving force for the evolution of bacterial defense strategies. In this study, we investigated the adaptive traits of A. hydrophila NJ-35, a carp pathogenic strain, in response to Tetrahymena thermophila predation. After subculturing with Tetrahymena, over 70% of A. hydrophila colonies were small colony variants (SCVs). The SCVs displayed enhanced biofilm formation, adhesion, fitness, and resistance to bacteriophage infection and oxidative stress as compared to the non-Tetrahymena-exposed strains. In contrast, the SCVs exhibited decreased intracellular bacterial number in RAW264.7 macrophages and were highly attenuated for virulence in zebrafish. Considering the outer membrane proteins (OMPs) are directly involved in bacterial interaction with the external surroundings, we investigated the roles of OMPs in the antipredator fitness behaviors of A. hydrophila. A total of 38 differentially expressed proteins were identified in the SCVs by quantitative proteomics. Among them, three lipoproteins including SurA, Slp, and LpoB, and a serine/threonine protein kinase (Stpk) were evidenced to be associated with environmental adaptation of the SCVs. Also, the three lipoproteins were involved in attenuated virulence of SCVs through the proinflammatory immune response mediated by TLR2. This study provides an important contribution to the understanding of the defensive traits of A. hydrophila against protistan predators. [ABSTRACT FROM AUTHOR]

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

Breeding maize for drought tolerance necessitates the knowledge on tolerant genotypes, molecular basis of drought tolerance mechanism, action, and expression pattern of genes. Studying the expression pattern and gene action of candidate genes during drought stress in the hybrids will help in choosing target genes for drought tolerance breeding. In the present investigation, a set of five hybrids and their seven parents with a variable level of tolerance to drought stress was selected to study the magnitude and the direction of 52 drought-responsive candidate genes distributed across various biological functions, viz., stomatal regulation, root development, detoxification, hormone signaling, photosynthesis, and sugar metabolism. The tolerant parents, HKI1105 and CML425, and their hybrid, ADWLH2, were physiologically active under drought stress, since vital parameters viz., chlorophyll, root length and relative water content, were on par with the respective well-watered control. All the genes were up-regulated in ADWLH2, many were down-regulated in HM8 and HM9, and most were down-regulated in PMH1 and PMH3 in the shoots and roots. The nature of the gene action was controlled by the parental combination rather than the parent per se. The differentially expressed genes in all five hybrids explained a mostly non-additive gene action over additivity, which was skewed toward any of the parental lines. Tissue-specific gene action was also noticed in many of the genes. The non-additive gene action is driven by genetic diversity, allele polymorphism, events during gene regulation, and small RNAs under the stress condition. Differential regulation and cross-talk of genes controlling various biological functions explained the basis of drought tolerance in subtropical maize hybrids. The nature of the gene action and the direction of the expression play crucial roles in designing introgression and hybrid breeding programmes to breed drought tolerant maize hybrids.