-
Plant Communications Jun 2024Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be...
Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species with slow LD decay. We generated RNA-Seq data of a soybean diversity panel, and identified the genetic expression regulation of 29,286 genes in soybean. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod color L2 was identified via TWAS and functionally validated by genome editing. By introducing the new exon proportion feature, we significantly improved the detection of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
PubMed: 38918950
DOI: 10.1016/j.xplc.2024.101010 -
Scientific Reports Jun 2024The decline of wild bee populations causes the decline of bee-pollinated plant populations through the deterioration of pollination services. Since high bee species...
The decline of wild bee populations causes the decline of bee-pollinated plant populations through the deterioration of pollination services. Since high bee species richness generally involves high functional group diversity, protecting areas of high bee species richness will help to maintain pollination services for plants. However, those areas do not always include the habitats of bee species with specialized functions that expand the range of plants being pollinated. To map important areas for protecting native bee species and their functions, we estimated the distributions and functional range of 13 bumble bee species and 1 honey bee species in Japan. The distributions were estimated from an ensemble of six species distribution models using bee occurrence data and environmental data. The functional range of bee species was estimated by combining the estimated distributions and proboscis length, which frequently corresponds to the floral shape of the plant species they pollinate. The estimated species richness was high in western Hokkaido and the estimated functional range was wide in central Honshu. Our method is useful to see whether areas important for high species richness of pollinators differ from those for rare species or their functions.
Topics: Bees; Animals; Pollination; Japan; Biodiversity; Ecosystem
PubMed: 38918494
DOI: 10.1038/s41598-024-61848-z -
Scientific Reports Jun 2024Although pesticide-free techniques have been developed in agriculture, pesticides are still routinely used against weeds, pests, and pathogens worldwide. These...
Although pesticide-free techniques have been developed in agriculture, pesticides are still routinely used against weeds, pests, and pathogens worldwide. These agrochemicals pollute the environment and can negatively impact human health, biodiversity and ecosystem services. Acetamiprid, an approved neonicotinoid pesticide in the EU, may exert sub-lethal effects on pollinators and other organisms. However, our knowledge on the scope and severity of such effects is still incomplete. Our experiments focused on the effects of the insecticide formulation Mospilan (active ingredient: 20% acetamiprid) on the peripheral olfactory detection of a synthetic floral blend and foraging behaviour of buff-tailed bumblebee (Bombus terrestris) workers. We found that the applied treatment did not affect the antennal detection of the floral blend; however, it induced alterations in their foraging behaviour. Pesticide-treated individuals started foraging later, and the probability of finding the floral blend was lower than that of the control bumblebees. However, exposed bumblebees found the scent source faster than the controls. These results suggest that acetamiprid-containing Mospilan may disrupt the activity and orientation of foraging bumblebees. We hypothesize that the observed effects of pesticide exposure on foraging behaviour could be mediated through neurophysiological and endocrine mechanisms. We propose that future investigations should clarify whether such sub-lethal effects can affect pollinators' population dynamics and their ecosystem services.
Topics: Animals; Bees; Insecticides; Flowers; Odorants; Neonicotinoids; Pollination
PubMed: 38918480
DOI: 10.1038/s41598-024-65388-4 -
PloS One 2024Land use change affects both pollinator and herbivore populations with consequences for crop production. Recent evidence also shows that land use change affects insect...
Land use change affects both pollinator and herbivore populations with consequences for crop production. Recent evidence also shows that land use change affects insect traits, with intraspecific body size of pollinators changing across landscape gradients. However, the consequences on crop production of trait changes in different plant interactors have not been well-studied. We hypothesized that changes in body size of key species can be enough to affect crop productivity, and therefore looked at how the field-realistic variation in body size of both an important pollinator, Bombus impatiens (Cresson), and a key pest herbivore, Lygus lineolaris (Palisot), can affect fruit size and damage in strawberry. First, we determined if pests vary in body size along land use gradients as prior studies have documented for pollinators; and second, we tested under controlled conditions how the individual and combined changes in size of an important pollinator and a key herbivore pest affect strawberry fruit production. The key herbivore pest was smaller in landscapes with more natural and semi-natural habitat, confirming that herbivore functional traits can vary along a land use gradient. Additionally, herbivore size, and not pollinator size, marginally affected fruit production-with plants exposed to larger pests producing smaller fruits. Our findings suggest that land use changes at the landscape level affect crop production not just through changes in the species diversity of insect communities that interact with the plant, but also through changes in body size traits.
Topics: Fragaria; Animals; Fruit; Body Size; Pollination; Herbivory; Bees
PubMed: 38917100
DOI: 10.1371/journal.pone.0305370 -
Plant Communications Jun 2024Transient heatwaves occur more frequently with climate warming, yet their impacts on crop yield are severely underestimated and even overlooked. Heatwaves spanning mere... (Review)
Review
Transient heatwaves occur more frequently with climate warming, yet their impacts on crop yield are severely underestimated and even overlooked. Heatwaves spanning mere days or even hours during sensitive stages (e.g., microgametogenesis and flowering) can significantly reduce crop yield by disrupting plant reproduction. Recently, advancements in multi-omics and GWAS analysis have shed light on specific organs (e.g., pollen, lodicule, and style), key metabolic pathways (sugar and reactive oxygen species (ROS) metabolisms, Ca homeostasis), and essential genes for transient heatwaves responses during the most sensitive stages in many crops. Based on this, this review places particular emphasis on the crop's heat-sensitive stages, using pollen development, floret opening, pollination, and fertilization as the central narrative thread. Complementing by key parts such as lodicule and tapetum, the multifaceted effects of transient heatwaves and their molecular basis are systematically demonstrated. A number of heat-tolerant genes for these processes have been identified in major crops such as maize and rice. The mechanisms and key heat-tolerant genes shared over different stages potentially facilitate the improvement of heat-tolerant crops more precisely.
PubMed: 38915200
DOI: 10.1016/j.xplc.2024.101009 -
Scientific Reports Jun 2024Haploid induction (HI) holds great promise in expediting the breeding process in onion, a biennial cross-pollinated crop. We used the CENH3-based genome elimination...
Haploid induction (HI) holds great promise in expediting the breeding process in onion, a biennial cross-pollinated crop. We used the CENH3-based genome elimination technique in producing a HI line in onion. Here, we downregulated AcCENH3 using the RNAi approach without complementation in five independent lines. Out of five events, only three could produce seeds upon selfing. The progenies showed poor seed set and segregation distortion, and we were unable to recover homozygous knockdown lines. The knockdown lines showed a decrease in accumulation of AcCENH3 transcript and protein in leaf tissue. The decrease in protein content in transgenic plants was correlated with poor seed set. When the heterozygous knockdown lines were crossed with wild-type plants, progenies showed HI by genome elimination of the parental chromosomes from AcCENH3 knockdown lines. The HI efficiency observed was between 0 and 4.63% in the three events, and it was the highest (4.63%) when E1 line was crossed with wildtype. Given the importance of doubled haploids in breeding programmes, the findings from our study are poised to significantly impact onion breeding.
Topics: Onions; RNA Interference; Plants, Genetically Modified; Haploidy; Plant Proteins; Gene Expression Regulation, Plant; Down-Regulation; Plant Breeding; Gene Knockdown Techniques
PubMed: 38914600
DOI: 10.1038/s41598-024-64432-7 -
European Annals of Allergy and Clinical... Jun 2024Grass and olive pollens have overlapping pollination periods and are common allergens in the Iberian Peninsula. The objective is to determine the sensitization pattern...
Grass and olive pollens have overlapping pollination periods and are common allergens in the Iberian Peninsula. The objective is to determine the sensitization pattern to major Phleum pratense and Olea europaea pollens in the Portuguese population with pollen allergic rhinitis (AR) using molecular allergen diagnosis (MAD). Seasonal AR patients (≥ 12 years), with positive skin prick tests (SPT) to Phleum and Olea were recruited from 16 centers. Using ALEX2, specific IgE to Phl p1, Phl p2, Phl p5, Phl p6, Phl p7, Phl p 12, Ole e1, Ole e7 and Ole e9 were determined. Immunoblotting of Olea allergic patients was performed. Included 175 patients (55.4% female; mean age 31.6 ± 13.3 years; 85.7% adults; 40% asthmatic, Coast 28%/Inland 72% and North 29.1%/Centre 20.6%/South 50.3%). Considering Phleum MAD, 85.7% were sensitized to Phl p1, 45.7% to Phl p2, 50.3% to Phl p5, 45.7%, to Phl p6, 10.9% to Phl p7 and 22.9% to Phl p12. Sensitization to Ole e1 was found in 56.6%, to Ole e7 in 1.7% and Ole e9 in 3.4% patients. Sensitization to Phl p7 was more frequent in asthmatics (17.4% vs 6.6%; p = 0.044). Sensitization to Phl p5, Phl p6, Phl p12 and Ole e1 was more frequent in inland. Regarding sensitization patterns: 53.1% patients were sensitized to both species genuine´ sIgE, 38.3% to Phleum and 3.4% only to Olea species' sIgE. Immunoblotting of Olea allergic patients showed a high intensity band that may correspond to Ole e12. MAD showed "genuine" Grass and Olea sensitization in approximately 50% of our patients.
PubMed: 38913398
DOI: 10.23822/EurAnnACI.1764-1489.347 -
Scientific Reports Jun 2024As natural landscapes are modified and converted into simplified agricultural landscapes, the community composition and interactions of organisms persisting in these...
As natural landscapes are modified and converted into simplified agricultural landscapes, the community composition and interactions of organisms persisting in these modified landscapes are altered. While many studies examine the consequences of these changing interactions for crops, few have evaluated the effects on wild plants. Here, we examine how pollinator and herbivore interactions affect reproductive success for wild resident and phytometer plants at sites along a landscape gradient ranging from natural to highly simplified. We tested the direct and indirect effects of landscape composition on plant traits and reproduction mediated by insect interactions. For phytometer plants exposed to herbivores, we found that greater landscape complexity corresponded with elevated herbivore damage, which reduced total flower production but increased individual flower size. Though larger flowers increased pollination, the reduction in flowers ultimately reduced plant reproductive success. Herbivory was also higher in complex landscapes for resident plants, but overall damage was low and therefore did not have a cascading effect on floral display and reproduction. This work highlights that landscape composition directly affects patterns of herbivory with cascading effects on pollination and wild plant reproduction. Further, the absence of an effect on reproduction for resident plants suggests that they may be adapted to their local insect community.
Topics: Herbivory; Flowers; Pollination; Animals; Reproduction; Agriculture; Insecta; Crops, Agricultural
PubMed: 38906942
DOI: 10.1038/s41598-024-65352-2 -
Evolutionary Applications Jun 2024Land-use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead...
Land-use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead to elevated inbreeding, lower genetic diversity, and poor fitness. Here we investigate the genetics of two rare and threatened plant species, and , and we compare them to a widespread congener . We also report the first phylogenetic study of the genus (Apocynaceae), including 10 of the 17 taxa and multiple sampling locations, to understand species relationships. We used a double digest restriction-site associated DNA sequencing (ddRADseq) approach to investigate the genetic diversity and gene flow of each species and to create a maximum likelihood phylogeny. The ddRADseq data was mapped to a reference genome to separate out the chloroplast and nuclear markers for population genetic analysis. Our results show that genetic diversity and inbreeding were low across all three species. The chloroplast and nuclear dataset in were highly structured, whereas they showed no structure for , while lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that is distinct and sister to , and together they are distantly related to . Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within . Interestingly, we show that in there was significant structure despite being pollinated by large, bodied hawkmoths that are known to be able to carry pollen long distances, suggesting that other factors are contributing to the structure observed among populations. Conservation efforts should focus on protecting all of the populations, as they contain unique genetic diversity, and a protection plan for needs to be established due to its limited distribution.
PubMed: 38903246
DOI: 10.1111/eva.13736 -
Molecular Plant Jun 2024Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of the maternal tissues (i.e., fruit ripening), has applications in...
Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of the maternal tissues (i.e., fruit ripening), has applications in crop production and breeding. However, the underlying molecular mechanism has yet to be elucidated. Here, we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination between distinct Malus domestica (apple) cultivars. We demonstrated that hundreds of mobile mRNAs originating from the seeds are delivered to the fruit. We also found that the movement of one of these mRNAs, ACC oxidase 3 (MdACO3), is coordinated with fruit ripening. Salicylic acid treatment, which can cause plasmodesmal closure, blocks MdACO3 movement, indicating that MdACO3 transcripts may move through plasmodesmata. To assess the role of mobile MdACO3 transcripts in apple fruit, we created MdACO3-GFP-expressing apple seeds using MdACO3-GFP-overexpressing pollen for pollination and showed that MdACO3 transcripts in the transgenic seeds move to the flesh where they regulate fruit ripening. Furthermore, we demonstrated that MdACO3 can be transported from the seeds to fruit in the fleshy-fruited species tomato and strawberry. These results underscore the potential of mobile mRNAs from seeds to influence fruit characteristics, providing an explanation for the xenia phenomenon. Notably, our findings highlight the feasibility of leveraging diverse pollen genomic resources, without resorting to genome editing, to improve fruit quality.
PubMed: 38902921
DOI: 10.1016/j.molp.2024.06.008