Genome-wide Analysis Research Articles

Molecular characterization and expression pattern analysis of Sirtuin family genes in the eastern honeybee, Apis cerana

Sirtuin proteins are a family of evolutionarily conserved NAD+-dependent deacetylase enzymes which play crucial roles in regulating insect metabolism, maintaining genome stability, and lifespan. However, there is no report on the genome-wide analysis of the Sirtuin gene family in the eastern honeybee, Apis cerana. Here, 6 Sirtuin genes (AcSirt1, AcSirt2, AcSirt4 ~ AcSirt7) were obtained in the A. cerana genome, which were located on 6 different chromosomes and were all single-copy genes. Gene structure analysis revealed that these 6 genes were all multi-exon genes. The Sirtuin family genes contained 9 conserved motifs and 5 conserved domains, which exhibited typical Sirtuin protein structural characteristics. The phylogenetic analysis of the Sirtuin family genes indicates that A. cerana lacked the Sirt3 gene, and the 6 Sirtuin encoding genes could be clustered into 5 groups and 6 branches, showing high homology with the Apis mellifera and the Apis dorsata. The results of the tissue and period expression profiles by qRT-PCR indicated that the 6 Sirtuin family genes showed transcriptional activity in different tissues of worker bees, and the gene expression level reached the peak in the 4-day-old larvae and pupa stages. It was speculated that Sirtuin genes expression level was affected by fasting behavior, caloric restriction and organ differentiation during different developmental stages of A. cerana. Meanwhile, the differential expression patterns of Sirtuin genes in various tissues further demonstrated the diversity and complexity of their functions, providing a basis for target selection in future studies on the functionality of Sirtuin genes.

Genome-wide association analysis identifies candidate genes for carcass yields in Peking ducks.

Poultry meat, particularly Peking ducks, holds a significant global market share, prized for their high meat yield and fat content. However, understanding of the molecular genetic mechanisms influencing carcass yield in ducks is limited. This research aims to use genome-wide association analysis to uncover single-nucleotide polymorphisms influencing carcass yield in Peking ducks, followed by identifying candidate genes linked to carcass traits. In this study, we analyzed seven traits of 643 Peking ducks at age 42 days and identified novel loci associated with these traits. A total of 35 significant loci were detected, with eight SNPs reaching genome-wide significance. KIF20B, AGBL5, SGSM1, MRO, PLAG1, XKR4, and TGS1 were considered as important candidate genes influencing carcass yield in ducks. This study adds to the list of genes affecting Peking duck body traits, aiding marker-assisted breeding and enhancing economic yield.

Genome-wide association analysis revealed genetic markers linked to grain yield and yield related traits in finger millet grown in acidic soils

Abstract Aim Soil acidity has a major impact on the finger millet yield and productivity as tolerant cultivars that perform well in acidic soils are limited. This study aimed at evaluating major finger millet phenotypic traits under acidic soils followed by identifying associated markers. Method A total of 288 finger millet genotypes were field evaluated for 8 major phenotypic traits including grain yield under acid soil conditions at two independent locations (Bako and Gute) in Ethiopia. In parallel, the same genotypes were subjected to genotyping-by-sequencing to generate single nucleotide polymorphism markers to be used in the association panel. Results Phenotypic data analysis revealed significant phenotypic variation in all the targeted traits among the studied genotypes. Genotypes Ec-100093, Ec-215803, and Ec-203322 were relatively high-yielding, whereas genotypes Ec-229721 and Ec-242110 had the lowest grain yield across the two locations. The broad-sense heritability of the traits ranged from 0.04 for the number of effective tillers (NET) to 0.78 for days to emergence (DE). The marker-trait association analysis revealed 23 SNP markers significantly associated with one or more traits. Among the 23 significant markers, one marker associated with DE, seven with days to heading (DH), four with days to maturity (DM), one with plant height (PH), two with number of fingers, two with ear length (EL), three with the number of effective tillers (NET) and three with grain yield (GY). Conclusions The identified novel markers associated with the targeted traits will potentially be useful for genomics-driven finger millet improvement in acidic soils.

Machine vision-assisted genomic prediction and genome-wide association of spleen-related traits in large yellow croaker infected with visceral white-nodules disease

High-resolution and high-throughput genotype-to-phenotype studies in fish are rapidly advancing, driven by innovative technologies that aim to address the challenges of modern breeding models. In recent years, machine vision and deep learning techniques, particularly convolutional neural networks (CNNs), have achieved significant success in image recognition and segmentation. Moreover, qualitative and quantitative analysis of disease resistance has always been a crucial field of research in genetics. This motivation has led us to investigate the potential of large yellow croaker visceral white-nodules disease (VWND) in encoding information on disease resistance for the task of accession classification. In this study, we proposed an image segmentation framework for the feature extraction of the spleen after VWND infection based on machine vision. We utilized deep CNNs and threshold segmentation for automatic feature learning and object segmentation. This approach eliminates subjectivity and enhances work efficiency compared to using hand-crafted features. Additionally, we employed spleen-related traits to conduct genome-wide association analysis (GWAS), which led to the identification of 24 significant SNPs and 10 major quantitative trait loci. The results of function enrichment analysis on candidate genes also indicated potential relationships with immune regulation mechanisms. Furthermore, we explored the use of genomic selection (GS) technology for phenotype prediction of extreme individuals, which further supports the predictability of spleen-related phenotypes for VWND resistance in large yellow croakers. Our findings demonstrate that artificial intelligence (AI)-based phenotyping approaches can deliver state-of-the-art performance for genetics research. We hope this work will provide a paradigm for applying deep learning and machine vision to phenotyping in aquaculture species.

Genetic analysis of cognitive preservation in the midwestern Amish reveals a novel locus on chromosome 2.

Alzheimer's disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). A total of 12 single nucleotide polymorphisms (SNPs) demonstrated suggestive association (P≤5×10-4) with cognitive preservation. Genetic linkage analyses identified>100 significant (logarithm of the odds [LOD]≥3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2. GWAS and linkage identified over 100 loci associated with cognitive preservation. One locus on Chromosome 2 retained significance over multiple analyses. Predicted TFBSs near rs1402906 regulate genes associated with neurocognition.

The Genetic Characteristics of FT-MIRS-Predicted Milk Fatty Acids in Chinese Holstein Cows

Fourier Transform Mid-Infrared Spectroscopy (FT-MIRS) can be used for quantitative detection of milk components. Here, milk samples of 458 Chinese Holstein cows from 11 provinces in China were collected and we established a total of 22 quantitative prediction models in milk fatty acids by FT-MIRS. The coefficient of determination of the validation set ranged from 0.59 (C18:0) to 0.76 (C4:0). The models were adopted to predict the milk fatty acids from 2138 cows and a new high-throughput computing software HiBLUP was employed to construct a multi-trait model to estimate and analyze genetic parameters in dairy cows. Finally, genome-wide association analysis was performed and seven novel SNPs significantly associated with fatty acid content were selected, investigated, and verified with the FarmCPU method, which stands for “Fixed and random model Circulating Probability Unification”. The findings of this study lay a foundation and offer technical support for the study of fatty acid trait breeding and the screening and grouping of characteristic dairy cows in China with rich, high-quality fatty acids. It is hoped that in the future, the method established in this study will be able to screen milk sources rich in high-quality fatty acids.

Genome-wide analysis of anterior-posterior mRNA regionalization in Stentor coeruleus reveals a role for the microtubule cytoskeleton.

Cells have complex and beautiful structures that are important for their function. However, understanding the molecular mechanisms that produce these structures is a challenging problem due to the gap in size scales between molecular interactions and cellular structures. The giant ciliate Stentor coeruleus is a unicellular model organism whose large size, reproducible structure, and ability to heal wounds and regenerate have historically allowed the formation of structure in a single cell to be addressed using methods of experimental embryology. Such studies have shown that specific cellular structures, such as the membranellar band, always form in particular regions of the cell, which raises the question: what is the source of positional information within this organism? By analogy with embryonic development, in which regionalized mRNA is often used to mark position, we asked whether specific regionalized mRNAs might mark position along the anterior-posterior axis of Stentor . By physically bisecting cells and conducting bulk RNA sequencing, we were able to identify sets of messages enriched in either the anterior or posterior half. We then conducted half-cell RNA-sequencing in paired anteriors and posteriors of cells in which the microtubule cytoskeleton was disrupted by RNAi of β-tubulin or dynein intermediate chains. We found that many messages either lost their regionalized distribution or switched to an opposite distribution, such that anterior-enriched messages in control became posterior-enriched in the RNAi cells, or vice versa. This study indicates that mRNA can be regionalized within a single giant cell and that microtubules may play a role, possibly by serving as tracks for the movement of the messages.

Cell wall alterations occurring in an evolved multi-stress tolerant strain of the oleaginous yeast Rhodotorula toruloides

The oleaginous yeast species Rhodotorula toruloides is a promising candidate for applications in circular bioeconomy due to its ability to efficiently utilize diverse carbon sources being tolerant to cellular stress in bioprocessing. Previous studies including genome-wide analyses of the multi-stress tolerant strain IST536 MM15, derived through adaptive laboratory evolution from a promising IST536 strain for lipid production from sugar beet hydrolysates, suggested the occurrence of significant modifications in the cell wall. In this study, the cell wall integrity and carbohydrate composition of those strains was characterized to gain insights into the physicochemical changes associated to the remarkable multi-stress tolerance phenotype of the evolved strain. Compared to the original strain, the evolved strain exhibited a higher proportion of glucomannans, fucogalactomannans, and chitin relative to (1→4)-linked glucans, and an increased presence of glycoproteins with short glucosamine derived oligosaccharides, which have been found to be associated to ethanol stress tolerance and physical strength of the cell wall. Furthermore, the evolved strain cells were found to be significantly smaller than the original strain and more resistant to thermal and mechanical disruption, consistent with higher proportion of beta-linked polymers instead of glycogen, conferring a more rigid and robust cell wall. These findings provide further insights into the cell wall composition of this basidiomycetous red yeast species and into the alterations occurring in a multi-stress tolerant evolved strain. This new information can guide yeast genome engineering towards more robust strains of biotechnological relevance.

Genome-wide analysis of the WRKY gene family and their response to low-temperature stress in elephant grass.

Elephant grass (Cenchrus purpureus) is a perennial forage grass characterized by tall plants, high biomass and wide adaptability. Low-temperature stress severely limits elephant grass biomass and geographic distribution. WRKY is one of the largest families of plant-specific transcription factors and plays important roles in plant resistance to low-temperature. However, the understanding of the WRKY family in grasses is limited. In this study, we conducted a genome-wide characterization of WRKY proteins in elephant grass, including gene structure, phylogeny, expression, conserved motif organization, and functional annotation, to identify key CpWRKY candidates involved in cold tolerance. In this study, a total of 176 WRKY genes were identified in elephant grass. It was found that 172 were unevenly distributed across its 14 chromosomes, while the remaining 4 genes were not anchored to any chromosome. The genes were classified into three groups based on their WRKY conserved domains and zinc finger motifs. There were 12, 8, 19, 27, 12, 18 and 80 CpWRKYs belonging to group I, group IIa, group IIb, group IIc, group IId, group IIe and group III, respectively. We hypothesized that the ancient subgroup IIc WRKY gene is the ancestor of all WRKY genes in elephant grass. Most CpWRKYs in the same group have similar structure and motif composition. A total of 169 duplicate gene pairs were identified, suggesting that segmental duplication might have contributed to the expansion of the CpWRKY gene family. Ka/Ks analysis revealed that most of the CpWRKYs were subjected to purifying selection during the evolution. It was also found that six genes (CpWRKY51, CpWRKY81, CpWRKY100, CpWRKY101, CpWRKY140 and CpWRKY143) exhibited higher expression in roots compare to leaves, and were significantly induced by low temperature stress. Among them, CpWRKY81 had the highest expression under low-temperature stress, and its over-expression significantly enhanced the cold tolerance in yeast. In this study, we characterized WRKY genes in elephant grass and further investigated their physicochemical properties, evolution, and expression patterns under low-temperature stress. This research provides valuable resources for identifying key CpWRKY genes that contribute to cold tolerance in elephant grass.

Genome-Wide Identification and Expression Analysis of the BTB Gene Superfamily Provides Insight into Sex Determination and Early Gonadal Development of Alligator sinensis.

The BTB gene superfamily is widely distributed among higher eukaryotes and plays a significant role in numerous biological processes. However, there is limited knowledge about the structure and function of BTB genes in the critically endangered species Alligator sinensis, which is endemic to China. A total of 170 BTB genes were identified from the A. sinensis genome, classified into 13 families, and unevenly distributed across 16 chromosomes. Analysis of gene duplication events yielded eight pairs of tandem duplication genes and six pairs of segmental duplication genes. Phylogenetics shows that the AsBTB genes are evolutionarily conserved. The cis-regulatory elements in the AsBTB family promoter region reveal their involvement in multiple biological processes. Protein interaction network analysis indicates that the protein interactions of the AsBTB genes are centered around CLU-3, mainly participating in the regulation of biological processes through the ubiquitination pathway. The expression profile and protein interaction network analysis of AsBTB genes during sex differentiation and early gonadal development indicate that AsBTB genes are widely expressed in this process and involves numerous genes and pathways for regulation. This study provides a basis for further investigation of the role of the BTB gene in sex differentiation and gonadal development in A. sinensis.

Comparative genomic analysis of pathogenic factors of Listeria spp. using whole-genome sequencing

Listeria monocytogenes is an important foodborne pathogen known for causing listeriosis. To gain insights into the pathogenicity, genetic characterization, and evolution of various Listeria species, in vitro cell adhesion and invasion ability assays and whole-genome sequencing were performed using four Listeria strains isolated from livestock and poultry slaughterhouses. The four Listeria strains exhibited adhesion and invasion abilities in Caco-2 and RAW264.7 cells. Pathogenic Liv1-1 and Lm2-20 had higher adhesion ability, but non-pathogenic Lin4-99 was more invasive than Lm2-20 (p < 0.05). Genetic characterization revealed the presence of a single chromosome without plasmid across four strains with similar whole-genome sizes and G + C% content. Analysis of key pathogenic genes underscored the presence of multiple virulence genes among the four Listeria strains. In contrast, non-pathogenic Listeria lacked LIPI-1, LIPI-2, and LIPI-3 genes, which could possibly be the cause of their non-pathogenicity despite their in vitro cell adhesion and invasion abilities. Thus, genetic determinants of Listeria do not necessarily predict cell adhesion and/or invasive ability in vitro. This study presents a comprehensive comparative genome-wide analysis of four Listeria strains, offering invaluable insights into the pathogenesis of the Listeria genus.

Genome-Wide Analysis of Potato CCT Family Genes and Its Response to Auxin Substances

The control of flowering time plays an important role in the growth and development of potato tubers. The CCT (CO, COL and TOC1) gene family is involved in the flowering process of plants. In this study, a total of 32 StCCT family genes were identified and further classified into five subfamilies, including COL (17 members), PRR (4 members), ZIM (3 members), ASML2 (6 members) and TCR1 (2 members), based on their phylogenetic relationship. An analysis of the gene structure, motif compositions and conserved domain provided support for this classification. The StCCT genes were unevenly distributed on 12 chromosomes of the potato plant. In total, six gene duplication events were observed, which played a crucial role in the expansion of the StCCT family genes in the potato. The expression profiles exhibited diverse expression patterns of the StCCT genes in six tissues (leaf, shoot, root, tuber, stolon, and flower), StCCT32 is only expressed in flowers, while StCCT19 and StCCT8 are highly expressed in flowers and tubers, respectively. The StCCT genes exhibit different expression patterns in response to IAA and TIBA treatments at different concentrations across three tissues (leaf, stem, and tuber). After IAA and TIBA treatments, it was found that the expression level of StCCT7 was low in leaves and stems but significantly increased in tubers. Collectively, this study provided valuable information for the further study of potato formation and development and provided candidate genes for molecular breeding in the potato.

Genome-wide characterization and expression analysis of WRKY transcription factors reveals biotic stress response potential mechanisms in Panax notoginseng

WRKY transcription factors (TFs), among the largest families of transcriptional regulators, are essential players in defense responses in plants. Panax notoginseng, a traditional and precious herbal medicine in China, is widely cultivated due to its excellent medicinal and edible value. However, P. notoginseng is frequently affected by various diseases (like Black blot disease, Root rot disease and Viral diseases). Therefore, the present study aimed to identify and characterize PnWRKYs in the P. notoginseng genome, reveal their structural attributes, regulatory elements, and potential functions in defense responses. 68 PnWRKY TFs that have conserved domains and different physicochemical characteristics were identified in the genome. They can be divided into four groups according to phylogenetic relationships and conserved domain structures. Furthermore, Group II WRKY TFs can be classified into five subgroups (IIa, IIb, IIc, IId, and IIe) according to their zinc finger-like motif. The PnWRKY family expands mainly via segmental duplication. Additionally, the promoter regions of PnWRKYs contain many hormone-responsive and stress-responsive elements. Expression patterns under different hormones (salicylic acid, methyl jasmonate, and melatonin) and disease (root rot disease, black blot disease, and virus disease) treatment analysis highlighted their wide involvement in plant hormone-induced disease defense responses. These findings affirmed the potential functions of PnWRKY TFs in disease-mediated defense responses and provided valuable insights for future agricultural applications.

Runs of Homozygosity Decipher Genetic Diversity in Cattle Breed Dwelling in the Colder Regions of the World

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia’s harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle. Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed. Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Elucidating the downstream pathways triggered by H2S signaling in Arabidopsis thaliana under drought stress via transcriptome analysis

ABSTRACT Hydrogen sulfide (H2S) is a crucial signaling molecule in plants. Recent studies have shown that H2S plays an equally important role as nitric oxide (NO) and hydrogen peroxide (H2O2) in plant signaling. Previous studies have demonstrated the involvement of H2S in regulating drought and other stressful environmental conditions, but the exact downstream molecular mechanisms activated by the H2S signaling molecule remain unclear. In this study, we conducted a comprehensive genome-wide transcriptomic analysis of both wild type (WT) and double mutant (lcd/des1). Arabidopsis thaliana plants were exposed to 40% polyethylene glycol (PEG) to induce drought stress and 20 µM sodium hydrosulfide (NaHS). The resulting transcriptome data were analyzed for differentially significant genes and their statistical enrichments in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The results indicated significant upregulation of genes related to photosynthesis, carbon fixation, plant secondary metabolite biosynthesis, inositol and phosphatidylinositol signaling pathways, and stress-responsive pathways in mutant plants under drought stress. Mutant plants with impaired H2S signaling mechanisms displayed greater susceptibility to drought stress compared to wild-type plants. In summary, all findings highlight the pivotal role of H2S signaling in stimulating other drought-responsive signaling pathways.

Identification and functional analysis of GmPsaL regulating pod color in vegetable soybean

BackgroundVegetable soybean is rich in nutrients and has a unique flavor. It is highly preferred by people because of its pharmacological activities, including those that regulate the intestines and lower blood pressure. The pod color of vegetable soybeans is an important quality that indicates their freshness and has a significant impact on their commercialization.ResultsIn this study, pod color was evaluated in 301 vegetable soybean accessions collected from various regions. Genome-wide association analysis was carried out using the Mixed linear model (MLM), a total of 18 quantitative trait loci including 117 SNPs were detected. Two significant QTLs located on chromosomes 6 (qGPCL4 /qGPCa1/qGPCb2) and 18 (qGPCL10/qGPCb3) were consistently detected across different variables. Based on gene functional annotation, 30 candidate genes were identified in these two candidate intervals. Combined with transcriptome analysis, Glyma.18g241700 has been identified as a candidate gene for regulating pod color in vegetable soybeans. Glyma.18g241700 encodes a chlorophyll photosystem I subunit XI. which localizes to the chloroplast named GmPsaL, qRT-PCR analysis showed that GmPsaL was specifically highly expressed in developing pods. Furthermore, overexpression of GmPsaL in transgenetic Arabidopsis plants produced dark green pods.ConclusionsThese findings may be useful for clarifying the genetic basis of the pod color of vegetable soybeans. The identified candidate genes may be useful for the genetic improvement of the appearance quality of vegetable soybeans.

Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

Genome-wide identification, characterization and expression pattern analysis of TIFY family members in Artemisia argyi

BackgroundPlant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value.ResultsA total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways.ConclusionTaken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.

Genomic variation of European beech reveals signals of local adaptation despite high levels of phenotypic plasticity

Local adaptation is key for ecotypic differentiation and species evolution. Understanding underlying genomic patterns can allow the prediction of future maladaptation and ecosystem stability. Here, we report the whole-genome resequencing of 874 individuals from 100 range-wide populations of European beech (Fagus sylvatica L.), an important forest tree species in Europe. We show that genetic variation closely mirrors geography with a clear pattern of isolation-by-distance. Genome-wide analyses for genotype-environment associations (GEAs) identify relatively few potentially adaptive variants after correcting for an overwhelming signal of statistically significant but non-causal GEAs. We characterize the single high confidence genomic region and pinpoint a candidate gene possibly involved in winter temperature adaptation via modulation of spring phenology. Surprisingly, allelic variation at this locus does not result in any apparent fitness differences in a common garden. More generally, reciprocal transplant experiments across large climate distances suggest extensive phenotypic plasticity. Nevertheless, we find indications of polygenic adaptation which may be essential in natural ecosystems. This polygenic signal exhibits broad- and fine-scale variation across the landscape, highlighting the relevance of spatial resolution. In summary, our results emphasize the importance, but also exemplify the complexity, of employing natural genetic variation for forest conservation under climate change.

Identification of Key Genes Controlling Sugar and Organic Acid Accumulation in Wampee Fruit (Clausena lansium) via Genome Assembly and Genome-wide Association Analysis.

Wampee (Clausena lansium) is an economically significant subtropical fruit tree widely cultivated in Southern China. To provide high-quality genomic resources for C. lansium, we report a chromosome-level genome sequence for the "JinFeng" cultivar. The 297.1 Mb C. lansium genome contained nine chromosomes with a scaffold N50 of 29.2 Mb and encoded 23,468 protein-coding genes. Selective sweep analysis between sweet and sour C. lansium varieties and genome-wide association analysis identified 14 candidate genes putatively involved in sugar and acid accumulation. ClERF061, encoding an ethylene response factor, and ClSWEET7, encoding a Sugars Will Eventually be Exported Transporters (SWEET) family protein, were proposed as key regulators of the sweet and sour tastes of the wampee fruit. ClERF061 and ClSWEET7 overexpression in tomatoes increased the total sugar and acid content in fruits. ClSWEET7 promoter activation by ClERF061 was confirmed via Nicotiana benthamiana transient expression. Our study provides valuable genomic resources for C. lansium genetics and breeding.