Genome-wide Single Nucleotide Polymorphism Data Research Articles

Protein quantitative trait loci identifies genetic biomarkers of proteins associated with measures of myocardial fibrosis in new-onset, treatment naive rheumatoid arthritis

Abstract Introduction The excess risk of cardiovascular disease (CVD) in patients with rheumatoid arthritis (RA) compared to the general population is attributed to chronic inflammation. Identifying the underlying mechanisms and shared inflammatory pathways more precisely would enable tailored treatment. Purpose To identify genetic variants associated with the cardio-metabolic-inflammatory proteomic signature in patients with early, treatment-naïve RA and low CVD risk. Methods The Coronary Artery Disease Evaluation in RA (CADERA) study was a bolt-on to a RCT of patients with early, treatment-naïve RA and low CVD risk profile (maximum of 1 traditional CVD risk factor and no diabetes mellitus). Normalised expression of 334 proteins from 75 CADERA patients who underwent cardiovascular magnetic resonance imaging (CMR) was measured using the Olink Proximity Extension Immunoassay across Inflammation, Cardiovascular II, III and Cardiometabolic panels. Genome-wide single nucleotide polymorphism (SNP) data were generated using the Illumina Global Screening Array and was imputed and checked for data quality using standard approaches. Proteins associated with CMR parameters were identified using Bayesian mixed effects linear regression. Protein quantitative trait locus (pQTL) analysis was then performed using linear regression models adjusted for age, gender, and systolic blood pressure. Cis-pQTLs were defined as SNPs within 1Mb of the protein-encoding gene, and significance threshold was set at 1e-5. Due to sample size, trans-pQTLs were not considered in this analysis. Linkage disequilibrium (LD) clumping was performed using PLINK software to identify index SNPs defined as the most significant variant in LD (r2 <0.5) within a region of +/- 250Kb. Results Following quality control 318 proteins and 5,971,781 SNPs were available for analysis in 75 CADERA patients. The median age was 51 years [inter-quartile range (IQR) 40 - 61] with 52/75 (69%) females, 40/75 (53%) current/ex-smokers, and median body mass index (BMI) 26.4kg/m2 (IQR 23.3 - 28). Participants had a median RA symptom duration of 21.9 weeks (IQR 14.4 - 32.7). Only 8/75 (10%) reported a history of hypertension, hypercholesteroaemia or family history of CVD. 54 out of 318 proteins were associated with CMR measures of myocardial fibrosis and/or vascular stiffness. 460 cis-pQTLs were identified for 20 out of the 318 proteins. LD clumping revealed 40 cis-pQTLs independently associated with these 20 proteins. Of these, NOTCH3 (rs34763630) was positively associated with extracellular volume, and SELPLG (rs7980427) was negatively associated with late gadolinium enhancement as detected on CMR (table 1). No other proteins with genetic support were associated with CMR measures. Conclusion This study for the first time, implicates genetic markers associated with two proteins as putative candidate biomarkers of CMR-identified myocardial fibrosis in new-onset RA that now warrant validation in an independent cohort.

Comparative Population Genomic Diversity and Differentiation in Trapdoor Spiders and Relatives (Araneae, Mygalomorphae).

Although patterns of population genomic variation are well-studied in animals, there remains room for studies that focus on non-model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome-wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within- and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small-bodied taxa. We also predicted greater genetic differentiation in small-bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation-by-distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species-rich animal clade.

Demographic history of Platypus quercivorus (Coleoptera: Curculionidae), a beetle causing mass mortality of oak trees, in eastern Japan

Abstract In recent years, Japanese oak wilt causing mass mortality of oak trees has exhibited a significant geographical expansion. Understanding the formation history of current local populations of Platypus quercivorus Murayama, a vector of Japanese oak wilt, is important foundational knowledge for effectively preventing forest damage. In this study, we used genome-wide single nucleotide polymorphism data to infer the population genetic structure and historical demography of P. quercivorus populations in eastern Japan, where Japanese oak wilt is rapidly expanding. We found at least 3 distinct genetic groups, each of which caused Japanese oak wilt in different areas. The supported scenario suggests that 1 of 2 genetic groups in the northeast first diverged from the ancestral population, then the other group diverged from the southwestern population, followed by gene flow between the 2 groups. Recent admixtures of the 2 northeastern groups were identified at certain sites. The geographic genetic structure of the populations suggested that each genetic group experienced recent range expansion. Although genetically independent populations had caused oak tree mass mortality in their original distribution range, our results support the hypothesis that the recent geographic expansion of Japanese oak wilt outbreaks is attributed to the range expansion of these P. quercivorus groups.

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens.

The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.

O-271 Two component resolution of mosaic samples in PGT-A: primary template amplification (PTA) and independent analysis using copy-number variation and allelic balance

Abstract Study question How does accurate, unbiased whole genome amplification and tiered, independent, two component analysis impact PGT-A results? Summary answer When compared to previous methods a PGT-A workflow utilizing PTA followed by a CNV and allelic balance-based analysis generated more conclusive results. What is known already Accurate PGT-A results require unbiased error-free whole genome amplification from the trophectoderm biopsy and smart bioinformatics utilities to fully analyze and consider the large complex datasets. PTA generates fewer errors, greater coverage, and reduced allele drop-out offering the best starting point to interpret the genome of each embryo. Current PGT-A platforms leverage either normalized CNV data OR allelic balance at single nucleotide polymorphisms (SNPs), to detect alterations in the embryonic genome. A pipeline leveraging improved amplification technology and consolidated CNV and SNP data, particularly for putative mosaic and segmental mosaic calls, could reduce uncertainty and provide more accurate PGT-A results. Study design, size, duration A retrospective analysis of PGT-A results was undertaken with samples originating from multiple clinics and processed in a single laboratory, from January through December, 2023. Approximately 500 samples were processed simultaneously through two independent PGT-A pipelines. The primary objective was to compare the performance of CNV-only PGT-A with a test leveraging both CNV and SNP data. A secondary objective was to observe the resolution of mosaic embryos. Participants/materials, setting, methods De-identified samples were amplified with PTA and sequenced with both shotgun (coverage-based CNV) and capture (SNP-based)-approaches. Method specific analysis was applied to the resulting data. An initial bioinformatics approach analyzed CNV data only for variations in copy-number along the genome, proposing stretches of aneuploidy or mosaicism. A second, tiered analysis extended this data and incorporated SNP-based allelic balance to evaluate candidate regions and confirm the presence of aneuploidy and/or quantify mosaic levels. Main results and the role of chance Genome-wide read coverage and SNP data confirmed that PTA accurately and completely amplified the genetic material in each sample with broad distribution of informative data and a low allele drop-out rate. High concordance (95%) was observed for euploid and full aneuploid (whole chromosome and segmental) embryos classified with CNV-alone and CNV/SNV combined analysis. SNP data was processed, and B-allele ratios were used to confirm aneuploidies with particular utility in resolving the location of segmental changes. The classification of mosaic samples was altered in the pipeline leveraging both CNV and SNP data. Of 54 mosaic samples tested, 75% remained mosaic after independent consideration of SNP data, ∼15% and 6% of high-level mosaics were resolved to full aneuploid and euploid, respectively, and ∼25% of low-level mosaics reverted to a euploid classification. The deep SNP data produced during targeted sequencing confirmed the altered allele ratio predicted by CNV data and re-confirmed the presence and proportion of aneuploid cells. Mosaic levels were highly correlated in 90% of re-confirmed mosaic samples. This suggests that the classification of these samples as mosaic is precise and accurate and suggests a strong utility for a two component PGT-A pipeline leveraging CNV and SNV data generated from PTA embryos. Limitations, reasons for caution This was a retrospective study with limited sample numbers. Wider implications of the findings The study highlights the strong advantages of a hybrid PGT-A pipeline, leveraging PTA and two component analysis of coverage and allelic balance, particularly to resolve mosaic embryos more accurately. Overall, this could reduce uncertainty and deliver more confident PGT-A results for embryo transfer decision making. Trial registration number not applicable

On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India.

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.

Shared Genetic Determinants of Schizophrenia and Autism Spectrum Disorder Implicate Opposite Risk Patterns: A Genome-Wide Analysis of Common Variants.

The synaptic pruning hypothesis posits that schizophrenia (SCZ) and autism spectrum disorder (ASD) may represent opposite ends of neurodevelopmental disorders: individuals with ASD exhibit an overabundance of synapses and connections while SCZ was characterized by excessive pruning of synapses and a reduction. Given the strong genetic predisposition of both disorders, we propose a shared genetic component, with certain loci having differential regulatory impacts. Genome-Wide single nucleotide polymorphism (SNP) data of European descent from SCZ (N cases = 53386, N controls = 77258) and ASD (N cases = 18381, N controls = 27969) were analyzed. We used genetic correlation, bivariate causal mixture model, conditional false discovery rate method, colocalization, Transcriptome-Wide Association Study (TWAS), and Phenome-Wide Association Study (PheWAS) to investigate the genetic overlap and gene expression pattern. We found a positive genetic correlation between SCZ and ASD (rg = .26, SE = 0.01, P = 7.87e-14), with 11 genomic loci jointly influencing both conditions (conjFDR <0.05). Functional analysis highlights a significant enrichment of shared genes during early to mid-fetal developmental stages. A notable genetic region on chromosome 17q21.31 (lead SNP rs2696609) showed strong evidence of colocalization (PP.H4.abf = 0.85). This SNP rs2696609 is linked to many imaging-derived brain phenotypes. TWAS indicated opposing gene expression patterns (primarily pseudogenes and long noncoding RNAs [lncRNAs]) for ASD and SCZ in the 17q21.31 region and some genes (LRRC37A4P, LINC02210, and DND1P1) exhibit considerable variation in the cerebellum across the lifespan. Our findings support a shared genetic basis for SCZ and ASD. A common genetic variant, rs2696609, located in the Chr17q21.31 locus, may exert differential risk regulation on SCZ and ASD by altering brain structure. Future studies should focus on the role of pseudogenes, lncRNAs, and cerebellum in synaptic pruning and neurodevelopmental disorders.

The role of historical biogeography in shaping colour morph diversity in the common wall lizard.

The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.

Phylogenetic relationships of Quercus species (Fagaceae) in Vietnam based on multiplexed inter simple sequence repeat genotyping by sequencing

Quercus is the largest genus of the family Fagaceae in the world and the second-largest in Vietnam, with approximately 50 species. However, the phylogeny study of the Quercus genus in Vietnam has yet to be thoroughly explored. In this study, we utilize the genome-wide single-nucleotide polymorphisms (SNPs) data obtained through Multiplexed Inter Simple Sequence Repeat Genotyping by sequencing (MIG-seq) to explore the phylogenetic relationships among Quercus species in Vietnam. The results of this study reveal that all Quercus species in Vietnam belong to subgenus Cerris and the phylogenetic analysis strongly supports the recognition of two infrageneric sections: Quercus and Ilex section for the Vietnamese Quercus. These results also confirm that the monophyly of Quercus in Vietnam is strongly supported by both morphological and molecular data. The results of this study also align entirely with previous research, indicating that Quercus species in Asia fall under the subgenus Cerris, comprising two sections: section Ilex and section Cyclobalanopsis.

Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)

Abstract Crescent butterflies of the Phyciodes tharos group have a long-standing reputation for taxonomic difficulty. We assessed species boundaries in the P. tharos group using genome-wide single-nucleotide polymorphism (SNP) data, focusing on sampling in western Canada, where 4 species (P. tharos, P. cocyta, P. batesii, and P. pulchella) have classically been recognized. Phylogenetic and cluster-based analyses confirm that there are indeed 4 species based on the maintenance of genomic integrity in the presence of occasional hybridization and low levels of gene flow. Mitochondrial cytochrome c oxidase I (COI) does not consistently distinguish species, with haplotypes extensively shared between species. Limited sampling of P. batesii indicates complex boundaries and interactions with other Phyciodes, especially with P. pulchella and P. cocyta. This study demonstrates the power of a genome-wide perspective to elucidate the integrity of boundaries between recently diverged species that remain capable of occasional hybridization.

Genomics Research of Lifetime Depression in the Netherlands: The BIObanks Netherlands Internet Collaboration (BIONIC) Project.

In this cohort profile article we describe the lifetime major depressive disorder (MDD) database that has been established as part of the BIObanks Netherlands Internet Collaboration (BIONIC). Across the Netherlands we collected data on Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) lifetime MDD diagnosis in 132,850 Dutch individuals. Currently, N = 66,684 of these also have genomewide single nucleotide polymorphism (SNP) data. We initiated this project because the complex genetic basis of MDD requires large population-wide studies with uniform in-depth phenotyping. For standardized phenotyping we developed the LIDAS (LIfetime Depression Assessment Survey), which then was used to measure MDD in 11 Dutch cohorts. Data from these cohorts were combined with diagnostic interview depression data from 5 clinical cohorts to create a dataset of N = 29,650 lifetime MDD cases (22%) meeting DSM-5 criteria and 94,300 screened controls. In addition, genomewide genotype data from the cohorts were assembled into a genomewide association study (GWAS) dataset of N = 66,684 Dutch individuals (25.3% cases). Phenotype data include DSM-5-based MDD diagnoses, sociodemographic variables, information on lifestyle and BMI, characteristics of depressive symptoms and episodes, and psychiatric diagnosis and treatment history. We describe the establishment and harmonization of the BIONIC phenotype and GWAS datasets and provide an overview of the available information and sample characteristics. Our next step is the GWAS of lifetime MDD in the Netherlands, with future plans including fine-grained genetic analyses of depression characteristics, international collaborations and multi-omics studies.

DdRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations

Turkey oak (Quercus cerris L.) is one of the most ecologically and economically significant deciduous tree species in the Central and Southeast European regions. The species has long been known to exhibit high levels of genetic and phenotypic variation. Recent climate response predictions for Turkey oak suggest a significant distribution extension in Europe under climate change. Since Turkey oak has relative drought-tolerant behaviour, it is regarded as a potential alternative for other forest tree species during forestry climate adaptation efforts, not only in its native regions but also in Western Europe. For this reason, the survey of existing genetic variability, genetic resources, and adaptability of this species has great significance. Next-generation sequencing approaches, such as ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow the attainment of high-resolution genome-wide single nucleotide polymorphisms (SNPs). This study provides the first highly variable genome-wide SNP data for Turkey oak generated by ddRAD-seq. The dataset comprises 17 607 de novo and 26 059 reference mapped SNPs for 88 individuals from eight populations, two from Bulgaria, one from Kosovo, and five from Hungary. Reference mapping was carried out by using cork oak’s (Quercus suber L.) reference genome. The obtained high-resolution genome-wide markers are suitable for investigating selection and local adaptation and inferring genetic diversity, differentiation, and population structure. The dataset is accessible at: https://doi.org/10.5281/zenodo.8091252

Modification of Huntington's disease by short tandem repeats.

Expansions of glutamine-coding CAG trinucleotide repeats cause a number of neurodegenerative diseases, including Huntington's disease and several of spinocerebellar ataxias. In general, age-at-onset of the polyglutamine diseases is inversely correlated with the size of the respective inherited expanded CAG repeat. Expanded CAG repeats are also somatically unstable in certain tissues, and age-at-onset of Huntington's disease corrected for individual HTT CAG repeat length (i.e. residual age-at-onset), is modified by repeat instability-related DNA maintenance/repair genes as demonstrated by recent genome-wide association studies. Modification of one polyglutamine disease (e.g. Huntington's disease) by the repeat length of another (e.g. ATXN3, CAG expansions in which cause spinocerebellar ataxia 3) has also been hypothesized. Consequently, we determined whether age-at-onset in Huntington's disease is modified by the CAG repeats of other polyglutamine disease genes. We found that the CAG measured repeat sizes of other polyglutamine disease genes that were polymorphic in Huntington's disease participants but did not influence Huntington's disease age-at-onset. Additional analysis focusing specifically on ATXN3 in a larger sample set (n = 1388) confirmed the lack of association between Huntington's disease residual age-at-onset and ATXN3 CAG repeat length. Additionally, neither our Huntington's disease onset modifier genome-wide association studies single nucleotide polymorphism data nor imputed short tandem repeat data supported the involvement of other polyglutamine disease genes in modifying Huntington's disease. By contrast, our genome-wide association studies based on imputed short tandem repeats revealed significant modification signals for other genomic regions. Together, our short tandem repeat genome-wide association studies show that modification of Huntington's disease is associated with short tandem repeats that do not involve other polyglutamine disease-causing genes, refining the landscape of Huntington's disease modification and highlighting the importance of rigorous data analysis, especially in genetic studies testing candidate modifiers.

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China.

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Contrasting patterns of genetic structure and population demography in two Dicraeus species feeding on bamboo flowers in Japan

Abstract Population outbreaks of insects provide an excellent opportunity to elucidate their evolutionary history. In this study, we uncovered the phylogenetic relationships of Dicraeus spp. in Japan and compared the population genetic structure of two bamboo-feeding Dicraeus spp., Dicraeus phyllostachyus and Dicraeus nartshukae, by leveraging a recent nationwide mass flowering event of several bamboo species in Japan. We performed analysis using mitochondrial COI gene sequencing and genome-wide single-nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). We found genetic similarity in COI haplotypes over a large geographical range in the two Dicraeus spp., but, for both species, no concordance was detected between the collected host plants and genetic structures. In the genome-wide single-nucleotide polymorphism data, no clear genetic clusters were detected for D. phyllostachyus populations, whereas D. nartshukae populations were divided into two groups, in the north and south of Japan. Demographic analysis indicated that D. phyllostachyus had greatly expanded its population recently compared with D. nartshukae. These contrasting patterns between the two species might reflect the differences in the demographic history between the species. Our study suggested that the mass flowering event might cascade to the genetic structure of the florivorous insects through trophic interactions.

The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data

BackgroundThe presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions.ResultsThe diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods.ConclusionsThis genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.

Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus).

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

Evidence for selfing in a vertebrate from whole-genome sequencing.

A growing number of recent genomic studies report asexual parthenogenetic reproduction in a wide range of taxa, including vertebrate species from the reptile, bird, and fish lineages. Yet, self-fertilization (selfing) has been recorded only in a single vertebrate, the mangrove killifish Kryptolebias marmoratus In cichlid fishes, sex determination is notably diverse and can be influenced by the environment, and sequential hermaphroditism has been reported for some species. Here, we present evidence for a case of facultative selfing in the cichlid fish Benitochromis nigrodorsalis, which is otherwise known as biparentally reproducing ovophilic mouthbrooder from Western Africa. Our laboratory observations revealed that a wild-caught individual produced repeatedly viable offspring in absence of a mating partner. By analyzing genome-wide single-nucleotide polymorphism (SNP) data, we compare that individual and two of its offspring to shed light on its reproductive mode. First, our results confirm uniparental reproduction. Second, overall heterozygosity is reduced in the offspring compared with outbred individuals. Retained maternal heterozygosity in the offspring is ∼51%, which is close to the theoretically expected value of a heterozygosity reduction of 50% by selfing. Heterozygosity patterns along individual chromosomes do not point to alternative parthenogenetic reproductive mechanisms like automixis by terminal or central fusion. Facultative selfing may represent an adaptive strategy ensuring reproduction when mating partners are absent and, hence, contribute to the cichlids' enormous evolutionary success.

Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population.

The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and . Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (NKAIN2, IGF1R, KISS1R, TYRO3, SPINT1, ADGRF5, APC2, PTBP1, CLCN3, CBR4, HPF1, FAM174A, SCP2, CLIC1, ZFYVE9, SPATA33, KIF5C, EPC2, GABRA2, and GABRA4) were identified. These findings provide novel insights into the genetic basis of pig litter traits and will be helpful for improving the reproductive performances of sows in pig breeding.