Genetic Structure Research Articles

Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan.

Africa is rich in wild species of Cucumis and is considered one of the origins of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analyzed the genetic structure of African melons, with emphasis on Sudan. Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR, and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan. African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian center of melon domestication. Large seed-type from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus, and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was the mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm that was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types. Melon of Ic lineage, including Tibish, originated from wild melon in the "western Sudan region," and independently of melon with Ia or Ib cytoplasm that originated in Asia. This clearly indicates the polyphyletic origin of melon.

First Report of Proctoeces maculatus (Digenea: Fellodistomidae) Infecting the Ribbed Mussel, Geukensia demissa: Detection of a Unique Haplotype in New England, USA.

Parasites play critical roles in ecosystems, influencing host populations and community dynamics. Despite their ecological significance, the diversity and genetic structure of parasites in the ribbed mussel, Geukensia demissa (Dillwyn), a key species in salt marsh ecosystems, remain poorly understood. This study provides the first record of the trematode Proctoeces maculatus (Looss, 1901) infecting G. demissa in the Herring River estuary, Cape Cod, Massachusetts. Among 50 mussels examined, P. maculatus prevalence was 66%, with infection intensities ranging from light (less than 20 sporocysts per individual) to over 300 sporocysts per individual. Heavily infected mussels displayed mantle discoloration, suggesting potential pathological impacts. Molecular analysis of the 28S ribosomal RNA gene identified a unique haplotype, GD1, restricted to G. demissa populations in Cape Cod. Haplotype network analysis revealed GD1's distinctiveness within P. maculatus populations, while genetic divergence (K2P: 0.001-0.003) indicated incipient host-associated differentiation rather than cryptic speciation. These findings highlight the role of ecological partitioning, such as the salt marsh-specific habitat of G. demissa, in shaping parasite genetic structure.

Genomic Analysis Reveals a New Cryptic Taxon Within the Anopheles gambiae Complex With a Distinct Insecticide Resistance Profile in the Coast of East Africa.

Anopheles mosquitoes are major malaria vectors, encompassing several species complexes with diverse life histories, transmission risks and insecticide resistance profiles that challenge malaria control efforts. This study investigated the genetic structure and insecticide resistance profiles of Anopheles gambiae complex mosquitoes in Tanzania. We analysed whole-genome sequence data of 300 mosquitoes collected between 2012 and 2015 across four regions in northern Tanzania and identified An. gambiae s.s., An. arabiensis and a distinct taxonomic group that was previously unknown. This distinct taxon has a unique profile of genetic diversity and appears restricted to the coastal region, and we refer to it as the Pwani molecular form. Analysis of insecticide resistance based on target-site mutations and copy number variations (CNV) showed that these markers were strikingly absent from the Pwani molecular form in contrast to other taxa. Our analysis also revealed a pattern of geographical isolation in the An. gambiae s.s. populations, with samples from the north-western site (Muleba) clustering separately from those collected in the north-eastern site (Muheza). These geographically isolated subpopulations also had differing resistance and selection profiles, with An. gambiae s.s. from the north-western site showing genomic evidence of higher resistance to pyrethroids compared with the north-eastern population. Conversely, An. arabiensis showed no geographical population structuring, with a similar insecticide resistance profile across all sampling locations, suggesting unrestricted gene flow. Our findings underscore the need to incorporate genetic data into malaria vector surveillance and control decisions and could inform the development and deployment of new interventions.

Fakta Kemanusiaan dan Subjek Kolektif dalam Film The Journey: Cerminan Struktur Sosial dalam Anime

<p><strong>The presence of anime, in addition to functioning as entertainment, often also reflects social structures through depictions of human reality and social identity, one of which is the anime The Journey. This anime presents a story in the context of Middle Eastern history and culture. This study aims to reveal how human facts and collective subjects are represented as a reflection of social structures in Anime. The research data are in the form of scenes, dialogues, and storylines of the anime film The Journey which was released in June 2021. The data collection technique was carried out using the listening and note taking technique. The results and discussion show that the anime The Journey depicts human facts and collective subjects Arab society through the social structure in the film. Through the genetic structuralism, prove that social structures in anime is not only fictional, but also a reflection of Arab society. This finding supports Lucien Goldmann's theory that literary works and popular culture can reflect social group. This study only focuses on two basic concepts of genetic structuralism, human facts and collective subjects. It is hoped that further research can continue research either with the same or different theories.<em></em></strong></p><p><strong><em>Keywords </em></strong><em>– Collective Subject, Genetic Structuralism, Human Facts.</em></p>

Population Genetic Diversity and Structure of Venturia carpophila on Peach and Almond in the U.S.A.

Scab of peach and almond is caused by Venturia carpophila but little is known regarding the population genetics of the pathogen, which aids understanding the epidemiology of the disease and guiding its management. Isolates (735) of V. carpophila were sampled from peach and almond orchards in the eastern U.S.A. and California, respectively. The aims were to determine population genetic diversity and structure of V. carpophila, compare populations of the pathogen from each host, and determine mating type ratios. Measures of gene and genotypic diversity indicated greater diversity among peach as compared to almond populations of the pathogen. Mating types were consistently at equilibrium (clone corrected) for populations from peach, but none of the populations from almond were at equilibrium. The MAT1-1-1 idiomorph was at low frequency or absent from almond populations. All populations on both peach and almond exhibited linkage disequilibrium. Analysis of molecular variance showed structure (71.8% of variance at the scale of the tree, and 25.3% at the scale of the geographic region, or crop). A discriminant analysis of principal components showed that the peach and almond populations clustered as independent groups. The results suggest that on peach in the southeastern U.S.A., V. carpophila is a sexually reproducing pathogen, but on almond in California, it is likely asexual. The confounded factors of geographic location and crop host may have both contributed to population differentiation. Although more research is needed, these results have implications for our understanding of the disease epidemiology and management in the two regions.

Genetic diversity and demography of Pteridium aquilinum (L.) Kuhn in Iran

Abstract Pteridium aquilinum, commonly known as bracken, is a fern species distributed in temperate and subtropical regions. In Iran, it primarily grows in isolated populations in the northern regions, and its genetic structure, gene flow and population genetics are not well understood. This study aimed to investigate gene flow and genetic diversity in 11 geographical populations of P. aquilinum in Iran for the first time. A total of 133 plants from different populations were examined, and both morphological and genetic diversity were assessed using start codon targeted (SCoT) molecular markers. Results showed genetic and morphological admixture within populations, likely due to the high mobility of dispersal units in this species. Significant genetic differences were found among populations, but a high degree of genetic variability was observed within individual populations. Additionally, there was a significant correlation between geographical and genetic distances, indicating gene flow between populations. The assignment test revealed genetic admixture among plants from different populations, and Gst analysis of SCoT loci yielded Nm = 0.95, confirming gene flow among the populations. Overall, this study demonstrates that the Iranian populations of P. aquilinum maintain substantial gene flow, which may contribute to the long-term survival and adaptability of this species in the region.

Genetic variation and molecular evolution of tomato yellow leaf curl China virus and its betasatellite DNA isolates in China

Tomato yellow leaf curl China virus (TYLCCNV) and its betasatellite DNA isolates (TYLCCNB), seriously threaten tomato crop production in China. The present work aimed to analyze the genetic diversity and population structure of TYLCCNV/TYLCCNB, collected from 168 leaf samples with apparent yellow and curly leaf disease symptoms in China. The study involves phylogenetic, recombination, and selection pressure analysis, based on the genome sequences of 57 TYLCCNV and 109 TYLCCNB isolates. It was found that the TYLCCNV/TYLCCNB populations collected from the same geographic regions exhibit a close relationship under phylogenetic analysis. The recombination analysis revealed 8 possible recombination sites in the TYLCCNV C1 and C4 genes, and 6 possible recombination sites in the TYLCCNB βC1 gene. The results showed that the TYLCCNV C4 gene was under positive selection pressure in the selection pressure analysis. Moreover, nucleotide and predicted amino acid sequence identities in C1 and C4 were significantly lower than other ORF region sequences. The lower gene flow and significant genetic differentiation between the geographic populations of Guangxi and Sichuan provinces suggested that environmental adaptation was an important evolutionary force in shaping the genetic structure of TYLCCNV/TYLCCNB. In addition, C1 and C4 ORFs of TYLCCNV were proved to be the major mutation regions in greenhouse and field inoculation experiments. A-rich region was the major mutant hot spot in the associated betasatellites such as TYLCCNB, TbCSB, and MYVB. A thorough investigation into the evolutionary factors affecting the population structure of TYLCCNV/TYLCCNB will provide vital information for systematic virus management.

Unveiling the heterosis pattern of modern maize breeding in Southwest China through population structure and genetic diversity analysis

Maize (Zea mays L.) is an important food crop throughout the world and is also one of the earliest crops to use heterosis. In this study, we evaluated the genetic diversity, population structure, and selective sweep of 100 elite inbred maize lines collected from the current breeding program in Sichuan province, Southwest China, using 5,261,175 high-quality single nucleotide polymorphisms (SNPs). We discovered an abundance of genetic diversities and classified them into four groups. By combining kinship relationships, these groups were further divided into Tropic-local A, Improved-tropic, Tropic-local B, and Improved-local. Genomic differentiation was assessed using Fst values (0.21–0.44) as well as genetic diversity (π = 6.07 × 10−4 − 6.61 × 10−4). We generated 900 (90 × 10) hybrids using 90 and 10 inbred maize lines from 100 diverse maize germplasms. All hybrids were evaluated for 10 traits in three replicate tests across two locations. We found that the patterns of G1 × G3, G1 × G4, G2 × G3, and G3 × G4 exhibited significant heterosis in yield-related traits and have been used in commercial breeding. In addition, we also explored the relationship between 10 traits of hybrid offspring and the number of heterozygous SNP. Under most heterosis modes, the best linear unbiased estimation (BLUE) value of the trait was highly consistent with the trend of deleterious SNPs, but there was a deviation in the G1 × G3 mode. Taken together, the results provide insight into the utilization of the current maize germplasm in Sichuan province to improve hybrid breeding.

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US.

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus, is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Mitochondrial genetic divergence of Chiton articulatus (Polyplacophora: Chitonida) in the Mexican Tropical Pacific

Context Chiton articulatus is a gonochoric, free-spawning mollusc with short-lived trochophore larvae inhabiting rocky shores along the fragmented and heterogeneous Mexican Tropical Pacific (MTP). Its limited dispersal in this patchy environment may lead to genetic divergence among populations. Aims Our objective was to characterise the genetic diversity and population structure of C. articulatus based on mitochondrial DNA. Methods We conducted a phylogeographic analysis using the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA collected from 100 C. articulatus organisms located across its geographic distribution. Key results The findings showed high levels of genetic diversity and a high number of private haplotypes. The structure analysis indicated six genetically distinct clusters with low connectivity. Divergence between the northern and southern populations was evident, with central mixing suggesting that gene flow adhered to the stepping-stone model. The historical demography indicated that the populations experienced sudden expansions during the late Pleistocene and early Holocene. Conclusions The northernmost and southernmost C. articulatus populations exhibit significant genetic divergence, suggesting the presence of distinct stocks in the MTP. Nevertheless, we recommend prioritising the conservation of central populations, as they serve as essential genetic reservoirs for all populations. Implications Our findings contribute to the broader understanding of how limited larval dispersal and habitat fragmentation shape population structure in marine invertebrates. The identification of distinct genetic stocks and central populations acting as genetic reservoirs underscores the importance of integrating genetic data into marine spatial planning and fisheries management. This research provides a framework for the conservation of other intertidal species with similar life histories in fragmented coastal environments.

Внутрипопуляционная генетическая дифференциация быков холмогорской породы Республики Коми по микросателлитам

The polymorphism of microsatellites was studied in 85 bulls – semen donors of the following breeds and types: the Kholmogory breed (38), the Holstein breed (10), the Pechora type of the Kholmogory breed (17), and the type obtained through crossing the Pechora type with the typical Kholmogory breed (20). Individuals were genotyped by 15 microsatellite loci. The largest number of specific alleles was revealed in the group of the Kholmogory breed bulls. The maximum genetic distance was identified between the Pechora-Kholmogory bulls and the Holstein bulls (DN 0.237, FST 0.045). The division of the entire array into two clusters in the program Strukture confirmed the high genetic differentiation between the crossed and purebred Pechora type bulls of the Kholmogory breed and the Holstein breed. The genetic difference between the Holstein and the typical Kholmogory breed was as high. The average probability of membership in the first cluster was 0.107±0.039, in the second cluster – 0.893±0.039 for Holstein bulls, 0.828±0.052 and 0.172±0.052 for Pechora type bulls of the Kholmogory breed, 0.860±0.019 and 0.140±0.019 for Pechora-Kholmogory bulls, and 0.633±0.046 and 0.367±0.046 for bulls of the typical Kholmogory breed, respectively. Information on number of effective alleles per locus, heterozygosity and fixation indices in animal groups of different genealogy and breeds did not provide any reliable and significant information on their intrapopulation genetic structure and differentiation that could be used in practical work to maintain the genetic diversity and reproduce the conserved gene pool of the breed. The cluster analysis at k=3 and k=4 allowed to identify and detail the structure and degree of genetic difference between groups and, thus, obtain additional information for planning and implementing gene pool conservation measures.

A rare variant in GPR156 associated with depression in a Mennonite pedigree causes habenula hyperactivity and stress sensitivity in mice

Major depressive disorder (MDD) is a leading cause of disability worldwide. Risk for MDD is heritable, and the genetic structure of founder populations enables investigation of rare susceptibility alleles with large effect. In an extended Old Order Mennonite family cohort, we identified a rare missense variant in GPR156 (c.1599G>T, p.Glu533Asp) associated with a two-fold increase in the relative risk of MDD. GPR156 is an orphan G protein-coupled receptor localized in the medial habenula, a region implicated in mood regulation. Insertion of a human sequence containing c.1599G>T into the murine Gpr156 locus induced medial habenula hyperactivity and abnormal stress-related behaviors. This work reveals a human variant that is associated with depression, implicates GPR156 as a target for mood regulation, and introduces informative murine models for investigating the pathophysiology and treatment of affective disorders.

Population genetic structure and demographic history of Dermacentor marginatus Sulzer, 1776 in Anatolia

Dermacentor marginatus is a medically important tick species due to its preference humans and domestic animals as hosts and its vectorial competence, yet it remains understudied in many regions. This study aimed to examine the population structure and demographic history of D. marginatus using the cox1 and ITS2 genes, focusing on populations from Central and Northeast Anatolia—two regions on either side of the Anatolian Diagonal, a natural biogeographical barrier. A total of 361 host-seeking adult D. marginatus ticks from 31 sampling sites were analyzed, revealing 131 haplotypes for cox1 and 104 genotypes for ITS2. Neutrality tests and mismatch distribution patterns rejected the null hypothesis of the neutral theory, indicating that the population of D. marginatus in Anatolia has undergone a recent demographic expansion. Significant genetic differentiation and population structuring were observed between the Central and Northeastern Anatolian populations of D. marginatus, correlating with geographic distance and suggesting that the Anatolian Diagonal acts as a potential barrier to gene flow. Intrapopulation gene flow was higher in Central Anatolian populations compared to Northeastern Anatolian populations. Bayesian phylogeny revealed a highly divergent D. marginatus haplotype within the Northeastern Anatolian population, clustering into a Central Asian clade. Additionally, phylogenetic trees of the subgenus Serdjukovia revealed taxonomic ambiguities, including the absence of a distinct clade for D. niveus and potential misidentifications of D. marginatus and D. raskemensis specimens. Furthermore, the monophyletic relationship between D. marginatus and D. raskemensis supports the likelihood of sympatric speciation. These findings enhance our understanding of the genetic structure, phylogeography, and evolutionary dynamics of D. marginatus while providing a framework for future research on tick populations.

Population genetic structure analysis of Anopheles kleini in the Republic of Korea based on the mitochondrial COI gene

BackgroundAnopheles kleini is a competent vector mainly observed in the northern, malaria-risk areas of the Republic of Korea (ROK). In this study, the population genetic structure of An. kleini was analysed for the first time in the ROK using the mitochondrial cytochrome c oxidase subunit I (COI) marker.MethodsThe genetic structure of 249 An. kleini was analysed from three statistically analysable regions, each including more than five mosquitoes.ResultsNetwork analysis identified 140 haplotypes organized into three clusters. Cluster II was related to An. kleini from eastern Russia and northwestern China. The pairwise genetic distance (FST) values among the populations showed regional genetic differences between Gangwon-do and Gyeonggi-do. Analysis of molecular variance (AMOVA) indicated that individual mosquitoes within the population had a significant influence on the total variation. The neutrality test, using three methods (Fu’s Fs, Fu, and Li’s D, and Fu and Li’s F), indicated that all values were negative, suggesting that An. kleini is an expanding population. Anopheles kleini in Yanggu has a significant difference in genetic distance from other regions.ConclusionThis study provides molecular epidemiologically information for understanding the spatial population structure of An. kleini and is helpful for malaria control in the ROK.

Variable time lags in genetic response of three temperate forest herbs to 70 years of agricultural landscape change

ContextAgriculture-driven land-use changes over the past decades have not only reduced the amount of habitat for species but also influenced the genetic exchange among the remaining fragmented populations. Many recent studies have found a delayed response in population genetic diversity and differentiation of species in fragmented habitats to past landscape disturbances, a so-called time lag. However, the specific role of species’ individual reproductive traits and the population genetic measures used remain poorly understood.ObjectivesWe examined the impact of past and current agricultural landscape composition in temperate Europe on the population genetic structure of three long-lived, slow-colonizing forest herb species – Anemone nemorosa, Oxalis acetosella and Polygonatum multiflorum, which vary in their reproductive traits.MethodsWe considered four time points in history (mid-1900s, 1985, 2000 and 2017) to identify the potentially different length of time that is needed by each species to respond to landscape change. We also explored the impact of using different genetic measures in quantifying the time lags.ResultsOur findings show that despite substantial landscape alterations about 70 years ago, the mid-1900s landscape composition was not reflected in the current genetic diversity and differentiation of the three species. This indicates a possible unexpected quick genetic adjustment of these species. Nevertheless, by combining the signals of multiple genetic measures, we found that O. acetosella, which reaches sexual maturity earlier than the other two species and is self-compatible, showed signs of faster genetic adjustment to these landscape changes. In contrast, A. nemorosa and P. multiflorum, which take longer to reach sexual maturity, might exhibit longer time lags that were beyond this study’s time frame.ConclusionsThis study underscores the importance of considering the species’ reproductive traits and especially the role of temporal scales of different genetic measures when investigating the impact of landscape history on current population genetic structures.

Population stratification in Northern shrimp (Pandalus borealis) off Iceland evident from RADseq analysis

The northern shrimp Pandalus borealis (ice. Stóri kampalampi) is a North Atlantic crustacean of significant commercial interest which has been harvested consistently in Icelandic waters since 1936. In Icelandic waters, the length at which this protandrous species transitions from male to female differs between the inshore and offshore populations, suggesting a biologically meaningful stratification which may or may not be plastic. Using reduced representative genomes assembled from RADseq data, sampled from 96 individuals collected at two time points (2018 and 2021), we compare the level of genetic structure across a gradient extending out of Skjálfandi bay, north Iceland. These data are compared to samples from a far offshore site, some 65 km out from the bay, as well as another inshore fjord in Arnarfjörður, in northwestern Iceland. Since 1999, no harvesting of inshore populations of P. borealis in Skjálfandi has been allowed due to stock decline, but harvesting of offshore stocks has continued. Uncertainty surrounding the extent of structure between the in- and offshore aggregations has remained. Here we report distinct genetic structure defining the inshore and offshore populations of northern shrimp, but find significant admixture between the two. Most importantly, we see that genetically inshore populations of northern shrimp extend far outside the harvest boundaries of inshore shrimp, and offshore individuals may exhibit punctuated migration into the inshore areas.

Molecular Characterization and Nutritional Regulation of Two Fatty Acid Elongase (elovl8) Genes in Chinese Perch (Siniperca chuatsi)

Proteins for elongation of very long-chain fatty acids (ELOVLs) are critical for the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), and they are one group of the rate-limiting enzymes responsible for the initial condensation reaction within the fatty acid elongation. Elovl8 is a newly identified member of the ELOVL protein family, and its evolutionary and functional characterizations are still rarely reported. Here, we identified two elovl8 paralogues (named Scelovl8 and Scelovl8b) from Chinese perch (Siniperca chuatsi), and then their molecular and evolutionary characteristics, as well as potential roles involved in LC-PUFA biosynthesis, were examined. The ORFs of both Scelovl8a and Scelovl8b genes were 810 bp and 789 bp in length, encoding proteins of 270 and 263 amino acids, respectively. Multiple protein sequence comparisons indicated that elovl8 genes were highly conserved in teleosts, showing similar structural function domains. Meanwhile, phylogenetic analysis showed that the elovl8 gene family was clustered into two subclades of elovl8a and elovl8b, and Scelovl8a and Scelovl8b shared close relationships with banded archerfish elovl8a and striped bass elovl8b, respectively. Genetic synteny and gene structure analyses further confirmed that elovl8b is more conserved in comparison to elovl8a in teleosts. In addition, Scelovl8a was found to be highly expressed in the liver, while Scelovl8b was most abundant in the gills. Long-term food deprivation and refeeding are verified to regulate the transcription of Scelovl8a and Scelovl8b, and intraperitoneal injection of fish oil (FO) and vegetable oil (VO) significantly modified their gene expression as well. In summary, our results in this study indicate that elovl8 genes were conservatively unique to teleosts, and both elovl8 genes might be involved in the endogenous biosynthesis of LC-PUFAs in Chinese perch. These findings not only expand our knowledge on the evolutionary and functional characteristics of both elovl8 genes but also lay a solid basis for investigating regulatory mechanisms of LC-PUFA biosynthesis in various teleosts.

Trans-ancestry GWAS identifies 59 loci and improves risk prediction and fine-mapping for kidney stone disease

Kidney stone disease is a multifactorial disease with increasing incidence worldwide. Trans-ancestry GWAS has become a popular strategy to dissect genetic structure of complex traits. Here, we conduct a large trans-ancestry GWAS meta-analysis on kidney stone disease with 31,715 cases and 943,655 controls in European and East Asian populations. We identify 59 kidney stone disease susceptibility loci, including 13 novel loci and show similar effects across populations. Using fine-mapping, we detect 1612 variants at these loci, and pinpoint 25 causal signals with a posterior inclusion probability >0.5 among them. At a novel locus, we pinpoint TRIOBP gene and discuss its potential link to kidney stone disease. We show that a cross-population polygenic risk score, PRS-CSxEAS&EUR, exhibits superior predictive performance for kidney stone disease than other polygenic risk scores constructed in our study. Relative to individuals in the third quintile of PRS-CSxEAS&EUR, those in the lowest and highest quintiles exhibit distinct kidney stone disease risks with odds ratios of 0.57 (0.51–0.63) and 1.83 (1.68–1.98), respectively. Our results suggest that kidney stone disease patients with higher polygenic risk scores are younger at onset. In summary, our study advances the understanding of kidney stone disease genetic architecture and improves its genetic predictability.

Molecular Analysis by Microsatellite Markers of Goji Plants (Lycium barbarum L.) Grown in Central Italy Reveal Genetic Distinction from Both L. barbarum and L. chinense Species

Lycium barbarum L. is a shrub native to China. It produces berries that are high in nutraceutical value. Its commercial appeal has led to the development of new plantations in Italy over recent decades. The majority of cultivated goji plants are derived from local nursery seedlings without the selection of varieties or clones. This study used nine simple sequence repeats (SSRs) from Lycium chinense L. to analyze the genetic structure and variability of heterogeneous, seed-derived accessions cultivated in an orchard located in central Italy (from here on referred to as field). The results were compared to accessions of known origin (LB, Lycium barbarum; LC, Lycium chinense). The study aimed to determine the genetic origin of seedlings and assess the feasibility of using microsatellite markers for individual fingerprinting. It also aimed to propagate the most adapted, productive plants while ensuring traceability and protection of potential clones throughout the production chain. The SSR markers used revealed that the field accessions were genetically distinct from both the L. barbarum and L. chinense accessions, whose seeds came from different European Botanical Gardens. The mean observed heterozygosity (Ho) across the three groups was 0.356, higher than the mean expected heterozygosity (He) of 0.314. The values of the inbreeding coefficient (FIS) ranged from −0.25 (field) to 0.05 (LC), confirming the high genetic variability in our dataset. The fixation index (FST) was 0.234, indicating medium to high genetic differentiation. The Bayesian analysis revealed three distinct clusters, indicating that three gene pools influenced the genetic structure of the studied populations. The orchard accessions form a distinct population, most likely a L. barbarum landrace, descended from two distinct ancestral populations that differ from the two known species. Our findings preliminarily lay the groundwork for the protection of some clonal lines of goji accessions for use in future planting more suited to the Mediterranean climate. This study also serves as a foundation for a more thorough characterization of cultivated L. barbarum, allowing for traceability and sustainable management of the genetic resource.

Exploring the genetic components and multi-omics sources of inflammatory bowel disease from the perspective of autoimmune disorders.

Inflammatory bowel disease(IBD) and autoimmune disorders result from immune system dysregulation. However, the genetic overlap between them remains unclear. Our study aimed to investigate the genetic mechanisms and structure of IBD from the perspective of autoimmune disorders. The genetic correlation (rg) between traits can provide valuable information about the shared underlying biological mechanisms. Utilizing summary statistics from genome-wide association studies, we delved into the genetic correlation, shared inheritance, and potential causality of IBD (N = 34,652) with autoimmune disorders (N = 1,755,610). We performed transcriptomics at the gene level, multi-marker analyses of genome annotations, and enrichment analyses of biological pathways to highlight shared and diverse perspectives. There were significant genetic correlations between IBD and ankylosing spondylitis (rg = 0.327), rheumatoid arthritis (rg = 0.242), type 1 diabetes (rg = - 0.061), psoriasis (rg = 0.246), and ankylosing spondylitis (rg = 0.308).We identified 110 unique regions(including 5p33.3, 10q25.3, and 22q13.31) after a consistent study at the gene levels. By implementing transcriptomics techniques, we discovered potential common biological mechanisms in several tissues, including blood, spleen, thyroid, and pancreas, revealing potential common biological mechanisms involving lincRNA, protein-coding, and pseudogenes. Our study demonstrated hypothesized pleiotropic genomic regions that provide important clues to delve into the genetic basis of IBD and autoimmune disorders on the basis of multi-omics. Moreover, we have identified shared pathogenic processes and potential common therapeutic targets among these diseases. Key Points • The finding provides a new perspective on the genetic basis of inflammatory bowel disease and autoimmune disease across multi-omics platforms. • Fine mapping of functional summary-based imputation and causal genomes has identified hypothesized pleiotropic genomic regions. • The identified genes and pathways may offer innovative targets for the prevention of immune-related diseases.