Genetic Structure Research Articles

Genetic structure and pyrimethanil resistance of Botrytis spp. causing gray mold on strawberry from greenhouses in Zhejiang, China

Gray mold caused by Botrytis spp. is a common disease on various hosts, including strawberries. In this study, we obtained 59 Botrytis isolates from strawberries from greenhouses in Zhejiang Province, China. Identification of the sampled isolates at species level was performed by a duplex PCR assay method, the result showed that, in Zhejiang, gray mold on strawberry fruits is caused by a complex of Botrytis groups including B. cinerea group N (47.5 %) and B. cinerea group S (52.5 %). The sensitivities of all Botrytis isolates to pyrimethanil were determined based on discriminatory dose method on L-asparagine-based agar medium plate. Our results showed that the isolates obtained from the greenhouses with continuous use of pyrimethanil developed severe resistance to pyrimethanil, and the resistance frequencies of B. cinerea group N and group S isolates were 89.3 % and 41.9 %, respectively. By sequencing, four different resistance-related point mutations were identified in 38 Botrytis isolates: Bcpos5L412F (16 isolates, 42.1 %), Bcpos5L412V (14 isolates, 36.8 %), Bcmdl1E407K (2 isolates, 5.3 %), and Bcpos5L412S⸱Bcmdl1E407K (1 isolate, 2.6 %). The exogenous addition of methionine could not completely alter the resistance of Botrytis isolates to pyrimethanil. In this study, the pyrimethanil resistance in Botrytis isolates was steadily inherited, and compared to the pyrimethanil-sensitive isolates, the resistant mutants exhibited good fitness in sporulation capacity, spore germination rate, and virulence on strawberries. In conclusion, our results provided a description of the genetic structure of Botrytis groups complex on strawberry fruits and reminded growers to focus on the stable pyrimethanil resistance in Botrytis isolates, caused by point mutations in BcPos5 and BcMdl1.

Introduced Herbivores Threaten the Conservation Genetics of Two Critically Endangered Single-Island Endemics, Crambe sventenii and Pleudia herbanica.

Crambe sventenii Pett. ex Bramwell & Sunding and Pleudia herbanica (A.Santos & M.Fernández) M.Will, N.Schmalz & Class.-Bockh. are two single-island endemic species from Fuerteventura (Canary Islands), inhabiting the same areas and similar habitats. They are under the "Critically Endangered" category due to historical herbivore pressure, mainly goats, leading to habitat fragmentation and poor population recruitment. The main aim of our study was to provide insights into the conservation genetics and habitat suitability of these two species. For this purpose, we sampled all known populations on the island and developed two new sets of microsatellite markers. Moreover, to assist restoration plans, we performed species distribution models to determine the most suitable areas for reintroduction. While Crambe sventenii is highly fragmented, with low genetic diversity indices in some populations, Pleudia herbanica's genetic structure is quite homogeneous, grouped in three main regions, with signs of inbreeding and an overall low genetic diversity. Both species could present moderate to high levels of autogamy. Our findings can provide guidance to local governments regarding conservation actions to be implemented in the field, like the identification of propagule sources and new suitable areas for restoration.

309 Synergistic optimization: Utilizing genomic insights to enhance strategies for joint selective (deep) phenotyping and recursive creation of genomic reference populations - Sponsored by EAAP

Abstract Synergistic optimization is a process combining different elements achieving better results than would be possible by optimizing each element individually. Our objective will be to design systems where genotyping and phenotyping complement each other to achieve superior performance. Deep phenotyping can be defined as a comprehensive and detailed approach to characterize traits of animals, including those based on the study of intermediate phenotypes representing not only the phenome, but also e.g., the metabolome, the proteome, and the transcriptome (i.e., -omics phenotypes). Often these phenotypes are also called high-throughput but this should not be considered being a synonym for being cheap. Interplay between genotyping and (deep) phenotyping has a major impact on the acquisition of genetic knowledge but could also be used in the context of genomic evaluations (i.e., as intermediate correlated features such as high-throughput or -omics phenotypes). While past studies have largely focused on ways to integrate deep phenotyping to gain new knowledge but also to support genetic and genomic evaluations, phenotyping and especially deep phenotyping currently requires massive investment, limiting its effective and widespread use under field, but also in experimental conditions. This problem extends to complex phenotype-taking as feed intake, methane emissions or in general use of expensive sensors. Even with all the possible investments, many phenotyping efforts are limited by the poor choice of animals. This presentation will address and introduce the topic of genome-enabled optimization of (deep) phenotyping taking into account the facts that genotypes are in many cases much cheaper than phenotyping, can be performed at early stages, and can help organize animal sampling in an efficient manner. The last point is also linked to validation techniques comparing predicted to observed phenotypes and closely related to recursive genomic reference population building issues. Techniques used in other fields such as chemometrics (i.e., infrared spectra prediction building) will be proposed to optimize covering genetic variability. In the context of recursively performed genomic evaluations (i.e., increasing reference population at each round) population accuracy and bias of prediction will be addressed. Moreover, long term genetic contribution and population structure issues will have to be considered. Based on literature and practical examples systematically organized sampling techniques will be presented to discuss basic principles as covering observed genomic and expected phenotypic diversity and long-term effects of recursively created genomic reference populations.

Genetic resources of African mahogany in Brazil: genomic diversity and structure of forest plantations

BackgroundAfrican mahogany species (Khaya sp.) have been introduced to Brazil gaining increasing economic interest over the last years, as they produce high quality wood for industrial applications. To this date, however, the knowledge available on the genetic basis of African mahogany plantations in Brazil is limited, which has driven this study to examine the extent of genetic diversity and structure of three cultivated species (Khaya grandifoliola, Khaya senegalensis and Khaya ivorensis) and their prospects for forest breeding.ResultsIn total, 115 individuals were genotyped (48 of K. grandifoliola, 34 of K. senegalensis and 33 of K. ivorensis) for 3,330 filtered neutral loci obtained from genotyping-by-sequencing for the three species. The number of SNPs varied from 2,951 in K. ivorensis to 4,754 in K. senegalensis. Multiloci clustering, principal component analysis, Bayesian structure and network analyses showed a clear genetic separation among the three species. Structure analysis also showed internal structure within each species, highlighting genetic subgroups that could be sampled for selecting distinct genotypes for further breeding, although the genetic distances are moderate to low.ConclusionIn our study, SNP markers efficiently assessed the genomic diversity of African mahogany forest plantations in Brazil. Our genetic data clearly separated the three Khaya species. Moreover, pairwise estimates of genetic distances among individuals within each species showed considerable genetic divergence among individuals. By genotyping 115 pre-selected individuals with desirable growth traits, allowed us not only to recommend superior genotypes but also to identify genetically distinct individuals for use in breeding crosses.

Genetic diversity and population structure of wild Salvia miltiorrhiza in China revealed by microsatellite markers and implication for conservation

AbstractSalvia miltiorrhiza is an outcrossing and perennial herb native to China. Although well-known for its medicinal value, there is a lack of knowledge regarding its natural population genetics. Here, we used 12 microsatellite markers to investigated population genetic diversity and structure of 215 samples from populations naturally distributed in central eastern China. A moderate level of genetic diversity was detected probably due to the over-mining of its roots. The allelic richness (AR) ranged from 3.034 to 4.889 with an average of 3.891. Moreover, pairwise estimates of FST among the populations of S. miltiorrhiza varied from 0.036 to 0.312 and two clusters were obtained by STRUCTURE and discriminant analysis of principal components. It is likely that the genetic differentiation of these two clusters was formed during glacial periods. Our result provides insights into the conservation of this valuable medicinal plant.

Assessment of Population Genetic Diversity of Medicinal Meconopsis integrifolia (Maxim.) Franch. Using Newly Developed SSR Markers.

Meconopsis integrifolia is an endangered Tibetan medicinal plant with significant medicinal and ornamental value. Understanding its genetic diversity and structure is crucial for its sustainable utilization and effective conservation. Here, we develop a set of SSR markers based on transcriptome data to analyze the genetic diversity and structure of 185 individuals from 16 populations of M. integrifolia. The results indicate that M. integrifolia exhibits relatively high genetic diversity at the species level (the percentage of polymorphic bands PPB = 91.67%, Nei's genetic diversity index He = 0.2989, Shannon's information index I = 0.4514) but limited genetic variation within populations (PPB = 12.08%, He = 0.0399, I = 0.0610). The genetic differentiation among populations is relatively high (the coefficient of gene differentiation GST = 0.6902), and AMOVA analysis indicates that 63.39% of the total variation occurs among populations. This suggests that maintaining a limited number of populations is insufficient to preserve the overall diversity of M. integrifolia. Different populations are categorized into four representative subclusters, but they do not cluster strictly according to geographical distribution. Limited gene flow (Nm = 0.2244) is likely the main reason for the high differentiation among these populations. Limited seed and pollen dispersal abilities, along with habitat fragmentation, may explain the restricted gene flow among populations, highlighting the necessity of conserving as many populations in the wild as possible.

JointPRS: A Data-Adaptive Framework for Multi-Population Genetic Risk Prediction Incorporating Genetic Correlation.

Genetic prediction accuracy for non-European populations is hindered by the limited sample size of Genome-wide association studies (GWAS) data in these populations. Additionally, it is challenging to tune model parameters with a small tuning dataset for methods that require tuning data, which is often the case for non-European samples. To address these challenges, we propose JointPRS, a novel, data-adaptive framework that simultaneously models multiple populations using GWAS summary statistics. JointPRS incorporates genetic correlation structures into the prediction framework, enabling accurate performance even without individual-level tuning data. Additionally, it uniquely employs a data-adaptive approach, providing a robust solution when only a small tuning dataset is available. Through extensive simulations and real data applications to 22 quantitative traits and four binary traits in five continental populations (European (EUR); East Asian (EAS); African (AFR); South Asian (SAS); and Admixed American (AMR)) evaluated using the UK Biobank (UKBB) and All of Us (AoU), we demonstrate that JointPRS outperforms six other state-of-art methods across three different data scenarios (no tuning data, tuning and testing data from the same cohort, and tuning and testing data from different cohorts) for most traits in non-European populations, while maintaining model simplicity and computational efficiency.

Analysis of the Genetic Diversity and Genetic Structure of Jiangshan Black Pigs Using Single Nucleotide Polymorphism (SNP) Chips.

The Jiangshan black pig is an indigenous pig breed in China, renowned for its superior meat quality and adaptability to roughage. However, the population of Jiangshan black pigs has dwindled due to the introduction of cosmopolitan pig breeds and the outbreak of African swine fever, putting them at risk of extinction. To offer insights into the conservation and breeding of Jiangshan black pigs, this study involved 118 Jiangshan black pigs as the research subjects and employed the Zhongxin-1 Porcine Breeding Array PLUS chip to detect whole-genome SNPs. Additionally, various software tools were utilized to accurately analyze the genetic diversity, phylogenetic relationship, inbreeding coefficient, and pedigree structure of the Jiangshan black pig conservation population. The findings indicated that the effective population size (Ne) of the Jiangshan black pig was 4.9, with an average inbreeding coefficient of 0.253 within the population. A genetic relationship analysis identified that the 16 male pigs were clustered into four families, and the 100 female pigs were also assigned to these familial groups. Furthermore, two female pigs were classified as "other" due to their distant genetic relatedness to all the males. These results contribute to a better understanding of the current status of the conservation of the Jiangshan black pig population and offer a theoretical foundation for the development of conservation strategies.

Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range.

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC-RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0-58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts.

Assessment of the Genetic Diversity of the Monogenean Gill Parasite Lamellodiscus echeneis (Monogenea) Infecting Wild and Cage-Reared Populations of Sparus aurata (Teleostei) from the Mediterranean Sea.

The diplectanid monogenean Lamellodiscus echeneis (Wagener, 1857) is a specific and common gill parasite of the gilthead seabream Sparus aurata Linnaeus, 1758, in the Mediterranean Sea. Few isolated molecular studies of this monogenean have been conducted, and its population structure and genetic diversity are poorly understood. This study represents the first analysis of the population genetics of L. echeneis, isolated from wild and cage-reared gilthead seabream from fifteen localities in both the Southern (Tunisia) and Northern (Italy and Spain) regions of the Mediterranean Sea, using nuclear ITS rDNA markers and a partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI). The phylogenetic trees based on the newly obtained dataset and the previously published sequences of L. echeneis corroborated the spread of only a single species throughout the Mediterranean Sea. The star-like haplotypes network, inferred by COI sequences, suggested a recent population expansion of L. echeneis. This is supported by the observed high haplotype diversity (Hd = 0.918) and low nucleotide diversity (Pi = 0.01595). Population structure-based AMOVA for two groups (the Adriatic Sea and the rest of the Mediterranean Sea) attributed 35.39% of the total variation to differences within populations, 16.63% to differences among populations within groups, and 47.99% to differences among groups. Fixation indices were significant, with a high FST value (0.64612), likely related to the divergence of the parasite populations from the Adriatic Sea and other Mediterranean regions. Phylogenetic analyses grouped all samples into the main clade corresponding to L. echeneis from several localities. This study provides insight into the genetic variation between L. echeneis populations, and did not show a clear genetic structure between populations of L. echeneis throughout Tunisian, Italian, and Spanish localities, which can be attributed to the considerable gene flow between the populations favoured by the potential for host dispersion within the Mediterranean Sea. Finally, haplotypes shared between wild and cage-reared hosts provided evidence for the potential for cross-infection between wild and farmed hosts in the Mediterranean Sea.

Geographic patterns and ecological adaptations of Manila clam (Ruditapes philippinarum) along the Chinese coast: Insights from migration dynamics and gene flow

The Manila Clam (Ruditapes Philippinarum) is one of the most economically significant marine bivalves along the China coast. In recent years, due to the escalating scale of aquaculture, the artificial activities of "cross-regional introduction" have to some extent exerted an influence on the genetic diversity and structure of clam larvae, leading to an ongoing occurrence of genetically mixed clam larvae populations and ambiguous genetic foundation of germplasm resources in China. Therefore, there is an imperative need to gain profound insights into the lineage, genetic structure, and assess the adaptability potential of clams originating from both northern and southern regions. We use Specific Locus Amplified Framents technology to simplify genome sequencing of wild clams along the coast of China. Through genetic diversity, genetic structure, gene flow, and selection elimination analysis, the results show that clams can be divided into distinct north-south lineages, with Wafangdian in Liaoning (RPLW), Zhangzi Island in Liaoning (RPLZ), and Laizhou in Shandong (RPSL) comprise the northern lineage, while Lianjiang in Fujian (RPFL) constitutes the southern lineage. The artificial relocation of clams in China has resulted in a blended population structure among local clams. The genetic functional differences between clams from the north and south are primarily manifest in energy metabolism, and the adaptive evolution of clams is mainly associated with temperature. This integrative research not only furnishes valuable insights into the genetic structure of clam populations, thereby contributing to the advancement of natural conservation and genetic breeding efforts for clams but also establishes the groundwork for a comprehensive exploration of clam adaptive evolution.

Genetic structure, selective characterization and specific molecular identity cards of high-yielding Houdan chickens based on genome-wide SNP

The high-yielding Houdan chicken (GGF) is characterized by high egg production and disease resistance. This study conducted whole genome resequencing of the GGF population and compared it to data from other breeds. Genetic diversity analysis revealed higher observed heterozygosity (Ho), Polymorphism information content (PIC), number of runs of homozygosity (ROH), and inbreeding coefficient (FROH) in GGF. Linkage disequilibrium (LD) decay was slowest in GGF, indicating intensive inbreeding and strong selection. These findings suggest a need for appropriate strategies to enhance genetic diversity conservation in this breed. Population structure analysis demonstrated that GGF was genetically distinct from both the red jungle fowl (RJF) and Chinese indigenous chicken (CIC) populations, highlighting GGF as a unique genetic resource warranting intensive protection and utilization. Selective sweep analysis identified genes under selection in GGF, primarily enriched in signaling pathways related to oocyte meiosis and progesterone-mediated oocyte maturation. Key candidate genes included: CCNE1, SKP1, CDC20, CDK2, ADCY8, RPS6KA6, PPP3CB, PDE3B, HSP90AB1, and AKT3. These findings provide a theoretical foundation for their potential application in poultry breeding. Additionally, this study combined bioinformatics analysis with PCR amplification and Sanger sequencing to identify 4 SNPs that can serve as a molecular identity card (ID) for GGF: SNP1 (Chr2: 136130976), SNP3 (Chr4:11705164), SNP4 (Chr4: 63255588), and SNP5 (Chr24: 3271008). This study provides a scientific basis for effective management and conservation of GGF genetic resources, and establishes a simple, economical, and accurate set of molecular IDs to combat the proliferation of inferior breeds and protect genetic resources.

Identification of a Novel β-Defensin Gene in Gilthead Seabream (Sparus aurata)

The excessive use of antibiotics in aquaculture favors the natural selection of multidrug-resistant bacteria, and antimicrobial peptides (AMPs) could be a promising alternative to this problem. The most studied AMPs in teleost fish are piscidins, hepcidins, and β-defensins. In this work, we have found a new gene (defb2) encoding a type 2 β-defensin in the genome of gilthead seabream, a species chosen for its economic interest in aquaculture. Its open reading frame (192 bp) encodes a protein (71 amino acids) that undergoes proteolytic cleavage to obtain the functional mature peptide (42 amino acids). The genetic structure in three exons and two introns and the six characteristic cysteines are conserved as the main signature of this protein family. In the evolutionary analysis, synteny shows a preservation of chromosomal localization and the phylogenetic tree constructed exposes the differences between both types of β-defensin as well as the similarities between seabream and European seabass. In relation to its basal expression, β-defensin 2 is mostly expressed in the intestine, thymus, skin, and gonads of the gilthead seabream (Sparus aurata). In head kidney leucoytes (HKLs), the expression was very low and did not change significantly when stimulated with various immunocompetent agents. However, the expression was significantly down-regulated in the liver, head–kidney, and blood 4 h post-injection with the fish pathogen Vibrio harveyi. When infected with nodavirus, the expression was downregulated in brain at 7 days post-infection. These results denote a possible complementarity between the expression patterns of β-defensins and hepcidins. Further studies are needed to analyze gene duplications and expression patterns of β-defensins and describe their mechanism of action in seabream and other teleost fish.

Development of a haplotype reference panel and analysis of genetic structure in Golden Pompano (Trachinotus ovatus)

Trachinotus ovatus, a valuable marine fish, is primarily farmed in the South China Sea. Intensive aquaculture can lead to genetic uniformity and disease risks. Additionally, the high cost of genome sequencing restricts knowledge of genetic variation, hindering genetic analysis and breeding advancements. This study investigated the genetic diversity and structure of Trachinotus ovatus populations within the South China Sea aquaculture context, with the goal of strengthening sustainability. Additionally, the study also enhanced breeding strategies by developing a high-quality haplotype reference panel and an efficient imputation process. Through high-throughput sequencing (depth＞20X), 173 samples from three key breeding sites (SanYa, Hainan; Zhanjiang, Guangdong; and Beihai, Guangxi) were analyzed, revealing substantial genetic diversity and distinct population structures. Notably, the Beihai (BH) population exhibited significant stratification, suggesting regional genetic uniqueness. Low levels of genomic inbreeding coefficient and the identification of unique SNP loci across populations underscored the genetic richness within these Trachinotus ovatus communities. A major constructed of this work is the creation of the first high-quality haplotype reference panel for the species, demonstrating genotype imputation's viability as a cost-effective alternative for large-scale genetic studies in aquaculture. In particular, a Shapeit reference panel with 5476,550 SNPs was created, excelling in accuracy across various depths, notably achieving up to 95.8 % imputation accuracy at 1X sequencing depth. This high accuracy across populations shows the importance of genetic diversity in the panel. This research not only advances the understanding of Trachinotus ovatus genetic foundations but also provides crucial insights for conservation efforts and genetic analysis. By establishing a robust haplotype reference panel for Trachinotus ovatus helps lower the costs of future genetic research and variation studies, this study lays the foundation for sustainable aquaculture practices and breeding programs.

Genetic homogeneity and weak signatures of local adaptation in the marine mussel Mytilus chilensis

The natural populations of the marine mussel Mytilus chilensis and the associated aquaculture industry forms a sensitive social-ecological system that relies on the released propagules for cultivation in the highly heterogeneous environment (temperature, productivity, and salinity) of northern Patagonia (42–44 °S). We assessed spatial genetic structure, signals of local adaptation, and population assignment of M. chilensis analyzing 5963 SNPs from 125 individuals across six natural populations sampled over two consecutive years along the southeast Pacific coast (39° 25′ to 43° 07′ S, ~ 430 km). Neutral and putatively adaptive loci revealed high genetic diversity and low genetic differentiation among populations. Of the whole dataset, less than 1% (50) of loci were identified as putatively adaptive through multiple approaches, with only 0.1% detected in by all of them, and only two loci of them were correlated with environmental variables. No evidence of Isolation by Environment (IBE) was found, albeit a slight differentiation in the southern sampling location (Yaldad). These results suggest that the genetic structure observed is primarily shaped by neutral processes with weak signals of local adaptation. Gene-flow appears to be the main evolutionary force influencing the species’ population genetic structure. Because of the importance for the industry, the probability of correct assignment of individuals to their population of origin using allelic frequencies was evaluated. Analyses exhibited relatively low probabilities (< 50% for four out of six sites) of accurately assigning individuals to their geographic origin, with a limited success of SNP markers the for such purposes. Likely, species' high dispersal capacity, seed translocation, and the spill-over effect of mussel aquaculture prevents population genetic differentiation through high effective gene flow, hindering local genetic adaptation.

Genomic diversity and population structure of Carniolan honey bee in its native habitat

BackgroundResearch into the genetic diversity of honey bee (Apis melliferaL.) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees (Apis mellifera carnica) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs.ResultsOur analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (FST), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee (Apis mellifera ligustica) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise FST values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained.ConclusionsThis study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.

Genome resequencing reveals genetic status of Macrobrachium rosenbergii populations in China

The giant freshwater prawn (Macrobrachium rosenbergii) has been widely cultured in China since 1990s. In this study, 189 individuals were sampled from 10 distinct populations, including original populations introduced from abroad and domesticated strains in China, namely Florida (FD), "Nantaihu No.2" (NT), Vietnam (YN), Sri Lanka (SK), Bangladesh (ML), Thailand (TG), Taiwan (TW), "Shufeng No.1" (SF), Zhengda (ZD) and New Myanmar (NMD). The genetic diversity and population structure of these populations were analyzed based on a dataset of 300,828 genome-wide SNP loci. The population structure analysis showed that the 10 populations shared 4 ancestors, and the domestic populations (i.e., SF, ZD, TW and NT) shared a common ancestor. The phylogenetic analysis showed that the 10 populations were grouped into 4 branches, with all the domestic populations clustering together. Estimation of fixation index (Fst) values revealed relatively lower Fst values among the domestic populations, in contrast to the more significant differences observed between domestic and foreign-origin populations. Gene flow analysis revealed three significant events of genetic exchange among the 10 populations: (1) from YN to the common ancestor of FD, TG and the domestic populations, (2) from NMD to the common ancestor of TG and FD, and (3) from the common ancestor of NMD, YN, ML and SK to ZD population. In addition, selective sweep analysis, utilizing Fst and nucleotide diversity (Pi) estimations, was conducted on representative populations (i.e., ML and SF), and 7 positively selected genes were identified, including Prospero Homeobox 1 (Prox1), Forkhead Box L1 (Foxl1), Tousled Like Kinase 2 (TLK2), G Protein Subunit Alpha 14 (Gna14), Uronyl 2-sulfotransferase (Ust), MAX Network Transcriptional Repressor (Mnt) and Importin-9 (Ipo9). These findings contribute to elucidating the breeding potential of the introduced populations and provide insights into the genetic status of the domestic breeding strains of M. rosenbergii in China.

Establishment and population genetic analysis of SNP fingerprinting of Chinese soft-shelled turtle (Pelodiscus sinensis)

Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquaculture species in China. However, with the continuous development of P. sinensis cultures, problems related to germplasm degradation and population mixing have become increasingly prominent. This has seriously affected the protection and utilization of germplasm resources by P. sinensis. To broaden the understanding of the germplasm resources of P. sinensis and improve the efficiency of germplasm identification, Super-GBS sequencing technology was used to conduct population genetic analysis of P. sinensis samples from six different populations distributed in five provinces. As a result, 1464,488 SNPs were identified. Genetic structure analysis revealed that the six P. sinensis populations could be divided into three sub-populations. The genetic differentiation coefficient of the DT and CY populations was very low (Fst=0.0088), indicating that differentiation had not yet occurred. Additionally, 15 KASP core markers for the identification of P. sinensis populations were developed using KASP typing technique for the first time. Genetic information can lay a foundation for the protection and utilization of germplasm resources by P. sinensis, and the fingerprinting database developed in this study provides a practical tool for authenticating P. sinensis.

Does rafting promote contemporary gene flow? Global and regional patterns of population genetic diversity and structure on the false limpet Siphonaria lateralis in the Southern Ocean

Rafting has been proposed as an effective mechanism for species without free-living pelagic larvae to achieve long-distance dispersal, theoretically preventing population differentiation over wide distributional ranges. Moreover, rafting has been advocated as a main dispersal mechanism for marine invertebrates with sub-Antarctic distributions, because of abundant buoyant kelps, driven by the Antarctic Circumpolar Current. Nonetheless, little attention has been given to the role of rafting to establish regular gene flow across the sub-Antarctic, and the geographic and temporal scales at which it occurs. Aiming to unravel these major questions about the extent of genetic connectivity across the Southern Ocean (SO), we studied the pulmonate limpet Siphonaria lateralis, a benthic species with encapsulated larvae, found on the rocky intertidal of sub-Antarctic islands and southern South America. Since S. lateralis is closely associated with D. antarctica, dispersal by rafting is plausible, as revealed by the absence of phylogeographic structure across the sub-Antarctic. We sampled 116 individuals from eight localities across the SO, and used 5,515 SNPs obtained through Genotyping-by-Sequencing, to determine contemporary genetic diversity, structure, and gene flow at two spatial scales; global, across the SO, and regional, within Kerguelen. Results identified substantial genetic structure, differentiating Patagonia, Falklands/Malvinas Islands, South Georgia and the Kerguelen archipelago, and low levels of contemporary gene flow. The most notable genetic differentiation was found between Patagonia/Falklands and South Georgia/Kerguelen. Structure was also significant between Patagonia and the Falkland/Malvinas Islands. Conversely, South Georgia and Kerguelen exhibited closer genetic affinity, and indications of recent but limited gene flow. Moreover, historical gene flow estimates between the four populations were low. At regional scale, noteworthy genetic structure persisted, and gene flow was insufficient to prevent genetic differentiation within Kerguelen. Consequently, rafting’s potential may be overestimated as a contemporary mechanism promoting gene flow across the SO, as these events may be sporadic, irregular, and unpredictable for marine invertebrates lacking a larval dispersal stage, since contemporary dispersal events don’t seem to facilitate high gene flow at both scales. Accordingly, other oceanographic factors or processes may hinder the establishment of species associated with macroalgae, and as consequence, contemporary genetic connectivity in the sub-Antarctic.

Analysis of Genetic Diversity of Some Vitis labrusca and Vitis spp. with Molecular Markers

Türkiye has a very suitable climate for viticulture, and different grape varieties have been grown in almost every region since ancient times. Although these grape varieties have different names, there are also grape varieties with the same genetic structure. In particular, in the Black Sea Region, Vitis labrusca, which is resistant to heavy rainfall and humidity, and hybrids of this species grow. However, it is known that different genotypes of this species are grown in the region. Genetic confusion exists in Vitis labrusca L. and its hybrids due to natural pollen transfer and crossing. This study evaluated the genetic similarities and differences among Vitis varieties and genotypes, mainly Vitis labrusca genotypes, with 18 different SSR primers. In the genetic relationship dendrogram, the varieties/genotypes showed similarity at rates ranging from 0.65% to 0.98%. The highest similarity rate between the varieties and genotypes used in the study was determined between the genotypes 5 '57 Gerze 04' and 6 '61 Of 04' with 92%. The results obtained have revealed different grape gene pools, especially in the Black Sea Region, and are expected to contribute to disease resistance breeding studies in the future significantly. Increasing consumer awareness of climate change will increase the interest in disease-resistant or tolerant grapes, such as Vitis labrusca species, in the coming years.