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The objective of this research was to describe the variation in breeding practices in the population of Arabian horses in Algeria in relation to the population size drop observed in the 2000s, due to an increase in the cost of food and a change in interest in racing, related to the black decade. As a result, the breeders had to face two opposite constraints: enhancing reproduction to counter the population decline and preventing the loss of genetic diversity. The aim of the study was to evaluate the genetic consequences of the decisions taken over a period of 30 years, starting from 1988 to 2018. The study was based on the analyses of the stud-book and on 11 microsatellite markers in a group of 943 horses, distributed into 13 age classes. Between 2004 and 2008, the breeders purchased foreign sires and dams, allowing a relative stability in unbiased heterozygosity of about 71%, due to the high genetic distances between foreign and local horses. As these importations stopped from 2009 on, there was a decrease in allele numbers of about 20%. Moreover, from 2010 on, we observe an excess of inbreeding and an increase in genetic drift relative to the starting population, due to population size decline. From the analysis of genetic distances between local individuals, it seems that the only constraint for sires and dams allowed to mate was a null coefficient of inbreeding. [ABSTRACT FROM AUTHOR]

The study of the state of Baikal endemic sponge populations is of great interest because of the occurrence of mass mortalities and disease in recent decades. To identify possible signs of species vulnerability to extinction, it is crucial to develop appropriate genetic markers that help developing measures for conservation. In this paper, we describe the population genetic structure of the Baikal endemic sponge Lubomirskia baikalensis examined with the set of microsatellite markers we developed. We analysed 251 samples from eight locations that cover all three basins of Lake Baikal. A genetic subdivision into three clusters was revealed. Such a structure can be explained mainly by the low ability of larvae to disperse. Despite the presence of dead and diseased individuals in all studied locations, all populations were in Hardy–Weinberg equilibrium and no bottleneck effect was found at all. This is the first time that a genetic connectivity study has been performed for L. baikalensis, a species endemic of Lake Baikal. Reconstruction of the changes in the effective population size agrees with the results obtained during drill sample analysis and it demonstrates that the effective population size was 55.5 times lower about 24,000 years ago, which indicates that apparently there is no threat of extinction of the Baikal endemic sponges at present. [ABSTRACT FROM AUTHOR]

The mite, Dermatophagoides farinae, is an allergen source that triggers allergy symptoms in humans. We studied how different habitats affect the genetic structure of D. farinae populations. We used 12 microsatellite loci to analyse the genetic structure of six D. farinae populations collected from four habitats: flour mill (FM), dormitory (DM), cotton mill (CM), and pillow (PL). The CM population had the highest genetic diversity (He = 0.641) while the FM population had less genetic diversity. AMOVA analysis showed 81% intrapopulation genetic variation and 19% interpopulation variation. The overall FST value of the six populations was 0.18531, indicating significant population genetic differentiation. Significant genetic differentiation occurred between the FM population and the other three habitat populations. Bayesian clustering analysis showed that the FM population was divided into two clusters. UPGMA tree and PCoA data supported the above results and indicated that the D. farinae populations from CM, PL, and DM1 had similar genetic ancestors. It was speculated that D. farinae could spread through the cotton-pillow-dormitory route. This study showed that D. farinae may have undergone habitat-associated differentiation and provides measures for preventing the dispersal of D. farinae. [ABSTRACT FROM AUTHOR]

Quercus griffithii is an ecologically and economically important tree species utilized for firewood, fodder, compost, and building-making. It is also a good source of food for wildlife. The genetic diversity of Q. griffithii is poorly understood; therefore, in the present study, 16 polymorphic SSR markers were used to assess the extent and pattern of genetic diversity in Q. griffithii samples collected from the northeastern region of India. The SSR markers revealed significant discriminating power (PIC range, 0.15˗0.81) and resulted in the amplification of 119 alleles. At the species level, it showed moderate levels of genetic diversity (Ho = 0.47; He = 0.52) with low genetic differentiation (FST = 0.06) and high gene flow (Nm = 3.91). Two genetic clusters, with high admixture populations were estimated in the Bayesian analysis of STRUCTURE, which was in accordance with clusters of UPGMA and PCoA. This is the first study to assess genetic diversity using SSR markers in Q. griffithii. The genetic information generated in this study will be helpful in the future conservation and restoration of Q. griffithii in the northeastern region of India. [ABSTRACT FROM AUTHOR]

Genetic diversity analysis provides the scientific basis for the preservation, evaluation, and utilization of the germplasm resources of tree species. We explored the genetic diversity and structure of Populus tomentosa elite trees in North China using 13 nuclear microsatellite markers. We compared nine groups of accessions including 20 originating from Beijing (BJ), 122 from Hebei (HB), 20 from Shandong (SD), 113 from Henan (HN), 270 from Shanxi (SX), 54 from Shaanxi (SAX), 8 from Gansu (GS), 10 from Anhui (AH), and 6 from Jiangsu (JS). All of the studied primer pairs were polymorphic and generated 125 alleles. Analyses of molecular variance revealed that 79%, 14%, and 8% of the total variation was due to variations within the individual, among individuals, and among populations, respectively. Based on principal coordinate and STRUCTURE cluster analyses, individuals distributed in the southern region (HN, SAX, AH, and JS) were roughly classified into one group, while those distributed in the northeastern region (BJ, HB, and SD) and northwestern regions (SX) were separately divided into one group each. Moreover, the northwestern region included two-thirds of the SX trees, and the remainder were in the northeast region. By analyzing genetic diversity and structure within populations, individuals with different genetic backgrounds were screened for constituent training populations (TRS), including broad allelic variation for related traits. This ensures that the genomic prediction model can accurately capture genetic effects and provide reliable predictions across a broad spectrum of genetic backgrounds. Therefore, our results will benefit genome breeding technology. [ABSTRACT FROM AUTHOR]

The giant freshwater prawn, Macrobrachium rosenbergii, is one of the most crucial crustacean species cultured in China. However, in recent years, M. rosenbergii aquaculture in China has encountered several challenges, including low productivity and growth retardation. A decline in genetic variation has been implicated in this phenomenon. This study aims to develop microsatellite multiplex PCR panels to elucidate the genetic diversity and differentiation of cultured M. rosenbergii populations in China. Based on our previous transcriptome sequencing, we developed 24 polymorphic molecular markers. The average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were 4.042, 0.535, 0.605, and 0.543, respectively. Two multiplex PCR panels involving six microsatellite loci were obtained by combining different amplicon lengths from these 24 loci. The panels were used to evaluate the genetic structure of six cultured M. rosenbergii populations in China, including one population in Guangxi (GX) and another in Guangdong (GD) province, along with two populations each in Jiangsu (JSA and JSB) and Zhejiang (ZJA and ZJB) provinces. Results revealed that the polymorphism among the six populations ranged from 0.365 to 0.682 with reduced genetic diversity in ZJA and JSB populations (PIC < 0.5). Pairwise FST, Nei's genetic distance, and STRUCTURE analysis revealed significant differentiation among the six cultured populations. ZJA and GD exhibited pronounced genetic distinctiveness from the other populations and were consequently assigned to distinct groups. Populations GX and JSB (FST=0.058, DA=0.045) and populations ZJB and JSA (FST=0.009, DA=0.016) were assigned to two clusters, respectively, suggesting they share similar origins. This study provided polymorphic microsatellite markers and genetic diversity assessment of cultured M. rosenbergii populations, laying a foundation for future breeding programs. [ABSTRACT FROM AUTHOR]

Abstract Background Soft ticks of the genus Ornithodoros are responsible for the maintenance and transmission of the African swine fever (ASF) virus in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of the Borrelia species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical Ornithodoros ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study is to design microsatellite markers that could be used for ticks of the Ornithodoros moubata complex, particularly Ornithodoros phacochoerus, to assess population structure and tick movements in ASF endemic areas. Methods A total of 151 markers were designed using the O. moubata and O. porcinus genomes after elimination of repeated sequences in the genomes. All designed markers were tested on O. phacochoerus and O. porcinus DNA to select the best markers. Results A total of 24 microsatellite markers were genotyped on two populations of O. phacochoerus and on individuals from four other Ornithodoros species. Nineteen markers were selected to be as robust as possible for population genetic studies on O. phacochoerus. Conclusions The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of O. phacochoerus. Graphical Abstract

Abstract Background Jackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers. Results The results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (H o ) and expected (H e ) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the ‘partitioning around medoids’ (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances. Conclusions Both morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers’ incomes. However, selecting germplasm based on morphology alone may be misleading.

Background: Soft ticks of the genus Ornithodoros are responsible for the maintenance and transmission of the African swine fever (ASF) virus in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of the Borrelia species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical Ornithodoros ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study is to design microsatellite markers that could be used for ticks of the Ornithodoros moubata complex, particularly Ornithodoros phacochoerus, to assess population structure and tick movements in ASF endemic areas. Methods: A total of 151 markers were designed using the O. moubata and O. porcinus genomes after elimination of repeated sequences in the genomes. All designed markers were tested on O. phacochoerus and O. porcinus DNA to select the best markers. Results: A total of 24 microsatellite markers were genotyped on two populations of O. phacochoerus and on individuals from four other Ornithodoros species. Nineteen markers were selected to be as robust as possible for population genetic studies on O. phacochoerus. Conclusions: The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of O. phacochoerus. [ABSTRACT FROM AUTHOR]

Lake Baikal, an ancient, massive lake in Siberia that holds 20% of the world’s fresh water reserves, is a unique center of speciation. Changes in the lake’s ecosystem in recent years require comprehensive monitoring activities to track the continuously evolving situation. Sponges are bioindicators of the state of aquatic ecosystems, and in Lake Baikal sponges are represented by both cosmopolitan and endemic species. However, the study of intra- and interspecific relationships between endemic sponges is complicated by the fact that standard molecular genetic markers are not suitable for these purposes. In this regard, the search for suitable high-resolution molecular genetic markers is especially relevant. Here we report on the development of a set of universal microsatellite markers that allows the interspecific relationships between Lake Baikal endemic sponges to be studied. We tested the effectiveness of this set of microsatellite markers on representatives of four endemic sponge species and achieved a reliable separation of representatives of all four genera of the endemic sponge family Lubomirskiidae. This is the first report of a set of highly variable molecular genetic markers that has been developed specifically for the study of interspecific relationships between Lake Baikal sponges. This set also has the potential to be a marker for species identification, which is important for monitoring activities in connection with events of mass death and diseases of sponges in Lake Baikal. The described approach can be used to study endemic sponges from other ancient lakes. It has great potential for use in the development of universal markers for identifying groups of closely related species. [ABSTRACT FROM AUTHOR]

Roupala montana var. brasiliensis is a timber tree species native to the Cerrado and Atlantic Forest areas of Brazil. The wood was exploited for international markets, but there is no information on the conservation status of its natural populations, nor on other key aspects, such as mating system, gene flow, and inbreeding depression, essential for the species' sustainable management and conservation. We report the first study of any Roupala species to apply a validated set of species-specific microsatellite markers to genotype adults, juveniles, and seedlings, and analyse genetic diversity, inbreeding, effective population size, and mating system. We studied four populations of the species in areas of mixed Ombrophilous forest with different disturbance levels (undisturbed to strongly disturbed) in southern Brazil. The species occurs at low frequency in the study forests, but the populations are genetically diverse without significant differences in genetic diversity levels related to disturbance. The study also indicated resistance to the severe fragmentation associated with low density of individuals, with a stable mating system showing preferential outcrossing, with some inbreeding (tm ≈ 0.83, F > 0.165). Despite being spatially isolated from each other, the populations are not reproductively isolated, receiving immigrant pollen from long distances, although there was no evidence of gene flow into the populations via seeds. Seedlings from self-fertilization show low levels of inbreeding depression, which may reflect earlier pre-germination selection events. There was loss of allelic wealth in the younger cohorts, which may be a warning of the fragility of the genetic diversity detected in populations. We consider the implications of the results for the development of ex and in situ conservation and tree improvement programs. [ABSTRACT FROM AUTHOR]

The sable (Martes zibellina L.) range extends from the western slopes of the Ural Mountains to the Far East. Sable has a complex intraspecific structure; geographic populations differ in a number of morphological traits. Unregulated sable hunting for several centuries, forest fires and industrialization of Siberia led to a sharp decline in the species' population size and the fragmentation of its habitat by the beginning of the twentieth century. In some regions of Siberia, the species was almost completely exterminated. To restore the sable population, along with a complete ban on hunting, large-scale sable reintroductions were made in the middle of the twentieth century. About 11.7–11.8 thousand animals were brought from the Baikal-Patom region of the Baikal Mountain Country to Western and Eastern Siberia. Reintroduced sables survived in the new territories and formed naturalized populations. We studied the allele frequency distribution of 15 microsatellite loci of 474 sable specimens from 14 native and six naturalized sable populations in the Central Siberian Plateau and adjacent territories. The results of the analysis of genetic diversity, differentiation and population structure indicate the presence of five clusters in the study area, four of which are formed by native populations and one that includes a native population from the Patom donor area and all six naturalized populations. Both large-scale reintroductions and a complete ban on hunting have contributed to the restoration of sable populations in Siberia, which have become a continuous sable range. An analysis of genetic structure in historical and geographic context can be useful in studying the effects of introduction or reintroduction when considering the stages of introduction-naturalization-invasion continuum. [ABSTRACT FROM AUTHOR]

AbstractWheat leaf rust caused by Puccinia triticina (Pt) is an important disease of bread wheat in Zimbabwe. This study was carried out to determine the distribution, avirulence/virulence profile(s) and genotypic variation among isolates of the pathogen. In total, 104 single-pustule isolates were established from infected wheat samples that were collected from the main wheat production regions in Zimbabwe in surveys conducted from 2019 to 2021. Phenotyping of the isolates on a set of 46 differential and additional wheat lines revealed a single Pt race, MCDS. For genotypic assessment, 48 Pt isolates, including eight South African races, were genotyped with 19 microsatellite markers. Using the Bayesian model, isolates were subdivided into three clusters in both a DARwin neighbour-joining tree and STRUCTURE analysis. The results confirmed a high genetic similarity between the Zimbabwean Pt isolates and the South African races MCDS, MCPS and MFPS. Furthermore, Pt isolates from Zimbabwe were clonal, which was in accordance with all 104 isolates that typed to race MCDS. [ABSTRACT FROM AUTHOR]

Seasonally Dry Tropical Forests (SDTFs) exhibit a patchy distribution throughout the Neotropics and are considered one of the most threatened tropical forests in the world. Nonetheless, their conservation has often been neglected in comparison to efforts directed towards other biomes. The distribution pattern of Anadenanthera colubrina (Vell.) Brenan var. cebil (Griseb) Altschul allows an adequate mapping of this biome. The main objectives of this work are to study the historical processes that determined the current distribution of A. colubrina var. cebil under the hypothesis that the demographic history of the remaining fragments of SDTFs in Argentina leads back to a single event of ancestral divergence, and identify Argentinean localities with priority for conservation. Plastid genetic diversity of A. colubrina var. cebil from northern Argentina is characterised using three plastid microsatellite loci. From this, genetic characterization, population genetics, and Bayesian inference were carried out. The results from approximate Bayesian computations show that the Misiones and Piedmont Subandean nuclei diverged from an ancestral population in the early Neogene while the Formosa population derived from the Misiones nucleus in the late Neogene. Two out of five locations from the Misiones nucleus and three of nine locations from the Subandean Piedmont nucleus are proposed as priority conservation areas. [ABSTRACT FROM AUTHOR]

Background: Jackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers. Results: The results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the 'partitioning around medoids' (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances. Conclusions: Both morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers' incomes. However, selecting germplasm based on morphology alone may be misleading. [ABSTRACT FROM AUTHOR]

Biodiversity conservation entails not only the preservation of specific taxa but also genetic diversity. Despite the crucial role of molecular data in freshwater fish conservation management, there is a scarcity of information regarding the genetic diversity of Luciobarbus Heckel, 1843 (Actinopterygii, Cyprinidae) populations in the Aral system. Therefore, the primary aim of this study was to provide genetic information on two native species of the Luciobarbus genus found in the Aral system: L. conocephalus (Kessler, 1872) and L. brachycephalus (Kessler, 1872). These species, like many others in the Aral system, confront the imminent threat of extinction due to system alterations. However, genetic studies on these species at the nuclear level are challenging because Luciobarbus is an allotetraploid genus. Consequently, genetic investigations thus far have focused mainly on sequencing mitochondrial genes due to their haploid nature. This study has successfully developed fifteen new polymorphic microsatellite loci, which can prove to be valuable for population genetics, conservation, and other pertinent research on these species. [ABSTRACT FROM AUTHOR]

Nitrogen is an essential element for maize growth, but excessive application can lead to various environmental and ecological issues, including water pollution, air pollution, greenhouse gas emissions, and biodiversity loss. Hence, developing maize hybrids resilient to low-N conditions is vital for sustainable agriculture, particularly in nitrogen-deficient soils. Combining ability and genetic relationships among parental lines is crucial for breeding superior hybrids under diverse nitrogen levels. This study aimed to assess the genetic diversity of maize inbred lines using simple sequence repeat (SSR) markers and evaluate their combining ability to identify superior hybrids under low-N and recommended conditions. Local and exotic inbred lines were genotyped using SSR markers, revealing substantial genetic variation with high gene diversity (He = 0.60), moderate polymorphism information content (PIC = 0.54), and an average of 3.64 alleles per locus. Twenty-one F1 hybrids were generated through a diallel mating design using these diverse lines. These hybrids and a high yielding commercial check (SC-131) were field-tested under low-N and recommended N conditions. Significant variations (p < 0.01) were observed among nitrogen levels, hybrids, and their interaction for all recorded traits. Additive genetic variances predominated over non-additive genetic variances for grain yield and most traits. Inbred IL3 emerged as an effective combiner for developing early maturing genotypes with lower ear placement. Additionally, inbreds IL1, IL2, and IL3 showed promise as superior combiners for enhancing grain yield and related traits under both low-N and recommended conditions. Notably, hybrids IL1×IL4, IL2×IL5, IL2×IL6, and IL5×IL7 exhibited specific combining abilities for increasing grain yield and associated traits under low-N stress conditions. Furthermore, strong positive associations were identified between grain yield and specific traits like plant height, ear length, number of rows per ear, and number of kernels per row. Due to their straightforward measurability, these relationships underscore the potential of using these traits as proxies for indirect selection in early breeding generations, particularly under low-N stress. This research contributes to breeding nitrogen-efficient maize hybrids and advances our understanding of the genetic foundations for tolerance to nitrogen limitations. [ABSTRACT FROM AUTHOR]

Simple Summary: Bactrocera dorsalis is a highly invasive fruit fly that is of major economic importance worldwide. In Burkina Faso, it is one of the main problems associated with mango production, and it is often responsible for the loss of the whole harvest in the most affected areas. Innovative strategies are being developed to improve the current means of controlling this pest. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male B. dorsalis were collected transversally in Burkina Faso in July 2021. The results showed that the abundance of B. dorsalis varied from 87 to 2986 flies per trap per day at the different sampling sites. The genetic variability was high at all sites, with an average Shannon diversity index of 0.72 per site. The migration rates were high between the study populations and ranged from 10.62 to 27.53 migrants. A genetic structural analysis identified three weakly separated genetic groups in the population of B. dorsalis in Burkina Faso. The results of this study will help to better guide control interventions against this pest. Bactrocera dorsalis Hendel is a highly invasive horticultural pest that is of major economic importance worldwide. In Burkina Faso, it is one of the main insect pests that affects the production and exportation of mangos. Understanding the biology and the genetic dynamics of this insect pest provides crucial information for the development of effective control measures. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male flies were collected transversally in Burkina Faso and analyzed by PCR using 10 microsatellite markers. The results showed an abundance of B. dorsalis varying from 87 to 2986 flies per trap per day at the different sampling sites. The genetic diversity was high at all sites, with an average Shannon's Information Index (I) of 0.72 per site. The gene flow was high between study populations and ranged from 10.62 to 27.53 migrants. Bayesian admixture analysis showed no evidence of structure, while Discriminant Analysis of Principal Components identified three weakly separated clusters in the population of B. dorsalis in Burkina Faso. The results of this study could be used to optimize the effectiveness of current control interventions and to guide the implementation of new, innovative, and sustainable strategies. [ABSTRACT FROM AUTHOR]

Abstract Background Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland. Results Chloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean A R = 12.35; mean H o = 0.769; mean H e = 0.542) but low differentiation based on nuclear microsatellites (F ST = 0.045). Significant spatial genetic structure, consistent with models of isolation by distance, was detected in 14 out of 23 populations. Estimated effective population size was moderate-to-high, with a harmonic mean of 57.5 individuals per population. Conclusions Genetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands.

Rainbow trout (Oncorhynchus mykiss) is a significant cold-water fish farmed in China. Currently, most molecular marker-assisted breeding applications in rainbow trout rely on SSR markers. Although many rainbow trout SSR markers have been developed, methods for mining many polymorphic SSR markers from the genome and identifying them efficiently and rapidly are still lacking. For this reason, this study used in silico simulation method to rapidly develop a large number of polymorphic SSR markers quickly. A total of 354,613 SSR loci with two to six nucleotide repeat motifs were mined from 32 chromosomes of the rainbow trout reference genome using GMATA. The chromosome sequences of the reference genome were then aligned to the whole genome sequencing data (10×) of 68 rainbow trout samples. In silico genotyping was performed using the HipSTR programme to compare and count the variation in the number of repeats of the motifs of the SSR loci in the samples. The loci with high deletion rates and monomorphism were discarded, while those with more than one nonreference allele were kept. The final set of polymorphic SSR loci screened was 78,828. Finally, 4,821 SSR loci were selected with more than 3 alleles and no deletion in all rainbow trout samples and were physically mapped. The average polymorphic information content of these loci was 0.692, indicating high levels of polymorphism. These SSRs were utilized to analyse the genetic diversity and population structure of the 68 rainbow trout samples. The results showed that these 68 samples were divided into two groups. These newly discovered polymorphic SSR markers will provide valuable information for evaluating the construction of rainbow trout family lines for genetic diversity and improvement. [ABSTRACT FROM AUTHOR]

Kelussia odoratissima Mozaff. (Apiaceae) is a native plant that has been traditionally consumed in Iran's food and pharmaceutical industries. Overharvesting of the taxon, especially at the beginning of the growing season, due to its considerable medicinal and economic value, is believed to be the main reason for the extirpating of this plant. The consequences of the severe anthropogenic impacts on the genetic diversity of populations are poorly known. In order to investigate the level of genetic variation and patterns of the genetic structure of K. odoratissima, we developed novel microsatellite markers using the 454 Roche next-generation sequencing (NGS) platform for the first time. Out of 1,165 microsatellite markers bioinformatically confirmed, twenty- five were tested, of which 23 were used to screen genetic variation across 12 natural populations. Our results showed that the average number of alleles per locus and the polymorphic information content (PIC) were 10.87 (range 7 to 27), and 0.81 (range 0.67 to 0.94), respectively. The mean observed and expected heterozygosities (± SD) across all populations were 0.80 ± 0.31 and 0.72 ± 0.14, respectively. The average pairwise FST among the populations was 0.37 (range 0.04 to 0.81). Bayesian and distance-based clustering, and principal coordinate analyses revealed at least four major genetic clusters. Although high level of structure can be explained by landscape topography and geographic distance, presence of admixed populations can be associated to seed or pollen dispersal. Contrary to expectations, the high level of genetic variation and lack of inbreeding suggest that overexploitation has not yet significantly purged the allelic variability within the natural populations in protected areas. [ABSTRACT FROM AUTHOR]

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The introduction of exotics is common in forestry, and majorly important species, like eucalypts, poplar, and Casuarina sp. occupy vast areas in the Indian subcontinent. Importantly, with the latest cost-effective sequencing techniques, genetic diversity research through molecular marker approaches on major exotics provides novel information for genetic improvement in economic traits with climatic adaptation. The study was carried out on Grevillea robusta to assess genetic relatedness and diversity among 228 genotypes belonging to five northwestern states in India. These genotypes were assayed using twelve simple sequence repeat (SSR) markers. A population structure analysis using structure software identified four major gene pool subgroups with clear-cut differences from each other. Principal coordinate analysis also supports the clustering patterns of the unweighted pair group method with arithmetic mean analysis. In the case of genetic diversity assessment, a total of seventy-three alleles were detected from twelve SSRs, with an average of 6.08 ± 0.71 per locus. Polymorphism information content ranged from 0.17 to 0.67 with a mean of 0.44 ± 0.045, indicating high levels of polymorphism across the genotypes. All the evaluated SSRs demonstrated moderate genetic diversity (observed heterozygosity = 0.31 ± 0.03; expected heterozygosity = 0.32 ± 0.03; and genetic differentiation = 0.295) among the sampled genotypes. These findings indicate significant genetic variability in the germplasm to warrant selection and have potential for a long-term tree improvement program of G. robusta in India. Study Implications: The study on population genetics of Grevillea robusta in exotic environments assessed probable gene pools, provenances, and genetic diversity in geographical distribution range of the species in the Indian scenario. The basic population genetic measures revealed the high diversity areas and probable seed zones of G. robusta in its exotic range. Importantly, the study will be helpful in the selection of candidate plus trees of G. robusta to further strengthen the genotype × environment interaction study for future breeding programs. Further, studying the genetic makeup for moderately diverse species offers valuable insights into evolutionary history, population dynamics, and ecological interactions, which may lead to conservation efforts and guidance for the management of trees such as G. robusta in their native and introduced regions. [ABSTRACT FROM AUTHOR]

Background: Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland. Results: Chloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean AR = 12.35; mean Ho = 0.769; mean He = 0.542) but low differentiation based on nuclear microsatellites (FST = 0.045). Significant spatial genetic structure, consistent with models of isolation by distance, was detected in 14 out of 23 populations. Estimated effective population size was moderate-to-high, with a harmonic mean of 57.5 individuals per population. Conclusions: Genetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands. [ABSTRACT FROM AUTHOR]

Simple Summary: We studied the flight dispersal of two congeneric beetle species (Ochthebius quadricollis and Ochthebius lejolisii) living in Mediterranean coastal rockpools; temporary and fragmented habitats with extreme environmental conditions (high salinity, high temperature, and strong desiccation). We used a multi-approach (experimental flying assays, wing morphology, and genetic markers) to measure flight capacity. We found that both species had similar flight behaviour, with most individuals flying when water was heated. Females had larger body sizes and wing areas and lower wing loading than males, which suggested higher dispersal capacity. The wing shape of both species was also shown to be an efficient adaptation to flight. However, the molecular data point to passive dispersal assisted by wind at small-to-medium spatial scales (<100 km). Flight dispersal is ecologically relevant for the survival of supratidal rockpool insects. Dispersal has important consequences for colonisation, gene flow, and evolutionary divergence. Here, we compared the flight dispersal capacity of two congeneric beetle species (Ochthebius quadricollis and Ochthebius lejolisii) that exclusively inhabit these temporary, fragmented, and extreme habitats. We estimated flight capacity and inferred dispersal in both species using different approaches: experimental flying assays, examination of wing morphology, and comparison of microsatellite markers between species. Our findings revealed that both species exhibited similar flight behaviour, with 60 to 80% of the individuals flying under water heating conditions. Notably, females of both species had larger body sizes and wing areas, along with lower wing loading, than males in O. quadricollis. These morphological traits are related to higher dispersal capacity and more energetically efficient flight, which could indicate a female-biassed dispersal pattern. The wing shapes of both species are characterised by relatively larger and narrower wings in relation to other species of the genus, suggesting high flight capacity at short distances. Molecular data revealed in both species low genetic divergences between neighbouring populations, non-significant differences between species, and no isolation by distance effect at the study scale (<100 km). These results point to passive dispersal assisted by wind. [ABSTRACT FROM AUTHOR]

The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy–Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied. [ABSTRACT FROM AUTHOR]

In China, the brown trout is a second-level key aquatic wildlife protection animal in the Tibet Autonomous Region. In order to protect the brown trout germplasm resources in the Tibet Autonomous Region, the Institute of Aquatic Sciences of the Academy of Agricultural and Animal Husbandry Sciences of the Tibet Autonomous Region and the Heilongjiang Institute of the Chinese Academy of Aquatic Sciences collaborated on research on the key technologies of brown trout family construction. A fast in silico simulation method was employed in this study to discover numerous polymorphic SSRs. A total of 1,115,563 SSR loci with two to six nucleotide repeat motifs were mined from 40 chromosomes of the brown trout reference genome by GMATA. The whole genome sequences (30×) of 30 brown trout samples were compared to the reference genome's chromosome sequence. Then, the HipSTR program was employed to carry out in silico genotyping through comparisons and enumerations of repeat count variants on the motifs of the SSR loci among the samples. The loci with monomorphism and high deletion in the SSR genotype data were removed, and the loci with more than one non-reference allele were retained. The final set of polymorphic SSR loci screened was 106,194. Forty-three SSR markers were randomly selected for characteristic analysis. The range of alleles per locus was 3 to 9 (mean = 5). Observed heterozygosity was in the ranged from 0.167 to 1.000. Expected heterozygosity was in the ranged from 0.155 to 0.823. Twenty-three loci significantly deviated from Hardy-Weinberg equilibrium. These SSR markers will provide valuable information for assessing the genetic diversity of constructed brown trout families and for the genetic improvement of brown trout. [ABSTRACT FROM AUTHOR]

• Genome sequencing of Primula denticulata at 15X coverage. • 31,584 microsatellite loci were identified, 100 primer pairs were synthesized and tested. Out of these, 64 microsatellite loci were polymorphic. • Cross-species transferability of polymorphic loci was tested in 14 different Primula species. • UPGMA dendrogram showed the phylogenetic relationship among species. • Study aids fast plant diversity assessment for climate vulnerability and conservation. The genus Primula (Primulaceae) harbours habitat-sensitive species. It is a valuable tool for monitoring and assessing the overall state of the ecosystem as it can serve as a reliable indicator of ecological health. Primula denticulata Sm. is one of the most prevalent Primrose species found in the Indian Himalayan region with a wide extent of distribution from 1500 m to 3500 m altitude. Considering the ecological importance of Primulas, it is imperative to develop microsatellite markers to study genetic variability which can offer valuable insights into the adaptive strategies of the plants in response to changing environmental conditions. In this study, we sequenced the P. denticulata genome by utilizing Illumina paired-end sequencing technology at ∼15X coverage. 27,196 sequences harbouring 31,584 microsatellite loci were identified. 100 primer pairs were synthesized and tested for amplification. Impressively, 84 of these primers exhibited robust amplification, and 64 of these displayed polymorphism. Primer pairs from trinucleotide motifs were identified as more polymorphic. To assess the broader applicability of these primers, we also tested cross-species transferability on 14 different Primula species representing different sections of the genus that were collected from different parts of Himalaya. Notably, one SSR locus, Next Generation Sequencing Primula_5 (NGSPr_5) was able to produce bands in all the species showing 100 % transferability. Primula atrodentata showed a maximum (88.23 %) while P. glabra exhibited minimum (19.60 %) cross-transferability. The UPGMA dendrogram clustered different sections of sub-genus Aleuritia , and species from subgenera Sphondylia and Auganthus separately into two major groups. The groupings are in accordance with the known relationship between the different species from the genus. [ABSTRACT FROM AUTHOR]

The successful management of coral reefs necessitates understanding the genetic characteristics of reefs' populations since levels of genetic diversity play a critical role in their resilience, enabling them to withstand environmental changes with greater efficacy. To assess the genetic diversity and connectivity of the widespread Indo-Pacific coral, Stylophora pistillata, eight microsatellite loci were employed on 380 tissue samples collected from eight sites along the northern Gulf of Eilat, Red Sea. We documented deviations from the Hardy–Weinberg equilibrium and observed low heterozygosity and high values of expected heterozygosity (0.59 and 0.82, respectively). The relatively high FST values and STRUCTURE analysis results showed population fragmentation along the short coastline (<12 km). These results signify isolation by distance, low gene flow between most populations, and possible non-random mating. These results are connected to this species' sexual reproduction traits, a brooding coral species with planulae that settle shortly upon release with limited connectivity that are most probably further exacerbated by anthropogenic impacts imposed on Eilat's reefs. This study provides insights into the connectivity and population genetics of S. pistillata residing in an urbanized northern Red Sea reef and reinforces the need for better management of the current MPA, employing future active coral reef restoration in the area. [ABSTRACT FROM AUTHOR]

Genetic diversity serves as the basis for selecting and genetically enhancing any culturable species in aquaculture. Here, two different strains of wild (River Ravi and River Kabul) and six captive-bred strains of Labeo rohita from various provinces were selected, and genetic diversity among them was evaluated using three different microsatellite markers, i.e., Lr-28, Lr-29, and Lr-37, and one mitochondrial CO1 (Cytochrome c oxidase subunit 1) gene. Different strains of L. rohita were collected, and part of their caudal fin was cut and preserved in ethanol for DNA extraction and determination of genetic diversity among them. Results indicated that selected markers were polymorphic with polymorphic information content (PIC) content values above 0.5 with the highest in Lr-28 followed by Lr-29 and then Lr-37. The observed heterozygosity (Ho) of all strains was higher (Avg: 0.731) but less than the expected heterozygosity (He). Moreover, TMs and WRs showed the highest He, while TKs showed the lowest, He. Overall, inbreeding coefficient (FIS) values observed for all strains with selected markers were positive. The DNA barcoding with the CO1 gene revealed genetic variation among various strains, as demonstrated by the clades in the phylogenetic tree separating the strains into two distinct clusters that then divided into sub-clusters. In conclusion, TMs showed the highest heterozygosity as compared to other strains. Overall results provide the baseline data for the initiation of the genetic improvement program.

Genetic diversity analysis provides the scientific basis for the preservation, evaluation, and utilization of the germplasm resources of tree species. We explored the genetic diversity and structure of Populus tomentosa elite trees in North China using 13 nuclear microsatellite markers. We compared nine groups of accessions including 20 originating from Beijing (BJ), 122 from Hebei (HB), 20 from Shandong (SD), 113 from Henan (HN), 270 from Shanxi (SX), 54 from Shaanxi (SAX), 8 from Gansu (GS), 10 from Anhui (AH), and 6 from Jiangsu (JS). All of the studied primer pairs were polymorphic and generated 125 alleles. Analyses of molecular variance revealed that 79%, 14%, and 8% of the total variation was due to variations within the individual, among individuals, and among populations, respectively. Based on principal coordinate and STRUCTURE cluster analyses, individuals distributed in the southern region (HN, SAX, AH, and JS) were roughly classified into one group, while those distributed in the northeastern region (BJ, HB, and SD) and northwestern regions (SX) were separately divided into one group each. Moreover, the northwestern region included two-thirds of the SX trees, and the remainder were in the northeast region. By analyzing genetic diversity and structure within populations, individuals with different genetic backgrounds were screened for constituent training populations (TRS), including broad allelic variation for related traits. This ensures that the genomic prediction model can accurately capture genetic effects and provide reliable predictions across a broad spectrum of genetic backgrounds. Therefore, our results will benefit genome breeding technology.

The implementation of a swift and economical molecular genetic approach, ensuring both efficacy and cost-effectiveness and facilitating population certification, is of utmost significance for breeders and the conservation of Turkiye's native pigeon biodiversity. In this study, we aimed to examine the genetic structure of racing pigeons (Columba livia domestica) raised in Turkiye using a genetic marker panel consisting of eight short tandem repeat (STR) loci. For this purpose, DNA was isolated from the shed feathers of 216 pigeons. Genomic DNA was amplified using the multiplex allele-specific PCR and subsequent capillary electrophoresis with ABI PRISM 3130XL Genetic Analyzer. Next, PCR products were analyzed in the GeneMapper Software program (Applied Biosystems). For parent testing, paternity index (PI), combined paternity index (CPI), and cumulative probability of paternity (CPP) were calculated. Furthermore, population genetic diversity was evaluated using heterozygosity (He), polymorphism information content (PIC), and Hardy-Weinberg equilibrium (HWE) testing. Results revealed that the total number of alleles is 81 and the number of alleles per locus varies between 4 and 19. The similarity rate between parent and offspring was calculated as 99.99% and above. Since no pedigree information was given when the samples were analyzed, obtaining this similarity ratio demonstrates the reliability of the panel. He values range from 0.362 to 0.919, and the PIC values range from 0.295 to 0.909. Loci PG-1, PG-2, and PG-3 show significant genetic diversity, with moderate to high PIC values reflecting varied allele frequencies in the population. Consequently, the set of seven STR markers (+ one sex marker) can be applied to identify and confirm parentage on a regular basis, thereby facilitating efficient breeding programs and ensuring genetic diversity conservation. This panel enables efficient pedigree analysis and gender determination, optimizing cost-effectiveness. The methodology presented in this study is ideal for pedigree analysis and breed certification in the Turkish pigeon breeding industry. Consequently, we affirm that the study data carries considerable national importance. [ABSTRACT FROM AUTHOR]

In this study, twelve polymorphic microsatellite loci were screened to evaluate the genetic diversity of five yellow drum (Nibea albiflora) populations in the Zhoushan Sea region of the East China Sea, including one wild population (WP), one artificially propagated population (common population, CP), and three breeding populations (parent population, F4; all-female population, AF; and neo-male population, NeoG). The results of genetic diversity analyses showed that all five yellow drum populations had relatively high genetic diversity, with the highest in WP and the lowest in NeoG. Genetic structure analyses showed that the level of genetic differentiation among populations was low, with that between CP and F4 being the largest, whereas that between CP and WP was the smallest. Mutation–drift equilibrium analysis showed that the five populations likely did not experience a recent bottleneck. Our results suggest the CP population was the most suitable for large-scale release for stock enhancement, and precautionary measures shall be taken for the AF population before it is used for cage culture to avoid potential genetic concerns of the wild population. Nevertheless, further genetic diversity monitoring is needed to evaluate genetic effects and avoid the negative impact of excessive genetic differentiation between breeding and wild populations. [ABSTRACT FROM AUTHOR]

Papaver somniferum L. is cultivated for its edible seeds and for the production of alkaloids. A serious problem in seed trade and processing is the intentional mixing of excellent food-quality seeds with non-food-grade-quality seeds. Tracking the correct or illegitimate handling of seeds requires an efficient method for discrimination and individualization of poppy varieties. As in human and animal forensics, DNA variable regions containing short tandem repeats (STRs) located either in non-coding DNA or in gene sequences (EST-STRs) are preferred markers for discrimination between genotypes. Primers designed for 10 poppy EST-STR loci not analyzed so far were tested for their discriminatory ability on a set of 23 related P. somniferum L. genotypes. Thirty-three EST-STR alleles were identified together. Their polymorphic information content (PIC) values were in the range of 0.175–0.649. The PI value varied in the range of 0.140–0.669, and the cumulative PI was 1.2 × 10−5. PIsibs values varied between 0.436 and 0.820 and the cumulative value was lower (5.0 × 10−3). All analyzed genotypes were distinguished mutually, each with its own unique EST-STR profile. These newly developed EST-STR markers more effectively discriminated P. somniferum L. genotypes, even those genotypes whose DNA profiles were previously identical. [ABSTRACT FROM AUTHOR]

Breeding habitat loss and depletion of genetic diversity can have critically negative impacts on species, and especially so for habitat specialists. The Aquatic Warbler Acrocephalus paludicola is a threatened European songbird that breeds in fens, which have been lost and fragmented over centuries. We used microsatellite loci to perform a spatial and longitudinal comparison, comparing samples collected recently (contemporary) with those obtained about two decades earlier (historical) from c. 25% of the breeding range (Biebrza and Polesie) of the Aquatic Warbler. With these data we explored changes in genetic diversity, expansions and reductions of population size, population structure, and gene flow. Allelic richness, expected heterozygosity, the number of effective and private alleles, and effective population size (NE ≈ 200) were low and comparable across time and space. We detected a genetic bottleneck in contemporary Biebrza, and a less certain bottleneck in both historical and contemporary Polesie. Across space, Biebrza and Polesie were not genetically differentiated in either period. All the historical samples clustered together, but in the contemporary samples a small part of Polesie clustered separately (FST = 0.011). Across time, Biebrza and Polesie showed low but significant differentiation (FST = 0.026–0.064), and historical and contemporary groups clustered apart. A principal coordinate analysis on genetic distance detected three groups, which spanned sampling locations. In the temporal comparison, the contemporary group and contemporary Biebrza had elevated mean within‐group pairwise relatedness. We did not recover signals for sex‐biased dispersal, asymmetric gene flow or isolation‐by‐distance using the molecular data. Our results suggest that the studied populations show: (1) impoverished genetic diversity, (2) a change in allele frequencies over the two decades studied and (3) high gene flow between distant breeding sites, implying high resilience to habitat fragmentation that should facilitate the success of recolonising restored habitat patches by Aquatic Warblers. [ABSTRACT FROM AUTHOR]

Polyandry, a fundamental aspect of honeybee biology, influences genetic diversity within bee colonies. The Csd gene, responsible for sex determination, exhibits a high intraspecific polymorphism, making it a promising candidate for studying patrilines. This study investigates the potential of the complementary sex-determiner gene (Csd) as a marker for genetic studies of honeybee colonies, comparing its efficacy with standard microsatellite markers. A worker bee brood from five colonies was genotyped using both Csd and microsatellite markers. The results showed that Csd alleles offer higher variability than microsatellite markers, providing a superior resolution in genotyping. The number of distinct Csd alleles in each colony surpassed microsatellite markers, demonstrating the potential of Csd for detailed genetic analyses. Despite challenges in Csd amplification efficiency, a two-step nested PCR protocol proved effective. Interestingly, Csd genotyping alone identified more patrilines than the set of five microsatellite markers, emphasizing its efficacy. Combining Csd and microsatellite genotyping enhances the resolution of genetic studies in honeybee colonies, offering valuable insights into genetic diversity, reproductive success, and social dynamics. The Csd gene emerges as a promising tool for advancing genetic studies in honeybee populations. [ABSTRACT FROM AUTHOR]

The rhizostomatid scyphozoan Rhopilema nomadica is one of the most notorious marine invasive species established in the eastern Mediterranean Sea. Using seven microsatellite loci, here, we examined the population genetic structures on 587 individual tissue samples collected from 21 sites along the Mediterranean coast of Israel over a period of 16 years. The results indicate unique microsatellite landscapes for all samples, which belong to a single unstructured population. The >20 alleles found in most loci, low fixation index (F) values (average 0.106), and high heterozygosity (average 0.667) suggest random or assortative mating. Additionally, the low overall differentiation (Fst) values (0.043) and pairwise Fst values between the samples collected in different years indicated gene flow and random mating over the years, potentially due to the long-lasting podocytes, scyphistomae, and adults causing a population overlap between the sampled months/years. Likewise, analyses were conducted between seasons, sites, and early/intermediate/late periods of collecting years. These results support the previous analyses performed on the mitochondrial gene cytochrome oxidase subunit I (COI) sequences, altogether indicating a highly polymorphic single unstructured R. nomadica population in the Levant, possibly backed by independent introductions. The results hint to the existence of highly functional connectivity with a genetically highly diverse source population. [ABSTRACT FROM AUTHOR]

Cattle are losing maximum breeds among the world's livestock. Genetic variability data is essentially required for conservation decision-making. Thutho is a recently registered Indian cattle breed (INDIA_CATTLE_1400_THUTHO_03047) from the northeast region (NE), a biodiversity hotspot. Genetic diversity in the Thutho population and its differentiation from the only other cattle breed of NE (Siri) and cattle (Bachaur) of the neighboring region was established using highly polymorphic, FAO-recommended microsatellite markers. Numerous alleles (253) were detected across the 25 loci. The mean observed and expected numbers of alleles in the population were 10.12 ± 0.5 and 4.5 ± 0.37, respectively. The observed heterozygosity (0.67 ± 0.04) was lower than the expected heterozygosity (0.73 ± 0.03) which indicated a departure from the Hardy–Weinberg equilibrium. A positive FIS value (0.097) confirmed the heterozygote deficiency in the Thutho population. Genetic distance, phylogenetic relationships, differentiation parameters, population assignment, and Bayesian analysis explicitly ascertained the unique genetic identity of the Thutho cattle. The population did not suffer any bottlenecks in the past. Thutho has minimum diversity among the three populations; hence, its scientific management needs to be initiated immediately. Interestingly, genetic variation is enough for formulating breeding programs for managing, improving, and conserving this precious indigenous cattle germplasm. [ABSTRACT FROM AUTHOR]

India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country. [ABSTRACT FROM AUTHOR]

Globally, maize is one of the most consumed crops along with rice and wheat. However, maize is sensitive to different abiotic stress factors, such as drought, which have a significant impact on its production. The aims of this study were to investigate (1) genetic variation among 41 maize-inbred lines and the relationships among them and (2) significant marker–trait associations (SMTAs) between 7 selected physiochemical traits and 200 simple sequence repeat (SSR) markers to examine the genetics of these traits. A total of 1023 alleles were identified among the 41 maize-inbred lines using the 200 SSR loci, with a mean of 5.1 alleles per locus. The average major allele frequency, gene diversity, and polymorphism information content were 0.498, 0.627, and 0.579, respectively. The population structure analysis based on the 200 SSR loci divided the maize germplasm into two primary groups with an admixed group. Moreover, this study identified, respectively, 85 SMTAs and 31 SMTAs using a general linear model (Q GLM) and a mixed linear model (Q  + K MLM) with statistically significant (p < 0.05 and <0.01) associations with the seven physiochemical traits (caffeic acid content, chlorogenic acid content, gallic acid content, ferulic acid content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity, leaf relative moisture content, total phenolic content). These SSR markers were highly correlated with one or more of the seven physiochemical traits. This study provides insights into the genetics of the 41 maize-inbred lines and their seven physiochemical traits and will be of assistance to breeders in the marker-assisted selection of maize for breeding programs. [ABSTRACT FROM AUTHOR]

India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (>0.6) and the average number of alleles per locus (>8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei's genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8–7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households. [ABSTRACT FROM AUTHOR]

Simple Summary: This study provides an example of the creation of a biobank of drone sperm of specific subspecies of Apis mellifera L. For subspecies identification, morphometric ("classical morphometry") and genetic (tRNAleu-COII mtDNA and nine SSR markers) methods were used. A honey solution was used as a cryopreservative. It was shown that the main values of frozen–thawed sperm decreased compared to those of fresh sperm. However, the use of honey in sperm cryopreservation has great potential. The cryopreservation of gametes and embryos is an important element of biodiversity conservation. One species in need of conservation is the honey bee Apis mellifera L. Changing environmental factors, especially the anthropogenic factor, have led to a reduction in the numbers of this insect species. In this study, we provide an example of the creation of a biobank of honey bee drone sperm. For sperm cryopreservation, drones of the most common subspecies of honey bees common in Russia were selected. These were the dark forest bee, Apis mellifera mellifera, from the Republic of Bashkortostan, with three subspecies (A. m. carnica, A. m. carpatica, and A. m. caucasica) from the southern regions of Russia, as well as two breeding stocks, the Far Eastern bee and Prioksky bee. For subspecies identification, morphometric and genetic methods were used. The subspecies of the studied samples were confirmed via the analysis of the tRNAleu-COII locus of mitochondrial DNA and nine microsatellite markers of nuclear DNA. It was shown that bees of the Prioksky breeding stock belong to the subspecies A. m. caucasica based on phylogenetic analysis, and the Far Eastern breeding stock is a stable hybrid, descending on the maternal line from the evolutionary lineage C or O. The results of the morphometric analysis are consistent with the results of the genetic analysis. For the cryopreservation of sperm, we used a cryoprotectant solution with honey. As a result, the viability of frozen–thawed sperm decreased by 20.3% compared to fresh sperm, and overall motility decreased 25-fold. The measurement of the sperm concentration in the spermatheca of artificially inseminated queens showed that it varied from 0.22 to 4.4 million/μL. Therefore, the use of honey in sperm cryopreservation has great potential. [ABSTRACT FROM AUTHOR]

Isolation-by-distance (IBD) pattern among bilberry (Vaccinium myrtillus L.) populations has previously been reported for this species in northern Europe. However, the number of molecular studies conducted on bilberry, using everything from isoenzymes, RAPDs to microsatellite markers, are very few and far between. Considering that Bosnia and Herzegovina (B&H) is a country rich with diverse fruit genetic resources, conducting a genetic characterization of the naturally occurring V. myrtillus populations could yield valuable data for the conservation and utilization of this resource. This study entailed genotyping samples collected from three bilberry populations located in Fojnica, Kladanj, and Srebrenica municipalities using seven polymorphic microsatellite or SSR (simple sequence repeats) markers. The obtained molecular data was used to calculate the correlation between the physical distance of the individual B&H populations and a parameter of the genetic differentiation (pairwise Fst). The results of the correlation analyses revealed an absence of a significant isolation-by-distance pattern among the three examined B&H bilberry populations. In addition, the most pronounced genetic differentiation was detected between the Srebrenica and each of the two remaining B&H populations. At the same time, the values for pFst were significant, albeit much lower, between the Fojnica and Kladanj populations. Bilberries from the sampled Srebrenica population appear to be distinct from the other B&H populations, possibly due to the different genetic origin of this population. [ABSTRACT FROM AUTHOR]

The direction and rate of gene flow between the perennial wild rice species, O. longistaminata and cultivated rice, O. sativa was investigated using nine Microsatellite (SSR) markers. The study involved characterization of parental lines of two cultivated rice varieties and O. longistaminata and their F1 progenies. Presence of crop-specific alleles in the wild species or vice-versa was used as an indicator of occurrence of gene flow between the two species. The study revealed that gene flow between O. longistaminata and each of the two varieties of O. sativa occurs naturally. The direction of gene flow was mainly from the cultivated to wild species. The rate (frequency) of gene flow was higher from cultivated (O. sativa) to wild rice (O. longistaminata) than from O. longistaminata to O. sativa and varied with cultivated rice variety. Higher rate of gene flow from cultivated to wild species could be due to floral structure and out-crossing nature of the wild species (O. longistaminata). Gene flow between O. longistaminata and O. sativa is likely to change genetic integrity of natural populations of the two species in areas where they occur sympatrically. However, isolation by distance can help to control gene flow between these species. [ABSTRACT FROM AUTHOR]

The aim of the present experiment was to study the genetic diversity in 79 individuals from the Rhodope Shorthorn cattle breed, raised in the region of Smolyan, Bulgaria. For the purpose of the experiment was used a panel of 11 microsatellite markers. A total of 103 alleles were identified and 7 of them were population-specific. The allele number per locus varied from 6 (BM1824) to 14 (TGLA53), with a mean number of 9.36. The highest number of heterozygotes (72) was observed in locus TGLA227 (n = 79). The lowest number of heterozygotes (41) was detected in locus ETH10 (n = 79). Microsatellite markers used in the current experiment showed PIC from 0.52 (ETH10) to 0.88 (ETH3), with a mean value of 0.897. Observed heterozygosity (Ho) varied from 0.767 (locus ETH10) to 0.946 (INRA23). Expected heterozygosity (genetic diversity - He) varied from 0.205 in locus ETH10 to 0.819 in locus TGLA227. Heterozygosity for all investigated loci was Ho = 0.897 and He = 0.586. Effective allele number (N) was between 7 (ETH10, INRA 23) and 14 (TGLA 53). Estimated values (PIC, Ho, He, and MNA) showed that all studied markers were polymorphic. All tested loci were with high Polymorphic information content (>0.5) and Ho > 0.6. [ABSTRACT FROM AUTHOR]

Simple Summary: Supratidal rockpools stand out as some of the most extreme environments on the planet. These pools are exposed to the wave's action, fluctuations in sea level, dramatic shifts in water temperature, high salinity levels, desiccation, and intense sunshine. As a result, only a handful of species can survive there, with aquatic beetles of the genus Ochthebius being the insects that dominate this kind of habitat on the Mediterranean coast. In this work, we genetically analysed four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) found along the Mediterranean coasts of Spain and Malta to develop microsatellite markers, which are repetitive DNA motifs, for the first time for this genus. Additionally, we obtained the complete mitochondrial genome of three species (O. lejolisii, O. subinteger, and O. quadricollis). These newly developed microsatellite markers and mitochondrial genomes for Ochthebius will be valuable in future studies for evolutionary and ecological research on the diversity of this genus: identification, genetic structure, population connectivity, etc. Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools. [ABSTRACT FROM AUTHOR]