Search

Numerous individuals of an amphipod previously unreported from the Black Sea were found in 2017 on structures of a mussel and oyster marine farm, near the outer roadstead of Sevastopol Bay, Crimea. The species discovered was morphologically especially similar to Stenothoe tergestina (Nebeski 1881) and provisionally identified as Stenothoe cf. tergestina. The morphology, population structure, and ecology of this species were studied. An analysis of the population structure of S. cf. tergestina in the years 2017–2022 showed that adult females, males, and juveniles were present in the samples year round. The animals preferred to dwell on surfaces overgrown with periphyton colonies of the hydroid polyp of the genus Aglaophenia Lamouroux 1812. In the collections of amphipods from the periphyton of the farm structures, S. cf. tergestina turned out to be the most abundant (70–90% of the total number of identified amphipod individuals). The length of adult females was up to 4.5 mm, while it reached up to 3.6 mm in males. [ABSTRACT FROM AUTHOR]

Background: Garlic (Allium sativum L.) is an important crop with significant medicinal and culinary uses. Understanding the genetic diversity and population structure of Himalayan garlic genotypes from Sikkim is crucial for effective breeding and conservation efforts. This study aims to analyze the genetic diversity among 60 Himalayan garlic genotypes collected from various altitudinal locations of Sikkim, India, using 27 Simple Sequence Repeats (SSR) markers. Methods and results: The genetic diversity was assessed using SSR markers, which revealed substantial variation among the genotypes. The number of alleles (Na) ranged from 1.13 to 2.00, while the major allele frequency (MAF) varied from 0.672 to 0.963. The observed heterozygosity (Ho) ranged from 0.0667 to 0.475, indicating moderate genetic diversity. Population structure analysis using STRUCTURE software grouped the genotypes into three distinct sub-populations, suggesting genetic differentiation not solely based on leaf morphology. Analysis of Molecular Variance (AMOVA) showed that genetic variation was more significant among individuals within populations (41%) than among populations (16%). UPGMA dendrogram and Principal Coordinates Analysis (PCoA) further confirmed the genetic relationships among the genotypes. Conclusions: This study reveals significant genetic diversity among Himalayan garlic genotypes from Sikkim, with clear genetic differentiation observed within and between populations. The results highlight the importance of both leaf morphology types and genetic structure in understanding the genetic basis of phenotypic variation in garlic. The finding provides valuable insights for future breeding programs and conservation strategies, emphasizing the need to consider morphological and genetic data for effective germplasm management and improvement of garlic cultivars. [ABSTRACT FROM AUTHOR]

Understanding the genetic diversity of crops is of fundamental importance for the efficient use and improvement of germplasm resources. Different molecular genotyping systems have been implemented for population structure and phylogenetic relationships analyses, among which, microsatellites (SSRs) and single nucleotide polymorphisms (SNPs) markers have been the most widely used. This study reports the efficacy of SNPs detected via double-digest restriction-site-associated DNA sequencing (ddRADseq) and SSRs analyzed via capillary electrophoresis (CE) and high-resolution melting (HRM) in tomato. In total, 21,020 high-quality SNPs, 20 CE-SSRs, and 17 HRM-SSR markers were assayed in a panel of 72 accessions that included a diversified set of landraces, long-shelf-life cultivars and heirlooms with different origins and fruit typology. The results showed how the population structure analysis was consistent using the three genotyping methods, although SNPs were more efficient in distinguishing cultivar types and in measuring the degree of accessions' similarity. Compared to CE-SSR, the analysis of microsatellites via HRM yielded a slightly higher number of alleles (98 vs. 96). HRM-SSR demonstrated a distinction between European and non-European germplasm, better resolving the collection's diversity and being more consistent with SNP data. Phylogenetic trees drawn with independent marker data, detected specific groups of accessions showing robust clusters, highlighting how heirlooms were less heterogeneous than landraces. In addition, the fixation index (FST) revealed a high genetic differentiation between heirlooms and long-shelf-life cultivars, with SNP and SSR-HRM data emphasizing the distinction between cherry and plum types and CE-SSR data between cherry and oxheart types. In all instances, a greater molecular variance was found within the different considered biological statuses, provenances, and typologies rather than among them. This work presents the first attempt to compare the three tomato genotyping techniques in tomato. Findings highlighted how the markers used are complementary for genetic diversity analysis, with SNPs providing better insight and HRM-SSR as a viable alternative to capillary electrophoresis to dissect the genetic structure. [ABSTRACT FROM AUTHOR]

Rice blast disease is one of the most disastrous diseases causing significant losses to the crop. In the humid weather conditions of north-eastern Himalayan region, the situation is highly devastating as the climate is very favorable to the fungus Magnaporthe oryzae. Development of resistant rice varieties is the most effective, economical, and environment-friendly way to control this disease. The study aimed to identify novel sources of resistant donor using agro-morphological and gene-based markers for their utilization in development of blast-resistant varieties with high yield potential. Phenotypic evaluation has classified the hundred landraces into resistant (13), moderately resistant (43), moderately susceptible (24), and susceptible (20). Fifty-nine genotypes were found to carry genes responsible for blast resistance, either singly or in combination. The genotype MN-62 was found to have a blast score of zero in field screening. The genetic frequencies of the major blast resistance genes ranged from 28 to 97%. The cluster analysis grouped the landraces into three major groups. Additionally, the association between blast genes was computed with blast score using a general linear model (GLM) and mixed linear model (MLM), revealing that the markers AP4007, AP56595, C1454, and RM208 were found to be associated with the trait. The landraces with six blast R-genes like Nungshang Phou, Ratkhara, Anandhi, RCPL 1–44, Ching Phou Khong Nombi, MN-31, Rona Yang, and RCPL-128 were also superior for agro-morphological traits. Similarly, the landraces MN-62, Tara Bali, Rato Bhan Joha, MN-47, RCPL 1–411, and CAU-R1 were promising regarding yield and blast resistance. The resistant lines with various combinations of blast resistance genes can be utilized for introgression of genes into the commercial varieties for durable resistance using marker-assisted backcrossing. [ABSTRACT FROM AUTHOR]

Population structure of Cannabis sativa L. was explored across nine independent collections that each contained a unique sampling of varieties. Hierarchical Clustering of Principal Components (HCPC) identified a range of three to seven genetic clusters across datasets with inconsistent structure based on use type indicating the importance of sampling particularly when there is limited passport data. There was broader genetic diversity in modern cultivars relative to landraces. Further, in a subset of geo-referenced landrace accessions, population structure was observed based on geography. The inconsistent structure across different collections shows the complexity within Cannabis, and the importance of understanding any particular collection which could then be leveraged in breeding programs for future crop improvement. [ABSTRACT FROM AUTHOR]

For wheat improvement, knowledge of diversity patterns and evolutionary relationships among the germplasm is essential for the sustainable conservation of valuable genetic materials. Therefore, this investigation aims to decipher the genetic diversity and population structure of wheat germplasm and identify diverse accessions to expedite the wheat breeding programs. In this study, a diverse set of 81 bread wheat genotypes, including derived doubled haploids, elite exotic lines, indigenous landraces and cultivars were used. Phenotypic and molecular characterization was conducted using 10 morpho-physiological traits and 68 microsatellite (SSR) markers, respectively. Among, the nine morphological descriptors the highest morphological variation (H) was observed for 1000 grain weight (1.06). The genotypes based on phenotypic traits were grouped into three clusters using Euclidian distance. Principal component analysis (PCA), revealed that the first four significant principal components accounted for 78% of the variance. A total of 58 alleles were generated from 27 polymorphic SSR primers with an average of 2.15 alleles per locus. The polymorphic information content (PIC) ranged from 0.26 (Wmc434) to 0.76 (Wmc47), with an average of 0.69. Molecular analyses by NTSYS-PC delineated the genotypes into four clusters, whereas while the cluster tree generated using neighbour-joining analysis identified three major clusters. Structure analysis grouped the genotypes into three sub-populations. When comparing agro-morphological and molecular clusters, seven genotypes (DH 194, DH 207, DH 215, DH 217, CIMMYT line 30 Entry No.10, Chamba landrace 18 and C 306) were identified as common. Notably, these genotypes were identified as distant and belong to different diversity clusters. Therefore, integrating morphological analysis with a polymorphic SSR survey may be effective in selecting diverse parental lines in wheat hybridization programs. [ABSTRACT FROM AUTHOR]

Papaya (Carica papaya L.) is a versatile tropical fruit crop with economic and nutritional benefits. Assessing genetic diversity of the germplasm is essential for effective collection, conservation management and utilization of resources for breeding purposes. Genetic variability and population structure were studied for 55 papaya accessions including landraces, cultivars, and exotic collections, using 15 simple sequence repeat (SSR) markers. SSR analysis data revealed a total of 95 alleles with an average of 6.3 alleles per marker and an average heterozygosity of 0.75. All the markers were polymorphic, with an average PIC value of 0.72. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on shared allele distance grouped the accessions into four main clusters. Genetic structure based on the structure algorithm identified two populations, whereas discriminant analysis of principal components revealed four distinct genetic clusters. Remarkably, these clusters were not linked to the geographic regions. The analysis of molecular variance (AMOVA) indicated a variation of 75% within individuals and 22% between populations. Fst = 0.216 and Nm = 0.205 showed moderate genetic relationship within populations. These findings have implications for marker-assisted breeding, improvement of conservation strategies, detection of duplicates, and framing policies for sustainable crop utilization. [ABSTRACT FROM AUTHOR]

Sweetpotato (Ipomoea batatas (L.) Lam), a vital root crop cultivated globally by small and marginal farmers, plays a pivotal role in combatting malnutrition and serves as a lifeline for underdeveloped nations. In order to optimize the utilization of germplasm for breeding purposes, it is crucial to comprehend the extent of genetic diversity it encompasses. The effective utilization of genetic diversity in germplasm resources hinges on assessing genetic relationships among diverse cultivars and landraces, facilitating improved breeding programs and sustainable agricultural practices. In this study, 31 sweetpotato genotypes were examined to assess genetic diversity using 21 simple sequence repeat (SSR) markers. A total of 704 amplicons were detected, averaging 33.52 per marker. Band frequency ranged from 0.33 to 0.69, while polymorphic information content ranged from 0.03 to 0.61. Utilizing the Dice similarity coefficient, the 31 genotypes were clustered into three primary clusters, demonstrating similarity scores from 0.09 to 0.92. Subsequent subdivision of these clusters revealed nuanced relationships within the dataset. Population structure analysis uncovered two well-stratified subpopulations, Subpop1 and Subpop2, with Fst values of 0.49 and 0.23, respectively. Average distances within Subpop1 and Subpop2 were 0.26 and 0.33, and the estimated allele-frequency divergence was 0.21. The SSR markers utilized in this study proved to be informative and polymorphic, offering insights into the genetic diversity of sweetpotato. These markers hold significant potential for enhancing breeding programs aimed at improving elite progenies in the future. [ABSTRACT FROM AUTHOR]

Quercus brantii var. persica and Quercus infectoria are two economically and ecologically important oak species widespread in the Zagros forest, located in the northwestern and southwestern parts of Iran. An effective study of the genetic diversity and population structure of these genetic resources is still unexplored. In the present study, 48 accessions of the mentioned oak species collected from different regions of Kermanshah province were subjected to a study of genetic diversity and population structure using two sets of markers (inter-simple sequence repeats [ISSR] and CAAT-box derived polymorphism [CBDP]). CBDP markers showed greater efficiency in detecting polymorphism in the oak individuals studied. The analysis of molecular variance [AMOVA] showed that the genetic variation within species, as well as within regions per species, was higher than between species. Quercus brantii var. persica had the highest values for all indicators of genetic variability. Moreover, at the regional level, the Dalahoo populations in both species showed the highest genetic diversity using the ISSR markers. This population, along with Gilan-e-Gharb had the highest genetic diversity using the CBDP markers. The results indicate a high level of genetic diversity in isolated regions, which in turn promotes the formation of population structure. Therefore, this may contribute to further conservation and genetic improvement of Iranian oak germplasm. [ABSTRACT FROM AUTHOR]

Biological invasions are a growing threat to native ecosystems, and genomic studies have become an increasingly useful tool for invasive species management by providing the ability to identify spatial population structure in the invaded range. In this study, we compared the spatial genetic structure of two ecologically distinct non-native lizard species both established and widespread throughout South Florida, a global hotspot for reptile invasions. We used an individual-based sampling approach to collect genetic samples of Agama picticauda, a rock specialist native to West Africa, and Basiliscus vittatus, a riparian specialist from Central and South America. We collected specimens across Miami-Dade County (the original site of introduction) and then genotyped ~ 4000 single nucleotide polymorphisms for each species. Both species exhibited fine-scale population structure at distances < 5 km for A. picticauda and < 10 km for B. vitattus, but at the county scale B. vittatus showed much stronger spatial structure compared to A. picticauda. Landscape genomic analysis revealed no significant landscape influence on A. picticauda genetic differentiation, while for B. vittatus low canopy cover was the best predictor of genetic connectivity. The genetic structure of both species may suggest human-aided dispersal is driving long distance movements, and A. picticauda appear more susceptible to these events likely due to their affinity for highly urbanized areas. By identifying variable dispersal patterns among two ecologically distinct species, we hope that this study will help combat the spread of these or similar species as they continue to arrive at urban centers across the globe. [ABSTRACT FROM AUTHOR]

Reductions in gene flow due to anthropogenic habitat fragmentation are often associated with reduced genetic diversity and increased population structuring in wildlife populations. We assessed fine-scale population structure and landscape factors influencing gene flow in threatened boreal woodland caribou (Rangifer tarandus caribou) based on genotypes for 337 individuals sampled at the southern extent of their distribution in Ontario. The impact of isolation by distance (IBD) and isolation by resistance (IBR) on gene flow was examined using resistance surface optimization and linear mixed-effects modelling. Genetic clustering algorithms failed to identify a biologically meaningful pattern of population substructure, consistent with the observed weak genetic differentiation of individuals across the study area. Although the inferred optimum resistance scenario differed based on the choice of genetic distance metric, roads were consistently included in the top resistance models. While our results support a growing body of evidence indicating a negative influence of roads on gene flow in woodland caribou, future studies are recommended to validate these finding given the conservation implications for this iconic boreal species. [ABSTRACT FROM AUTHOR]

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species. [ABSTRACT FROM AUTHOR]

Indigenous landraces are heterogeneous and exhibit greater gene diversity, and are therefore an excellent source of variation and material for crop improvement. However, they are very prone to genetic erosion, therefore exploration of genetic variability in landraces is essential step for crop breeding. Discovery of the genetics of a character in rice, that cope adverse condition, is important for maintaining world-food supply. In this study, fifty rice genotypes were assessed for the phenotypic and genetic diversity and their relatedness using morpho-physiological traits of the genotypes. Further clustering and population structure analysis were performed using phenotypic and simple sequence repeat (SSR) markers data through unweighted pair group method with arithmetic mean (UPGMA) and STRUCTURE analysis. Significant variation among yield components were identified. Phenotypic and genotypic coefficients of variability were higher for filled grains, whereas heritability was highest for plant height. Panicle number and 100-grain weight displayed significant relationship with yield. Phylogenetic clustering of the agromorphological traits divided the genotypes into eight clusters, whereas SSR markers yielded ten clusters. SSR markers produced a total of 138 alleles varying from two to nine with 77.53% polymorphic allele having 3.69 alleles per locus (average). The polymorphic information content indices and observed number of alleles varied among markers with an average of 0.649, exhibiting RM336, RM316, and RM287 have the greatest potentiality in exploring genetic diversity among genotypes. Among the genotypes, Dolkochu, Jolduba, BRRI Dhan-32, and Mokbul displayed significant variability, suggesting their suitability as potential parents in hybridization programs. Population structure study demonstrated that the genotypes were structurally diverse that grouped the accessions into two subpopulations (K = 2). Therefore, this research aimed to identify potential genotypes and suitable traits of rice germplasms for breeding programs. [ABSTRACT FROM AUTHOR]

The results of a comparative study of the genetic structure, parameters of intraspecific genetic diversity, and spatial differentiation of 35 populations of Picea abies–P. obovata–P. koraiensis species complex, located within the areas of distribution of "pure" species and in the contact zones of their ranges were presented. P. abies populations from Eastern Europe (Belarus, Poland); spruce populations from the European part of Russia, the Urals, and the West Siberian Plain, located in the zone of P. abies and P. obovata introgressive hybridization; P. obovata populations from various parts of the extensive range of this species in Siberia and Mongolia; and P. koraiensis populations from the Russian Far East and Northeast China were analyzed. The study of genetic variability and differentiation of populations was based on the analysis of variability of three microsatellite loci: Pt63718, Pt71936, and Pt26081, developed on the basis of Pinusthunbergii Parl chloroplast genome. The use of these DNA markers made it possible to obtain data indicating a fairly high degree of P. koraiensis genetic divergence from two other spruce species included in the complex, P. abies and P. obovata. Korean spruce growing in the Far East differs significantly from the populations of these species in the number and composition of haplotypes, the level of genetic diversity, and population structure, which gives us reason to consider it as a separate species. [ABSTRACT FROM AUTHOR]

In order to describe large-scale spatial structure of sockeye salmon on the Asian part of the range, the variability of 45 SNP loci was analyzed in 22 samples from the Northwest coast of the Pacific Ocean. Three large regional population complexes were identified: Southwest Kamchatka, Kamchatka River basin, and the Northeast (comprising stocks from Koryak Highlands). Populations within the identified complexes are connected by gene migration and have a common origin, close geographic proximity, comparable climatic, landscape, and environmental conditions in the freshwater and early marine periods of sockeye salmon life. Populations confined to watersheds of the North coast of the Sea of Okhotsk (Palana and Okhota rivers), along with island populations, displayed distinctions from the isolated population complexes. It is hypothesized that the marked divergence observed in island populations is primarily caused by genetic drift occurring during long periods of isolation. The pronounced divergence of Palana River population may be the result of both genetic drift and natural selection, driven by the challenging smoltification and specific conditions of freshwater period in this watershed. At the same time in the Okhota River population, demographic factors such as genetic drift and bottlenecks played a key role. [ABSTRACT FROM AUTHOR]

Colombian Creole pigs have adapted to tropical conditions for over 500 years. They have been modified by natural and artificial selection in different regions. At present, the diversity and current introgression status are unknown. The objective was to estimate the genomic diversity, linkage disequilibrium, population structure, and admixture of four Colombian pig breeds and their relationship with other breeds worldwide. Three Colombian pig breeds (SPE-San Pedreño, 11 samples; ZUN-Zungo, 11 samples; CM-Casco de Mula, ten samples) from the conservation nucleus and one biotype not recognized as a breed (CCH-Criollo Chocoano, seven samples) were genotyped using the Illumina GGP-Porcine80K chip. Open-access data from seven international breeds were also included. Colombian Creole pigs showed moderate genetic differentiation (FST 0.14) globally, but several groups of animals separated, suggesting local clustering due to geographical isolation or different founding effects. Colombian Creole pigs showed breed imprinting and specific grouping in all analyses except for CCH, which, like the Ecuadorian Creole, was a cluster of admixtures. The Colombian Creole pigs revealed a significant relationship with the Iberian pig and some other breeds to varying degrees. However, good maintenance of the conservation nucleus was evidenced. Potential adaptive genes, mainly related to immunological functions, were found, according to FST and pcadapt analyses. This study provides a foundation and scientific data for policy decisions on zoogenetic resources. [ABSTRACT FROM AUTHOR]

Lumpy skin disease (LSD) is a transboundary, viral disease of cattle with a significant economic impact on the livestock industry. This study describes the epidemiological investigations of outbreaks of LSD that occurred in 2022 in three Indian states viz., Haryana, Himachal Pradesh and Rajasthan and the genetic characterization of Lumpy skin disease viruses (LSDVs). Also, the population structure analysis of LSDVs was carried out. Out of 138 scab samples tested from suspected cattle for LSDV, 106 were found positive. Of these, nine representative scab samples were further genetically characterized. Phylogenetic analysis based on the P32 and EEV gene sequences depicted that the LSDV strains of the present study had nucleotide identity of 100% and 99.10–99.45%, respectively with the LSDV/2019 field strains of India. Multiple sequence alignment of the EEV glycoprotein gene sequences revealed nucleotide polymorphisms at three positions viz., G178A, G253A and A459G in circulating LSDV/2022 field strains. Based on the median joining network analysis of the EEV gene, 12 haplotypes were identified among the LSDV populations. Population structure analysis corresponding to the EEV gene revealed high haplotype (0.8486 ± 0.026) and low nucleotide diversities (0.00636 ± 0.0006) and negative values for neutrality indices, indicating a high number of closely related haplotypes and the studied population may have undergone a recent expansion. The findings will help in understanding the distribution and dynamics of LSDV populations, which will prove pivotal in designing and implementing effective management and control strategies. [ABSTRACT FROM AUTHOR]

The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species. [ABSTRACT FROM AUTHOR]

The meta-analysis was used to summarize the results of previously performed studies on variability of 45 single-nucleotide polymorphism loci and 13 microsatellite loci in Asian sockeye salmon Oncorhynchus nerka populations from the eastern coast of Kamchatka and Chukotka. Allelic frequencies of both types of markers were analyzed using congruent statistical approaches in 53 sample sets from 13 sockeye salmon reproduction watersheds on the west coast of the Bering Sea and the western Pacific Ocean. The spatial structure of the species in considered part of its distribution range was assessed and four major regional population complexes were identified: the Koryak Plateau and Chukotka, the Karaginsky Gulf, the Kamchatka River Basin, and southeastern Kamchatka. The formation of the geographic structure of the sockeye salmon on the Asian Pacific coast is associated with the history of colonization of the region by the species and its adaptation to reproductive conditions in the river and lake-river systems of eastern Kamchatka and Chukotka. [ABSTRACT FROM AUTHOR]

The Artemisia genus is a group of valuable medicinal plants that are found in the temperate regions of the world. These plants have many pharmacological benefits. Iran is known to be one of the main centers of distribution for various Artemisia species, however, there is limited information available about their genetic diversity and population structure at the molecular level. In this study, 50 Artemisia accessions belonging to five species (A. fragrans Wild., A. absinthium L., A. scoparia Waldst. & Kit., A. biennis Rchb., and A. annua L.) were evaluated for genetic diversity and population structure using several start codon-targeted polymorphism (SCoT) and CATT-box derived polymorphism (CBDP) markers. Ten SCoT and eight CBDP primers were used, yielding 69 and 77 fragments, respectively. Out of these fragments, 63 and 64 were found to be polymorphic. The results showed that the CBDP marker technique was more efficient compared to SCoT due to higher values of informativeness indices. An analysis of molecular variance (AMOVA) based on all two markers and combined data revealed a higher distribution of genetic variation among species. Furthermore, A. absinthium species showed a high level of genetic diversity due to the maximum values for genetic variation parameters. Hence, this species can be attended to in future genetic and metabolomics research. The obtained clustering patterns of studied accessions by all molecular data were similar to each other and were further supported by the principal coordinate analysis (PCoA). All investigated accessions were grouped into five separate clusters. In conclusion, the results of this study suggest that SCoT and CBDP markers can be suitable for use in fine mapping research because they are more efficient for the detection of genetic polymorphism in Artemisia germplasm. [ABSTRACT FROM AUTHOR]

Knowledge of genetic diversity is one of the most essential tasks for sustainable management of medicinal plants. In the present study, the molecular variability and population structure in a set of Ferula assafoetida accessions collected from different geographical regions of Iran were evaluated using start codon targeted polymorphism (SCoT) and universal rice primer (URP) markers. Based on results, SCoT (12 primers) and URP (12 primers) markers amplified 192 and 149 polymorphic fragments, respectively. The polymorphism information content (PIC) estimated by URP and SCoT ranged from 0.31 to 0.43, and 0.34 to 0.44, respectively. The analysis of molecular variance revealed the greater genetic variation within population compared to among them. The Kerman's population showed the highest values for the heterozygosity (He), percentage of polymorphic bands (PPB), Shannon's information index (I), and effective number of alleles (Ne). The neighbor joining (NJ) clustering algorithm grouped all investigated accessions into six and five main groups based on URP and SCoT data, respectively. The results of structure analysis based on both marker systems showed that all accessions were divided into five subpopulations. Furthermore, principal coordinate analysis (PCoA) supported these findings. In conclusion, our results revealed a high level of genetic diversity and gene flow between F. assafoetida populations. Moreover, the SCoT markers were more effective than URP in detecting the genetic diversity in F. assafoetida populations. Hence, the use of SCoT markers in further genetic research such as genetic fingerprinting and association analysis would be recommended. [ABSTRACT FROM AUTHOR]

This work is part of a program for the conservation and enhancement of Tunisian genetic resources of orchardgrass (Dactylis glomerata L.). This species is of great interest, especially from an agronomic point of view. However, little information is available regarding agronomic characterization and genetic variation in Tunisian orchardgrass. This study aims to evaluate the genetic diversity of nine natural populations of orchardgrass collected in the north of Tunisia through the analysis of 16 morpho-phenological traits and 14 simple sequence repeat (SSR) markers developed from different grass species. Our results showed that the analysis of variance and multivariate analyses of quantitative parameters revealed a significant morphological and phenological variation within and among the populations mainly relating to the precocity and vigor of the plants. Moreover, the population structure was independent from the geographic origin and bioclimatic stage. At the molecular level, the 14 selected SSR markers are highly transferable and exhibited amplification in Dactylis glomerata. An average of 5.27 alleles with a polymorphism information content (PIC) of 0.69 per locus set was detected among the populations studied. The average polymorphic rate for this species was 86.08%, suggesting a high degree of genetic diversity. A high level of genetic diversity (Gst = 65.49%) was observed among the populations. Bayesian clustering based on SSR data clearly segregated populations into two groups. The results of this study will be useful to identify suitable populations that could be used in breeding programs for the improvement of Tunisian orchardgrass. [ABSTRACT FROM AUTHOR]

The complexity of citrus phylogeny and taxonomy, influenced by polyembryony, genetic diversity, and extended generation cycles, necessitates assessing genetic relationships for improved production and disease resilience. DNA polymorphism markers are pivotal in genotyping and resolving phenotypic varietal ambiguities through accurate and objective genetic relatedness and distinctiveness assessments. In this study, 27 accessions of kagzi and ornamental lime were evaluated at morphological (based on IPGRI citrus descriptor), biochemical, and molecular levels using DNA-based markers, namely, random amplified polymorphic DNA (RAPD), start codon targeted (SCoT) polymorphism, and simple sequence repeats (SSR). Morphological analysis unveiled significant variation in leaf lamina attachment, shape, margins, fruit characteristics, and texture across all parameters. Biochemical research noted minimal differences, with total soluble solids (TSS) ranging from 5.7° to 8.0° Brix and titratable acidity (TA) from 0.36 to 0.50%. Notably, ornamental lime accessions exhibited higher TSS:TA ratios of 16.00. Molecular markers (RAPD, SCoT, and SSR) corroborated these findings, yielding 115, 74, and 64 amplicons, respectively, with polymorphic percentages varying from 33.33 to 100%. Polymorphic information content ranged from 0.20 to 0.90 for RAPD, 0.41 to 0.99 for SCoT, and 0.07 to 0.67 for SSR markers. Analysis of molecular variance (AMOVA) substantiated significant genetic differences among the kagzi and ornamental lime accessions (RAPD PhiPT = 0.267, SCoT PhiPT = 0.351, SSR PhiPT = 0.107). Furthermore, STRUCTURE software 2.3.4 revealed a ΔK value of two (K = 2), indicating two distinct genetic pools within the accessions, possibly attributable to bud mutations generating varying morphological traits within the same plant. Molecular marker-based germplasm characterization can mitigate confusion linked to morphological characteristics and multiple cultivar registrations. [ABSTRACT FROM AUTHOR]

Grape is a type of fruit widely grown globally and in Türkiye thanks to its importance in human nutrition and diversity of usage areas. Türkiye has a long history of grape cultivation, and the genetic diversity of local grapes grown in some regions has still not been revealed. This study showed the genetic diversity between 60 local grape genotypes selected from north Central Anatolia and nine reference grape cultivars;10 inter simple sequence repeats (ISSR) and 7 inter-primer binding site (IPBS) retrotransposon primers were used. The mean values of genetic diversity indices in ISSR and IPBS retrotransposon primers were calculated as expected allelic frequency (p) 0.476/0.195, observed allelic frequency (q) 0.524/0.805, number of effective alleles (Ne) 1.326/1.378, Shannon's information index (I) 0.308/0.367, expected heterozygosity (He) 0.199/0.232 and unbiased expected heterozygosity (uHe) 0.201/0.234, respectively. Unweighted pair group method with arithmetic mean (UPGMA) and model-based STRUCTURE analysis divided the studied germplasm into two groups. However, local genotypes were not grouped per the regions where they grew. As a result of the analysis of molecular variance (AMOVA) analysis, the inter-population variation was determined to be 11%, and the intra-population variation was determined to be 89%. The mean genetic differentiation value (Fst) between populations was 0.303. The results showed that ISSR and IPBS retrotransposon primers effectively explained the genetic diversity. [ABSTRACT FROM AUTHOR]

Azadirachta indica (neem) is a multipurpose tree species that is distributed in Asian and African countries. It is used in food, medicine and agriculture. Our study used 20 neem-specific polymorphic simple sequence repeat (SSR) markers to investigate the genetic diversity among 170 neem germplasm from three distinct populations [North Central (NC), West Central, and South Eastern (SE)]. The study revealed moderate levels of genetic diversity. The SE population exhibited the highest genetic variation, as indicated by the observed heterozygosity (Ho = 0.63) and expected heterozygosity (He = 0.64) values, while the NC population showed the lowest genetic diversity. Furthermore, evidence of inbreeding was exhibited by the overall positive value of the fixation index (F = 0.13). The polymorphic Information content value 0.583 indicates a moderate level of marker diversity within the populations. The significant genetic differentiation coefficient (Fst) was 0.25. Analysis of molecular variance revealed that 12% of the total genetic variation was observed among the populations, whereas 88% was found within populations. Principal component analysis, clustering, and structure analysis were in correspondence with each other and identified three populations of A. indica with slight admixtures. The results of this study provide a genetic diversity of the A. indica germplasm for harnessing its genetic potential and conservation. [ABSTRACT FROM AUTHOR]

Avocado (Persea americana Mill.) is a fruit tree species that grows in different regions of the world. The edible fruit and other parts of the avocado tree have immense nutritional, oil-bearing, and medicinal value. The plant is native to Guatemala but was introduced to Ethiopia by missionaries in 1939. In southern Ethiopia, where coffee is the main cash crop, it is used as a shade for plants. However, in the past 25 years, many farmers and urban dwellers have begun to use avocados as a valuable source of income. Hence, there is a need for quality avocado trees for commercial purposes. Although there is conjecture about the wide variation in avocados in Ethiopia, the diversity and population structure of this plant has not been described. This study aims to fill this gap by comparing avocado germplasm from Guatemala and Ethiopia. A sample of 298 avocados was collected from three and four populations in Guatemala and Ethiopia, respectively. Population diversity and structure were assessed using 12 simple sequence repeat (SSR) markers. The SSR marker profile detected 112 alleles, with an average of 10.21 per locus and an average PIC value of 0.84. Genetic diversity was high, with an average of 10.2 alleles per locus, a mean Shannon index value of 1.65, and observed and expected heterozygosity of 0.51 and 0.71, respectively. The expected heterozygosity varied between populations and was highest in West Guatemala (0.85) and lowest in Gamo (0.55). An analysis of molecular variance showed that 18% of the genetic variation was between the continents and only 2% among the populations. The pairwise genetic differentiation coefficient ( F ST ) indicated high differentiation between populations. The phylogenetic tree, structure, discriminant analysis of the main components, and Nei's genetic distance analysis confirmed three groups of avocados. The Wondo Genet population was more genetically diverse than the populations from the Sidama, Wolaita, and Gamo regions. Furthermore, it revealed little genetic exchange with these populations, unlike the Guatemalan avocado, indicating the presence of unique alleles among avocados in Ethiopia. The landraces from Sidama, Wolaita, and Gamo appeared to have experienced historical drift events. [ABSTRACT FROM AUTHOR]

Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica. Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, FST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, FST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (Ne = 62.4–147.1). Genetic diversity was variable across sites and watersheds (He = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity. [ABSTRACT FROM AUTHOR]

Pyricularia (syn. Magnaporthe) oryzae is responsible for the blast disease in rice resulting in a greater extent of yield loss. However, some of the cultivars of rice have the ability to survive this devastating infection due to the presence of R (resistance) genes. Therefore, genome wide association study (GWAS) was undertaken using a panel of 400 rice landraces (ARC panel) and a set of filtered 38,723 single nucleotide polymorphisms (SNPs). The highest SNPs were mapped to chromosome 1 with a number of 4332 SNPs and lowest (2252) in chromosome 12. The ARC panel was evaluated phenotypically which revealed that 6% of the selected cultivars has resistance to rice blast disease with SES score of 1. The majority of the resistant cultivars belong to the group Asra of the panel. The population structure analysis was executed wherein three genetic subpopulations were identified namely RC1, RC2, RC3 and an admixture population constituting 48 accessions. Further, GWAS detected 15 significant association signal with P value in the range of 1.03E−05 to 1.03E−04, effect ranged from − 1.18 to 1.06, phenotypic variance explained was from 0 to 7.14%, R2 of 0.047 to 0.058, and minor allele frequency of 0.107 to 0.444. Eleven (Os01g39980, Os01g56130, Os01g67100, Os01g67110, Os03g41030, Os04g33310, Os07g42104, Os09g06464, Os09g08920, Os09g38800, Os12g37680) out of these 15 significant associations were identified as the candidate loci for the blast resistance in rice that will serve as an important genetic resistance source to be introgressed into an elite rice line in future breeding programs for deciphering blast resistance in rice. The GWAS study presented in this article helped to uncover significant gene regions which encode proteins to resist blast infection in rice plant. This is the first report on the GWAS analysis for blast resistance in unique landraces of rice from Northeast India employing single nucleotide polymorphism. [ABSTRACT FROM AUTHOR]

Color polymorphisms in poison frogs have intrigued evolutionary ecologists, as understanding the mechanisms that sustain them is of great interest. Temporal variation in selection is considered crucial for maintaining color polymorphism, and monitoring aposematic signals provides valuable insights into such temporal dynamics. We conducted a six-year study on red-belly toads, Melanophryniscus rubriventris, analyzing color patterns and body size variation across five reproductive seasons. Our findings show stable color morph ratios over time, with no discernible differences between sexes and no interdependence between dorsal and ventral patterns. Notably, darker morphs, mostly melanic, comprised only about 25% of the population, contrasting with the higher frequency of conspicuous aposematic combinations. Intermediate morphs were more prevalent, while the most extreme conspicuous dorsal pattern was rare. Regarding body size, females were significantly larger and in better body condition than males. We observed a significant decrease in snout-vent length for males between 2021 and 2022, while females showed a significant increase between 2020 and 2022. Interestingly, there was a phenotypic association between color patterns and body size, with males exhibiting black bellies having smaller snout-vent lengths compared to those with other ventral patterns, particularly red bellies. Our study suggests that dorsal and ventral color patterns may respond differently to selection. The stability of color patterns within the population could be upheld through complex interactions involving stabilizing and sexual selection. We emphasize the importance of long-term studies and recommend that future research considers reproductive ecology and individual behavioral decisions in this polymorphic aposematic species. By incorporating these aspects, we can gain a more comprehensive understanding of the mechanisms driving phenotypic variation. [ABSTRACT FROM AUTHOR]

Adoption of a rational management in dairy farms would improve the milk quality and farmers' income. In the current study, we aimed to describe bovine mastitis in 32 dairy herds, identify the main cow- and herd-associated risk factors, and analyze both epidemiological along with molecular characteristics of Staphylococcus aureus infecting udders. Based on Californian Mastitis Test and clinical examination, the prevalence of mastitis in cows was 52.25% (116/222), of which 6.3% was clinical mastitis and 45.94% was subclinical mastitis. Overall, 218 (24.54%) quarters suffered from mastitis, whose 29.81% (65/218) infected with S. aureus. Mastitis was lowest in mid-lactation with OR = 0.371 with 95% confidence interval (CI) of 0.141–0.976, and in cows separated from their calves (OR = 0.164, 95% CI 0.056–0.477) than suckler cows. Similar results were obtained from S. aureus related mastitis. To assess the genetic lineages of S. aureus isolates, we determined clonal complexes (CC) using DNA microarray hybridization profiles and performed spa typing. The strains were assigned to nine clonal complexes, and 19 spa types; with CC97 (44.77%), and CC22 (40.29%) were the most predominant lineages and t223 (40.29%), t7136 (10.44%), t359 (8.95%) and t267 (5.97%) were the most common spa types. A total of 88.05% (n = 59) isolates were resistant to at least one tested antibiotic while only 4.47% were multi-drug resistant strains. Higher rates of resistance were observed for penicillin (86.5%) and tetracycline (14.9%) respectively. Our results show the need for adoption of feasible mastitis program with special emphasis on sub-clinical mastitis and associated risk factors. [ABSTRACT FROM AUTHOR]

The abrupt decline in sardine catches in the Sea of Japan and the East China Sea (SJ-ECS) in 2014 and 2019 and the recovery in the following years call into question the current assumption that sardines in the SJ-ECS form a self-recruiting subpopulation. To test this hypothesis, we analysed otolith stable oxygen and carbon isotope profiles (δ18O, δ13C) of age-0 and age-1 sardines from 2010 and 2013–2015 year-classes captured in the SJ-ECS, as geographic markers for nursery areas. Age-0 sardines generally showed a significant ontogenetic decrease in otolith δ18O from larval to juvenile stages. However, the majority of age-1 captured in spring 2011, 2015 and 2016 showed non-decreasing otolith δ18O profiles, suggesting that the age-0 off the Japanese coast were not the main source of recruitment. Different migration groups were thus indicated: the “locals” growing up off the Japanese coast and the migrating “nonlocals”. The isotope profiles of the “nonlocals” overlapped with those of age-0 captured in the subarctic North Pacific, suggesting that they may be migrants from the Pacific, or perhaps an unobserved northward migration group in the SJ-ECS. Our results highlight the considerable uncertainty in the population structure assumed in current stock assessment models for Japanese sardine. [ABSTRACT FROM AUTHOR]

A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods ("delta" and two FST-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure. [ABSTRACT FROM AUTHOR]

Background: The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model. Results: The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83. Conclusion: Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume. [ABSTRACT FROM AUTHOR]

Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015–2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation. [ABSTRACT FROM AUTHOR]

In this study, 38 elite breeding pepper lines were genetically analyzed using SRAP markers and tested for resistance to PVY, TSWV, and PMMoV viruses using molecular markers. In the virus resistance tests, 1 line (37-H–D-6) from the Three-lobs population was found to be resistant to all 3 viruses tested. The 19 SRAP primer combinations used for genetic diversity yielded a total of 85 bands, 57 of which were polymorphic among pepper lines. While 2–8 bands per primer were obtained, the number of polymorphic bands ranged from 1 to 6. The average polymorphism rate of the primers was 66.44%. The PIC values ranged from 0.06 to 0.40 (with a mean of 0.18). In addition, the average gene diversity, effective allele number, and Shannon information index values of the primers were 0.21, 1.34, and 0.31, respectively. STRUCTURE analysis showed that the pepper lines were grouped into 4 clusters. PCoA and Q-matrix plots supported the cluster distribution. Some lines of the Sivri and Three-lobs pepper populations were observed as outliers in the plots. Kapia and Three-lobs were more similar to each other. This study showed that SRAP markers can be successfully used for genetic diversity of pepper breeding lines. [ABSTRACT FROM AUTHOR]

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H.pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high Fis and low Ne, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise Fst, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus. [ABSTRACT FROM AUTHOR]

Wheat is one of the most important staple food crops in Ethiopia and elsewhere in the world. Knowledge of its genetic diversity provides breeders a chance to develop new, improved cultivars with desirable traits. In this research the genetic diversity and population structure of 180 bread wheat germplasms representing eight populations was analyzed using 10 Inter simple sequence repeat (ISSR) markers used. Based on diversity indices all the ISSR markers were polymorphic and highly informative. High within-populations genetic diversity with a mean allele values of 1.47, effective alleles of 1.33, Shannon's Information index of 0.29, Nei's gene diversity of 0.19, and percent polymorphic loci of 80.5% were obtained in this research. Among the populations, those from the International Septoria Observation Nursery (ISEPTON) showed relatively, the highest observed number of alleles (1.47), effective number of alleles (1.33), Shannon's Information index (0.4) and Nei's gene diversity (0.19). Thus, the ISEPTON lines could be a good source of useful alleles to be used in wheat improvement programs. Analysis of molecular variance revealed that 95% of the total genetic variation resides within populations, while the remaining 5% is accounted to among populations. Clustering using unweighted pair group method with arithmetic mean, principal coordinate analysis and population structure analysis did not group the wheat populations into genetically distinct clusters following their breeding objectives. In the present research adequate polymorphism and reproducible fingerprint profiles were explored from of the genetic structure analysis in the wheat germplasms. The information obtained could thus be useful in future bread wheat breeding programs as well it its sustainable use. [ABSTRACT FROM AUTHOR]

As a renowned tea with a historical significance in China, Gushan semi-rock tea originated from the Gushan Mountain in Fujian, China. This study describes the genetic diversity, population structure, and distribution characteristics of 76 tea samples collected from Gushan Mountain and neighboring regions, using single nucleotide polymorphism (SNP) markers. The results show that the average information index (I) is 0.490, the average observed heterozygosity (Ho) is 0.384, the average expected heterozygosity (He) is 0.329, and the average fixation index (F) is − 0.132. The genetic variation mainly comes from intraregional variation, which accounts for 82% of the total variation. Furthermore, there is a closer connection between tea plants in Southern, Northern, and Eastern Fujian. The frequency of genetic exchange between tea plants in the Gushan semi-rock tea and those in Southern, Northern, and Eastern Fujian is relatively low, showing obvious uniqueness. The findings of this study help fill the gap in tea genome research in the Gushan semi-rock tea and provide valuable information on the genetic diversity of tea resources in Gushan area. The results can be utilized in future genomics, phylogeny, and breeding programs aimed at developing new tea cultivars. [ABSTRACT FROM AUTHOR]

Genetic diversity and population structure analysis is vital for germplam conservation and efficient utilization. A set of 188 tetraploid wheat (Triticum turgidum spp) genotypes, including 166 landraces and 22 improved cultivars, were genotyped using high density genotyping by sequencing by diversity arrays technology sequencing. We investigated the genetic diversity and population structure for the study panel as well as the landraces, separately based on 10,349 DArTSeq markers distributed across A and B genomes. The whole tetraploid wheat study panel was clustered into two populations: pop1 and pop2 comprising 150 landraces and three released cultivars and 19 released cultivars and 12 landraces, respectively. Further population structure analysis of the tetraploid wheat landraces revealed two subgroups of the landraces. Population structure based on the analysis of molecular variance (AMOVA) revealed significant (P < 0.001) variation between populations and within populations for both the study panels and the landraces. Total variation within population (88%, 97%) was higher than total variation between populations (12%, 3%) for both study panel and the landraces. The AMOVA result was also verified by the population structure analysis based on genetic differentiation (Fst), which was reported to be little (Fst = 0.028) and moderate (Fst = 0.117) for the landraces and the study panel, respectively, thereby implying no significant differentiation among populations. The lower genetic differentiation led to more gene flow in the study panel (Nm = 1.891) and in the landraces (Nm = 8,612) which is an indication of more gene exchange preventing genetic differentiation among populations implying a low level of diversity among subpopulations, that was confirmed by the AMOVA result. The genetic indices of the study panel revealed that pop2 (I = 0.523, Ne = 1.612, He = 0.353, uHe = 0.359) was more diverse than pop1 (I = 0.415, Ne = 1.423, He = 0.263, uHe = 0.264), which comprised of 98.04% landraces along with 1.96% released cultivars. Likewise, pop2 (I = 0.432, Ne = 1.442, He = 0.276, uHe = 0.277) of the landraces was more diverse than Pop1 (I = 1.380, Ne = 1.380, He = 0.234, uHe = 0.236). Furthermore, principal component analysis (PCA) of the tetraploid wheat study panel grouped the released cultivars together and the landraces separately. However, PCA of the landraces did not show clear groupings. The first two components together explained 77% (PC1 = 65%, PC2 = 12%) and 68% (PC1 = 48%, PC2 = 20%) of the total variation in the tetraploid wheat study panel and landraces, respectively. The total number of different alleles in pop1 (4762, 4624) and pop2 (4708, 4760) were revealed in the study panel and the landraces, respectively. 127 genotypes were reported to have one or more private alleles at 755 loci, an indication of key adaptive genes at these loci to be exploited in breeding program. In conclusion, high genetic diversity was detected in Ethiopian tetraploid wheat germplasm, which could be utilized for future wheat breeding program. Furthermore, the higher genetic variation observed within populations than between populations reveal that more attention should be given to individual accessions within populations to explore the existing genetic diversity. [ABSTRACT FROM AUTHOR]

A key goal of coral restoration is to re-establish self-sustaining coral populations and ensure resilience to future stressors, which requires that genetic diversity is maximised. However, coral genetic and genotypic (clonal) diversity is variable across reef sites via success of sexual recruitment, and cryptic species diversity can complicate breeding efforts. Assessing genotypic and genetic diversity of colonies to be used in restoration is therefore critical to avoid founder, inbreeding or outbreeding effects. Considering recent efforts to upscale coral propagation on the Great Barrier Reef (GBR), we examined species, population and clonal structure of a commonly out-planted tabular Acropora species—Acropora hyacinthus (Dana, 1864). A total of 189 colonies were sampled from six reef systems throughout the northern-central GBR and genotyped using an Acropora-specific Affymetrix microarray, which resulted in 1387 variant sites that passed quality control. Cryptic species were readily resolved and all sampled A. hyacinthus colonies represented unique genotypes within sites at three reefs. At reefs that contained multi-ramet genets (clonal genotypes), the mean and maximum between-ramet distances were 0.68 and 1.99 m, respectively. Therefore, sampling colonies > 2 m apart increases the likelihood these colonies represent distinct genets. Such a sampling design therefore maximises genotypic diversity when sourcing colonies for propagation and out-planting. Based on these variant sites, we found no between-reef genetic divergence based on locality. Furthermore, through unintentional sampling of non-target tabular Acroporid species, we show how this genotyping method may be used for resolving taxonomic uncertainty as well as population dynamics. [ABSTRACT FROM AUTHOR]

Main conclusion: The pilot-scale genome-wide association study in the US proso millet identified twenty marker–trait associations for five morpho-agronomic traits identifying genomic regions for future studies (e.g. molecular breeding and map-based cloning). Proso millet (Panicum miliaceum L.) is an ancient grain recognized for its excellent water-use efficiency and short growing season. It is an indispensable part of the winter wheat-based dryland cropping system in the High Plains of the USA. Its grains are endowed with high nutritional and health-promoting properties, making it increasingly popular in the global market for healthy grains. There is a dearth of genomic resources in proso millet for developing molecular tools to complement conventional breeding for developing high-yielding varieties. Genome-wide association study (GWAS) is a widely used method to dissect the genetics of complex traits. In this pilot study of the first-ever GWAS in the US proso millet, 71 globally diverse genotypes of 109 the US proso millet core collection were evaluated for five major morpho-agronomic traits at two locations in western Nebraska, and GWAS was conducted to identify single nucleotide polymorphisms (SNPs) associated with these traits. Analysis of variance showed that there was a significant difference among the genotypes, and all five traits were also found to be highly correlated with each other. Sequence reads from genotyping-by-sequencing (GBS) were used to identify 11,147 high-quality bi-allelic SNPs. Population structure analysis with those SNPs showed stratification within the core collection. The GWAS identified twenty marker–trait associations (MTAs) for the five traits. Twenty-nine putative candidate genes associated with the five traits were also identified. These genomic regions can be used to develop genetic markers for marker-assisted selection in proso millet breeding. [ABSTRACT FROM AUTHOR]

Understanding how bovine tuberculosis (TB) is maintained in wildlife reservoirs is critical for the management of this disease impacting cattle in many countries. For the primary wildlife reservoir of the disease in New Zealand, the brushtail possum (Trichosurus vulpecula), transmission of this contagious bacterial disease among possums is often assumed to be linked to home range overlap. Identifying drivers of possum home range, and home range overlap between individuals, is thus important for informing wildlife reservoir TB management in New Zealand. We monitored four sub-populations of free-living possums in New Zealand native forests during 10 consecutive months using live trapping, to give the first direct insight into how the frequency and area of overlaps alters with density, sex and age. A total of 832 individuals were captured (average 9.3, range from 1 to 40 captures per animal with a median value of 7) and 35,820 home range overlaps were recorded. Both the number and area of overlaps were significantly associated with age class, with 66.6% of overlaps occurring between adults, 30% between adults and juveniles, and only 3.4% between juveniles. Overall, adult males showed significantly higher numbers of overlaps than expected, while adult and juvenile females showed significantly lower numbers of overlaps than expected and no differences were observed in juvenile males. In addition, males exhibited more and larger overlaps than females. The number and size of overlaps per individual decreased with increasing local population density. Understanding shared areas of activity among individuals can provide insights into the interactions occurring and potential pathways for diseases transmitted by contact such as TB. These results can inform to develop effective strategies for the control of diseases carried and dispersed by possums. [ABSTRACT FROM AUTHOR]

India's rich diversity encompasses individuals from varied geographical, cultural, and ethnic backgrounds. In the field of population genetics, comprehending the genetic diversity across distinct populations plays a crucial role. This study presents significant findings from genetic data obtained from the Sikkimese population of India. Autosomal markers were crucial for evaluating forensic parameters, with a combined paternity index of 1 × 109. Notably, Penta E emerged as a distinguishing marker for individual identification in the Sikkim population. Fst genetic distance values revealed insights into genetic isolation among different groups, enhancing our understanding of population dynamics in the central Himalayan region. The NJ-based phylogenetic tree highlighted close genetic relationships, of the Sikkim population with the Nepalese population surrounding neighbouring Himalayan populations providing glimpses into common ancestry. In summary, this study contributes valuable data to population genetics and underscores the importance of genetic variation in comprehending population dynamics and forensic applications. [ABSTRACT FROM AUTHOR]

Differences in migratory behavior have been suggested to drive speciation, but the genetics underlying this process remain unknown. Identification and study of migratory divides can help us understand how differential migration can lead to reproductive isolation. Here, we genotyped Willow Warblers Phylloscopus trochilus, from the Åland islands, located in between the ranges of the differentially migrating subspecies P. t. trochilus and P. t. acredula. We found that Willow Warblers on the Åland islands were genetically intermediate to allopatric populations of both parental subspecies, providing evidence that the islands constitute a previously unknown hybrid swarm, likely to be a migratory divide. [ABSTRACT FROM AUTHOR]

Hyalomma anatolicum, an Anatolian hard tick is a well-recognized vector involved in the transmission of various pathogens to animals and humans. The present study elucidated the population structure and haplotype network of H. anatolicum based on the mitochondrial large subunit ribosomal RNA (16S rRNA) gene sequence. The population structure and haplotype network analysis of 75 sequences archived in the GenBank, including the 15 sequences generated herein, yielded 24 haplotypes. Haplotype 1 (Hap_1) was the predominant haplotype consisting of 45 sequences from India, China, Pakistan, Turkey, Egypt, Iraq, and Tajikistan. The complete haplotype network exhibited a stellate conformation, highlighting a recent population expansion. The overall dataset, together with the sequences corresponding to India, China, and Pakistan, showed a high haplotype (0.638 ± 0.065, 0.671 ± 0.103, 0.753 ± 0.099, and 0.854 ± 0.061, respectively) and low nucleotide (0.00407 ± 0.00090, 0.00525 ± 0.00196, 0.00680 ± 0.00233, and 0.00453 ± 0.00056, respectively) diversity, further emphasized a recent population expansion. The neutrality indices including Tajima’s D, Fu and Li’s D, and Fu and Li’s F for the complete dataset (− 2.661, − 6.008, and − 5.649, respectively) as well as for the sequences from India (− 2.223, − 3.414, and − 3.567, respectively) were negative, suggesting deviation from neutrality and a recent population expansion. The present study provided novel insights into the population structure and haplotype networks of H. anatolicum based on the mitochondrial 16S rRNA gene, and the different tests inferred a low genetic differentiation and suggested a recent population expansion of this economically important tick species. [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]

Three sardine species of Harengula and one of Opisthonema (Clupeiformes, Clupeidae) are known in the Western Atlantic, where the Amazon-Orinoco plume has been recognized as a major biogeographic barrier, albeit permeable to larger and generalist species. Here we used mitochondrial cox1 gene DNA sequences to check the lineage delimitation of both genera, testing the influence of the Amazon-Orinoco barrier (AOB) and marine provinces on their phylogeographic structure. Results indicate that the two genera are differently affected by the AOB, including cryptic speciation in Harengula and population structure in Opisthonema. Harengula show a broad distribution in the Brazilian Province (BRA) distinct from H. clupeola and H. jaguana from the Greater Caribbean Region (GCR). Divergence time between Harengula from the GCR vs. BRA was estimated as about 2.4 Mya, which coincides with the period of increasing sediment and freshwater discharge of the Amazon River in the Atlantic. Results also indicate the existence of a single species of Opisthonema, albeit with population structuring related to the marine provinces. Since species of both genera are relevant to artisanal fisheries and the maintenance of oceanic ecosystems, these results may help in fisheries management of these important marine resources. [ABSTRACT FROM AUTHOR]

Increasing rates of hybridization and introgression in managed populations of freshwater fish are a major threat to the long-term viability of native species. The conservation challenge begins with identifying native gene pools. For brown trout (Salmo trutta Linnaeus, 1758) in the Upper Danube drainage, this task is complicated by the presence of both naturally and anthropogenically induced admixture of highly divergent lineages (Atlantic and Danubian). Herein, a ddRADseq protocol was used to type 377 individuals from 24 populations in the Upper Danube in Austria and Germany, and from reference populations from adjacent drainages and commercial hatcheries. High genetic differentiation at small geographic scales was found among pure Danubian-lineage populations, especially in the Kalkalpen National Park (Austria). In the Upper Danube drainage of Germany, as well as in the Rhine and Elbe drainages, brown trout populations were predominantly of Atlantic-lineage origin – as were those of all commercial hatcheries. Most populations, however, showed various degrees of admixture between Danubian and Atlantic lineages, hypothesized to be the result of both natural and anthropogenic processes. We highlight the conservation value of pure Danubian-lineage populations, and the challenges promoting conservation of naturally admixed populations, while discouraging continued stocking and admixture via management activities. [ABSTRACT FROM AUTHOR]

The genetic diversity of Egyptian rice has received diminished attention recently, resulting in a weakened genetic foundation that renders it more vulnerable to environmental fluctuations. Developing durable rice cultivars necessitates the ongoing exploration of genetic resources and the utilization of diverse germplasm. The examination of rice diversity was conducted by researchers utilizing 27 rice genotypes and 23 polymorphic microsatellite markers. The microsatellite comprises 106 alleles that have been observed (Na), with an effective allele count of 67.36 (Ne). The average number of alleles per locus is 4.61, with a standard deviation of 2.93. On average, the values of polymorphism information content (PIC) were found to be 0.580. A noteworthy correlation was observed between the number of alleles and both gene diversity (r = 0.713) and polymorphic information content (PIC) (r = 0.785). The results of our study provide empirical evidence supporting the existence of both the P1 and P2 subgroups; P1 comprises twelve distinct rice genotypes, while P2 encompasses fifteen different rice genotypes. The analysis of molecular variance determined that individual variations contributed to 34.22% of the observed variance, while population differences accounted for the remaining 65.78%. The gene flow coefficient was determined to be 0.481, whereas the fixation index exhibited a statistically significant value of 0.342. The presence of admixtures within the population suggests a significant likelihood of gene transfer between different genotypes. The principal component analysis (PCA) encompassed 27 components, with only the initial four components (PC1, PC2, PC3, and PC4) regarded as variation representatives. In that order, the initial four components exhibited the highest eigenvalues, specifically 18.413, 10.759, 7.618, and 7.031. The findings underscore the importance of investigating and establishing connections between genetic diversity and developing Egyptian rice breeding and enhancement strategies. Selecting genotypes as possible donors in a crop breeding approach to improve rice quality requires examining genetic diversity within populations. The distribution of alleles within subpopulations reveals valuable loci for genetic diversity research. This study contributes to developing environmentally sustainable cultivars by providing insights into the mechanisms of gene flow and genetic structure in Egyptian rice. [ABSTRACT FROM AUTHOR]

The relationship between the genetic diversity and genetic characteristics of wild plant germplasm can provide insights for better utilization and conservation of genetic resources. Bunchgrass species in the genus Elymus are important for forage and grassland restoration in Northwest China. In this study, eight phenotypic traits were evaluated in 81 accessions of four Elymus species in the northwest region of China, and genetic diversity analysis was performed using 16 simple sequence repeat (SSR) markers. In the phenotypic trait analysis, Elymus sibiricus had the highest coefficient of variation for single-plant weight (58.24%) and the lowest coefficient of variation for the number of spikelets (0.005%). Clustering based on phenotypic traits placed cultivars into four groups, which were also supported by principal component analysis (PCA). A total of 16 pairs of SSR markers were screened with high polymorphism, with a polymorphism information content (PIC) range of 0.3648–0.7794 and an interspecific PIC range of 0.465–0.611 in Elymus species. The unweighted pair-group method with arithmetic mean approach applied to SSR marker data also divided the 81 accessions into four groups, similar to the results based on phenotypic traits. The results of PCA and population structure analysis based on SSR data were similar. The findings presented here will facilitate the collection and conservation of Elymus germplasm resources and provide theoretical references for the future classification, breeding, innovation, utilization, and conservation of germplasm. [ABSTRACT FROM AUTHOR]