Search Results (53)

In nature, orchid seed germination is extremely low, making in vitro asymbiotic seed germination essential for the propagation and conservation of endangered Vanda coerulea. This study optimized a micropropagation protocol and evaluated the genetic homogeneity of regenerated orchids. The synergistic effect of kinetin (KN) with auxins in the Mitra (M) medium best supported protocorm formation and seedling development. The highest shoot multiplication (5.62 ± 0.09) was achieved with 1.2 mg L⁻¹ KN and 0.6 mg L⁻¹ IBA (indole-3-butyric acid) in the medium. Enhanced leaf production (4.81 ± 0.37) was observed when 3.2 mg L⁻¹ KN was combined with 1.8 mg L⁻¹ IAA (indole-3-acetic acid), while root development was superior when 3.2 mg L⁻¹ KN together with 2.4 mg L⁻¹ IAA was incorporated in the medium. Anatomical sections confirmed well-developed leaf and root structures. Genetic fidelity assessment using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), inter-primer binding site (iPBS), and start codon targeted (SCoT) markers revealed 97.17% monomorphism (240/247 bands) and low Nei’s genetic distances (0.000–0.039), indicating high similarity among the regenerants. Dendrogram clustering was supported by a high cophenetic correlation coefficient (CCC = 0.806) and strong resolution in Principal Coordinate Analysis (PCoA) (44.03% and 67.36% variation on the first two axes). The Mantel test revealed a significant correlation between both ISSR and SCoT markers with the pooled marker data. Flow cytometry confirmed the genome stability among the in vitro-propagated orchids, with consistently low CV (FL2-A) values (4.37–4.94%). This study demonstrated the establishment of a reliable in vitro protocol for rapidly propagating genetically identical V. coerulea via asymbiotic seed germination. Full article

Background/Objectives: The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. Materials and Methods: A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite markers. Genetic diversity parameters (e.g., allele number, heterozygosity, F-statistics) were calculated using GeneAIEX (v.6.503) and Fstat software (v.2.9.4). Parentage analysis was conducted using Cervus software. Bayesian clustering analysis was performed using STRUCTURE software (v.2.3.4), and a phylogenetic tree was constructed based on Nei’s genetic distance to reveal the population genetic structure. Results: A total of 191 alleles were detected, with an average allele number of 11.969, observed heterozygosity of 0.481, and expected heterozygosity of 0.787. Parentage testing showed a cumulative exclusion probability (CEP) of 0.9652999 when one parent’s genotype was known and 0.9996999 when both parents’ genotypes were known, achieving an accuracy of 99%. Genetic differentiation analysis revealed moderate genetic divergence among populations (FST = 0.128) and moderate inbreeding levels (FIS = 0.396). Bayesian clustering analysis (K = 4) indicated that the Yanqi horse population could be divided into four genetic clusters, reflecting the impact of geographical isolation on genetic structure. Conclusions: The Yanqi horse conservation population exhibits moderate genetic diversity, high accuracy in parentage identification, and moderate genetic differentiation and inbreeding. The findings provide a scientific basis for the conservation and sustainable utilization of Yanqi horse genetic resources. Future efforts should focus on strengthening conservation measures, optimizing breeding strategies, and further investigating the genetic background using genomic technologies to ensure the sustainable development of the Yanqi horse population. Full article

Background: The patterns of inbreeding coefficients (F_IS) and fine spatial genetic structure (FSGS) were evaluated regarding the mating system and inbreeding depression of food-deceptive orchids, Dactylorhiza majalis, Dactylorhiza incarnata var. incarnata, and Dactylorhiza fuchsii, from NE Poland. Methods: We used 455 individuals, representing nine populations of three taxa and AFLPs, to estimate percent polymorphic loci and Nei’s gene diversity, which are calculated using the Bayesian method; F_IS; F_ST; FSGS with the pairwise kinship coefficient (Fij); and AMOVA in populations. Results: We detected a relatively high proportion of polymorphic fragments (40.4–68.4%) and Nei’s gene diversity indices (0.140–0.234). The overall F_IS was relatively low to moderate (0.071–0.312). The average Fij for the populations of three Dactylorhiza showed significantly positive values, which were observed between plants at distances of 1–10 m (20 m). F_ST was significant in each Dactylorhiza taxon, ranging from the lowest values in D. fuchsii and D. majalis (0.080–0.086, p < 0.05) to a higher value (0.163, p < 0.05) in D. incarnata var. incarnata. Molecular variance was the highest within populations (76.5–86.6%; p < 0.001). Conclusions: We observed concordant genetic diversity patterns in three food-deceptive, allogamous, pollinator-dependent, and self-compatible Dactylorhiza. F_IS is often substantially higher than Fij with respect to the first class of FSGSs, suggesting that selfing (meaning of geitonogamy) is at least responsible for homozygosity. A strong FSGS may have evolutionary consequences in Dactylorhiza, and combined with low inbreeding depression, it may impact the establishment of inbred lines of D. majalis and D. incarnata var. incarnata. Full article

Alnus glutinosa plays a crucial role in flood control, riverbank stabilization, and water purification. Recognized for its ecological significance, it is listed in the Red Book of Kazakhstan. This study investigated the genetic variability of A. glutinosa populations in Kazakhstan, analyzing 78 trees from seven populations in the Bayanaul mountain forest massif and the northern Turgay regions using 12 SSR markers. The study identified an average of 6.3 alleles and 2.783 effective alleles, as well as observed and expected heterozygosities of 0.570 and 0.562, respectively, reflecting genetic diversity. Among the populations, KS1 (northern Turgay) and PVL3 (Bayanaul) displayed the highest diversity, while PVL5 (Bayanaul) showed slightly lower diversity. The analysis of molecular variance results indicated that 86% of the genetic diversity occurred within populations, with 14% attributed to differences between populations. A UPGMA tree based on Nei’s genetic distance revealed three distinct clusters, suggesting geographically structured genetic variability in A. glutinosa populations. Full article

The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185 male foals sired by nine stallions. As females could not be sampled, we could not make inferences on all yearlings and test whether there are differences in the genetic population parameters between both sexes. The mean number of progeny was 19.92 with a range of 2–32, caused by the length of the service period per stallion. The average observed and unbiased expected heterozygosity was 0.688 and 0.631, the mean number of alleles was 4.448, and Wright’s F_IS was −0.173. Pairwise genetic distances (F_ST and Nei’s unbiased genetic distances) were significant and varied between 0.038 to 0.091 and 0.085 to 0.290, respectively. Neighbor-joining dendrogram plots clustered a large proportion of the paternal progeny groups in different branches. Posterior Bayesian analyses using seven paternal half-sib groups with 10–74 members supported a maximum of six clusters, with two paternal progeny groups not differing, and a median of five clusters, with two groups of two sires each falling into the same clusters. When sires were employed in non-consecutive years, progeny from these different years of the same sires were grouped in the same cluster, whereas the progeny of one sire from two consecutive years were in different clusters. We were able to distinguish male progeny from Dülmen wild horse stallions and to show the effects of stallion use on the genetic substructure in the Dülmen wild horse herd. In conclusion, the analyses showed the genetic potential of the Dülmen wild horse stallions to maintain a high genetic diversity and also the effects in which breeding seasons and for how long stallions are used to sire foals. The selection of stallions may be sensitive for the further development of genetic diversity and preserve this closed population as a valuable resource for further studies on the evolution of the horse. Full article

By using 14 SSR primer pairs, we here analyzed and compared the amplification results of 534 DNA samples from six red sugar beet germplasm resources under three treatments. These data were used to explore the sampling strategy for the aforementioned resources. Based on the sampling strategy results, 21 SSR primer pairs were used to evaluate the genetic diversity of 47 red sugar beet germplasm resources. The six population genetic parameters used for exploring the sampling strategy unveiled that individual plants within the population had a relatively large genetic distance. The genetic parameters Ne, I, and Nei’s of the randomly mixed sampling samples increased rapidly between 10 and 30 plants before decreasing. Therefore, when SSR technology was used to analyze the genetic diversity of the red sugar beet germplasm resources, the optimal sampling gradient for each population was the adoption of a random single-plant mixed sampling sample of no less than 10 plants and no more than 30 plants. The 21 SSR primer pairs were used to detect genetic diversity in 30 random mixed samples of 47 resources. The average polymorphic information content (PIC) was 0.5738, the average number of observed alleles (Na) was 4.1905, the average number of effective alleles (Ne) was 2.8962, the average Shannon’s information index (I) was 1.1299, the average expected heterozygosity (Nei’s) was 0.6127, and the average expected heterozygosity (He) was 0.6127. The genetic distance of the 47 germplasm resources ranged from 0.0225 to 0.551 (average: 0.316). According to the population structure analysis, the most suitable K value was six, which indicated the presence of six populations. Based on the clustering analysis results, the 47 germplasm resources were segregated into six groups, with obvious clustering and some germplasm resources noted for having groups with close genetic relationships. We here established a more accurate and scientific sampling strategy for analyzing the genetic diversity of red sugar beet germplasm resources by using SSR molecular markers. The findings provide a reference for collecting and preserving red sugar beet germplasms and protecting their genetic diversity. Full article

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei’s gene diversity (H) was 0.200, Shannon’s information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei’s gene diversity (H) was 0.132, Shannon’s information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei’s genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation. Full article

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of −0.035. Pairwise genetic distances (F_ST, Nei’s standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski’s horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication. Full article

Ilex chinensis Sims. is an evergreen tree species native to China and mainly distributed in the region south of the Qinling Mountains and the Huai River. This species has important ornamental, medicinal, ecological, and economic values, and plays a positive role in improving the environment and people’s lives. To reveal the genetic diversity and genetic structure of 401 individuals from 14 populations in the major distribution area of I. chinensis, 11 pairs of SSR primers were selected for PCR amplification. The products were then subjected to capillary electrophoresis, and the genetic diversity of Ilex individuals was analyzed using relevant software. The results showed that the genetic diversity of I. chinensis was at a moderate-to-high level. A total of 54 alleles were detected at 11 SSR loci in the 14 Ilex populations, with an average of 4.831 alleles per locus. AMOVA analysis indicated that the genetic variation of I. chinensis populations mainly originated within populations. A STRUCTURE analysis divided the 401 I. chinensis individuals into four different genetic clusters. The unweighted pair group methods using arithmetic averages (UPGMA) clustering based on Nei’s genetic distance revealed that the population from Xinping of Yuxi, Yunnan Province (XP), and the population from Longan of Qianxinan, Guizhou Province (LoA) were located in the outermost layer of the phylogenetic tree, indicating the furthest genetic relationship between these two population and other populations. The remaining populations could be roughly divided into two groups. Principal coordinate analysis (PCoA) demonstrated that the 401 individuals were clearly divided into three groups, which was consistent with the results of the STRUCTURE analysis and UPGMA clustering. This study identified the hotspots of genetic diversity of I. chinensis, as well as units for the conservation of individuals. It also revealed the patterns of genetic variation and population distribution of I. chinensis in different regions, providing a molecular basis for the geographical zoning and formulation of breeding programs for I. chinensis, as well as germplasm resource management. Full article

Feijoa sellowiana (O. Berg) is a broadly widespread fruit tree species at a very early stage of domestication. Although appreciated for its flavored berries rich in nutrients and nutraceuticals, and as an ornamental plant, feijoa is still considered an underutilized species and little information is available about its genetic background, cultivar traceability and divergence. This study aimed to investigate, for the first time, the genetic diversity of feijoa through the application of AFLPs. Specifically, twenty cultivars from different countries and six wild types (WTs) from their area of origin (Misiones, Argentina) were analyzed. The AFLPs proved to be informative, revealing the values of the percentage of polymorphic loci (PPB), Nei’s genetic diversity (h), and the Shannon index (I) at 69.36%, 0.27, and 0.43, respectively, consistent with the average of long-lived perennial and outcrossing species. However, despite the limited number of WTs examined, the genetic variability (h) was higher (approximately 37%) within the six samples compared to cultivars. The population structure analysis identified three clusters, with WTs forming a separated cluster (III) as expected. Cultivars were divided into two clusters (I and II), with cluster I exhibiting a closer genetic proximity to WTs compared to cluster II. This finding was further confirmed using the UPGMA dendrogram based on Provesti distances. This work raised awareness of the genetic variability among the feijoa’s widespread cultivars and demonstrated that the limited genetic breeding programs over the last decades resulted in low diversity among them. Moreover, these results confirm the hypothesis that all varieties are derived from a single narrow ancestral population. The potential of this species is considerable and needs to be further investigated to exploit its peculiarities. Full article

Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation. Full article

Metarhizium rileyi is an entomopathogenic fungus that naturally infects the larvae of Spodoptera frugiperda, and has biocontrol potential. To explore more natural entomopathogenic fungi resources, a total of 31 strains were isolated from 13 prefectures in Yunnan Province. All the strains were identified using morphology and molecular biology. The genetic diversity of the 31 isolates of M. rileyi was analyzed using inter-simple sequence repeat (ISSR) techniques. Seven primers with good polymorphism were selected, and fifty-four distinct amplification sites were obtained by polymerase chain reaction amplification. Among them, 50 were polymorphic sites, and the percentage of polymorphic sites was 94.44%. The thirty-one strains were divided into eight subpopulations according to the regions. The Nei’s gene diversity was 0.2945, and the Shannon information index was 0.4574, indicating that M. rileyi had rich genetic diversity. The average total genetic diversity of the subpopulations in the different regions was 0.2962, the gene diversity within the populations was 0.1931, the genetic differentiation coefficient was 0.3482 (>0.25), and the gene flow was 0.9360 (<1). The individual cluster analysis showed that there was no obvious correlation between the genetic diversity of the strains and their geographical origin, which also indicated that the virulence of the strains was not related to their phylogeny. Thus, the genetic distance of the different populations of M. rileyi in Yunnan Province was not related to the geographical distance. The virulence of those 32 strains against the 3rd-instar larvae of S. frugiperda were varied with the differences in geographical locations. On the 10th day of inoculation, seventeen strains had an insect mortality rate of 70.0%, and seven strains had an insect mortality rate of 100%. The half-lethal times of the M. rileyi SZCY201010, XSBN200920, and MDXZ200803 strains against the S. frugiperda larvae were less than 4 d. Thus, they have the potential to be developed into fungal insecticidal agents. Full article

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats. Full article

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (H_obs) and the expected heterozygosity (H_exp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (N_a), the average effective number of alleles at the locus (N_e), the F_ST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ²-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering. Full article

The genetic variability of five populations of Quercus petraea originating from the Transylvania and Maramureș regions of Romania was investigated in this study to provide insights into the species’ adaptability, population dynamics, and potential for preservation in the face of environmental challenges. To achieve this, sequence-related amplified polymorphism (SRAP) markers, in conjunction with a set of 18 primer combinations, were employed. The outcomes of the analysis revealed a range of polymorphisms spanning from 69.78% to 85.75%. Additionally, the assessment of genetic diversity using Shannon’s information index (I) yielded values ranging between 0.2887 and 0.3955, while Nei’s gene diversity (He) exhibited a spectrum from 0.1833 to 0.2582. The analysis of genetic variability, conducted via molecular variance (AMOVA), unveiled that 9% of the genetic variation was attributable to differences among the populations, while a substantial 91% resided within the populations. A further investigation of the population structure revealed that the construction of a UPGMA dendrogram based on Nei’s genetic distances elucidated the presence of two principal genetic clusters, a finding that was reinforced by a Principal Coordinate Analysis (PCoA). The genetic diversity revealed by Quercus petraea using SRAP molecular markers offers promising potential for upcoming breeding programs to identify optimal genitors, facilitating the development of well-adapted oak populations in the Transylvania and Maramureș regions. Full article