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Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics. [ABSTRACT FROM AUTHOR]

The most important goal in cotton breeding is to increase the fiber yield which can be increased by improving a key trait, lint percentage (LP). However, narrow genetic background of upland cotton resulting in stagnant yield. In order to effectively dissect the genetic mechanism and enrich the gene loci of LP in cotton, the genetic diversity and population structure and a genome-wide association study (GWAS) was conducted using 204 upland cotton accessions based on 191 pairs of polymorphic microsatellite markers. The results were as follows: (1) The agronomic traits of the materials especially LP varied widely. (2) The SSRs revealed relatively high degree level of genetic diversity at DNA level. (3) Similarity coefficient cluster analysis of SSR markers indicated the influence of male parent on female parents was different after cross, the variation sites of agronomic traits could be further excavate in F1. (4) The GWAS revealed that 3 SSR markers were associated with LP: BNL3649-2, GH0132-2, CIR0246-3. There were two genes, Gh_D02G0125 and Gh_D11G2610, near the three SSR loci. These results provided a theoretical basis for improving fiber yield. [ABSTRACT FROM AUTHOR]

Bambara groundnut is a valuable leguminous crop with many landraces. A study was carried out to establish genetic diversity and phylogenetic relationship, among 33 Bambara groundnut accessions based on simple sequence repeat (SSR) markers. The nine microsatellite markers amplified a total of 27 alleles with a mean of 6.00 alleles per locus. Marker P 36 had the highest number of polymorphic bands while makers P131 and P68 were monomorphic. Genetic distance among the accessions based on Jaccard's similarity coefficient ranged from 0.84 to 1.00. Cluster analysis resolved the accessions into five major groups with subgroups. Each group had a combination of distinct accessions from different geographical origin. A substantial level of intra-accession polymorphism was obtained among the evaluated collection of Bambara groundnut. The significant genetic diversity observed can support the selection of appropriate parental genotypes for the improvement of Bambara groundnut through various breeding programmes. [ABSTRACT FROM AUTHOR]

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population's ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations. [ABSTRACT FROM AUTHOR]

Flamingos are highly mobile waterbirds that can be found in tropical and subtropical regions worldwide. The large distribution range of flamingos, the inaccessibility of most of their breeding sites and the lack of species-specific molecular markers, such as microsatellites, have hampered population genetics studies of these majestic birds. Here, we developed a library of microsatellite loci primers using high-throughput sequencing technology that could be used for further genetic studies on Phoenicopteriformes. Microsatellite and mitochondrial markers were employed for the genetic characterization of individuals of all flamingo species and their hybrids, and to conduct a population genetics study of the Caribbean flamingo. The phylogeny of Phoenicopteriformes was confirmed with six species grouped in two major clades that diverged approximately 13 Mya. This suggests the existence of two genera of flamingos, not three, as is currently accepted. The analysis of the genetic structure of the Caribbean flamingo shows that all Cuban demes constitute a single population isolated from the Bonairean colony. This supports suggestions of the existence of limited connectivity between northern and southern Caribbean colonies. The small Galápagos colony was confirmed as an isolated population with low genetic diversity; thus, it should be considered as threatened. [ABSTRACT FROM AUTHOR]

Lima bean (Phaseolus lunatus L.) is a crop that stands out for its economic and social importance throughout the world, including in Northeast Brazil. Evidence points to high levels of genetic diversity in this crop in this region. Monitoring the levels of genetic diversity in lima beans is necessary for predicting the possible processes of genetic erosion. In this study, we compared the genetic diversity of 12 lima bean genotypes collected in the 1980s with that of 42 genotypes collected in 2014–2016 in Northeast Brazil, using eight microsatellite loci (SSRs), to assess the occurrence of genetic erosion. The genetic diversity (HE) for the genotypes collected in 2014–2016 ranged from 0.144 to 0.47, indicating a wide diversity among the lima bean germplasms cultivated in Northeast Brazil. The Garza–Williamson index showed values below 0.70 for both the periods (1980s and 2014–2016). Moreover, the results obtained suggest a recent genetic bottleneck for the 2014–2016 genotypes, which may be related to the management and production techniques used by farmers owing to the growing market demand for improved lima bean varieties in recent years. [ABSTRACT FROM AUTHOR]

The pathogenic variants of genes encoding proteins, participating in the formation and functioning of epidermis and dermo-epidermal junctions, create a large variety of clinical phenotypes from: small localized to severe generalized dermatitis, as well as early, or even, prenatal death due to extensive epidermis loss. The diagnostic panel in this study was developed for the purposes of identifying these pathogenic genetic variants in 268 Russian children, who possessed the epidermolysis bullosa symptom complex in a selection of 247 families. This panel included the targeted areas of 33 genes, which are genetic variants that can lead to the development of the phenotype mentioned above. The usage of next generation sequencing allowed the revelation of 192 various altered alleles (of which 109 alleles were novel, i.e., had not been described previously). In addition, it allowed the definition of the genetic variants that are both typical for most of the examined children and for the separate ethnic groups inhabiting modern Russia. We found that the most characteristic mutations for the Dargin and Chechen ethnic groups are the c.3577del deletion in the COL7A1 gene and the c.2488G>A missense mutation in the COL17A1 gene, respectively. In addition, the study of haplotypes of microsatellite markers, which we managed to conduct in the Dargin population, confirmed the presence of the founder effect. [ABSTRACT FROM AUTHOR]

Ampelopsis grossedentata is an important national medicine in China. It is mainly used commonly by the Yao, Miao, Dong, and other ethnic minorities of China. The current literature, however, contains no study on the molecular genetics and taxonomy of A. grossedentata, which had led to potential problems in the conservation and utilization of this resource. Therefore, the present study was aimed to use simple sequence repeat (SSR) markers for assessing the levels and the distribution of genetic diversity in a sample set of 225 individuals from nine populations of A. grossedentata in China. The genetic differentiation among the nine populations was estimated at the level of 27 microsatellite loci. All loci were polymorphic in the nine populations analyzed. The average value of the Wright's fixation index (Fis) was -0.1154, with the range of -0.4627 to 0.2399, at the population level. The average Fit value was -0.0119, with the range of -0.3523 to 0.3563, at the population level. The Fst value was 0.0928 on average, ranging from 0.0463 to 0.1567. The SSR analysis revealed high levels of genetic variations within the studied populations, while the genetic differentiation among the populations was low. This finding probably reflected the historical association among the different populations of A. grossedentata. It is possible that sexual reproduction in the natural breeding system of A. grossedentata increased the levels of genetic variation within the populations while it reduced the genetic differences among the populations. The genetic cluster analysis revealed that the basal clade comprised populations from South China and that the different populations of A. grossedentata were categorized into five branches, which had continuous southeastward and southwestward distributions. The genetic structure of the populations and the levels of genetic diversity of A. grossedentata observed in the present study could provide important insights into the current status and the protection value of this species. [ABSTRACT FROM AUTHOR]

Simple Summary: The genetic characterization of native sheep breeds from the Tunisian-Italian Mediterranean corridor, the earliest westward introduction route of sheep breeding from the domestication center, was carried out using microsatellite markers in order to compare the genetic diversity level between both Mediterranean sides' local sheep breeds, and to investigate their level of risk for conservation purposes. Sampling concerned both private and public/institutional farms of all the native Tunisian breeds in the case of the southern Mediterranean side, and one center Italian and the Venetian native breeds from the northern side. The results revealed that the genetic diversity level of the Tunisian native breeds was higher than that of the Italian ones, with a lower inbreeding level. The comparison between private and public farms in terms of genetic diversity, consanguinity, and conservation decisions highlighted the superiority of the public/institutional breeding management strategies over private ones in both Tunisian and Italian cases. The present study illustrated the efficiency of genomic characterization in making genetic diversity evaluations and preservation decisions of native and well-adapted sheep breeds in both developing and developed countries' rearing conditions. Non-commercialized sheep breeds known as local or native breeds are well adapted to their environmental constraints and constitute precious genetic resources that need prioritization for genetic diversity characterization and preservation. The aim of the present study was to assess the genetic diversity level and the related preservation decisions of very old and traditional native Mediterranean sheep breeds from Tunisia and Italy using 17 microsatellite markers. In total, 975 sheep were sampled from five Tunisian, one Center Italian, and four Venetian native breeds. Both private and publicly available farms were considered for each breed for breeding strategies' comparison purposes. The microsatellite set used was highly informative (PIC = 0.80 ± 0.08), with a total of 383 alleles. Moderate genetic differentiation was revealed between the native sheep of the two Mediterranean sides (global overall loci FST = 0.081). The genetic diversity level was higher in the case of the Tunisian native breeds compared to the Italian ones, as evidenced by higher mean allelic richness, higher expected and observed heterozygosities, and lower inbreeding levels. Priority for conservation suggestions was carried out for each private or public breed population based on the contribution of each population to the diversity of the whole data. The four Venetian breeds, already undergoing conservation, the Tunisian dairy breed, and the very ancient Maghrebian breed, would be favored for conservation. In conclusion, our results highlighted the importance of the analyzed Mediterranean native sheep breeds as valuable inherited genetic reservoirs and supported previous conservation decisions made for the threatened breeds. [ABSTRACT FROM AUTHOR]

Introduction: Durum wheat is one of the most important crops in the world. Various environmental stresses such as drought stress can affect grain yield. Drought stress is one of the most important and common causes of wheat yield decline in most parts of the world. A large part of Iran's wheat cultivated lands is located in a Mediterranean climate. In these areas, the main part of rainfall is in winter and early spring, and from mid-spring, along with reduced rainfall and ambient humidity, the air temperature also rises sharply. Drought tolerance is a slightly complex trait controlled by many genes, and it is one of the most challenging traits to study and describe. Nevertheless, existing studies on drought have shown that the drought resistance mechanism of plants is morphological, physiological, and molecular, and strategies have been developed to deal with drought stress such as mass screening, modification, marker selection, and the use of exogenous hormones. Therefore, it is necessary to find a way to grow plants with limited water in areas deprived of water.Materials and methods: The study was conducted to identify molecular markers associated with the studied traits using SSR markers in rain-fed and supplementary irrigation conditions. The seeds of 150 genotypes of durum wheat, including two germplasm of durum wheat of ICARDA and germplasm of durum wheat of Iran, originated from the Seed and Plant Research Improvement Institute of Karaj, were planted in two cropping years 2018-2019 and 2019-2020. The experiment was performed in an augmented design with four controls in 6 blocks in the Farm of the Agricultural and Natural Resources Campus of Razi University of Kermanshah in supplementary irrigation and rainfed sites. The traits of plant height, peduncle length, weight of main stem, spike length, number node, weight spike, number grain per spike, weight grain per spike, thousand kernel weight were selected randomly and measured in 10 plants.Results: Based on the results, the GWM513 marker in the supplementary irrigation environment and the marker of GWM448-1 in the rain-fed environment showed the highest correlation with the number of seeds per spike (35% and 30%, respectively). GWM153 and GWM408 markers are suggested due to the high explanation coefficient (18-35%) and the most significant relationship with yield traits as the most suitable markers to improve most of the traits related to yield in rain-fed conditions.Conclusion: In the supplementary irrigation environment, a total of 24 significant markers were identified with the studied traits; among them, the number of seeds per spike had the highest amount of changes explained (30%) by the associated marker. In the rain-fed environment, a total of 21 significant associations of markers with the studied traits were identified among them; the number of seeds per spike had the highest coefficient explained (35%) by the associated marker. In the supplementary irrigation environment, 17 SSR markers significantly related to the studied traits, five markers, and in the rain-fed environment, out of 13 markers related to traits in this environment four markers participated in more than one feature.

Dromedary camels (Camelus dromedarius) are widespread in the desert and semi-desert areas of Africa, the Arabian Peninsula, some parts of southwest Asia and Australia. In the Arabian Peninsula, these well-adapted species have been classified based on their ecology into Desert camels, found mainly in the north and center of the Peninsula, Mountain camels, distributed along the west and south of the Peninsula, and Beach camels, populating the west to southwest of the Peninsula. Here, we aimed to investigate the genetic relationship between 386 camels corresponding to 12 dromedary populations from different geographical locations and ecology in the Arabian Peninsula with the genotyping of 17 microsatellite loci. No significant deviation was observed in heterozygosity, allelic richness, Fis (inbreeding coefficient) among the studied populations had a mean value of 0.5849, 4.808 and 0.04, respectively. A mean Fst (fixation index) value of 0.0304 was calculated for the various populations with the highest value obtained between racing Omani and Awarik camel populations (0.079). Both the neighbor-joining phylogenetic tree and the STRUCTURE analysis divided the populations into three different groups corresponding to their Arabian Peninsula geographic location (North, Central and West, South-West, and South-East of the Arabian Peninsula), rather than their ecological classification, with a high level of genetic admixture and gene flow among them. Investigating the genetic relationship of dromedary populations in the Arabian Peninsula can be considered as the first milestone to conserve this well-adapted species. The results obtained here need to be further validated using whole genome sequencing data.

The high economic value of olive oil has prompted the European Union to support efforts to protect and valorise the olive oil industry through the introduction of designations of origin (PDO/PGI). This review provides an overview of the European regulation on certified PDO and PGI extra virgin olive oils highlighting the importance and the impact of these labels. It examines the main fraudulent practices affecting extra virgin olive oil and the methods of analysis used to detect frauds, with a particular focus on DNA-based methods for varietal and sometimes, geographical identification. Moreover, an in-depth study was carried out on the varieties authorized in PDO and PGI extra virgin olive oils in Europe, addressing the issue of synonyms and the availability of SSR marker profiles. Finally, the data collected were used for the detection of private alleles. All the data and the information collected represent a useful and reliable tool for the varietal traceability and authentication of European PDO and PGI extra virgin olive oils. • European Geographical Indication protects products with unique characteristics. • The high economic value of olive oil leads to a wide range of frauds. • DNA-based methods allow the authenticity assessment of certified olive oils. • The availability of microsatellite markers is useful for the certified olive oil traceability. • Private alleles detection is an instrument for the agrifood traceability. [ABSTRACT FROM AUTHOR]

The proper use, further development, testing and deployment of animal genetic resources is essential to enhancement of food security and sustainable intensification of food production. For Red Mangalita conservation, we studied four microsatellite markers (SO228, SW72, SW911 and SW936) in order to genetic characterization of two populations. The results showed that both populations are in genetic imbalance, but also indicate high population variability, without the risk of genetic drift.

Dalbergia nigra is a long-living tree endemic to the Atlantic Rain Forest. Due to its high commercial value, this species has been widely exploited for timber production and is now endangered. It is widely known that understanding patterns of genetic structure is paramount for conserving threatened species. We analyzed the genetic diversity of 140 individuals from four different forest fragments in the southern region of Bahia, Brazil, to verify the possible effects of fragmentation on these populations and provide information for conservation initiatives. High polymorphism levels were detected from the genotyping of nine microsatellite loci (mean HE = 0.733). All populations showed high genetic diversity; however, a reduction of genetic diversity was detected in each population (HO < HE). The average fixation index was high and significant (f = 0.167), which could be due to the occurrence of inbreeding, the Wahlund effect, reproductive system, or from null alleles. Genetic differentiation among populations was high (mean θP = 0.118), suggesting strong isolation, a pattern consistent with historically low gene flow. The Bayesian analysis revealed five different genetic groups, among which three groups correspond to three different forest fragments, and two groups showed the genetic subdivision of individuals from the other forest fragment. Based on our results, the suggested conservation strategy for D. nigra populations in the southern region of Bahia, Brazil, involves high environmental investments to protect all sampled forest fragments and individuals. Another strategy would be to collect seeds from all individuals from the sampled fragments and start a new population with human interference in its evolutive history inside a protection unit.

Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity analysis using 10 quantitative traits, and 82 simple sequence repeat (SSR) markers. Out of 82 SSRs, 33 were polymorphic and the mean polymorphism information content (PIC) value was 0.38. Marker, JY-003 revealed a maximum (0.81) PIC value and, the number of alleles per locus ranged from 2 to 7 (average 3.46). The value of gene diversity showed the presence of a significant level of polymorphism among these genotypes. The unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into two major clusters of which Cluster I comprised mostly small and medium-fruited genotypes of both M. charantia var. charantia and M. charantia var. muricata, whereas Cluster II included mostly long and extra-long fruited genotypes. Furthermore, these genotypes were divided into six distinct groups based on population structure analysis. The diversity analysis based on 10 quantitative traits revealed that earliness and high-yielding ability were exhibited by the predominantly gynoecious line DBGS-21-06 followed by DBGS-48-00. The principal component analysis (PCA) revealed that the first two components exhibited more than 50% of the total genetic variation. The present study deciphered a higher magnitude of agro-morphological and genetic diversity in 96 bitter gourd genotypes. Therefore, trait-specific genotypes identified in this study could be utilized in breeding programmes directed towards the development of improved cultivars and hybrids of bitter gourd.

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.

The Michurinsk State Agrarian University (Michurinsk SAU) is one of the leading centers for breeding apple clonal rootstocks. A diverse collection of apple rootstocks, founded in 1930s by V.I. Budagovsky, is maintained at the Michurinsk SAU. In the present study, 87 rootstocks from this collection were analyzed using 18 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was rather high compared to the previous estimates of apple rootstock genetic variability. A total of 199 alleles were detected with an average of 11.1 alleles per locus. Among the detected alleles, 67 (33.67%) were rare and 43 (21.61%) were unique. The average PIC value was 0.73, and the expected and observed heterozygosity averaged 0.76 and 0.69, respectively. All the studied accessions except two could be identified with the used marker set. Cluster analysis revealed several groups according to the rootstocks’ pedigrees and genetic origin. Furthermore, Structure analysis revealed two main groups of the studied rootstock accessions. No significant differentiation of the studied sample according to dwarfing ability was detected, while weak differentiation was detected according to leaf color. SSR genotyping data can be used for rootstock fingerprinting and pedigree verification and will facilitate collection management. In addition, data on the genetic diversity and structure of the studied collection may be useful for further development of the Michurinsk SAU rootstock breeding program.

The sessile oak is a broadleaved tree species of great ecological and silvicultural importance. Oaks are the second most widespread deciduous tree species in the Czech Republic, and ongoing climate change negatively affects the abundant and often monocultural Norway spruce. Therefore, a proportional increase of more resilient tree species such as sessile oak has emerged. This study aimed to depict population genetic diversity when analysing 272 individuals from 10 subpopulations selected across the Czech Republic. Targeted populations were chosen based on the minimal expected human impact on the stand (presumably autochthonous stands). All individuals were genotyped using 18 polymorphic microsatellite markers (SSRs) assembled into two amplification multiplexes. The high discriminatory power of SSR markers was tested and confirmed by the probability of identity analysis. The genetic differentiation of the subpopulations was low yet significant, quantified by Wright's F-statistics within the range from 0.012 to 0.029. Based on discriminant analysis of principal components (DAPC), we detected two populations with geographic genetic correlation (the 15th meridian east being a north-south boundary line) and one with a distinct genetic pattern. We assume that the population might previously be established from seed sources outside the Czech Republic. Moreover, to some extent, our findings advocate the legitimacy of the legislative rules for forest reproductive material (FRM) transfer.

An inbred strain limits the segregating variance and provides more power and requires fewer experimental animals to produce good reproducibility. This study was undertaken with the aim to assess the impact of sex of offsprings and sex specific microsatellite variants on performance and fitness traits in F4 inbred Swiss albino mice. The phenomics of different performance and fitness traits were estimated on 506 F4 inbred mice population. Two ‘X’ chromosome specific microsatellite loci (DXMit187 and DxMit172) were used for PCR-Microsatellite genotyping of 102 F4 inbred population. PIC estimates showed that both the loci were informative for the population. In the current population, with the increasing level of “F” a declining trend was observed for Body weight at birth (BWB), Body weight at weaning (BWW), Litter size at weaning (LSW) and Litter weight at weaning (LWW). In F4 inbred population, BWW and ABW for males (17.32±0.32g and 30.81±0.31g) were significantly (p

In the tropical and semi-arid regions of Africa, sorghum [Sorghum bicolor (L.) Moench] is mainly grown as a major food security crop. Understanding the extent and pattern of genetic variability is a prerequisite criterion for sorghum improvement and conservation. The genetic diversity and population structure of 100 genotypes of sorghum were profiled using 15 microsatellite loci. A total of 108 alleles, with an overall mean of 7.2 alleles per locus, were produced by all of the microsatellite loci used due to their high polymorphism. Polymorphic information content values ranging from 0.68 to 0.89 indicated that all of the loci are effective genetic tools for analysing the genetic structure of sorghum. Different diversity metrics were used to evaluate genetic diversity among populations, and Nei's gene diversity index ranged from 0.74 to 0.81 with an overall mean of 0.78. Poor genetic differentiation (FST: 0.02; p

Okra [Abelmoschus esculentus (L.) Moench] also known as bhindi or lady’s finger is an important vegetable crop in India, West Africa, South Africa, Brazil, USA and Turkey. It belongs to the family Malvaceae. Okra is mainly grown in tropics and subtropics of the world. The studies regarding the molecular marker development are very limited; still there is no SSR development from comprehensive transcriptome data in this crop. This study presents the first comprehensive transcriptome data, using RNA from different parts of okra such as root, stem, leaf, bud, flower, different stages of developing pod and from twenty days old plantlets of heat, drought and salt stressed. A total of 10,492 SSRs were identified in this study. Among these tri repeats (2112) were found to be predominant followed by di (1285), tetra (149), penta (24) and hexa. Thirty four SSRs were standardized for PCR and screened for 36 okra genotypes and accessions. Among these 18 SSR primers were found to be highly polymorphic with the PIC values more than 0.5. And the overall results of analysis showed that expected heterozygosity ranged from 0.000 to 0.971 with a mean of 0.593; the values for observed heterozygosity ranged from 0.000 to 0.794 with the mean of 0.254; the number of allele per locus ranged from 1 to 30 and the Polymorphic Information Content (PIC) ranged from 0.000 to 0.940 with the mean value of 0.5546. The genic SSR markers developed will help in germplasm characterization mapping, genetic diversity studies, molecular assisted breeding and also in gene discovery.

Eucalyptus benthamii is an important species used in monoclonal and hybrid forest plantations around the world. Few natural populations of the species remain, and as such it has been placed on the list of endangered species. We sampled 111 seeds of Eucalyptus benthamii from nine progenies across two provenances (Candói - two progenies; Vale do Corisco - seven progenies). Samples were genotyped using 19 microsatellite loci. A high number of alleles (from 80 to 114) were found in the studied progenies.

Bambara groundnut is a valuable leguminous crop with many landraces. A study was carried out to establish genetic diversity and phylogenetic relationship, among 33 Bambara groundnut accessions based on simple sequence repeat (SSR) markers. The nine microsatellite markers amplified a total of 27 alleles with a mean of 6.00 alleles per locus. Marker P 36 had the highest number of polymorphic bands while makers P131 and P68 were monomorphic. Genetic distance among the accessions based on Jaccard’s similarity coefficient ranged from 0.84 to 1.00. Cluster analysis resolved the accessions into five major groups with subgroups. Each group had a combination of distinct accessions from different geographical origin. A substantial level of intra-accession polymorphism was obtained among the evaluated collection of Bambara groundnut. The significant genetic diversity observed can support the selection of appropriate parental genotypes for the improvement of Bambara groundnut through various breeding programmes.

We identified and characterized 11 polymorphic microsatellite markers suitable for routine testing (three in the MHC class I sub-region, four in MHC class II and four in the MHC class III sub-region) of dromedaries and Bactrian camels. In total, 38 dromedaries and 33 Bactrian camels were genotyped, and interspecific differences were observed in the numbers of alleles and in allelic frequencies, as well as in the observed heterozygosity. These loci may be used as markers to study the adaptive genetic diversity of the MHC region in Old World camels. [ABSTRACT FROM AUTHOR]

Simple Summary: Knowledge of genetic diversity is crucial to improve conservation plans for endangered species and ensure their long-term persistence. However, it may be difficult to accurately estimate genetic diversity when it is unfeasible to obtain sufficiently large sample sizes, which is often the case for marine endangered species. Here, we use Patella ferruginea as a model to investigate how small sample sizes affect genetic diversity estimates. We show that small sample sizes do not always hamper the detection of genetic patterns in endangered marine species, even though caution is needed when genetic divergence among populations is weak. Knowledge of Genetic diversity and its spatial distribution is crucial to improve conservation plans for endangered species. Genetic tools help ensure species' long-term persistence by unraveling connectivity patterns and evolutionary trajectories of populations. Here, microsatellite genotypes of individuals from populations of Patella ferruginea are used to assess the effect of sample size on metrics of within-and between-population genetic diversity by combining empirical and simulated data. Within-population metrics are slightly to moderately affected by small sample size, albeit the magnitude of the bias is proportional to the effective population size and gene flow. The power of detecting genetic differentiation among populations increases with sample size, albeit the gain of increasing the number of sampled individuals tends to be negligible between 30 and 50. Our results line up with those of previous studies and highlight that small sample sizes are not always a hindrance to investigating genetic patterns in endangered marine species. Caution is needed in interpreting genetic patterns based on small sample sizes when the observed genetic differentiation is weak. This study also highlights the importance of carrying out genetic monitoring in seemingly well-preserved but potentially isolated populations. [ABSTRACT FROM AUTHOR]

The Meadow and Steppe viper, Vipera ursinii-renardi complex is a well-studied group that is divided into several morphological subspecies. In this study, we combine the analyses of two mitochondrial genes with 9 microsatellite markers to compare both phylogenetic signals. Whereas the signal is similar between both genomes within most subspecies, the relative relationships between subspecies are more differentiated. Moreover, the nuclear phylogenetic reconstruction supports genetic homogeneity within V. u. macrops (in contrast to mtDNA). Both genetic portions show an unexpected differentiation between a population from Bistra Mountain and other V. u. macrops populations. Globally, the microsatellite markers suggest high genetic diversity in most subspecies, even in V. u. rakosiensis which is highly threatened; only V. u. macrops showed a limited genetic diversity. Within lowland subspecies, the differentiation between populations is globally limited compared to the distance between them (except in some populations of V. u. moldavica). The limited differentiation might be the consequence of a recent isolation (few decades) of previously large populations. Nevertheless, the only way to maintain this genetic diversity and to avoid an increase in genetic differentiation between populations in the future is to recreate suitable habitats and reconnect the populations. [ABSTRACT FROM AUTHOR]

The aim of the study was to evaluate the genetic structure of the reconstituted native Carpathian goat breed based on information from microsatellite markers. The study analysed of 14 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) for goats individual identification and parentage testing. Blood samples were taken from 249 Carpathian goats from 14 farms. All microsatellite markers deployed in this analysis showed sufficient polymorphism to assess genetic variation in Carpathian goats and the ISAG-recommended panel for goat individual identification and parentage testing is a highly useful one. The present study showed the status of the genetic structure of the reconstituted population of Carpathian goats. Carpathian goats maintained in Poland were characterized by relatively high genetic diversity (the average of alleles per locus was 9.143), high values of heterozygosity and a low level of inbreeding coefficient. The obtained parameters indicate the correctness of the breeding activities carried out within the framework of the programme for the protection of genetic resources and give guidelines for taking further steps related to the breeding of this valuable native breed. [ABSTRACT FROM AUTHOR]

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations -- with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country. [ABSTRACT FROM AUTHOR]

Powdery mildew, caused by Oidium heveae, is a major threat to rubber plantations worldwide. Population studies are scarce for this pathogen due to the lack of polymorphic molecular markers. In this study, sixteen polymorphic microsatellite loci were identified using DNA extracted from single lesions based on the whole-genome sequences of the pathogen. Primers of these loci were applied to 138 O. heveae samples from five counties in Hainan, China. The number of alleles per locus ranged from 2 to 11 and the gene diversity varied from 0.014 to 0.728. In total, 119 multilocus genotypes (MLGs) were observed for the 138 samples. However, only one sample was significantly distinct from the other samples base on DAPC analysis. Further study indicated that there were three subclusters for the other 137 samples, but no evidence for regional genotypic subdivision was identified. The microsatellite markers developed are very useful to study the genetic structure and the dispersal route of O. heveae, especially as it can use DNA extracted directly from infected leaves. [ABSTRACT FROM AUTHOR]

Various markers can be used for accurate identifications of plant genotypes and cultivars. Since microsatellite markers of simple sequence repeats (SSRs) are abundant and reliably reproducible, 14 pairs were used for evaluating polymorphic levels among 33 apple genotypes. All 14 pairs of primers had high degrees of polymorphism, ranging from three alleles (in the case of primers CH01h01 and CH02d12) to 12 alleles in primer CH05d04. In total, 83 polymorphic alleles appeared in these 14 SSR loci (with an average of 5.92 alleles per gene locus), and the polymorphic information content averaged 0.71. Dendrograms for molecular data were drawn based on the UPGMA method, and genotypes were divided into six main groups. The genotypes of Shahrood 20 and Shahrood 21 (95%) had the highest similarity with each other, while Shahrood 3 and Palestinian Malayer (14%) had the lowest. Principal component analysis confirmed the results of cluster analysis to determine relationships between the genotypes. [ABSTRACT FROM AUTHOR]

The whitefly Bemisia tabaci (Gennadius) is a large complex of cryptic species and is considered an invasive pest transmitting many plant viruses. It is a highly polyphagous insect that causes damage and economic losses to many plant species including vegetables, cotton, ornamentals, and weeds either in the open field or the greenhouses. A two-year survey (2016 to 2018) was conducted to biotype B. tabaci for B (MEAN1) and Q (MED) biotypes putative species. 18 host plants were screened from 14 different locations with a total of 101 samples that were collected and tested. Microsatellite markers and mitochondrial cytochrome oxidase I (mt COI) gene sequencing were used. The results showed that biotype B is dominant and prevailed in all surveyed locations. [ABSTRACT FROM AUTHOR]

Summary: The potato rot nematode, Ditylenchus destructor , causes serious disease limiting the production of many crops. This disease usually decreases sweet potato yield by 20-50%, and in heavily infested fields the crop may be completely lost. Although the nematode has economic importance in China, its transmission route and genetic diversity are unknown. In this study, a collection of 1761 contigs of the D. destructor genome was mined for simple sequence repeat (SSR) markers, which resulted in the identification of 9745 SSRs. A total of 150 pairs of SSR primers were further developed and used for validation of the amplification rate and assessment of the polymorphism. Nine SSR markers were finally identified and analysed using 96 individual specimens of D. destructor sampled from four provinces in China. These loci were found to be moderately polymorphic with 2-8 alleles per locus. The observed and expected heterozygosity across the four populations ranged from 0.000 to 0.833 and from 0.000 to 0.666, respectively. This is the first report of the development and characterisation of genomic SSR markers in D. destructor. Our study demonstrated the obvious gene differentiation among different populations of D. destructor in China. This suggests that D. destructor in China may have been introduced from multiple origins. Much more work is needed on this species to identify patterns of spread, and the microsatellite loci we develop here should be useful in many regions for modelling range expansion, studying the evolution of resistance, and increasing the effectiveness of pest management strategies. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (FIS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (FST) and among-individual differentiation (FIT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso. [ABSTRACT FROM AUTHOR]

We analysed nine microsatellite markers for 260 individuals representing Sophora tomentosa and 15 species from across the geographic range of Sophora sect. Edwardsia. The purpose of the study was to characterise the Sophora species from Pacific Ocean islands and South America and determine their relationships to the eight New Zealand species, with relationships of the extinct Rapa Nui/Easter Island S. toromiro a particular focus. Structure, PCoA and NeighborNet analyses showed S. tomentosa was distinct from species of sect. Edwardsia. Among the species of sect. Edwardsia, S. cassioides, S. howinsula, S. longicarinata, S. prostrata and S. toromiro were genetically distinct as each comprised a high proportion of membership of individuals assigned to them. The remaining species were assigned to four genetic groups, each of which had one species with a high proportion of membership and other species with lower proportions of membership. The S. chrysophylla group also included high proportions of S. macrocarpa, S. denudata and S. raivavaeensis. The S. fulvida, S. godleyi and S. molloyi genetic groups mostly included low proportions of other New Zealand species. In the PCoA, S. toromiro specimens clustered together and were placed at the margin of a large sect. Edwardsia group. Sophora toromiro comprised four specimens representing the Melbourne Botanic Gardens (Australia) genotype and two specimens in the Allan Herbarium (CHR) obtained from cultivated specimens in Valparaíso (Chile) during the early 1970s. One specimen from Valparaíso was originally identified as S. toromiro, while the other was misidentified as Sophora macnabiana (now S. cassioides). The lack of genetic variation in S. toromiro suggests they were perhaps derived from the last surviving tree on Rapa Nui / Easter Island. A cultivated plant from New Zealand known as the 'Victoria Park toromiro' had its identity confirmed as S. godleyi, which is consistent with its morphological identification. [ABSTRACT FROM AUTHOR]

Background: The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species. Methods and results: The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy–Weinberg equilibrium. Conclusions: The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii. [ABSTRACT FROM AUTHOR]

Chrysoporthe deuterocubensis is the causal agent of a serious canker disease of Eucalyptus spp. in tropical and sub‐tropical areas of Asia. Where the disease occurs, Eucalyptus spp. are non‐native and the native hosts of the pathogen have not been conclusively determined. The chance discovery of C. deuterocubensis on native Melastoma malabathricum growing in the understory of Eucalyptus trees in Indonesia raised the possibility that this woody shrub could be a native host of C. deuterocubensis, which would then have undergone a host jump to Eucalyptus. Four populations of C. deuterocubensis were collected from cankers on Eucalyptus and Melastoma trees in Indonesia and Malaysia. These were subjected to population genetic analyses using microsatellite markers. The genetic diversity for isolates in all four populations was relatively low (H¯ = 0.166–0.316) and unlikely to represent a native source. The maximum percentage of genotypic diversity was high for all four populations (Gmax = 60.0–71.5%) irrespective of the host. Structure analyses and haplotype networks showed no structure related to the host plant species. Overall, the results failed to provide evidence that the indigenous M. malabathricum is the native host or origin of C. deuterocubensis infections on the Eucalyptus trees studied. [ABSTRACT FROM AUTHOR]

The genetic diversity of natural populations is a key factor in the success of long-term ecosystem protection. We studied the genetic diversity and spatial genetic structure (SGS) in three endangered shrub birch (Betula humilis) populations using seven nuclear microsatellite loci. The highest genetic variation was found in the restored Szuszalewo population in Biebrza National Park, where active prevention of thicket forest succession was recently conducted. The results of bottleneck tests were not statistically significant in each locality, although a genetic indication for population reduction was detected in the Rospuda stand, which is not actively protected. The Bayesian clustering, principal coordinates analysis, and FST estimates revealed the greatest difference between Magdzie Bagno and Rospuda samples. SGS was found in all B. humilis stands; however, it was the strongest in the Rospuda locality, where pollen and seed dispersal was limited by dense clusters of shrub birch ramets scattered among forest and brushwood plants. The weakest SGS, also supported by finding some sibling pairs in distant locations, was observed in the Szuszalewo population. The aforementioned results indicate that the active protection practices may impose an immediate beneficial effect on the restoration and maintenance of the B. humilis populations. [ABSTRACT FROM AUTHOR]

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds' differentiation level (Wright's fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies. [ABSTRACT FROM AUTHOR]

To monitor and control the Japanese orange fly Bactrocera tsuneonis (Miyake) (Diptera: Tephritidae), it is important to determine their dispersal ability. Therefore, to determine the genetic structure of this species, we developed microsatellite markers at 17 loci for B. tsuneonis. A total of 80 adult females and males randomly collected from abandoned orchards in the Oita and Yamaguchi Prefectures, in the western part of Japan, were used for polymorphism analysis using the microsatellite markers. The average number of alleles was 2.65 for the 17 loci, in which two loci did not show polymorphism. The expected heterozygosity ranged from 0 to 0.663, although the observed heterozygosity was relatively low between 0 and 0.105. The null allele frequencies varied among populations. Moreover, no polymorphism was found in the three larval populations collected in the Oita Prefecture. These results suggested a high degree of inbreeding for this species. Significant genetic differentiation between females and males of the same population was not observed, although it was observed between the Oita and Yamaguchi populations. A bottleneck effect was detected in Yamaguchi but not in Oita, and this is congruent with the history of an expanding distribution in this species. These markers could be used for population discrimination and to expand the geographic history of this species, potentially contributing to the pest management of B. tsuneonis. [ABSTRACT FROM AUTHOR]

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana: Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy–Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations: Tswana (He = 0.7895 ± 0.033 vs Ho = 0.631 ± 0.091) and Tuli (He = 0.8123 ± 0.033 vs Ho = 0.556 ± 0.021). The inbreeding coefficient was 0.200 ± 0.002 and 0.332 ± 0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding programme is likely to result in minimal heterosis and therefore not recommended. [ABSTRACT FROM AUTHOR]

Corylopsis Seibold & Zucc. is a genus of flowering shrubs with few cultivars and little information on genome size, ploidy levels, and genetic relationships among taxa. The United States National Arboretum and collaborating gardens in North America maintain a diverse germplasm collection of Corylopsis including cultivated and wild-collected taxa. The objectives of this study were to determine genome size, ploidy, and genetic diversity in Corylopsis. Flow cytometry revealed a ploidy series of diploid, tetraploid, pentaploid, and hexaploid taxa in Corylopsis with 2C genome sizes ranging from 1.9 pg to 5.7 pg. Representative taxa were selected for root tip cytology, revealing diploid (C. platypetala Rehder & E.H. Wilson), tetraploid (C. gotoana Makino), pentaploid (unnamed hybrid selection), and hexaploid (C. willmottiae Rehder & E.H. Wilson) taxa. Seventeen genomic simple sequence repeat markers were developed and used to determine the genetic diversity of Corylopsis. These markers had an average of 7.4 alleles per locus with a range of three to 17 alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient to visualize genetic relationships and ploidy series within taxa. Information gained from this study will further breeding efforts and aid management of germplasm collections of Corylopsis. [ABSTRACT FROM AUTHOR]