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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]

Background: Cashew (Anacardium occidentale L.) is a widely cultivated tree with great economic significance. In cashew, several elite cultivars have been developed for commercial cultivation, which form the underpinning for the cashew-based industries and the several billion-dollar world trade. However, frequently the genetic purity of the planting material is not maintained, resulting in great economic losses. Therefore, there is a need to develop a reliable method for the identification of cultivars to avoid economic losses to the cultivators and the protection of cultivars by the breeders. Methods and results: In this study, 35 new microsatellite/simple sequence repeat (SSR) markers were developed, and a set of 20 highly polymorphic and reproducible markers were used for DNA fingerprinting and genetic diversity analysis in 32 cashew cultivars. The polymorphic information content (PIC) of newly developed markers varied from 0.19 to 0.67, with an average of 0.44. The probability of identifying any two genotypes with identical fingerprints using the 20 SSR markers used for fingerprinting here in cashew cultivars was less than 2.8 × 10–11. Of the set of 20 markers, eight were sufficient for uniquely fingerprinting all the cultivars. Genetic diversity analysis by the neighbor-joining (NJ) method grouped 32 cultivars into three main clusters, and the grouping had no relationship to the geographic regions or the pedigree. Conclusions: The findings of this study are useful for the conservation and protection of cultivars under the PVP Act for ensuring the trading of quality planting material and are also useful for cashew breeding programs. [ABSTRACT FROM AUTHOR]

Background: Paratuberculosis, caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic granulomatous enteritis that affects domestic and wild ruminants and camelids. The disease has rarely been reported in alpacas in Germany. This publication describes epidemiologically independent cases of paratuberculosis in two alpacas in Germany. Case presentation: Two alpacas, a 26-year-old female zoo animal (case 1) and a 2.5-year-old breeding stallion from a private owner (case 2), presented with progressive emaciation, leading to death (case 2) or euthanasia (case 1) because of deteriorating general condition. In both cases typical granulomatous lesions in the intestinal mucosa and mesenteric lymph nodes were found. In case 2, other lymph nodes were severely enlarged and MAP was detected in the mandibular lymph node, lung, and liver by qPCR. The MAP isolates differed between the alpacas, with two distinct phylogenetic clades (Clade 1 and 8) within Subgroup A of the MAP-C type group and two distinct INMV profiles (INMV 2 and 1) found. These genotypes have been identified in cattle and goats in different regions in Germany. The genotype isolated from case 1 has been detected in goats from the zoo since 2011, indicating transmission between these species. Conclusions: MAP can cause severe clinical disease in alpacas of variable age and under different husbandry conditions. Therefore, paratuberculosis should be considered for differential diagnosis in alpacas with emaciation and poor general condition. Although not definitely shown, cross-species infection between ruminant species and camelids is exceedingly likely. [ABSTRACT FROM AUTHOR]

Background: Corema album, a wild shrub endemic to the Atlantic coastal dunes of Iberian Peninsula, has important ecological and medicinal value. Corema album has been listed as an endangered plant due to threats associated with anthropogenic events. Conservation of the species is therefore critically important. Objective: The aim of this study was to assess the genetic diversity and population structure of four well-characterized populations to support pre-breeding programs aimed at enhancing species knowledge for a future berry crop culture, with the ultimate goal of protecting and conserving the threatened species C. album. Methods: The set of 128 C. album accessions was genotyped using six EST-SSR primers and one genomic-SSR primer. Results: A total of 65 alleles were obtained with a mean of 9.285 alleles per locus. The genetic diversity was found to be high, with mean values of observed heterozygosity (Ho) and expected heterozygosity (He) at 0.594 and 0.756, respectively. Moderate genetic differentiation among populations (FST = 0.095) was observed. STRUCTURE analysis and multivariate analyses roughly categorized the accessions into a complex mixed group. The STRUCTURE analysis revealed no correlation between genetic structure and geographical distribution; however, it facilitated the identification of pure accessions within each population. Conclusions: The results aid in the understanding the population structure and genetic diversity and are crucial to optimize conservation strategies as well as the utilization of genetic resources of C. album for a deeper genetic study of the species. [ABSTRACT FROM AUTHOR]

Centranthus is a small genus belonging to the family Caprifoliaceae, comprising approximately 16 taxa (nine species plus seven subspecies). Currently, it is incorporated into the Valeriana genus, which is the most species-rich in the world (> 400 species), even though its phylogeny is not clear. Despite its botanical relevance, genetic markers for assessing the genetic diversity and population structure of its members are scarce, thus hindering the management and conservation of wild populations. In this study, we conducted a genome screening of the critically endangered C. trinervis to develop a set of nuclear microsatellite markers (SSRs) for population genetic studies across this species and five congeneric species. After data filtering, we selected 8747 contigs from which 100 primer pairs were tested in PCR. Amplification profiles returned 37 candidate microsatellites, with 13 proving informative for C. trinervis. These markers successfully cross-amplified in C. calcitrapae (9/13), C. lecoqii (7/13), C. longiflorus (9/13), C. nevadensis (8/13), and C. ruber (8/13). The observed high level of polymorphism and the favourable amplification rates in other congeneric species underscore the utility of these microsatellite markers as valuable tools for conservation and population genetic studies in a genus such as Centranthus or Valeriana. [ABSTRACT FROM AUTHOR]

Determination of the distinctness, uniformity and stability (DUS) of plant cultivars is an important means of protecting the original innovations of breeders, increasing the enthusiasm of breeders and promoting the development of plant breeding. In this study, combinations of simple sequence repeat (SSR) markers and DUS morphological characteristics were used to identify cultivars. The genetic diversity of 30 flax plant cultivars was analyzed using 20 SSR markers and 18 DUS morphological characteristics. The results of the morphological characteristic analysis showed that the 30 flax cultivars had high genetic diversity. Ninety allelic variations were detected in 20 polymorphic SSR molecular markers, and 2–10 allelic variations were detected in each pair of primers. The diversity index (H) of Nei's gene range was 0.10–0.39, with a mean value of 0.23; the Shannon information index (I) range was 0.19–0.57, with a mean value of 0.37; and the polymorphism information content (PIC) range was 0.25–0.82, with a mean value of 0.51. Cluster analysis revealed that there were correlations between the SSR markers and morphological characteristics, and there were also some differences. These results show that these two methods have good potential for future research, especially for DUS analysis of hundreds of cultivars. Therefore, the use of molecular markers can reduce the cost and duration of resource consumption, and more importantly, identify and protect highly specific plant cultivars. [ABSTRACT FROM AUTHOR]

Central Asia contains rich genetic resources for apricots. With its mountainous geography, Kyrgyzstan is the country where wild and cultivated apricot forms are preserved. The present study revealed genetic diversity and population structures in 91 apricot accessions from different regions of Kyrgyzstan. Fifteen simple sequence repeat (SSR) primers were used, capillary electrophoresis was performed, and the number of alleles per primer ranged from 4 to 11. A significant level of variation was determined among apricots originating from Kyrgyzstan. In the resulting dendrogram, all apricot accessions were divided into five groups, and the materials belonging to the northern and southern regions were grouped separately. At the same time, the population structure of apricots was analyzed. Accordingly, individuals have 0.80 or more membership coefficients; therefore, they are likely pure and non-admixed. There were 34 apricot accessions that have been determined as pure. The remaining 53 individuals had varying membership coefficients and were likely to be admixed by at least two subpopulations. This study is the most comprehensive research on Kyrgyzstan-origin apricots, providing vital information on their identification, preservation, and use in future research. [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]

Simple Summary: As a key economic species in China, the breeding of new strains of Chinese mitten crab (Eriocheir sinensis) has been undertaken across various regions to address genetic resource degradation caused by the industry's rapid expansion. Limited pond space often resulted in different families of Eriocheir sinensis being raised together, complicating the preservation of distinct family lines. Microsatellite markers are widely used to assess the genetic diversity and assign parentage, but they can be expensive to develop and apply. Advances in high-throughput sequencing technology have made these markers more accessible, while multiplex PCR can significantly reduce costs. In this study, 100 highly polymorphic SSR markers were developed from the transcriptome, four multiplex PCR panels were constructed, and a parentage assignment method was created for Eriocheir sinensis. The results demonstrated that 100% of offspring were accurately assigned to their parents across six crab families when three or four panels were used. This method provides an efficient and cost-effective solution for breeding and family management, promoting the sustainable development of the industry. Background: The development of genetic markers is crucial for aquaculture and population genetics. Polyallelic microsatellite markers are widely used for breeding and family management of Eriocheir sinensis (E. sinensis), contributing to the sustainable development of the industry. Methods: Through transcriptome analysis, 100 highly polymorphic SSR markers were identified and developed. From these, four multiplex PCR panels, each containing 16 markers, were constructed and applied to parentage assignment in six E. sinensis families. Results: The number of alleles (Na) ranged from 7 to 21, the observed heterozygosity (Ho) varied from 0.356 to 0.951, and the expected heterozygosity (He) varied from 0.656 to 0.909. The polymorphism information content (PIC) ranged from 0.633 to 0.900. The CERVUS analysis showed that using only the two most informative multiplex PCR panels, assignment success rates exceeded 90.34%, with 100% accuracy in assigning offspring to parents when three or four panels were used. Conclusions: This method significantly enhances the efficiency of microsatellite marker analysis, which provides a convenient and cost-effective method for breeding programs and family management of E. sinensis. [ABSTRACT FROM AUTHOR]

Introduction: The epidemic spread of the harmful bacterium Xylella fastidiosa causing the "olive quick decline syndrome", decimating olive trees in southern Italy, in the region of Apulia, prompted investigations to search for olive genotypes harbouring traits of resistance. Methods: A prospecting survey was carried out to identify, in the heavily infected area of Apulia, olive genotypes bearing resistance. Given the limited genetic diversity in the commercial olive groves with few cultivars widely cultivated, surveys targeted predominantly spontaneous olive genotypes in natural and uncultivated areas. Trees, selected for the absence of symptoms, were subjected to diagnostic tests and parentage analysis to disclose their genetic background. Transcriptomic analyses were also employed to decipher the molecular pathways in resistant genotypes. Artificial inoculations were carried out to confirm the resistant phenotypes of four open-pollinated seedlings of the cultivar Leccino. Results: Among the 171 olive collected genotypes, 139 had unique simple sequence repeat (SSR) profiles, with the cultivars Leccino, Cellina di Nardò, and Ogliarola salentina being the most frequent candidate parents. Among the Leccino progeny (n. 61), 67% showed a highly resistant (HR), resistant (R), or tolerant (T) phenotype to infection by X. fastidiosa. The occurrence of such phenotypes among those deriving from Cellina di Nardò and Ogliarola salentina was 32% and 49%, respectively. Analyses of the transcriptomic profiles of three Leccino-bearing genotypes, naturally infected and not showing symptoms, unravelled that a total of 17,227, 13,031, and 4,513 genes were found altered in the expression, including genes involved in photosynthesis, cell wall, or primary and secondary metabolism. Discussion: Indeed, transcriptomic analyses showed that one of these genotypes (S105) was more resilient to changes induced by the natural bacterial infection than the remaining two (S215 and S234). This study consolidates the evidence on the presence and heritage of resistance traits associated with the cv. Leccino. Moreover, valuable insights were gathered when analysing their transcriptomic profiles, i.e., genes involved in mechanisms of response to the bacterium, which can be used in functional genetic approaches to introduce resistance in susceptible cultivars and initiate strategies in olive-breeding programs through marker-assisted selection. [ABSTRACT FROM AUTHOR]

Excellent germplasm resources are the foundation for cultivating high-quality, disease-resistant, and stress-tolerant varieties. In this study, simple sequence repeat (SSR) markers were used to identify 138 potato accessions collected from worldwide, and genetic cluster analysis was used to characterize the genetic diversity of the tested germplasm resources. The Potato virus Y (PVY) resistance of these potato accessions was identified by artificial friction inoculation combined with molecular marker detection, and potato accessions with different PVY resistance were screened based on disease index and incidence rate. Using SSR markers, 138 potato accessions were identified, and the results showed that the genetic distances between the tested potato germplasm resources ranged from 0.025 to 0.660, and the genetic similarity coefficients ranged from 0.489 to 0.975. The 138 accessions could be clustered into five subgroups using Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Among them, Z173, Biyin No. 4, Suyin No. 2, XN995, XN987, Biyin No 22, Bibiao104, Sarpo mira, XN996, XN979, Desiree, RUNSHI, Actrice, Jia 1219, Heyin No 12, and Moyin No.1 have relatively distant genetic relationship with another 122 accessions. Based on the disease index, the following different accessions were screened: five highly resistant, 11 resistant, 45 moderately resistant, 35 susceptible, and 42 highly susceptible. Fourteen resource materials with good resistance (disease index ≤ 33.74%, and a grading of high resistance (HR) or medium resistance (MR); incidence rate ≤ 67.58%) were identified. By combining genetic cluster analysis and PVY resistance identification, six accessions showed PVY resistance and had distant genetic relationships with other accessions selected which provided important materials for disease resistance breeding and quality improvement of potato. In this study, the genetic diversity and PVY resistance of global potato germplasm resources was explored, and potato germplasm materials with important utilization value were screened. The results obtained in this study could provide important references for the research and utilization of global potato germplasm resources. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Excellent germplasm resources are the foundation for cultivating high-quality, disease-resistant, and stress-tolerant varieties. In this study, simple sequence repeat (SSR) markers were used to identify 138 potato accessions collected from worldwide, and genetic cluster analysis was used to characterize the genetic diversity of the tested germplasm resources. The Potato virus Y (PVY) resistance of these potato accessions was identified by artificial friction inoculation combined with molecular marker detection, and potato accessions with different PVY resistance were screened based on disease index and incidence rate. Using SSR markers, 138 potato accessions were identified, and the results showed that the genetic distances between the tested potato germplasm resources ranged from 0.025 to 0.660, and the genetic similarity coefficients ranged from 0.489 to 0.975. The 138 accessions could be clustered into five subgroups using Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Among them, Z173, Biyin No. 4, Suyin No. 2, XN995, XN987, Biyin No 22, Bibiao104, Sarpo mira, XN996, XN979, Desiree, RUNSHI, Actrice, Jia 1219, Heyin No 12, and Moyin No.1 have relatively distant genetic relationship with another 122 accessions. Based on the disease index, the following different accessions were screened: five highly resistant, 11 resistant, 45 moderately resistant, 35 susceptible, and 42 highly susceptible. Fourteen resource materials with good resistance (disease index ≤ 33.74%, and a grading of high resistance (HR) or medium resistance (MR); incidence rate ≤ 67.58%) were identified. By combining genetic cluster analysis and PVY resistance identification, six accessions showed PVY resistance and had distant genetic relationships with other accessions selected which provided important materials for disease resistance breeding and quality improvement of potato. In this study, the genetic diversity and PVY resistance of global potato germplasm resources was explored, and potato germplasm materials with important utilization value were screened. The results obtained in this study could provide important references for the research and utilization of global potato germplasm resources. [ABSTRACT FROM AUTHOR]

Eleven microsatellite markers previously developed from gooseberry sequences were tested on red and black currants. The results showed amplification of all microsatellite loci on black currant accessions, while on red currant accessions, there was no amplification at three loci (RucANS, RucDFR2-1, RucDFR1-3). Polymorphic loci were identified in both black and red currants. In the MTT-7 locus of the studied black currant genotypes, amplification of three fragments was observed, suggesting duplication of this locus. At the same time, in the MTT-7 locus of red currant, amplification typical of a monolocus microsatellite was observed. The RucHLH-1 and RucUFGT loci were tested on a hybrid red currant family (Belaya Potapenko × 1426-21-80). Using linkage mapping approach, the RucHLH-1 locus was mapped to the linkage group 4 of the red currant genome, and the RucUFGT locus (presumed), to the linkage group 1. The set of microsatellite loci for the genus Ribes is currently limited. This study shows that some of the SSR markers developed from gooseberry are amplified and reveal polymorphism on currants too, and can also be used to study both black and red currants. [ABSTRACT FROM AUTHOR]

Identifying the genomic regions (quantitative trait loci (QTL)) significantly linked to grain yield under drought stress could expedite the development of novel rice cultivars suited for rainfed areas through marker‐assisted breeding. This study identified QTL regions linked to plant phenology and production traits by evaluating 122 recombinant inbred lines (RILs) of Danteshwari × Daggaddeshi under different environmental conditions. A consistent QTL region associated with grain yield under water stress (60.4 Mbp) was mapped on chromosome 1 between RM428 and RM24 with an LOD score of 4.0. Another QTL region (9.4 Mbp) linked to plant height under all environmental conditions was mapped on chromosome 1 between RM1‐HvSSR1‐87 with a LOD score of 7.5 and phenotypic variance of 25%. A core set of 402 diverse rice accessions was also evaluated under water stress conditions and subjected to genome‐wide association analysis. Twelve markers linked to grain yield under drought were identified, out of which five were significantly associated with grain yield and days to flowering under drought. The markers linked to grain yield were compared between the bi‐parental population and germplasm accessions to identify the common markers. Three markers (RM1, RM259 and RM201) were found to be consistently linked to drought stress across the seasons in both bi‐parental population and germplasm accessions studied and could be potential candidates for application in marker‐assisted selection for improving grain yield under drought stress in rice. [ABSTRACT FROM AUTHOR]

This study examines the challenges of peacebuilding in the Democratic Republic of Congo (DRC) through the lens of the shadow state framework. Despite earlier applications of the shadow state concept to African states, the relevance of the notion of a shadow state to post-conflict settings remains underexplored. The paper argues that the persistence of shadow state dynamics, fueled by patrimonialism and wartime alliances, significantly impedes peace efforts. Conventional top-down peacebuilding approaches, such as DDR and SSR, often fail to address the complex realities of shadow states. Overall, the study highlights the inadequacies of these methods and sheds new light on how entrenched shadow state networks undermine peacebuilding in DRC. [ABSTRACT FROM AUTHOR]

The date palm (Phoenix dactylifera L.) is a dioecious plant, and its sexual characteristics remain indiscernible until it reaches the reproductive stage, typically between 4 and 5 years of age. The Medjool variety is widely grown in Palestine and the neighboring regions. Early identification of male and female seedlings could significantly benefit date palm cultivation and breeding efforts. This study aimed to confirm the effectiveness of microsatellite markers in distinguishing between male and female date palms within the cv. Medjool variety. Out of eight microsatellite or simple sequence repeat (SSR) primers used, four markers (mPdCIR015, mPdCIR035, mPdCIR078 and mPdCIR093) were able to determine the sex of the date palm tree (cv. Medjool) at an early stage. Practically, a combination of any of these two SSR markers could be used to determine the sex of date palm at seedling stage cv. Medjool. mPdCIR010 and mPdCIR093 produced male specific bands (325 bp) and (156 bp) respectively. On the other side, mPdCIR015 and mPdCIR078 produced unique female bands (160 and 128 bp), respectively. 15 loci were identified, averaging 2.1 loci per primer. SSR markers were able to provide a reliable technique for sex determination in date palm (cv. Medjool) at an early stage. The utilization of SSR markers will not only advance but also facilitate the establishment of a commercial date palm cultivation through the breeding program in Palestine and the surrounding region. Primer mPdCIR035 (325 bp) and mPdCIR093 (156 bp) occurred in all date palm male samples and absent in all female samples indicates a promising candidate markers to detect the sex in date palm seedlings at early stage. [ABSTRACT FROM AUTHOR]

Mezcal is a distilled alcoholic beverage made from different species of agaves. In the state of Durango (Mexico) mezcal production depends on Agave durangensis or "maguey cenizo". This process of distillation of fermented juices, regulated since 1994, remains artisanal, supporting the economy of several families in the state, although, recently, several companies have emerged with industrial processes. Due to the increase in both national and international mezcal demand, natural populations of this species are threatened as well as their ecosystem in which a balanced plant-human interaction has been established for centuries. In this work, the genetic diversity and structure of four A. durangensis populations in the most important mezcal producing municipalities of Durango, are analysed with 10 nuclear simple sequence repeat (SSR) loci. Results show high heterozygosity levels in equilibrium and no defined structure between populations, which could be reflecting the conservation status of these population before the Mezcal Denomination of Origin was established. [ABSTRACT FROM AUTHOR]

Knowledge of the genetic diversity and population structure of species can facilitate conservation and guide management programs. However, the type of molecular markers used can affect estimates of genetic divergence and population structure. Here three types of molecular markers were used to estimate the genetic diversity and population structure of Euterpe edulis, a palm endemic to the Atlantic Forest and economically and ecologically important. The objective was to estimate the parameters of genetic diversity and population structure for two other types of molecular markers (SNP and SilicoDArT) in addition to the commonly used one (SSR) to the species. We used single nucleotide polymorphism (SNP), SilicoDArT, and microsatellite (SSR) markers in 138 E. edulis individuals sampled from 15 sites. Euterpe edulis individuals were grouped into 11 clusters using SNPs and SilicoDArT and six groups using SSR data. The SNP and SilicoDArT data showed less divergence between the individuals within each cluster in comparison to the results derived from the SSR data. The probability of reassigning individuals to their cluster of origin revealed an average association with the original clusters was 0.92 for SNPs (n = 100), 0.71 for SSR (n = 8), and 0.99 for SilicoDArT (n = 445). The genetic divergence is high among sites using SNP markers, whereas SSRs showed the largest genetic divergence is found within each site. The overall heterozygosity values for each site in the eight SSR (He = 0.69; Ho = 0.59) markers were almost four times higher than those values inferred using SNPs (data 7833 SNP, He = 0.15; Ho = 0.13; data 100 SNP, He = 0.14; Ho = 0.12). Within each site, we found low inbreeding rates using both markers (SNP and SSR). In addition, population structure analysis identified two strongly supported geographical groups, one northern and one southern Brazilian Atlantic Forest group, for both markers. This study contributes to the understanding of the population genetics and population structure of E. edulis and may have important implications for its conservation. In addition, our results suggest that SNP and SilicoDArT markers are more effective for evaluating population structure, but SSR is more capable of detecting diversity among individuals for this species. [ABSTRACT FROM AUTHOR]

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Genic codominant multiallelic markers are essential to identify the genetic variation, population diversity and evolutionary history of a species. Soybean (Glycine max) is a major legume crop having importance in both a protein-rich pulse as well as a high recovery oilseed crop. To date, no genome-wide genic SSR markers have been elucidated in this crop of high importance. This article aims to identify and validate regulatory gene-derived SSR markers in soybean. The coding sequences of Glycine max were downloaded from PlantTFDB and used for the identification, followed by the localization of SSRs by using a Perl 5 script (MISA, MIcroSAtellite identification tool). The flanking primers to SSRs were designed and chromosomal distribution and Gene ontology searches were performed using BLAST2GO. Twenty random SSR markers were validated to check cross-species transferability and genetic diversity study was performed. A set of 1138 simple sequence repeat markers from transcription factor coding genes were designed and designated as TF-derived SSR markers. They were anchored on 20 G. max chromosomes, and the SSR motif frequency was one per 4.64 kb. Trinucleotide repeats were found abundant and tetra, as well as pentanucleotide frequency, was least in soybean. Gene Ontology search revealed the diverse role of SSR-containing TFs in soybean. Eight soybean accessions were analyzed for identified twenty candidates for genic SSR diversification, and a principal co-ordinate analysis, a genic dissimilarity-based unweighted neighbour-joining tree, was constructed. Our findings will serve as a potential functional marker resource for marker-assisted selection and genomic characterization of soybean. [ABSTRACT FROM AUTHOR]

Precise Point Positioning (PPP) and Network Real-Time Kinematic (NRTK) have historically been known as two independent precise positioning techniques due to their respective evolutions and applications. While both rely on a network of stations to estimate corrections to be broadcast to the user, PPP uses a global network while NRTK uses a local network. The local nature of NRTK allows access to precise atmospheric corrections, which enables real-time, instantaneous, centimeter-level user positioning. However, fundamental differences exist between PPP and NRTK corrections. In this work, the unexplored possibility of using state-space representation (SSR) local NRTK corrections in an ambiguity-resolved PPP (PPP-AR) solution is assessed. Novel research results show that instantaneous ambiguity resolution can indeed be consistently achieved in a PPP-AR engine, where GNSS corrections are only estimated from a local network without global constraints from a global solution. The results are preceded by an in-depth and insightful analysis of differences between NRTK and PPP at both the SSR correction and position levels. The analysis presented here is insightful and necessary to open the door for a convergence of PPP and NRTK thanks to the possibility of processing GNSS corrections from a local network in a PPP-AR engine, which may eventually lead to a more robust and hybrid NRTK/PPP solution. Such a hybrid solution could potentially be useful in challenging areas for PPP such as dense urban environments. [ABSTRACT FROM AUTHOR]

Allelic variation is a valuable tool for displaying high levels of polymorphism within species and is closely correlated with crop productivity. In Marathawada, there is a significant amount of phenotypic heterogeneity among sorghum landraces. However, molecular variability needs to be reevaluated in order to identify any potential barriers that can interfere with current improvement initiatives. In the current work, we used 5 SSR markers to categorize 20 genotypes of elite (Sorghum bicolor L. Moench) accession from the Marathwada region, including one standard cultivar from various agro-economic zones. According to the results of this study, 14 alleles were found among the 20 genotypes, with a PIC value that ranged from 0.37 to 0.70 and a mean of 0.44 per locus. Each locus had anything from 1 (gpsb089) and 5 (mSbCIR223), with an average of 2.80 alleles per locus. A neighbor-joining tree was constructed and showed clustering of genotypes into two groups; this indicates that there is considerable diversity in genotypes compared with advanced cultivar for desired genotype (IS1042) by using SSR markers. Results show that most diverse cultivars were IS-4564, IS18357, and IS-18381, and significant variation was also reported in IS4566 and IS18379. [ABSTRACT FROM AUTHOR]

Castanopsis argentea is an endangered tree naturally distributed in Java and Sumatera Island and considered a keystone species in the submontane forest ecosystem. A laboratory study was conducted to test the cross-amplification potential of seven pairs of Castanopsis cuspidata var. sieboldii microsatellite markers to be used for Castanopsis argentea. The rate of cross-amplification success, average number of alleles per locus (NA), observed heterozygosity (HO), expected heterozygosity (HE), and fixation index (FIS) were determined, and cross-amplification potential was investigated. The rate of amplification success was 85.71% (6 out of 7 markers were successful amplified), NA was 7.67, HO ranged from 0.467 to 0.923, HE ranged from 0.441 to 0.745, and the fixation index (FIS) ranged from −0.413 to 0.278. Results indicate the high transferability of C. cuspidata var. sieboldii microsatellite markers to C. argentea. Six markers were suitable for genetic diversity and population genetic studies on C. argentea.

In the present global warming scenario, it is urgent to impart heat tolerance into the popular high yielding rice (Oryza sativa L.) varieties to reduce yield loss to a great extent. Uma (a prevalent red-grained rice variety in Kerala) was crossed with Nagina 22 (N22), the popular donor for heat tolerance. From the seven promising heat-tolerant F3 plants previously identified through marker assisted selection and field screening, F4 lines (58 nos.) were raised and characterised morphologically. Heat tolerance was scored under natural heat stress during hot summer months in field conditions. Among the evaluated F4 progenies, 26 promising plants registered >75% spikelet fertility. Double panicles were observed in some of the tillers of fourteen F4 plants. During the selection with reported polymorphic markers between parents, all the 26 F4 plants produced the corresponding amplicon for RM5749 (linked marker for heat tolerance in the parental cross Uma x N22) and also for RM9, RM201, RM208, RM225, RM242, RM495, RM3586, RM6100, RM6836, and RM26212, corresponding to the heat tolerant parent N22. Genomic analysis revealed 64% recovery of the Uma genome in seven F4 plants, with maximum genomic regions of Uma on the chromosomes 3 and 5. These promising F4 plants could be forwarded to generate stable and high yielding heat tolerant rice varieties. The identified markers could be used for linkage analysis and QTL mapping in future.

Watermelon (Citrullus lanatus L.) is grown in tropical and temperate regions and an economically important crop. Characterization studies of watermelon may provide valuable information for breeding and research programs. The objectives of this study were to determined of morphological, phytochemical, genetic diversity and population structure among the watermelons. Morphological and phytochemical variations including sugar contents were determined in 96 watermelon genotypes grown in the field. The average number of fruits per plant was determined as 2.52 ± 0.06, and the average yield was determined as 6.2 ± 0.11 kg/m2. The mean total sugar was determined as 6.27 ± 0.12 %, and the lowest value was measured in genotype 234 (1.1%); the highest value was measured in genotype number 184 (8.66%). A total of 62 SSR (Simple Sequence Repeat) primers were used in the molecular characterization study. The similarity coefficients among the 96 genotypes varied between 0.23 and 0.99. This study indicates that there is a wide morphological and sugar parameters variation among watermelon genotypes but narrow molecular genetic diversity. It also provides useful information for watermelon breeding studies.

Abstract Background Heat stress is one of the abiotic stresses that make wheat crops vulnerable, which significantly impacts crop production around the world. An increase in temperature during the reproductive phase (anthesis) beyond the optimal range of 15–20 °C leads to decreased crop production, poor quality of the grain, and altered physiological and biochemical processes. To study the association between high temperature and physio-biochemical traits under normal and late sown, a set of fifteen genotypes was utilized. Results Relative water content under high temperatures had an overall decrease of 8.7%. However, grain protein and malondialdehyde content were higher in the stressed conditions than in the control, with increases of 20.2% and 38.9%, respectively. Marker Xgwm67, located on chromosome 5B, was found to be significantly associated with malondialdehyde content (R 2 = 21%) and Xgwm570, located on 6A, was closely linked to relative water content as well as grain protein content (R 2 = 16%) revealed by regression analysis. The correlation matrix displays a positive association between the control and stressed condition by R 2 = 0.92, 0.82, and 0.53 in malondialdehyde, relative water content, and grain protein, respectively. However, there was a negative correlation between water content–malondialdehyde and malondialdehyde–grain protein, though there was only a 4% correlation between grain protein content (control) and relative water content (stressed). Based on the tolerance matrix, WH730 and RAJ4079 were heat tolerant, and DBW173 and HD3086 were sensitive. Conclusions These findings indicate that to identify tolerant genotypes, physiological and biochemical traits can be utilized as an alternate criterion, and these closely associated markers can be applied for improved late-planted wheat production through MAS. The breeding scheme and genome editing by recognizing novel genes through physio-biochemical parameters, marker-assisted selection, and prospective screening of tolerant genotypes are proclaimed by the study.

Abstract Background Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics. Results In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes. Conclusion These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Abstract Key message Populations of the European white elm (Ulmus laevis Pall.) in Switzerland can be considered natural. They show no evidence of genetic differentiation from other European populations. In the past, the U. laevis populations were probably more widespread and continuous in Switzerland with a larger gene flow. Context In Switzerland, at the margin of its distribution range, U. laevis is rare and considered endangered. Whether the species is native to Switzerland has been disputed, and it is often surmised to be solely cultivated, without any natural population in the country. Aims The structure of genetic diversity among Swiss populations of U. laevis and comparison to European populations are expected to shed light on the origin of local populations and support their management. Methods We analyzed 19 populations (194 individuals) in Switzerland and 15 populations (158 individuals) from other European countries, using a set of five microsatellite loci. Results (1) 90% of the genetic variation in European and Swiss populations occurs within populations. (2) We did not detect isolation by distance at the regional or continental scale. (3) Clustering analysis did not reveal any spatial pattern in the level of admixture of individuals within Swiss or other European populations. Conclusion Moderate levels of genetic diversity and evidence for recent gene flow between populations indicate that habitat deterioration, loss, and fragmentation are the main threats to the persistence of U. laevis populations in Switzerland.

Abstract Clematis nannophylla is a perennial shrub of Clematis with ecological, ornamental, and medicinal value, distributed in the arid and semi-arid areas of northwest China. This study successfully determined the chloroplast (cp) genome of C. nannophylla, reconstructing a phylogenetic tree of Clematis. This cp genome is 159,801 bp in length and has a typical tetrad structure, including a large single-copy, a small single-copy, and a pair of reverse repeats (IRa and IRb). It contains 133 unique genes, including 89 protein-coding, 36 tRNA, and 8 rRNA genes. Additionally, 66 simple repeat sequences, 50 dispersed repeats, and 24 tandem repeats were found; many of the dispersed and tandem repeats were between 20–30 bp and 10–20 bp, respectively, and the abundant repeats were located in the large single copy region. The cp genome was relatively conserved, especially in the IR region, where no inversion or rearrangement was observed, further revealing that the coding regions were more conserved than the noncoding regions. Phylogenetic analysis showed that C. nannophylla is more closely related to C. fruticosa and C. songorica. Our analysis provides reference data for molecular marker development, phylogenetic analysis, population studies, and cp genome processes to better utilise C. nannophylla.

Background: Heat stress is one of the abiotic stresses that make wheat crops vulnerable, which significantly impacts crop production around the world. An increase in temperature during the reproductive phase (anthesis) beyond the optimal range of 15–20 °C leads to decreased crop production, poor quality of the grain, and altered physiological and biochemical processes. To study the association between high temperature and physio-biochemical traits under normal and late sown, a set of fifteen genotypes was utilized. Results: Relative water content under high temperatures had an overall decrease of 8.7%. However, grain protein and malondialdehyde content were higher in the stressed conditions than in the control, with increases of 20.2% and 38.9%, respectively. Marker Xgwm67, located on chromosome 5B, was found to be significantly associated with malondialdehyde content (R2 = 21%) and Xgwm570, located on 6A, was closely linked to relative water content as well as grain protein content (R2 = 16%) revealed by regression analysis. The correlation matrix displays a positive association between the control and stressed condition by R2 = 0.92, 0.82, and 0.53 in malondialdehyde, relative water content, and grain protein, respectively. However, there was a negative correlation between water content–malondialdehyde and malondialdehyde–grain protein, though there was only a 4% correlation between grain protein content (control) and relative water content (stressed). Based on the tolerance matrix, WH730 and RAJ4079 were heat tolerant, and DBW173 and HD3086 were sensitive. Conclusions: These findings indicate that to identify tolerant genotypes, physiological and biochemical traits can be utilized as an alternate criterion, and these closely associated markers can be applied for improved late-planted wheat production through MAS. The breeding scheme and genome editing by recognizing novel genes through physio-biochemical parameters, marker-assisted selection, and prospective screening of tolerant genotypes are proclaimed by the study. [ABSTRACT FROM AUTHOR]

Introduction: The first small scale cultivation of potatoes in the Nordic countries began roughly 300 years ago, and later became an important staple food in the region. Organized conservation efforts began in the 1980s, and today, potato landraces, improved varieties, and breeding lines are conserved in genebanks at the Nordic Genetic Resource Center (NordGen), Sweden, and the Norwegian Genetic Resource Centre (NGS), Norway, as well as at potato breeding companies across Nordic countries. All these collections house a diverse array of genotypes with local names and local growing histories from the whole region. However, the presence of duplicates, and inconsistent naming has led to confusion. Methods: In this study, 198 accessions of cultivated potato (Solanum tuberosum L.) have been genotyped with 62 microsatellite (SSR) markers. The analyzed accessions came from three collections: 43 accessions from the Danish Potato Breeding Foundation in Vandel (LKF-Vandel), 90 from NordGen and 65 from NGS. Results and discussion: The genetic analysis revealed 140 unique potato genotypes and 31 groups/clusters of duplicates, most of which contained duplicate pairs and the others three to ten accessions. Several accessions with distinct names were genetically identical or very similar, suggesting historical sharing, and regional distribution of seed potatoes, leading to the emergence of diverse local names. Moreover, many improved varieties from early potato breeding were revealed to have duplicates that have been considered Nordic landraces. Furthermore, potato accessions with identical names but originating from different collections were confirmed to be duplicates. These findings have already influenced management decisions and will further improve management practices for Nordic potato collections. Additionally, this new knowledge will benefit Nordic potato breeding efforts and allow for the dissemination of more accurate information to other users of potato diversity. [ABSTRACT FROM AUTHOR]

【Objective】 Genetic diversity analysis and evaluation of introduced potato varieties is a necessary method for screening good parental materials. 【Method】SSR fluorescent marker capillary electrophoresis was used to analyze the genetic diversity of 51 introduced potato varieties and construct molecular ID cards. 【Result】The 41 pairs of primers amplified a total of 327 alleles, and 311 alleles were differentiated at the same position, and the percentage of polymorphism was 95.11%. The primer polymorphism information index (PIC) ranged from 0 to 0.89, with an average of 0.71. Shannon's (I) ranged from 0 to 0.54, with an average of 0.32. The genetic similarity coefficient (GS) of the introduced potato varieties was 0.32. In the genetic similarity coefficient GS of 0.76, the test materials were categorized into six major groups: Group I having 14 varieties, group II having 30 varieties, group III having three varieties, group V having two varieties, and group IV and VI having one variety each. Cluster analysis revealed that four varieties, Vilas, Dingshu 4, Kexin 33 and Dongnong 312 could be used as potato breeding materials. 【Conclusion】Three pairs of core primers, STM0037, SSR0387 and SSR01054, were selected to construct fingerprints and molecular IDs of 51 potato varieties. [ABSTRACT FROM AUTHOR]

Increasing the yield potential of wheat, as the most important grain product in the world, is undoubtedly important in solving the consequences of world hunger. The aim of this study was to identify the genomic regions controlling traits related to grains (grain length, grain width, and grain weight per spike) and leaves (flag leaf length, flag leaf width, leaf number, second leaf length, and second leaf width). This study involved a mapping population consisting of 120 recombinant inbred lines of the F8 generation of bread wheat resulting from a cross of Kohdasht (KHD) and Gonbad (GND) cultivars during and phenotyped for 2 years (2019 and 2020). The experiment was performed as an alpha lattice design. Genetic linkage map was provided using 521 polymorphic alleles of SSR (423 alleles), CBDP (21 bands), ISJ (58 bands), and SCoT (19 bands) markers. The length of the map was 3167.9 cM with an average distance of 1.6 cM between adjacent markers. In total, for 2 years, 10 quantitative trait loci (QTLs) were identified on chromosomes 1A, 1B, 3B, 3D, 4D, and 7D for 3 traits related to grain. Four QTLs explained 15% phenotypic variance and were reported as large-effect QTLs for grain length traits. Detected three and four large-effect QTLs were for leaf-related traits in 2019 and 2020, respectively. In 2019, two QTLs, qFLW-1B (flag leaf width) and qLEL-1B (second leaf length), and, in 2020, three QTLs, qFLL-1B (flag leaf length), qFLW-1B (flag leaf width), and qLEL-1B (second leaf length), were located at 166.34 cM on chromosome 1B and linked to Xgpw7577-1B. For flag leaf length, two stable QTLs (qFLL-2B and qFLL-3A) were located at 78.30 and 22.22 cM on chromosomes 2B and 3A, respectively. For flag leaf width, a stable QTL (qFLW-1B) was identified at 166.34 cM on chromosome 1B and linked to Xgpw7577-1B. For the second leaf length, QTLs qLEL-1B and qLEL-6A were stable on chromosomes 1B and 6A. The work will help to understand the genetic mechanisms of grain and leaf of wheat and lay a foundation for further marker-assisted breeding programs. [ABSTRACT FROM AUTHOR]

In many contexts in the Mediterranean, Security Assistance (SA) is perceived to have contributed to state fracture or prolonged conflict. In Tunisia, in contrast, SA has increased the performance and capacities of the security forces in matters of counterterrorism and migration control. However, in this article, by analysing SA's reordering impacts, I argue that it has interacted with political developments to reconfigure Tunisia's volatile political landscape in two ways. Firstly, SA programmes have acted to reinforce the coercive capacities of Tunisia's security forces vis-à-vis the general population. Secondly, vertical SA practices contributed to the reconfiguration of power dynamics between different actors in Tunisia's security sector, helping consolidate power in the increasingly authoritarian hands of the executive as well as the increasingly politicized security forces. Furthermore, in the final section of this article, I reflect upon the entanglements between security assistance, Tunisian political economy and the economic interests of many provider states. In doing so, I make the case for a 'recoupling' of security studies and political economy in analysis of external interventions in the Mediterranean to better understand their reordering impacts. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Moringa oleifera Lam. is a plant with nutritional and nutraceutical properties. It was introduced from India to Mexico, and some of its ecotypes are cultivated for industrial use. These ecotypes show morphological variations, indicating genetic variation. Therefore, the purpose of this study was to evaluate eight simple sequence repeat (SSR) loci to assess the genetic diversity of 10 cultivated M. oleifera populations collected from the southeast of Mexico. All markers generated a total of 127 alleles, with 15.8 alleles per locus. The polymorphic information content of markers was 0.869, with an average heterozygosity of 0.194. At the population level, the Nei's gene diversity was found to be 0.66, with 4.9 different alleles per locus and 5.2 genotypes on average per accession. The distribution of genetic variation was 20 % among populations, 58 % between individuals, and 22 % within individuals. The principal coordinate analysis (PcoA) plot and unweighted pair group method with arithmetic mean (UPGMA) linkage revealed three groups, corresponding to the three original genetic populations identified through structure analysis (Delta K = 3). Results showed significant differences in genetic diversity in M. oleifera populations stablished in Southeastern Mexico, which can be leveraged to increase the use of this germplasm. [ABSTRACT FROM AUTHOR]

Direct-seeded rice (DSR) is gaining popularity among farmers due to its environmentally safe and resource-efficient production system. However, managing the rice root-knot nematode (RRKN), Meloidogyne graminicola, remains a major challenge in DSR cultivation. Developing genetic resistance is a pragmatic and effective approach compared to using hazardous pesticides. Pusa Basmati 1121 (PB1121) is the most popular Basmati rice variety, but it is highly susceptible to RRKN. In contrast, Phule Radha (PR) has shown highly resistant reaction to RRKN, as reported in our earlier study. We generated an F2:3 population from the cross of PB1121/PR and evaluated it for RRKN resistance-related traits under artificial inoculation conditions. The distribution pattern of traits in the F2:3 population indicated that resistance may be governed by a few major-effect genes and many minor-effect genes. The molecular markers reported to be associated with QTLs governing RRKN resistance traits were used to test in the current population. Although the simple linear regression identified significant associations between the markers and RRKN resistance-associated traits, these associations were spurious as the LOD score was below the threshold limit. This indicates that PR possesses novel genomic regions for resistance to RRKN as it does not possess any of the earlier reported QTLs. [ABSTRACT FROM AUTHOR]

Background: Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics. Results: In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes. Conclusion: These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat. [ABSTRACT FROM AUTHOR]

Key message: Populations of the European white elm (Ulmus laevis Pall.) in Switzerland can be considered natural. They show no evidence of genetic differentiation from other European populations. In the past, the U. laevis populations were probably more widespread and continuous in Switzerland with a larger gene flow. Context: In Switzerland, at the margin of its distribution range, U. laevis is rare and considered endangered. Whether the species is native to Switzerland has been disputed, and it is often surmised to be solely cultivated, without any natural population in the country. Aims: The structure of genetic diversity among Swiss populations of U. laevis and comparison to European populations are expected to shed light on the origin of local populations and support their management. Methods: We analyzed 19 populations (194 individuals) in Switzerland and 15 populations (158 individuals) from other European countries, using a set of five microsatellite loci. Results: (1) 90% of the genetic variation in European and Swiss populations occurs within populations. (2) We did not detect isolation by distance at the regional or continental scale. (3) Clustering analysis did not reveal any spatial pattern in the level of admixture of individuals within Swiss or other European populations. Conclusion: Moderate levels of genetic diversity and evidence for recent gene flow between populations indicate that habitat deterioration, loss, and fragmentation are the main threats to the persistence of U. laevis populations in Switzerland. [ABSTRACT FROM AUTHOR]

AbstractSpot blotch (SB), caused by Bipolaris sorokiniana is becoming an important barley disease in humid, temperate growing regions, including Uruguay. The narrow genetic base of current donors of resistance and recent changes in pathogen virulence have driven the search for novel sources of resistance. In this study, a diverse collection of 39 barley genotypes was evaluated for SB resistance, and genetic relationships, population structure, and haplotype diversity were investigated using 27 simple sequence repeats (SSRs) and eight sequence-tagged sites (STS) markers linked to nine QTL for SB resistance located on chromosomes 1H, 2H, 3H, 4H, and 7H. Fourteen barley genotypes expressed high and moderate SB resistance at seedling and adult plant stages. Distance and model-based cluster analyses revealed that the 14 selected lines clustered in four groups consistent with geographical origin and pedigree relatedness. Reference SB resistant haplotypes were poorly represented. Based on these results, we suggest that these 14 lines are likely candidates to carry novel genes or alleles for SB resistance. Further research may expand the understanding of the genetic architecture of this trait. [ABSTRACT FROM AUTHOR]

The red swamp crayfish (Procambarus clarkii) has become one of China's most important freshwater aquaculture species. As the epicenter of crayfish cultivation, Hubei province provides the majority of germplasm resources for breeding applications. However, the genetic diversity and population structure of P. clarkii in this area remains largely incomplete, hindering the effective utilization of these germplasm resources. In this study, 20 polymorphic microsatellites were developed and used to investigate genetic diversity and differentiation in representative P. clarkii populations from five cultivated and five wild populations in Hubei province. A total of 169 alleles were discovered at these loci, and the average polymorphic information content was calculated as 0.584. Diversity index of expected heterozygosity (He) indicated a relatively medium genetic diversity across all populations (0.431 ~ 0.565), while wild populations exhibited higher genetic diversity (He = 0.542) compared to that in cultured populations (He = 0.478). The average value of pairwise population differentiation index (Fst) was 0.108, manifesting a moderate level of genetic differentiation among populations. Analysis of molecular variance between ten populations revealed that genetic variation mostly resided within individuals (79.4%), with slightly higher variation observed in cultured populations (84.79%) compared to that in wild populations (80.52%). Bayesian assignment, dendrogram, and principal component analysis grouped the genotypes into three clusters with wide variation among the accessions. These results reflected substantial genetic differentiation presented in P. clarkii populations. Our findings shed light on the diversity status of P. clarkii in Hubei province and will be great value for genetic improvement through selective breeding. [ABSTRACT FROM AUTHOR]

This article studies norm translation of the Women, Peace and Security agenda by interrogating the ways in which external support can contribute to gendering the security sector in conflict-affected countries. Through a case study of a Norwegian-led Specialized Police Team which provided capacity building in crime scene management to Malian Security Forces as part of the UN mission in Mali, it analyses how different understandings of gender inform gender mainstreaming practice. The analysis shows that while the Norwegian officers worked actively to promote gender equality and women's participation, the possibilities for capacity building to contribute to a gendering of the security sector are limited by the lack of more transformative understandings of gender to inform practice. [ABSTRACT FROM AUTHOR]

Forest musk deer (Moschus berezovskii) is one of the most endangered medicinally important wild animals in the world. Forest musk deer farming is the main way of production of musk. However, the single provenance and lack of genetic information lead to reduced genetic diversity of forest musk deer. Therefore, more SSR markers need to be developed to identify forest musk deer germplasm. In this study, bone marrow derived mesenchymal cells were used to construct cDNA library for transcriptome sequencing. The datasets were de novo assembled and annotated. 9 polymorphic simple sequence repeat (SSR) markers were finally identified and used to detect population genetic diversity. 6.07 Gb clean data were generated using Illumina sequencing technology, and de novo assembled into 138,591 transcripts and 81,553 unigenes. 5,777 simple sequence repeats (SSRs) were identified, in which there were 578 repeating motif types, with mono-nucleotide and tri-nucleotides comprising 55.88% and 25.60%, respectively. 100 primer pairs were designed to validate amplification and polymorphism using DNA from fecal samples. 9 polymorphic SSRs were developed and used to detect population genetic diversity of 122 forest musk deer in 2 farms. The average number of alleles per locus varied from 4 to 15 (average = 8.3). The observed heterozygosity (HO) per locus ranged from 0.102 to 0.941, while the expected heterozygosity (HE) per locus was from 0.111 to 0.651. All loci deviated significantly from the Hardy–Weinberg equilibrium (p < 0.001). The polymorphism information content (PIC) of these loci varied from 0.108 to 0.619. 9 polymorphic SSR markers were developed in this research. These sites can be used for breeding planning and conservation of germplasm resources. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Shenyang Agricultural University is the property of Journal of Shenyang Agricultural University Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Erwinia amylovora, the causative agent of fire blight of pome fruits and other rosaceous plants belongs to the group of regulated quarantine pests. The aim of this work was to characterize the populations of E. amylovora in Norway and their geographical distribution. A total of 238 E. amylovora isolates recovered from symptomatic host plants in Norway between 1986 and 2004 were genotyped by means of a short sequence repeat (SSR) marker (ATTACAGA) on plasmid pEa29. The SSR region was amplified and amplicon size determined using fluorescent labelling and rapid, automated capillary gel electrophoresis. All isolates contained the pEa29 plasmid harbouring the investigated marker. In total, ten genotypes were identified, of which two were detected only once. The number of repeats varied from 3 to 13, with 43% of the isolates containing five repeats. Of 17 isolates collected between 1986 and 1991, all but one contained five repeats, whereas more variation was observed in isolates from the period 2000 to 2004. Most of the isolates (80%) originated from Cotoneaster bullatus, hence no relationship between genotype of the isolate and host species that it was isolated from could be detected. This historic data suggests multiple introductions of E. amylovora to Norway. [ABSTRACT FROM AUTHOR]

Despite tea [Camellia sinensis (L.) O. Kuntze] is one of the top non-alcoholic beverages consumed around the world; its genetic and phenotypic diversity is less understood compared to other plantation crops. The study's aims were to undertake phenotypic and genotypic characterization of Sri Lankan and Indian tea germplasm and to identify diverse accessions to accelerate tea breeding programmes in both countries. A total of 171 tea accessions, comprising 94 Sri Lankan and 77 Indian accessions were used. All the accessions were subjected to phenotyping and genotyping using 28 polymorphic simple sequence repeat (SSR) markers. Based on 16 morphological characters, the first three principal components explained 57.61% and 58.43% of the total variability of Sri Lankan and Indian accessions, respectively. Young shoot pubescence, young shoot pigmentation, serration of leaf margin, and mature leaf colour contributed positively to the grouping of accessions. Based on Neighbor-joining analysis, all Sri Lankan accessions grouped in a single cluster, whereas Indian accessions grouped in two distinct clusters. The Gower's distance method was the most appropriate than other methods for developing core subsets. Among 21 Sri Lankan core accessions selected, 11 accessions belong to introductions, five TRI-developed cultivars and five estate selections. Among 18 Indian core accessions selected, 11 belong to China types, two Assam types and five Indian recommended cultivars. The current study is the first study to compare tea germplasm of both countries and the results are useful for tea crop improvement programme, conservation and utilization of tea germplasm in India and Sri Lanka in the future. [ABSTRACT FROM AUTHOR]

Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. By analyzing 21 SSR markers, an average of 11.6 alleles per locus were amplified and an average PIC value of 0.711 was determined. We determined the heterozygous status of the individuals and variability in the set using the SSR analysis on the basis of expected heterozygosity (He, 0.477), observed heterozygosity (Ho, 0.675), Shannon's index (I, 0.820), and fixation indices (FST, FIS, FIT). Based on the SSR analyses, the lower level of expected heterozygosity in the analyzed set of Tartary buckwheat genotypes was observed compared to common buckwheat. With the help of a hierarchical cluster analysis using the UPGMA algorithm, Structure analysis, and PCoA analysis for the SSR markers, we divided the buckwheat varieties in the dendrogram into two main clusters according to the species. The AMOVA analysis showed that genetic variability between the individuals prevails in the analyzed set. The SSR technique proved to be a suitable tool for the determination of intra- and inter-varietal genetic variability and for analysis of diversity. [ABSTRACT FROM AUTHOR]