Management Of Genetic Resources Research Articles

Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East

Key messageGenotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.

Assembly and Comparative Analyses of the Chloroplast Genomes of the Threatened Plant Rosa anemoniflora

Due to insufficient molecular biology and genetic research on Rosa anemoniflora, this endangered plant has not yet received effective protection. Therefore, the complete chloroplast genome sequence of R. anemoniflora, along with comparative analysis of the chloroplast genomes of related species, is necessary and crucial for reconstructing phylogenetic relationships and developing genetic markers to conserve these species. A series of analyses, including genome structure, GC content, gene number, selection pressure, and nucleotide diversity, were performed by comparing the chloroplast genomes of R. anemoniflora and its relatives. The results indicate that the chloroplast genomes of R. anemoniflora and its close relatives are highly conserved in all genome characteristics, and all protein-coding genes in R. anemoniflora have not experienced significant positive or negative selection pressures. Comparative analysis revealed several variation hotspots, such as the atpH-atpI region, which can serve as a DNA barcode for distinguishing R. anemoniflora from its close relatives. Finally, the results confirmed that R. anemoniflora belongs to Rosa section Synstylae and that R. anemoniflora and its close relatives likely originated from the Fujian and Taiwan regions of China and diverged approximately 3.24 million years ago. This study provides crucial information for future biodiversity conservation and genetic resource management.

Preliminary cytogenetic study of <em style="mso-bidi-font-style: normal;">Ctenopoma kingsleyae</em> from Esa-Odo water reservoir, Osun State, Nigeria

Ctenopoma kingsleyae belongs to the family Anabantidae covers a wide geographic region. It has been morphologically described by a number of authors, yet it is lacking in adequate cytogenetic information, which is a setback to understanding its karyotypic evolution. This study, therefore, describes the karyotype of C. kingsleyae (n = 10) from Esa-Odo, Reservoir, Osun State, Nigeria. Metaphase chromosome spread was obtained from the gills of fish after intraperitoneal injection with 0.05% colchicines. Slides prepared were stained with Giemsa stain, images of metaphase spread were taken digitally and a karyogram was prepared. The study revealed a karyotypic formula of 2n = 48t with uniarmed chromosomes. This study has provided needful information on C. kingsleyae karyotype and will serve as the basis for further study on its evolution, genetic resource management and production.

Characterization of genetic diversity in Curcuma longa L. cultivars using Start Codon Targeted (SCoT) markers

Curcuma longa L. (Family- Zingiberaceae), commonly called turmeric, is one of the most important commercial spices. Being a center of turmeric's diversity, India boasts of more than fifty cultivars with variable agronomic characters and curcumin content. However, the quest for calibrating their genetic variability remains debatable as popular molecular marker-based studies have yielded inconsistent results. A promising PCR-based approach, known as the Start Codon Targeted (SCoT)-PCR system has been established to be more efficient than random DNA marker systems because this technique can generate more information on genetic polymorphism patterns. Hence, the present study proposes to use Start Codon Targeted (SCoT) markers to assess inter-cultivar genetic diversity of turmeric. We report an orthogonal L16 (45) design-based approach to investigate the influence of five crucial factors (dNTPs, Taq DNA polymerase, primer, template DNA and annealing temperature of primer) on the efficiency of the polymerase chain reaction (PCR) for development of an optimized Start Codon Targeted (SCoT) amplification protocol using twenty-seven different cultivars of C. longa. The optimized PCR protocol yields best results with a 20 uL reaction mixture, containing 10×PCR Buffer (with 15 mM MgCl2), 2.5 mM dNTPs, 10 mM SCoT primer, Taq polymerase (2 U), template DNA (50 ng), which was verified by using twenty-five SCoT primers. This standardized rapid protocol of SCoT-PCR reported here was employed to examine genetic diversity among twenty-seven Indian cultivars of turmeric, revealing high range of polymorphism ranging from 81.25 % to 100 %. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data segregated the twenty-seven cultivars into two main clusters. The first cluster comprised of nine cultivars (36 % of the cultivars) which was further divided into three sub-clusters and the second one consisted of eighteen cultivars (64 %) which further divided into four sub-clusters. From the results of this study, it can be inferred that the employment of SCoT markers can be an effective tool for analysing genetic variability, phylogenetic relationships and develop a rich genetic resource management system for C. longa cultivars.

Genetic resources of common ash (Fraxinus excelsior L.) in Poland

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

Genomic scan of endangered moroccan endemic trees (Argania spinosa L. Skeels) along a latitudinal gradient: Exploring gene-environment correlations

Understanding the adaptive mechanism of trees to climate change and effective management of genetic resources necessitate a comprehensive knowledge of the relationship between environmental factors and their adaptive power. This study focuses on the endangered Moroccan endemic tree, Argania spinosa L., known for its remarkable adaptive power in the Mediterranean climate and heavily impacted by climate change. Through genomic scans along a latitudinal gradient, we aimed to identify genomic regions associated with convergent or divergent selection by searching the genome for outlier loci demonstrating high population differentiation. Variation of dominant markers (Amplified Fragment Length Polymorphism) was correlated with variation of environmental factors to discern signals of natural selection in 13 natural populations of Argania spinosa L. along a latitudinal transect.Genotyping of 130 individuals with 477 AFLP markers revealed six outlier loci exhibiting elevated population differentiation values within argan forests. The BayeScan v2.1 software was used to detect outlier loci, and the (MLM) method strongly associated these loci with at least five environmental factors, particularly bioclimatic variables. Notably, all outlier loci exhibited significant correlations with Soil Moisture, with additional associations with Temperature, Precipitation, Landforms, and Soil Type, influencing the local adaptation of Argania spinosa L.The outlier AFLP loci may not be the direct targets of natural selection, but locate closely to genes that are potential involved in local adaptation. Consequently, further investigations are imperative to validate these candidate loci. This research underscores the significance of considering bioclimatic variables, especially Soil Moisture, in understanding the local adaptation of Argania spinosa L. amid climate change in Morocco.

Phenotypic Diversity of Quinoa Landraces Cultivated in the Ecuadorian Andean Region: In Situ Conservation and Detection of Promising Accessions for Breeding Programs

Quinoa (Chenopodium quinoa Willd.) is an ancestral crop in the Ecuadorian Andean region, and its landraces have always been of great social and food importance for the native population. Currently, there is no updated information about their phenotypic diversity and conservation status nor about the changes that have occurred in the last decades. A total of 268 accessions of quinoa landraces collected at two different times (1978–1988 and 2014–2015) in three representative Ecuadorian Andean provinces (Imbabura, Cotopaxi and Chimborazo) were evaluated for forty agro-morphological (17 quantitative and 23 qualitative) traits. Most of the quantitative traits showed high variability, some of them with great importance for commercialization and germplasm selection for breeding programs (e.g., panicle width, grain width, 1000-grain weight or seed yield per plant). Ten quantitative and eleven qualitative descriptors were significantly different between both collections. Regarding the presence/absence of saponin, all the accessions collected four decades ago had saponin, while it was found in only 18% of accessions collected more recently. The phenotypic relationships in the dendrogram did not show clustered accessions by their geographical origin or by collection. A selection index allowed us to detect a few accessions recently collected in Chimborazo with high promises for future breeding programs, with high seed yields per plant values and a reduced or no saponin content. The agro-morphological information obtained may be very useful for the suitable management and conservation of this ancestral plant genetic resource, both on the farm by indigenous farming communities and ex situ by the Germplasm Bank of the Ecuadorian National Institute for Agricultural Research (INIAP).

Study of the physicochemical characteristics, antimicrobial activity, and in vitro multiplication of wild blackberry species from the Peruvian highlands

The Peruvian Andes are the natural habitat of several wild blackberry species that are little known and exploited due to the lack of technological and scientific development to support their agricultural potential. In this context, a study was conducted to understand the physicochemical composition, bioactive compounds, antimicrobial activity, and in vitro multiplication of four wild blackberry (Rubus sp.) species from the northern Peruvian highlands. The results indicate that fruits of R. floribundus presented the highest content of total soluble solids (9.58 ± 1.83°Brix) and titratable acidity (1.88 ± 0.07% citric acid). The fruits of R. weberbaueri recorded the highest total phenolic content (415.06 ± 8.69 mg GAE/100 g Ff). The antioxidant capacity determined by the DPPH assay varied significantly among species, with the highest value found in fruits of R. andicola (50.27 ± 0.11 mg TE/100 g Ff). The fruit extracts of R. weberbaueri and R. andicola showed better antimicrobial activity, with Staphylococcus aureus being the most sensitive bacterium. In the in vitro multiplication phase, the results show that BAP (6-Benzylaminopurine) has a significant effect at a dose of 1.5 mg l−1 on shoot number, leaf number, and shoot length. The results may help in the management of genetic resources.

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.

In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.

Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring

We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012–0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.

Human‐associated genetic landscape of walnuts in the Himalaya: implications for conservation and utilization

AbstractAimsA comprehensive understanding of the genetic variation of walnuts (Juglans regia and J. sigillata) in the Himalaya and its potential drivers are essential for the conservation and sustainable utilization of these plant genetic resources. In this study, we aimed to uncover the genetic landscape of walnuts and potential drivers in the Himalaya for better utilization, awareness, sustainable management and conservation of the extant genetic resources of walnuts in the vast Himalayan landscape.LocationThe Himalaya biodiversity hotspot.MethodsA total of 1410 wild or feral walnut trees from 65 populations of J. regia and J. sigillata across four countries in the Himalaya were collected. The genetic diversity, population structure, hybridization and gene flow were thoroughly investigated based on the chloroplast genome and 31 nuclear microsatellite markers. The patterns and drivers of the walnut genetic landscape were further explored.ResultsWe detected three genetic groups of J. regia (JR1, JR2, JR3), one of J. sigillata (JS) and two hybrid types (JR1 × JS and JR3 × JS) of walnut in the Himalaya, with the western Himalaya identified as the genetic diversity hotspot of J. regia. The spatial genetic pattern of the J. regia was significantly influenced by geographic and climatic factors. Human‐mediated dispersal probably promoted the hybridization and gene introgression between J. regia and J. sigillata, which reshaped the genetic landscape of walnut populations in the Himalaya.Main ConclusionsThe extant genetic landscape of walnuts in the Himalaya was driven by natural and anthropogenic forces. Regarding conservation, the western and eastern Himalaya are the genetic reservoir of J. regia and J. sigillata, and hence, pure individuals should be urgently protected from frequent hybridization and introgression. In addition, we propose the utilization of natural hybrid resources coupled with new breeding techniques that combine genomic and phenotypic data.

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing.

Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

Genetic Characterization of Myf5 and POU1F1 Genes in Different Egyptian Local Rabbit Breeds and Their Association with Growth Traits.

Genetic characterization and its association with quantitative traits in local breeds are important tools for the genetic improvement and sustainable management of animal genetic resources. Myogenic regulatory factor 5 (MYf5) and POU class 1 homeobox 1 (POU1F1) are candidate genes which play important roles in growth and development of mammals. The present study aims to detect the genetic diversity of the MYf5 and POU1F1 genes in four local Egyptian rabbit breeds and their association with growth traits, using PCR-restriction enzyme (PCR-RFLP), PCR-single-strand conformational polymorphism (PCR-SSCP), and direct sequencing techniques. The results showed that MYF5 exon 1 was observed with two genotypes in Baladi Black (BB), Gabali (GB) and New Zealand White (NZW) breeds while APRI-line (APRI) presented one genotype. The genetic diversity of Myf5 exon 2 between breeds showed two genotypes in APRI compared to three in NZW and four genotypes in BB and GB breeds. The genetic diversity of the POU1F1 gene (intron 5 and partial cds) in different rabbit breeds was two genotypes in NZW and three genotypes in BB, GB, and APRI breeds with different frequencies for each genotype. Based on the statistically significant difference between genes genotypes and growth weight, the results suggested that the genotypes of Myf5 exon 2 (1 and 2) of the BB breed, Myf5 exon 2 genotype 2 of the APRI breed, and genotype 1 of Myf5 exon 1 and genotype 1 of POU1F1 of the NZW breed compared to genotypes for each gene can be considered candidate molecular markers associated with the improvement of growth traits in these breeds.

Assessment of genetic diversity and population structure of groundnut cultivarsusing morphological characters

Forty six germplasm of groundnut (Arachis hypogaea L.) evaluated under kharif season have been classified using Principal component analysis (PCA) based on correlation matrix yielding eigen values and eigen vectors. Multivariate analysis of phenotypic characters extracted eight principal components (PC) using the mean performance of the genotypes and showed that the first three principal components contributed 61.75% of observed variability amongst the 46 genotypes with the eigen value >1 and PC1 accounted for 25.60% of the total morphological variation for the traits. The information given in this paper will be valuable in the efficient management and utilization of the groundnut genetic resources.

Characterization and Evaluation of Mulberry Genetic Resources for the Identification of Promising Accessions

Mulberry is a dioecious species but, is usually cultivated as low bush or dwarf tree form by repeated pruning. Apart from its importance in silkworm rearing, it is also valued for its delicious fruits, medicinal properties in infusions, and ornamental shade tree. The conservation of mulberry genetic resources for future use and their subsequent usage in plant breeding are two critical areas of action in any genetic resource management programme. The current study used morphological, reproductive, anatomical, biochemical, propagation, growth, and yield variables to know the potential value of 22 mulberry accessions. Based on multiple trait analysis, the accessions MI-0946, MI-0945, MI-0953, MI-0948, MI-0935, MI-0948, MI-0936 and MI-0952 were identified as top performers for anatomy, propagation, biochemical, growth and yield parameters. These accessions may serve as potential parents for the future breeding program.

Updates in psoriasis diagnosis and treatment status in China: results from the National Psoriasis Center Registry.

Updates in psoriasis diagnosis and treatment status in China: results from the National Psoriasis Center Registry.

Local Chickens Farming System Characteristics and Their Genetic Resources Management in Seno Province of Burkina Faso

Local Chickens Farming System Characteristics and Their Genetic Resources Management in Seno Province of Burkina Faso

Fertility Variation and Gene Diversity in Forest Populations

Fertility variation, defined as a difference in the ability to create progeny (i.e., reproductive success) among individuals, was reviewed using the related available theoretical and practical literature in an attempt to contribute to and improve future studies on the subject. Fertility variation is a useful guide for various purposes such as gene conservation, seed production programs, forest genetic resource (i.e., seed sources) management, other forestry practices (e.g., regeneration), and evolutional and physiological studies. Many papers and proceedings have been published, including both theoretical and practical approaches, on how fertility variation has improved in the last two decades. Large variations in fertility were widely reported among populations within species and among species. We reviewed the literature and combined our diverse knowledge to examine fertility variations and their linkage parameters. Fertility variations and their related parameters (e.g., gene diversity, status number, effective parent number, parental–balance curves) estimated based on reproductive characteristics have been studied for many years using easy and cheap surveys that are used for different purposes in forest sciences. Their importance is increasing and their use is becoming more widespread because of these advantages, leading to improvements in research papers. While many research papers have recently been published on fertility variations and linkage parameters, a review paper has not been published to date. Therefore, a review paper is needed based on a literature survey and unpublished experience, as a guide for future studies.

Farmers' perception on severity, crop loss and management practices of variegated grasshopper (Zonocerus variegatus L.) on cassava (Manihot esculenta Crantz) in Sierra Leone

Farmers' perception on the severity and management practices on cassava has not been fully investigated particularly across agro-ecologies in Sierra Leone. This study assessed the perception of smallholder cassava farmers on the severity of Z. variegatus L., its impacts on yield and indigenous coping management practices utilized to mitigate the infestation of grasshoppers in their cassava farms. The population of the study comprised 300 cassava farmers sampled from the north, south and eastern provinces of Sierra Leone. The study involved questionnaire research instrument administered to smallholder farmers who were farming for household consumption, those producing for sale and household consumption and those who were mainly producing for sale because their primary goal was to produce for the market. Findings revealed that farmers had perceived abilities about agro-ecological distribution of grasshoppers, making them to be familiar with cassava crop damage severity pattern and easy identification. Farmers have ability to recognize and identify adult grasshoppers, and part(s) of cassava mostly affected by grasshoppers. Cassava leaves and stems are destroyed by the pest during either preferential feeding or as a result of ‘choice, no choice feeding’. The study established that smallholder farmers have perceived abilities to identify damage symptoms, stage(s) in the life cycle of the pest that is/are more destructive leading to crop losses and utilization of best practices to mitigate grasshopper infestation on cassava that could be exploited for increased production, management and conservation of cassava genetic resources. Moreover, 52.3% of variation in extent of crop loss by grasshopper infestation is attributable to life cycle stage(s) of the grasshoppers, identification of part(s) of cassava plant mostly destroyed by grasshoppers, cassava variety preference by grasshoppers and the best practices that contribute to increased cassava productivity.

Enhancing Breeding Potential and Genetic Conservation: A Comprehensive Approach to Plus-Tree Selection for Tilia amurensis Improvement

The timber degradation and overexploitation of Tilia amurensis necessitate strategic genetic resource management. This study presents a comprehensive approach to plus-tree selection, focusing on growth evaluation. Drawing from the procedures developed for evergreen oak, it encompasses base population selection, criteria establishment, forest stand investigation, standardized measurements, and tree selection. This study advances the baseline selection methods by emphasizing growth differentiation through age and environmental adjustments. A total of 62 superior individuals were selected from 176 candidates across 20 populations, effectively expanding the geographical boundaries. This growth-centric improved approach offers practical insights for selective breeding and genetic conservation, and addresses the ecological characteristics of the species. This study underscores the need for further exploration of genetic differentiation and biological traits to provide a foundation for refining T. amurensis tree improvement programs. In a broader context, these findings contribute to the understanding and sustainable management of diverse broadleaf forests.