Genetic Diversity and Population Structure of Medemia argun (Mart.) Wurttenb. ex H.Wendl. Based on Genome-Wide Markers

Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (H-T) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (F-ST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise F-ST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.Peer reviewe

Demographic and Clinical Aspects of Congenital Hypothyroidism (Dyshormonogenesis) in Sudan

Introduction: Congenital hypothyroidism is the most common congenital endocrine disorder worldwide. Approximately 80 to 85% of cases are caused by defects in thyroid development (dysgenesis), the remaining 15 to 20% are due to errors of thyroid hormone biosynthesis (dyshormonogenesis). Congenital hypothyroidism is also the most common preventable cause of mental retardation. Its neurological defects can only be reversible if diagnosed and treated early. Its incidence rate is 1 out of 3000/4000 live births worldwide However, this incidence rate is higher in developing countries such as Sudan (1 of 1400/2200 newborn infants) in which its population is characterized by consanguinity (25-70%). The present study aimed to assess the demographic and clinical pattern of congenital hypothyroidism (dyshormonogenesis) in Sudan.Material and Methods: A total of 54 patients referred to Gaffar Ibn Auf Children Hospital presented with clinical features suggesting congenital hypothyroidism (dyshormonogenesis) were enrolled in this study. Demographic and clinical data was obtained by a predesigned questionnare. Data were analyzed using SPSS 13 software. Descriptive statistics (frequencies and percentages) were obtained for categorical variables.Results: Most patients enrolled in this study (85.7%) are descendants of consanguineous marriages. There were 11 reported families, comprising 74.3% of cases, with more than one affected member, of those family members, 68.6 % were in fact siblings. Patients from consanguineous marriage had a 96.6% positive family history. The majority of patients (97.1%) developed complications. According to the tribal origin, the vast majority of patients (65.7%) were from Afro-Asiatic tribes, whereas 34.3% were from Nilo-Saharan tribes. There was a large variation in the geographical distribution of patients. Biochemical analysis and ultrasound findings were concordant with the clinical presentation of patients.Conclusion: 1) Early diagnosis and treatment are crucial to prevent both cognitive and motor detrimental effects of the disease. 2) Consanguineous marriages are a major risk factor in patients with congenital hypothyroidism. 3)There is a wide range of tribal variation of both Afro-Asian (65.7%) and Nilo-Saharan (34.3%) tribes. 4) Poor education and unawareness of the disease were major factors in late diagnosis, treatment and further complications.Keywords: Congenital Hypothyroidism, Dyshormonogenesis, Sudan

Taatelipalmun geneettinen monimuotoisuus ja sopeutuminen

Acquiring sufficient information on the genetic variation, genetic differentiation, and the ecological and genetic relationships among individuals and populations are essential for establishing guidelines on conservation and utilization of the genetic resources of a species, and more particularly when biotic and abiotic stresses are considered. The aim of this study was to assess the extent and pattern of genetic variation in date palm (Phoenix dacttylifera L) cultivars; the genetic diversity and structure in its populations occurring over geographical ranges; the variation in economically and botanically important traits of it and the variation in its drought adaptive traits, in conservation and utilization context. In this study, the genetic diversity and relationships among selected cultivars from Sudan and Morocco were assessed using microsatellite markers. Microsatellite markers were also used to investigate the genetic diversity within and among populations collected from different geographic locations in Sudan. In a separate investigation, fruits of cultivars selected from Sudan, involved morphological and chemical characterization, and morphological and DNA polymorphism of the mother trees were also investigated. Morphological and photosynthetic adjustments to water stress were studied in the five most important date palm cultivars in Sudan, namely, Gondaila, Barakawi, Bitamoda, Khateeb and Laggai; and the mechanism enhancing photosynthetic gas exchange in date palm under water stress was also investigated. Results showed a significant (p < 0.001, t-test) differentiation between Sudan and Morocco groups of cultivars. However, the major feature of all tested cultivars was the complete lack of clustering and the absence of cultivars representing specific clones. The results indicated high genetic as well as compositional and morphological diversity among cultivars; while, compositional and morphological traits were found to be characteristic features that strongly differentiate cultivars as well as phenotypes. High genetic diversity was observed also in different populations. Slight but significant (p < 0.01, AMOVA) divergence was observed for soft and dry types; however, the genetic divergence among populations was relatively weak. The results showed a complex genetic relationships between some of the tested populations especially when isolation by distance was considered. The results of the study also revealed that date palm cultivars and phenotypes possess specific direct or interaction effects due to water availability on a range of morphological and physiological traits. Soft and dry phenotypes responded differently to different levels of water stress, while the dry phenotype was more sensitive and conservative. The results indicated that date palm has high fixation capacity to photosynthetic CO2 supply with interaction effect to water availability, which can be considered as advantageous when coping with stresses that may arise with climate change. In conclusion, although a large amount of diversity exists among date palm germplasm, the findings in this study show that the role of biological nature of the tree, isolation by distance and environmental effects on structuring date palm genome was highly influenced by human impacts. Identity of date palm cultivars as developed and manipulated by date palm growers, in the absence of scientific breeding programmes, may continue to mainly depend on tree morphology and fruit characters. The pattern of genetic differentiation may cover specific morphological and physiological traits that contribute to adaptive mechanisms in each phenotype. These traits can be considered for further studies related to drought adaptation in date palm.Väitöskirjatutkimuksessa pyrittiin selvittämään taatelipalmun (Phoenix dactylifera) lajikkeiden geneettistä monimuotoisuutta ja populaatiorakennetta sekä muuntelua taloudellisesti ja kasvitieteellisesti merkittävissä ja myös kuivuudenkestoon sopeutumiseen liittyvissä ominaisuuksissa. Viitekehyksenä oli sekä taatelipalmun geenivarojen suojelu että sen hyötykäyttö. Tutkimusmateriaali oli peräisin Sudanista ja Marokosta. Geneettistä vaihtelua populaatioiden sisällä ja välillä sekä lajikkeiden välisiä suhteita tutkittiin genomin mikrosatelliittialueisiin kohdistuvien geenimerkkien avulla. Lisäksi analysoitiin eri lajikkeiden hedelmien kemiallista koostumusta ja morfologiaa sekä emopuiden morfologista ja DNA-tason muuntelua. Sudanin viidelle tärkeimmälle taatelilajikkeelle (Gondaila, Barakawi, Bitamoda, Khateeb ja Laggai) suoritettiin kasvatuskokeita ja fysiologisia analyysejä kuivuudenkeston ja kuivuuteen sopeutumisen selvittämiseksi. Erityisenä kiinnostuksen kohteena olivat taatelipalmun yhteyttämisen eli fotosynteesin toiminnan mekanismit kuivuusstressin aikana. Tulokset osoittivat, että Sudanista ja Marokosta peräisin olevat lajikkeet eroavat geneettisesti toisistaan selvästi. Keskeinen tulos oli silti, että taatelipalmulla on runsaasti sekä geneettistä että morfologista vaihtelua ja että lajikkeet eivät muodosta selkeitä paikallisia ryhmiä tai klooneja. Hedelmätyypin perusteella pehmeään tai kuivaan päätyyppiin ryhmitellyt lajikkeet eroavat kuitenkin geneettisesti, morfologisesti ja fysiologisesti tosistaan ja ne reagoivat eri tavoin kuivuusstressiin. Taatelipalmulla on sopeutumismekanismeja, joiden avulla se pystyy selviämään hyvin kuivissakin olosuhteissa. Nämä piirteet voivat tulla nykyistäkin tärkeämmiksi ilmastonmuutoksen myötä. Vaikka taatelipalmulla ei ole varsinaista jalostusohjelmaa tutkimusalueella, viljelijät ovat muokanneet lajikkeiden koostumusta puiden morfologian ja hedelmälaadun perusteella. Tämä suoritettu valinta ja materiaalin vaihtaminen viljelijöiden kesken on vaikuttanut oleellisesti biologisten tekijöiden ohella taatelipalmun geneettiseen koostumukseen. Nyt valmistunut väitöskirjatutkimus antaa tärkeitä tietoja taatelipalmun geenivaroista ja sopeutumisesta erityisesti kuivuuteen. Saatuja tietoja voidaan käyttää tulevaisuudessa taatelipalmun jalostustoiminnan apuna

Variation in height and survival among northern populations of pedunculate oak (Quercus robur L.): results of a 13-year field study

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Genetic diversity and connectivity shape herbivore load within an oak population at its range limit

Host genetic diversity and genotypic identity have been reported to affect the abundance, species richness and species diversity of associated herbivore communities. Recent work, however, suggests that these effects are highly context-dependent and that the magnitude and direction of the effects may vary with e.g., spatial factors and the amount of genetic variation present in the host population. Here, we use observational data on a Finnish oak (Quercus robur) population to examine whether low genetic diversity within peripheral populations reduces the impact of host genotype on associated herbivore communities. We first compared measures of genetic variation within Finnish oak populations with those recorded in more central parts of the species' range, confirming that genetic variation within the Finnish populations is comparatively low. Despite this result, we found consistent imprints of host genetic diversity on herbivore communities: herbivore load, but not the species richness, increased with host genetic diversity in both years and both spatial scales examined. Spatial connectivity of hosts increased herbivore diversity as well as abundance. While the similarity of herbivore communities increased with the genetic similarity among hosts, the effect of geographic distance was stronger. Overall, our findings identify a major role for spatial context in structuring oak-associated herbivore communities-but we still trace detectable imprints of host genotype at multiple spatial scales even in this peripheral, genetically impoverished oak population.Peer reviewe

Fragmentation-related patterns of genetic differentiation in pedunculate oak (Quercus robur) at two hierarchical scales

Populations at species' range margins are expected to show lower genetic diversity than populations at the core of the range. Yet, long-lived, widespread tree species are expected to be resistant to genetic impoverishment, thus showing comparatively high genetic diversity within populations and low differentiation among populations. Here, we study the distribution of genetic variation in the pedunculate oak (Quercus robur L.) at its range margin in Finland at two hierarchical scales using 15 microsatellite loci. At a regional scale, we compared variation within versus among three oak populations. At a landscape scale, we examined genetic structuring within one of these populations, growing on an island of ca 5 km(2). As expected, we found the majority of genetic variation in Q. robur to occur within populations. Nonetheless, differentiation among populations was markedly high (F-ST = 0.12) compared with values reported for populations of Q. robur closer to the core of its range. At the landscape level, some spatial and temporal sub-structuring was observed, likely explained by the history of land-use on the island. Overall, Q. robur fulfils the expectation of the central-marginal hypothesis of high differentiation among marginal populations, but the notable population differentiation has most likely been influenced also by the long, ongoing fragmentation of populations. Finnish oak populations may still be adjusting to the drastic habitat changes of the past centuries. Preservation of genetic variation within the remaining stands is thus an important factor in the conservation of Q. robur at its range margin.Peer reviewe

Assessing Molecular Signature for Some Potential Date (Phoenix dactylifera L.) Cultivars from Saudi Arabia, Based on Chloroplast DNA Sequences rpoB and psbA-trnH

Phoenix dactylifera L. (date palm), being economically very important, is widely cultivated in the Middle East and North Africa, having about 400 different cultivars. Assessment of date cultivars under trading and farming is a widely accepted problem owing to lack of a unique molecular signature for specific date cultivars. In the present study, eight different cultivars of dates viz., Khodry, Khalas, Ruthana, Sukkari, Sefri, Segae, Ajwa and Hilali were sequenced for rpoB and psbA-trnH genes and analyzed using bioinformatics tools to establish a cultivar-specific molecular signature. The combined aligned data matrix was of 1147 characters, of which invariable and variable sites were found to be 958 and 173, respectively. The analysis clearly reveals three major groups of these cultivars: (i) Khodary, Sefri, Ajwa, Ruthana and Hilali (58% BS); (ii) Sukkari and Khalas (64% BS); and (iii) Segae. The economically most important cultivar Ajwa showed similarity with Khodary and Sefri (67% BS).The sequences of the date cultivars generated in the present study showed bootstrap values between 38% and 70% so these sequences could be carefully used as molecular signature for potential date cultivars under trading and selection of genuine cultivars at the seedling stage for farming

Assessment of genetic relationships among native and introduced Himalayan balsam (Impatiens glandulifera) plants based on genome profiling

We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from native and non-native regions of their distribution. When genetic relationships were explored by PCoA using SNP and SilicoDArT marker data, the first, second, and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada, and Pakistan were grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK-Canada-Pakistan group based on SilicoDArT markers. Constructed trees differentiated individuals into clusters resembling the PCoA patterns. The Bayesian BAPS analysis performed for the SNP data revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan, and the combination of the UK and Canada. Similar clustering was visible in the UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The BAPS analyses conducted for the SilicoDArT data differ slightly: The individuals were distributed in nine clusters, and the Indian cluster exhibited ancestral gene flow with the mixed cluster including Canadian, Pakistani, and UK samples, and one Finnish sample. The AMOVA showed that 45% and 26% of variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. The Bayesian BAPS analyses and the gene flow networks were the most informative tools for resolving relationships among native and introduced plants. It is notable that the small sample sizes for non-Finnish plant materials may affect the accuracy of the gene flow and other estimates.Peer reviewe

Genetic profiling of the critically endangered palm species Medemia argun using newly developed chloroplast DNA markers

Background: Medemia argun is a rare wild palm tree species. Its global existence is assumed to include the main population of about 1000 trees in the Nubian Desert of Sudan and some scattered individuals in southern Egypt. The species had previously been assumed to be extinct, but then reported to be extant about 20 years ago. Aims: To assess genetic variation and explore population genetic structure of M. argun, through development and analysis of microsatellite markers. Methods: The genome sequence mining approach was applied in order to identify microsatellites in the chloroplast genome of Bismarckia nobilis, a species closely related of M. argun. A set of 49 markers were designed, and their characteristics are now provided. Seven chloroplast DNA markers were developed for use in the genetic characterisation of this threatened species. Results: Five markers were found polymorphic in M. argun, which enabled the assessment of the genetic diversity of the species. Significant genetic differentiation was observed among generations and collection sites, accompanied by low genetic variation. The seven markers developed were polymorphic among the wild relatives Hyphaene thebaica and Borassus aethiopum. Conclusions: This is the first study to report molecular markers for M. argun. Our results suggest that the genetic consequences of population fragmentation in M. argun are beginning to be evident.Peer reviewe