Unique Genetic Resource Research Articles

Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation

BackgroundNile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques.ResultsThe samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq.ConclusionsThe results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.

Domestic chicken diversity: Origin, distribution, and adaptation.

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

Mitochondrial genomes from modern and ancient Turano-Mongolian cattle reveal an ancient diversity of taurine maternal lineages in East Asia.

Turano-Mongolian cattle are a group of taurine cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3119 and T3055) were identified as specific of Turano-Mongolian cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian cattle breeds, which have been shaped by ancient migrations and geographic barriers.

Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers.

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

Screening of Onion (Allium cepa L.) Genotypes for Drought Tolerance Using Physiological and Yield Based Indices Through Multivariate Analysis.

Drought is a leading abiotic constraints for onion production globally. Breeding by using unique genetic resources for drought tolerance is a vital mitigation strategy. With a total of 100 onion genotypes were screened for drought tolerance using multivariate analysis. The experiment was conducted in a controlled rainout shelter for 2 years 2017–2018 and 2018–2019 in a randomized block design with three replications and two treatments (control and drought stress). The plant was exposed to drought stress during the bulb development stage (i.e., 50–75 days after transplanting). The genotypes were screened on the basis of the drought tolerance efficiency (DTE), percent bulb yield reduction, and results of multivariate analysis viz. hierarchical cluster analysis by Ward’s method, discriminate analysis and principal component analysis. The analysis of variance indicated significant differences among the tested genotypes and treatments for all the parameters studied, viz. phenotypic, physiological, biochemical, and yield attributes. Bulb yield was strongly positively correlated with membrane stability index (MSI), relative water content (RWC), total chlorophyll content, antioxidant enzyme activity, and leaf area under drought stress. The genotypes were categorized into five groups namely, highly tolerant, tolerant, intermediate, sensitive, and highly sensitive based on genetic distance. Under drought conditions, clusters II and IV contained highly tolerant and highly sensitive genotypes, respectively. Tolerant genotypes, viz. Acc. 1656, Acc. 1658, W-009, and W-085, had higher DTE (>90%), fewer yield losses (<20%), and performed superiorly for different traits under drought stress. Acc. 1627 and Acc. 1639 were found to be highly drought-sensitive genotypes, with more than 70% yield loss. In biplot, the tolerant genotypes (Acc. 1656, Acc. 1658, W-085, W-009, W-397, W-396, W-414, and W-448) were positively associated with bulb yield, DTE, RWC, MSI, leaf area, and antioxidant enzyme activity under drought stress. The study thus identified tolerant genotypes with favorable adaptive traits that may be useful in onion breeding program for drought tolerance.

Microalgal Diversity Study of Lake Basaka, Metehara, Ethiopia

Lake Basaka is characterized by a Na-HCO3-Cl type of water which is typical feature of saline water. Such saline environments may harbors unique microbial genetic resource which have wide industrial applications. This study was conducted with the objective of describing algal diversity of the lake Basaka. For algal diversity study 90 water samples were collected in October, 2015. Microscopic study of the water samples showed that phylum Chlorophyta and Diatoms were dominated the Lake during sample collection. Scenedesmus, Selenastrum, Volvox, Navicula and Nitzschia species were observed with high frequencies. Moreover, few algal species belong to Phylum Euglinophyta were observed.

Conservation of criollo livestock in the United States: challenges and solutions

Conservation of criollo breeds in the USA provides for the survival of unique genetic resources that remain productive in challenging environments. Conservation is difficult because most criollo breeds are local and have no formal organization of breeders. Successful conservation has depended on establishing accurate breed definitions and investigations of phenotype, history, and genetics. Organization of breeders and of breeding has been essential for the final success of conservation efforts. Each specific breed has met its own unique challenges. Among cattle breeds, Texas Longhorns needed an accurate breed definition as well as genetic investigations, whereas Florida Crackers needed organization. Spanish goats required definition, organization, and research into their productive potential. This has led to the Spanish goat now being secure as a popular choice for extensive production of goat meat. Navajo Churro sheep are maintained by ongoing phenotypic evaluation at each generation and careful attention to the frequency of phenotypic characteristics within the population. The other criollo sheep breeds in the USA (Louisiana, Gulf Coast, and Florida) have benefitted from genetic studies that demonstrate differences among the breeds and guide conservation of each of these related types in isolation one from the others. The organization of criollo swine has lagged behind the others, with the Duroc standing out as an exception that has become one of the main breeds in commercial hog production.

Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p &lt; 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

Genetic status of lowland-type Racka sheep colour variants

Lowland-type Racka is an indigenous sheep breed that beside Hungarian Grey cattle and Mangalitza pig is one of the national symbols of Hungary. However, the genetic description of Racka sheep has not yet been conducted based on whole-genome screening. By using the Geneseek Ovine SNP50 BeadChip, we have sampled the genome of 126 Black and 128 White Racka sheep. For comparative purposes, we used 134 Hungarian Merinos and further 3345 animals from 81 different breeds have been included from an available database. Performance of a multidimensional scaling plot showed that White and Black Rackas represent well-separated groups among other sheep breeds and clustered separately from each other. However, the number and total length of Runs of Homozygosity was similar to other sheep breeds, except Soay. The inbreeding coefficients (method-of-moments relatedness F coefficient) of Black and White Racka were 0.147 and 0.133, respectively. Based on multidimensional scaling and admixture analyses and on comparisons of genetic distances of the investigated 84 populations, we suggest considering the colour variants of Racka as genetically differentiated breeds. The most differentiated markers between Black and White Racka highlight several candidate genes including 5-Hydroxytryptamine Receptor 5A, Insulin Induced Gene 1, Cyclin Dependent Kinase 5 and Melanocortin 1 Receptor. The results of this study help the recognition of Racka as a unique genetic resource among sheep and pave the way of application of genome screens to guide the resolution of questions arising among breeders.

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species.

Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe×niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

Assessment of genetic diversity of Cervus albirostris (white-lipped deer) by microsatellite markers

Cervus albirostris (white-lipped deer) is a unique plateau deer in China. In order to conserve the white-lipped deer population and maintain its sustainable development in Liaoyang, China, ten microsatellite markers was used to analyze the genetic diversity of 42 white-lipped deer, an ex-situ conservation population from Yushu (Qinghai) to Liaoyang (Liaoning). The results showed that expected heterozygosity ranged from 0.399 to 0.825 with a mean of 0.6071, while observed heterozygosity varied from 0.081 to 0.692 with a mean of 0.4456. This study contributes to the study of the unique genetic resources in this ex-situ conservation population and provides a perspective for better implementation of ex-situ conservation of white-lipped deer population in Liaoyang, China.

Genetic diversity of pear cultivars using SSR markers and their reactions to pear rust (Gymnosporangium fuscum)

Commonly grown in different ecological conditions of Turkey and the world, pear (Pyrus communis L.), as a plant species, has a long cultivation history in Turkey. However, its unique genetic resources are in danger of extinction due to changes in the agro-ecosystem and genetic erosion. In addition, pear rust caused by Gymnosporangium fuscum is one of the significant diseases of pear. Severe economic losses have been reported in some pear orchards near the extensive juniper populations. In the present study, the genetic diversity and sensitivity level to pear rust (Gymnosporangium fuscum) of 25 local and commercially important pear varieties grafted on seedling and Quince A (QA) was determined using 13 SSR primers. The selected verities were clustered into two major groups that were closely related. The SSR markers provided reliable genotyping and demonstrated their usefulness for identifying pear genetic diversity. The difference between years and rootstocks according to disease severity rates was found to be statistically significant. Although none of the pear varieties assessed in these experiments were resistant to rust, the disease severity of the pear varieties of QA rootstock was generally higher than that of the seedling varieties.

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

BackgroundChaka sheep, named after Chaka Salt Lake, are adapted to a harsh, highly saline environment. They are known for their high-grade meat quality and are a valuable genetic resource in China. Furthermore, the Chaka sheep breed has been designated a geographical symbol of agricultural products by the Chinese Ministry of Agriculture.ResultsThe genomes of 10 Chaka sheep were sequenced using next-generation sequencing, and compared to that of additional Chinese sheep breeds (Mongolian: Bayinbuluke and Tan; Tibetan: Oula sheep) to explore its population structure, genetic diversity and positive selection signatures. Principle component analysis and a neighbor-joining tree indicated that Chaka sheep significantly diverged from Bayinbuluke, Tan, and Oula sheep. Moreover, they were found to have descended from unique ancestors (K = 2 and K = 3) according to the structure analysis. The Chaka sheep genome demonstrated comparable genetic diversity from the other three breeds, as indicated by observed heterozygosity (Ho), expected heterozygosity (He), runs of homozygosity (ROH), linkage disequilibrium (LD) decay. The enrichment analysis revealed that in contrast to Mongolian or Tibetan lineage groups, the genes annotated by specific missense mutations of Chaka sheep were enriched with muscle structure development (GO:0061061) factors including insulin-like growth factor 1 (IGF1), growth differentiation factor 3 (GDF3), histone deacetylase 9 (HDAC9), transforming growth factor beta receptor 2 (TGFBR2), and calpain 3 (CAPN3), among others. A genome-wide scan using Fst and XP-CLR revealed a list of muscle-related genes, including neurofibromin 1 (NF1) and myomesin 1 (MYOM1), under potential selection in Chaka sheep compared with other breeds.ConclusionsThe comprehensive genome-wide characterization provided the fundamental footprints for breeding and management of the Chaka sheep and confirmed that they harbor unique genetic resources.

Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs).

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population , which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

Diversity of Native and Exotic Fruit Genetic Resources in Nepal

Diversity in fruit genetic resources in Nepal is contributed by wild, indigenous and exotic sources. This study was carried out to bring together the available fruit species and cultivars at various stations of Department of Agriculture (DoA), Nepal Agricultural Research Council (NARC), Agriculture and Forest University (AFU) and private farms until the Fiscal Year 2017/2018. Altogather there were 47 species of fruits from tropical zone of Terai (Tarahara, Janakpur, Sarlahi, Parwanipur and Khajura) to cold temperature zone of high hills (Marpha, Rajikot and Satbanj) across the country. Apple diversity was found at Horticulture Research Station, Rajikot, Jumla and has introduced 25 spur type cultivars. National Citrus Research Programme (NCRP), Dhankuta was citrus most diversity areas and has maintained 130 exotic and indigenous germplasms of citrus species followed by NCFD, Kirtipur. Mango diversity was noted at RARS, Tarahara (16 cultivars), RARS, Parwanipur (25 cultivars), Farm of DoA-Sarlahi (30 cultivars), Farms of DoA-Janakpur (18 cultivars), AFU-Rampur (17 cultivars). Some of the private nurseries like Everything Organic Nursery, Patlekhet, Kavre and international organization like Technology Demonstration Centre of ICIMOD, Godawari, Lalitpur were also found to be a diversity centre of many exotic and indigenous germplasms of fruit species. These indigenous fruit genetic resources were also used to develop varieties such as Sunkagati-1 and Sunkagati-2 and Tehrathum Local of acid lime, Khoku Local of mandarin orange, 'Malbhog' of banana which were notified by the National Seed Board, SQCC. The unique fruit genetic resources were ‘Pharping Local’ (Asian sand pear), ‘Sindhuli Junar’ (sweet orange), ‘Dhankuta Local’ and ‘Manakamana Local’ (mandarin), Local Malbhog (banana), Bhaktapure Lapsi (Nepalese hog plum) etc. which have superior traits than exotic fruits. Unique and wild fruit species were yellow, black and red raspberries (Rubus ellipticus, R. foliolosus and R. acuminatus respectively), bale (Aegle marmelos), pummelo (Citrus grandis), citron (Citrus medica), sweet lime (Citrus limettoides), butter tree or chiuri (Basia buttyacea), tamarind (Tamarindus indica), black plum (Syzygium cumini), wild apple (Mallus baccata), rough lemon (Citrus jambhiri), bayberry (Myrica esculanta), edimayal (Pyrus pashia), black and white ebony (Diospyrus malbarica), wild species of olive (Olea ferruginea and O. glandulifera), wild kiwifruit (Actinidia callosa) etc. Most of the diversity studies were based on phenotypic descriptions. We believe that the number of species and genotypes listed in this article would be increased if detail survey is further carried out. Way forward to utilize these valuable genetic resources has also been discussed in this manuscript.

Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection.

Soybean breeding relies on the use of wild (Glycine soja Sieb. and Zucc.) and domesticated [Glycine max (L.) Merr.] germplasm for trait improvement. Soybeans are self-pollinating and accessions can be maintained as pure lines, however within-accession genetic variation has been observed in previous studies of some landraces and elite cultivars. The objective of this study was to characterize within-line variation in the accessions housed in the USDA Soybean Germplasm Collection. This collection includes over 20,000 accessions, each previously genotyped using the SoySNP50K Chip. Each SoySNP50K genotype was developed by pooling approximately three individuals per accession. Therefore, clusters of SNPs called as heterozygous within an accession can be inferred to represent putative regions of heterogeneity between the three individuals sampled. In this study, we found high-probability intervals of heterogeneity in 4% of the collection, representing 870 accessions. Heterogeneous loci were found on every chromosome and, collectively, covered 98.4% of the soybean genome and 99% of the gene models. Sanger sequencing confirmed regions of genomic heterogeneity among a subset of ten accessions. This dataset provides useful information and considerations for users of crop germplasm seed banks. Furthermore, the heterogeneous accessions and/or loci represent a unique genetic resource that is immediately available for forward and reverse genetics studies.

English

This study reviews the introduction of the exotic breeds and cross breeding of local chicken in Ethiopia, solution to genetic erosion and needs for conservation with aim of delivering in the short form and clear information for beneficiaries and to whom it may concern. Poultry production and its product consumption are progressively increasing globally. In Ethiopia, chicken production plays a great role as a primary supply of eggs and meat in rural and urban areas and as a source of income for smallholder farmers. The interest of the farmers to maximize poultry products is increasing. Therefore, the different parts of the farmers are practicing crossbreeding unsystematically. However, crossbreeding is not advised and recommended by government due to its impact on genetic diversity and losing of the important traits of local chickens; thus, policy of the government has prepared different strategies to improve livestock development. There is no good breeding scheme introduced so far to avoid such kind of impacts or else regulator laws to avoid uncontrolled breeding activities. Therefore, conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. And even if the indigenous chickens are low in productive performance, it has its unique and important characteristics such as brooding, tolerance of the disease and harsh environment of tropics, and giving good product under management condition. Therefore, adjusting the proper breeding strategies in the country, especially upgrading the local chicken for higher production through selective breeding system rather than cross breeding with exotic breeds and conservation of the genetic resource is needed. Key words: Conservation, cross breeding, exotic and local chickens breed, genetic erosion, Ethiopia

Endemic plants of Crete in electronic trade and wildlife tourism: current patterns and implications for conservation

BackgroundThe island of Crete is a biodiversity hotspot having 223 endemic vascular taxa (species and subspecies) as a result of its long isolation and the wide range of habitats it includes. We explore trends and patterns in the electronic trade of these unique genetic resources and in their involvement in wildlife tourism, the ways these two activities are performed and the associated potential threats on the plants’ wild populations, and we also identify priority taxa requiring special attention. The main part of the study was conducted in 2016–2017 using English as a search language; an additional search was conducted in 2019 using German and French.ResultsWe found e-commerce for 28 (13%) endemic taxa. These are traded by 65 nurseries from 14 countries, the UK primarily. Among the traded plants, 16 face extinction risk and/or are under protection status. Prices vary largely for the same taxon and form of sale. Lamiaceae is the family with the highest number of e-traded taxa, Tulipa bakeri is the most traded species, and the living plant is the commonest form of sale. Thirty-seven endemic taxa are advertised in the websites of travel agencies involved in wildlife tourism. Tulipa doerfleri is the most frequently encountered taxon in these websites, whereas Lamiaceae, Liliaceae and Orchidaceae are similarly represented. The additional search showed a very rapid increase in the e-trade of the Cretan endemis.ConclusionThe two examined markets are similar in that geophytes play a prominent role and Lamiaceae rank first among the represented plant families, but differ in several aspects: only 22.6% of the taxa detected are common in both, obedience to rules exhibited by travel agencies is not usually the case with nurseries, and potential threats to wild populations are estimated as considerably higher for the traded plants. Sixteen endemic taxa of Crete were identified as requiring special attention.

A comprehensive study of metabolite genetics reveals strong pleiotropy and heterogeneity across time and context

Genetic studies of metabolites have identified thousands of variants, many of which are associated with downstream metabolic and obesogenic disorders. However, these studies have relied on univariate analyses, reducing power and limiting context-specific understanding. Here we aim to provide an integrated perspective of the genetic basis of metabolites by leveraging the Finnish Metabolic Syndrome In Men (METSIM) cohort, a unique genetic resource which contains metabolic measurements, mostly lipids, across distinct time points as well as information on statin usage. We increase effective sample size by an average of two-fold by applying the Covariates for Multi-phenotype Studies (CMS) approach, identifying 588 significant SNP-metabolite associations, including 228 new associations. Our analysis pinpoints a small number of master metabolic regulator genes, balancing the relative proportion of dozens of metabolite levels. We further identify associations to changes in metabolic levels across time as well as genetic interactions with statin at both the master metabolic regulator and genome-wide level.