High Level Of Genetic Diversity Research Articles

Genetic diversity studies between Ipomoea wild species and cultivated sweet potato (Ipomoea batatas (L.) Lam.) using SSR markers

Sweet potato (Ipomoea batatas (L.) Lam) is one of the major tuber crops in Asian countries, including India, yet the interrelationship and genetic variability among the cultivar and its crop wild relatives remain obscure. The wild relatives of sweet potato represent a vital source of untapped genetic diversity in the breeding programs. In this study, a set of 12 Simple Sequence Repeats (SSR) markers were utilized to understand the extent of genetic diversity and relationship within and between 20 sweet potato accessions, 23 wild Ipomoea species and two Merremia species for utilization in breeding programmes. The SSR primers produced 84 polymorphic alleles within the range of 105-393 bp, collectively showing an average polymorphism of 94.5%. The average Polymorphic Information Content (PIC) value of 0.67 showed that all the primers were polymorphic in nature. Similarity coefficient based dendrogram and Principal Component Analysis (PCA) scatter plot clearly differentiated all the cultivars and wild species. The cluster dendrogram analysis revealed the close relationship of cultivars with I. triloba and I. trifida at a similarity index of 0.75. Our analysis showed a high degree of genetic variability within and between hexaploid sweet potato and diploid wild species, whereas lower within the cultivars, which shows that there is a high level of genetic diversity exists within the Ipomoea species for its utilization in breeding programs. Thus, the two wild species, I. trifida and I. triloba could be used in hybridization for improvement of sweet potato through ploidy manipulation.

Consistent accumulation of transposable elements in species of the Hawaiian Tetragnatha spiny-leg adaptive radiation across the archipelago chronosequence

Abstract The ecological and phenotypic diversity observed in oceanic island radiations presents an evolutionary paradox: a high level of genetic variation is typically required for diversification, but species colonizing a new island commonly suffer from founder effects. This reduction in population size leads to lower genetic diversity, which ultimately results in a reduction in the efficiency of natural selection. Then, what is the source of genetic variation which acts as the raw material for ecological and phenotypic diversification in oceanic archipelagos? Transposable elements (TEs) are mobile genetic elements that have been linked to the generation of genetic diversity, and evidence suggests that TE activity and accumulation along the genome can result from reductions in population size. Here, we use the Hawaiian spiny-leg spider radiation (Tetragnatha) to test whether TE accumulation increases due to demographic processes associated with island colonization. We sequenced and quantified TEs in 23 individuals representing 16 species from the spiny-leg radiation and 4 individuals from its sister radiation, the Hawaiian web-building Tetragnatha. Our results show that founder effects resulting from colonization of new islands have not resulted in TE accumulation over evolutionary time. Specifically, we found no evidence for increase in abundance of specific TE superfamilies, nor an accumulation of ‘young TEs’ in lineages which have recently colonized a new island or are present in islands with active volcanoes. We also found that the DNA/hAT transposon superfamily is by far the most abundant TE superfamily in the Tetragnatha radiation. This work shows that there is no clear trend of increasing TE abundance for the spiny-leg radiation across the archipelago chronosequence, and TE accumulation is not affected by population oscillations associated with island colonization events. Therefore, despite their known role in the generation of genetic diversity, TE activity does not appear to be the mechanism explaining the evolutionary paradox of insular diversification in the Tetragnatha spiny-leg radiation.

Multidrug-resistant Escherichia coli strains isolated from swine manure biofertilizer in Brazil.

Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters

BackgroundAspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.ResultsPangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.ConclusionIn summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.

Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed

Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (HE = 0.373) and observed (HO = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise FST estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Effects of past riverine connectivity on the population structure and species distribution of ‘Geophagus’ brasiliensis (Cichlidae) complex in a Neotropical hotspot

Abstract Once fishes and rivers are intrinsically connected, historical events such as river captures and the reconfiguration of palaeodrainages affect population structure and species distribution. However, direct evidence of these events remains limited. We aimed to directly infer putative connections between adjacent river basins to understand genetic and geographical patterns in populations and species of the ‘Geophagus’ brasiliensis complex. For that, we analysed 174 sequences of the mitochondrial gene cytochrome c oxidase subunit I (COI) from five species along 35 sites within and near a coastal basin in northeastern Brazil. Based on haplotype network, palaeodrainage reconstruction, geological inferences of river captures and analyses of molecular variance (AMOVAs), we tested how the genetic structure could be associated with variable patterns of habitat connectivity through time. In general, high levels of genetic variation were identified, including shared haplotypes among drainages for most species. AMOVA suggested that drainage rearrangements between adjacent basins were the main drivers of genetic diversification in the ‘G.’ brasiliensis complex. Our study refuted dispersal routes via the continental shelf, whereas eight putative river captures suggested historical connections that enabled gene flow among drainages until recent interruption. These results provide novel insights on the role of riverscape evolution on the biogeography of neotropical ichthyofauna.

Advancing utilization of diverse global carrot (Daucus carota L.) germplasm with flowering habit trait ontology.

Biennial vegetable crops are challenging to breed due to long breeding cycle times. At the same time, it is important to preserve a strong biennial growth habit, avoiding premature flowering that renders the crop unmarketable. Gene banks carry important genetic variation which may be essential to improve crop resilience, but these collections are underutilized due to lack of characterization for key traits like bolting tendency for biennial vegetable crops. Due to concerns about introducing undesirable traits such as premature flowering into elite germplasm, many accessions may not be considered for other key traits that benefit growers, leaving crops more vulnerable to pests, diseases, and abiotic stresses. In this study, we develop a method for characterizing flowering to identify accessions that are predominantly biennial, which could be incorporated into biennial breeding programs without substantially increasing the risk of annual growth habits. This should increase the use of these accessions if they are also sources of other important traits such as disease resistance. We developed the CarrotOmics flowering habit trait ontology and evaluated flowering habit in the largest (N=695), and most diverse collection of cultivated carrots studied to date. Over 80% of accessions were collected from the Eurasian supercontinent, which includes the primary and secondary centers of carrot diversity. We successfully identified untapped genetic diversity in biennial carrot germplasm (n=197 with 0% plants flowering) and predominantly-biennial germplasm (n=357 with <15% plants flowering). High broad-sense heritability for flowering habit (0.81 < H2< 0.93) indicates a strong genetic component of this trait, suggesting that these carrot accessions should be consistently biennial. Breeders can select biennial plants and eliminate annual plants from a predominantly biennial population. The establishment of the predominantly biennial subcategory nearly doubles the availability of germplasm with commercial potential and accounts for 54% of the germplasm collection we evaluated. This subcollection is a useful source of genetic diversity for breeders. This method could also be applied to other biennial vegetable genetic resources and to introduce higher levels of genetic diversity into commercial cultivars, to reduce crop genetic vulnerability. We encourage breeders and researchers of biennial crops to optimize this strategy for their particular crop.

Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus).

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.

Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia.

Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.

Genetic variation and structure of endemic and endangered wild celery (Kelussia odoratissima Mozaff.) quantified using novel microsatellite markers developed by next-generation sequencing.

Kelussia odoratissima Mozaff. (Apiaceae) is a native plant that has been traditionally consumed in Iran's food and pharmaceutical industries. Overharvesting of the taxon, especially at the beginning of the growing season, due to its considerable medicinal and economic value, is believed to be the main reason for the extirpating of this plant. The consequences of the severe anthropogenic impacts on the genetic diversity of populations are poorly known. In order to investigate the level of genetic variation and patterns of the genetic structure of K. odoratissima, we developed novel microsatellite markers using the 454 Roche next-generation sequencing (NGS) platform for the first time. Out of 1,165 microsatellite markers bioinformatically confirmed, twenty-five were tested, of which 23 were used to screen genetic variation across 12 natural populations. Our results showed that the average number of alleles per locus and the polymorphic information content (PIC) were 10.87 (range 7 to 27), and 0.81 (range 0.67 to 0.94), respectively. The mean observed and expected heterozygosities (± SD) across all populations were 0.80 ± 0.31 and 0.72 ± 0.14, respectively. The average pairwise FST among the populations was 0.37 (range 0.04 to 0.81). Bayesian and distance-based clustering, and principal coordinate analyses revealed at least four major genetic clusters. Although high level of structure can be explained by landscape topography and geographic distance, presence of admixed populations can be associated to seed or pollen dispersal. Contrary to expectations, the high level of genetic variation and lack of inbreeding suggest that overexploitation has not yet significantly purged the allelic variability within the natural populations in protected areas.

High levels of genetic variation and differentiation in wild tropical gourds provide a novel resource for cucurbit crop improvement

Social Impact StatementThe genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement.Summary Crop wild relatives (CWR) are reservoirs of genetic diversity and they are important for the maintenance of crop evolutionary potential. Mexico is the centre of domestication and diversity for many CWR. The genus Cucurbita originated in America, where at least six independent domestication events took place. Nonetheless, Cucurbita CWR have been seldom studied. In the present study, we test the role of incomplete lineage sorting (ILS) and secondary contact in the divergence of C. okeechobeensis subsp. martinezii and C. lundelliana. Additionally, we seek to understand the role of environmental differentiation in their divergence. We obtained 1,638 single nucleotide polymorphisms (SNPs) for 107 individuals from the most recently diverged wild species in this genus, encompassing 25 localities of C. lundelliana and nine localities of C. okeechobeensis subsp. martinezii in Mexico. We found higher genetic variation in C. lundelliana (HE = 0.227) than in C. okeechobeensis subsp. martinezii (HE = 0.187). Each taxon constitutes a well‐differentiated genetic group, with an area of introgression in Pantanos de Centla. We found candidate loci associated to hydric and thermal stress, which could be valuable for crop improvement. Our study supported a scenario of ILS followed by secondary contact, where divergence was probably driven by Pleistocene climate change. These CWR represent important phytogenetic resources for crop improvement given their high levels of genetic variation and differentiation and their SNPs associated to different climatic variables.

Genome-wide scans for selection signatures in indigenous chickens reveal candidate genes associated with local adaptation

Population growth and climate change pose challenges to the sustainability of poultry farming. The emphasis on high-yield traits in commercialized breeds has led to a decline in their adaptability. Chicken varieties adapted to the local environment, possessing traits that facilitate adaptation to climate change, such as disease resistance and tolerance to extreme weather conditions, can improve hybridization outcomes. In this study, we conducted an analysis of the population structure and genetic diversity of 110 chickens representing indigenous breeds from southern China and two different commercial breeds. Further, we performed comparative population genomics, utilizing nucleotide diversity and fixation statistics, to characterize genomic features of natural selection and to identify unique genetic traits and potential selection markers developed by indigenous breeds after adapting to the local environment. Results based on genetic diversity and population structure analyses showed that indigenous varieties exhibited high levels of genetic diversity. Commercial breeds that have been indigenously bred demonstrated higher levels of genetic diversity than those that have not, and breeds with different selection practices displayed significant differences in genetic structure. Additionally, we further searched for potential genomic regions in native chicken ecotypes, uncovering several candidate genes related to ecological adaptations affecting local breeds, such as IKBKB, S1PR1, TSHR, IL1RAPL1 and AMY2A, which are involved in disease resistance, heat tolerance, immune regulation and behavioral traits. This work provides important insights into the genomic characterization of ecotypes of native chicken in southern China. The identification of candidate genes associated with traits such as disease resistance, heat tolerance, immunomodulation, and behavioral traits is a significant outcome. These candidate genes may contribute to the understanding of the molecular basis of the adaptation of the southern native chicken to the local environment. It is recommended that these genes be integrated into chicken breeding programs to enhance sustainable agriculture and promote effective conservation and utilization strategies.

Genetic and pathogenic characterization of Rhizoctonia solani AG-4 isolates obtained from common bean

Common bean (Phaseolus vulgaris L.) is the most important grain legume. Crop production of common bean is affected by a number of diseases, such as Rhizoctonia root rot, being detected worldwide. Herein, we aimed to genetically and pathologically characterize Rhizoctonia solani isolates obtained from different provinces in Turkey. Anastomosis groups (AG) and subgroups of isolates were identified based on the sequence analysis of the rDNA-ITS region. The most prevalent subgroup was AG-4 HGIII, according to BLAST analysis and the phylogeny of resultant sequences, followed by AG-4 HGI and AG-4 HGII, respectively. iPBS retrotransposons highly supported the phylogenetic tree and provided a high level of genetic variability among isolates to discriminate AG subgroups. The results indicated that the iPBS DNA marker system based on retrotransposons could be used to discriminate Rhizoctonia isolates relying on AG grouping. The virulence of the pathogen isolates changed from 3.67 to 5 based on the agar-plate assay on the susceptible cv. Gina. The reactions of thirty common bean cultivars were also evaluated against the most aggressive isolate in each subgroup. The reaction assay showed significant differences among both isolates and cultivars; the highest disease severity among cultivars was observed to AG-4 HGI, followed by AG-4 HGIII and AG-4 HGII, respectively. None of the cultivars showed resistance to all AG subgroups. Screening of AGs among the isolates and selecting cultivars are critical to managing Rhizoctonia disease due to the range of host suitability according to AG subgroups.

Genetic diversity of food-medicinal Lycium spp. in China: Insights from chloroplast genome

ObjectiveGoji (fruits of Lycium spp.) is commonly consumed as food and medicine. The increasing market demand for goji has led to its wide cultivation and broad breeding, which might cause loss of genetic diversity. This study aims to uncover the genetic diversity of the cultivated and wild Lycium. MethodsThe chloroplast genome (CPG) of 34 accessions of Chinese food-medicinal Lycium spp., including the popular cultivars and their wild relatives, was re-sequenced and assembled, based on which the genetic diversity was evaluated. ResultsSequence structural comparison shows that CPG is comparatively conserved within species. Phylogenetic analysis indicates that CPG is sufficient for the discrimination of Lycium species; combined with nuclear ribosomal internal transcribed spacer (Nr ITS) sequences, materials with mixed genetic backgrounds can be identified. Nucleotide diversity analysis reveals that the modern cultivars are probably with a common maternal parent, while the wild accessions are with higher level of genetic diversity. ConclusionFor the first time this study reveals the intraspecies genetic diversity of Lycium spp. using CPG, highlighting the urgent conservation demand of wild genetic resources of Lycium. Our study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity conservation. This CPG-based technology will contribute to the sustainable development of medicinal plants broadly.

Genetic diversity of mitochondrial DNA D-loop sequence in Bang Troi chicken breed

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima’s test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtD-loop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds.

Genetic structure and diversity of semi-captive populations: the anomalous case of the Asian elephant

AbstractWild species living in captivity are subject to loss of genetic diversity, inbreeding depression, and differentiation among populations. Only very few species have been under human care for centuries but have not been selectively bred, have free-ranging movements most of the time, and retain porous barriers to gene flow between wild and captive populations. Such captive populations are expected to retain high levels of genetic diversity and anthropogenic factors should result in a limited genetic differentiation from wild populations. Asian elephants have been trained and used by humans for at least 4000 years as war animals, mounts of kings and draught animals. In Myanmar and Laos, elephants are still being used for hauling timber in the forest while retaining traditional management practices including seasonal release, free mating and movement. However, habitat fragmentation, isolation and reduced gene flows are threatening both semi-captive and wild pools. We genotyped 167 semi-captive elephants from Laos and Myanmar using a panel of 11 microsatellite loci to estimate the genetic diversity and population structure. We found that elephants of both countries presented high levels of genetic diversity and a low degree of inbreeding, if any. This agrees with the expected high level of genetic diversity in semi-captive populations. We found a weak differentiation along a geographical gradient from southern Laos to northern Myanmar but no differentiation between wild-caught and captive-born pools. The potential value for conservation of a large population of semi-captive elephants has been recognized but the conservation community has yet to fully explore the potential role semi-captive elephants could play in maintaining gene flows.

Species Identification and Genetic Diversity Analysis of Medicinal Plants Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz.

The classification system for the genus Aconitum is highly complex. It is also the subject of ongoing debate. Aconitum pendulum Busch and Aconitum flavum Hand.-Mazz. are perennial herbs of the genus Aconitum. Dried roots of these two plants are used in traditional Chinese medicine. In this study, morphological observations and ISSR molecular markers were employed to discriminate between A. flavum and A. pendulum, with the objective of gaining insights into the interspecies classification of Aconitum. The pubescence on the inflorescence of A. flavum was found to be appressed, while that on the inflorescence of A. pendulum was spread. UPGMA (unweighted pair-group method with arithmetic average) cluster analysis, PCoA (principal coordinates analysis), and Bayesian structural analysis divided the 199 individuals (99 individuals from DWM population and 100 individuals from QHL population) into two main branches, which is consistent with the observations of the morphology of pubescence on the inflorescence. These analyses indicated that A. flavum and A. pendulum are distinct species. No diagnostic bands were found between the two species. Two primer combinations (UBC808 and UBC853) were ultimately selected for species identification of A. flavum and A. pendulum. This study revealed high levels of genetic diversity in both A. flavum (He = 0.254, I = 0.395, PPB = 95.85%) and A. pendulum (He = 0.291, I = 0.445, PPB = 94.58%). We may say, therefore, that ISSR molecular markers are useful for distinguishing A. flavum and A. pendulum, and they are also suitable for revealing genetic diversity and population structure.

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BackgroundThe sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.ResultsIn this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.ConclusionOur findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.