Genetic Diversity Of Wild Species Research Articles

QTL Mapping of Fiber- and Seed-Related Traits in Chromosome Segment Substitution Lines Derived from Gossypium hirsutum × Gossypium darwinii.

A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using G. darwinii accession 5-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC1 population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including GH_A01G1096 (ARF5) and GH_A10G0141 (PDF2) for lint percentage, and GH_D01G0047 (KCS4) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton.

Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity

Abstract Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

Functional immune diversity in reindeer reveals a high Arctic population at risk

Climate changes the geographic range of both species as well as pathogens, causing a potential increase in the vulnerability of populations or species with limited genetic diversity. With advances in high throughput sequencing (HTS) technologies, we can now define functional expressed genetic diversity of wild species at a larger scale and identify populations at risk. Previous studies have used genomic DNA to define major histocompatibility complex (MHC) class II diversity in reindeer. Varying numbers of expressed genes found in many ungulates strongly argues for using cDNA in MHC typing strategies to ensure that diversity estimates relate to functional genes. We have used available reindeer genomes to identify candidate genes and established an HTS approach to define expressed MHC class I and class II diversity. To capture a broad diversity we included samples from wild reindeer from Southern Norway, semi-domesticated reindeer from Northern Norway and reindeer from the high Artic archipelago Svalbard. Our data show a medium MHC diversity in semi-domesticated and wild Norwegian mainland reindeer, and low MHC diversity reindeer in Svalbard reindeer. The low immune diversity in Svalbard reindeer provides a potential risk if the pathogenic pressure changes in response to altered environmental conditions due to climate change, or increased human-related activity.

Bringing together approaches to reporting on within species genetic diversity

Abstract Genetic diversity is one of the three main levels of biodiversity recognised in the Convention on Biological Diversity (CBD). Fundamental for species adaptation to environmental change, genetic diversity is nonetheless under‐reported within global and national indicators. When it is reported, the focus is often narrow and confined to domesticated or other commercial species. Several approaches have recently been developed to address this shortfall in reporting on genetic diversity of wild species. While multiplicity of approaches is helpful in any development process, it can also lead to confusion among policy makers and heighten a perception that conservation genetics is too abstract to be of use to organisations and governments. As the developers of five of the different approaches, we have come together to explain how various approaches relate to each other and propose a scorecard, as a unifying reporting mechanism for genetic diversity. Policy implications. We believe the proposed combined approach captures the strengths of its components and is practical for all nations and subnational governments. It is scalable and can be used to evaluate species conservation projects as well as genetic conservation projects.

Genetic diversity in some domestic and wild sheep and goats in Iran

In present study, genetic diversity of domestic and wild Iranian sheep and goats were evaluated using inbreeding coefficients (FGRM, FHOM and FROH), linkage disequilibrium (LD), and effective population size (Ne). Genomic data of Iranian sheep and goat species were obtained from the NEXTGEN project. Animals consisted of 20 domestic sheep (Ovis aries), 14 wild sheep (Ovis orientalis), 20 domestic goats (Capra hircus) and 18 wild goats (Capra aegagrus). Mutations equivalent to the IlluminaSNPchip50 K were extracted to study mutations for each animal. Based on FGRM, FHOM and FROH, higher rates of inbreeding were observed in wild species than domestic species. Wild sheep had the highest rate of inbreeding among studied populations. Our results showed a decreasing in LD with increasing in distance between pairs of SNPs so that the average LD in short distance was in the range of 0.11−0.12, and in long distance was in the range of 0.091−0.093. The analysis of LD also demonstrated higher genetic diversity in domestic sheep and goat than wild species and wild sheep had the lowest genetic diversity among studied populations. The results indicated that Ne in 13 generations ago was higher in domestic species compared to wild species. In general, present results revealed that wild species had lower genetic diversity compared to the domestic species in Iran. Meanwhile, wild sheep population is in critical conditions from genetic diversity point of view and required more attention. Designing appropriate breeding programs to improve genetic diversity in wild species, especially in wild sheep in Iran is necessary to protect them from extinction.

Reversing a downward trend in threatened peripheral amphibian (Triturus cristatus) populations through interventions combining species, habitat and genetic information

Conserving genetic diversity in wild species is vital for preserving adaptations to local environmental conditions. We conducted a habitat creation project for a flagship European Protected Species of amphibian (northern great crested newt Triturus cristatus) at its north-western range edge in the Scottish Highlands, combining existing knowledge about the species’ local habitat requirements and the genetic structure of existing populations. Reconciled by a spatial connectivity model, we determined the best locations for the creation or restoration of 25 ponds to facilitate their natural colonisation, and to reconnect areas with similar genetic makeup whilst preserving differences between populations belonging to separate genetic clusters. A dynamic occupancy model based on data derived from standardised surveys revealed that both detection and occupancy probabilities strongly depended on habitat features known to be locally favourable for T. cristatus. At least 12 of the 25 new ponds were colonised within six years, representing a 26% increase in number of breeding ponds in the region and offsetting a gradual decline in number of pre-existing breeding sites recorded over the last 3 decades. Combining genetic evidence, spatial modelling and historical knowledge with local stakeholder engagement led to a habitat creation and management scheme that has met its immediate and evidence-based conservation goals in a way which is transferable to a range of different systems.

Genetic diversity in wild species and cultivars of strawberry for the FanAAMT gene controlling fruit flavor volatiles

Background. An important consumer trait of strawberry fruits is their aroma. Methyl anthranilate makes a considerable contribution to the fruit flavor. The methyl anthranilate content in strawberry fruits is controlled by the FanAAMT (аnthranilic acid methyltransferase) gene. Identification of genetic determinants for this trait facilitates targeted selection of promising forms based on diagnostic DNA markers. The purpose of this study was to study the allelic diversity of the FanAAMT fruit flavor gene in wild strawberry species and strawberry cultivars for identification of promising genotypes.Materials and methods. The objects of this study were wild species of Fragaria L. as well as F. × anaschata Kantor. and F. × ananassa Duch. cultivars of different ecogeographic origin. The FanAAMT gene was identified with the dominant marker FanAAMT.Results and conclusion. In the analyzed collection of strawberry genotypes, the FanAAMT gene was identified in 36.4% of the forms, including the wild species F. vesca L., F. moschata Duch. and F. virginiana subsp. platypetala (Rydb.) Staudt, and cv. ‘Kupchikha’ (F. × anaschata). Among the analyzed F. × ananassa cultivars, the FanAAMT gene was found in 31.6% of the tested forms, specifically in 27.3% of the 22 Russian cultivars, and 37.5% of the analyzed foreign ones. Promising sources of high methyl anthranilate content in fruits were identified: wild spp. F. moschata, F. vesca, and F. virginiana subsp. platypetala; cv. ‘Kupchikha’ (F. × anaschata); Russian garden strawberry cvs. ‘Bylinnaya’, ‘Zenit’, ‘Lastochka’, ‘Neznakomka’, ‘Feyerverk’ and ‘Tsarskoselskaya’; and foreign garden strawberry cvs. ‘Karmen’, ‘Ostara’, ‘Samson’, ‘Symphony’, ‘Troubadour’ and ‘Vima Tarda’, in which the functional allele of the FanAAMT gene was found. In the remaining studied strawberry genotypes the marker FanAAMT was not detected, which presumably indicates that the FanAAMT gene is absent. cells (R9.4.1).

Chromosome Stability of Synthetic-Natural Wheat Hybrids.

Primary allopolyploids are not only ideal materials to study species evolution, but also important bridges in incorporating genetic diversity of wild species into crops. Primary allopolyploids typically exhibit chromosome instability that a disadvantage trait in crop breeding. Newly synthesized hexaploid wheat has been widely used in wheat genetics and breeding studies. To better understand the cytological and genetic basis of chromosome instability, this study investigated the chromosomes of a large number of seeds derived from the synthetic wheat SHW-L1 and its hybrids with natural wheat. SHW-L1 exhibited persistent chromosome instability since we observed a high frequent chromosome variation de novo generated from euploid SHW-L1 plants at the 14th generation of selfing (F14). High frequent chromosome variations were also observed in the F2 hybrids and most of the analyzed recombinant inbred lines (RILs) at F14, derived from the cross of SHW-L1 with common wheat variety Chuanmai 32. Chromosome instability was associated with frequent univalency during meiotic metaphase I. The experiment on reciprocal crosses between SHW-L1 and Chuanmai 32 indicated that cytoplasm has not obvious effects on chromosome instability. An analysis on 48 F14 RILs revealed chromosome variation frequency was not associated with the Ph1 alleles from either SHW-L1 or Chuanmai 32, rejecting the hypothesis that chromosome instability was due to the Ph1 role of synthetic wheat. In the analyzed RILs, chromosome instability influences the phenotype uniformity, showing as obvious trait differences among plants within a RIL. However, the analyzed commercial varieties only containing ∼12.5% genomic components of synthetic wheat were chromosomally stable, indicating that chromosome instability caused by synthetic wheat can be effectively overcome by increasing the genetic background of common wheat.

The use of museum skins for genomic analyses of temporal genetic diversity in wild species

Analyses of museum specimens can help illuminate temporal changes in wildlife genetics and distributions, and the objective of our study was to evaluate the suitability of skin samples from the past century for genomic analyses. We examined two European species with extensive genomic resources and existing data: the wild boar (Sus scrofa) and the wolf (Canis lupus). Populations of both species declined during the twentieth century, followed by a strong recovery. Moreover, Carpathian Mountain wolves are genetically divergent from Northern European lowland wolves, and their evolutionary history is incompletely understood. We analysed genetic variation from skins of 14 European and Near Eastern wild boars (1903–1948) and 18 Carpathian and Northern wolves (1938–1998). Samples were genotyped in duplicates with standard Illumina single nucleotide polymorphism (SNP) arrays (wild boar 60 K and wolves 170 K), and we retained SNPs with a genotyping rate of > 90%. We obtained a final set of 1595 SNPs for six wild boars (genotyping rate 0.99) and 1806 SNPs for 18 wolves (genotyping rate 0.96). We merged the best performing duplicate with modern data and calculated polymorphism (P), observed (HO) and expected (HE) heterozygosity per population. Our findings underline the difficulties in obtaining quality genomic profiles from museum skins, though a limited number of SNPs provided insights for future research. Wild boars exhibited lower polymorphism in historical than modern samples. In contrast, patterns in wolves appeared spatial rather than temporal, with higher P, HO and HE observed in Carpathian than Northern wolves across historical and modern samples.

Strengthening the Link between International Conservation Policy and Plant Conservation Genetics to Achieve More Effective Plant Conservation

Although both international conservation policymakers and conservation geneticists have the shared goal of halting the loss of biodiversity, currently these communities have very little interaction. Because the targets of international conservation policy focus very little on the conservation of genetic diversity in wild species, they have received little attention from the plant conservation genetics community. Conservation policymakers should more explicitly include the conservation of genetic diversity of wild species in future targets to ensure that this important aspect of biodiversity is not overlooked for the majority of species on earth and to attain more buy-in from the plant conservation genetics community; I highlight specific ways in which policymakers may more explicitly include genetic diversity in international policy targets. For their part, conservation geneticists need to conduct work that will advance the big-picture goals of conservation policy; here, I discuss specific actions that plant conservation geneticists can take, such as measuring the proportion of genetic diversity that is protected, designing experiments in such a way to measure genetic erosion, and developing protocols to increase the efficiency of ex situ collection efforts. By working together, plant conservation geneticists and conservation policymakers will more effectively accomplish the shared goal of halting the loss of plant biodiversity.

Urbanisation versus agriculture: a comparison of local genetic diversity and gene flow between wood mouse Apodemus sylvaticus populations in human‐modified landscapes

Urbanisation and agriculture dramatically modify the landscapes available for use by wildlife, affecting key aspects of their ecology such as survival, foraging, predation, competition and reproductive success. Relatively little is known about the effects of urbanisation and agriculture on the genetic structure, gene flow and genetic diversity of wild species. Here, landscape genetic techniques were applied to compare local genetic diversity and gene flow between wood mouse populations in urban and arable landscapes. Using nine microsatellite markers, individuals were genotyped from six arable and seven urban sample sites. Inter‐population genetic differentiation was significantly greater in urban than arable habitat, while allele richness, private allele richness and heterozygosity were higher for arable sample sites, with varying degrees of significance. These suggest that urban habitat was sufficiently fragmented to limit gene flow. To test the effect of landscape features on gene flow, several cost‐distance measures were generated. Overland distance and Euclidean distance correlated best with inter‐population genetic differentiation in arable habitat, whereas distances that accommodated differences in habitat quality better explained differentiation in urban habitat. There was no evidence that margins adjacent to roads, rivers or railways facilitated gene flow. Together, the results indicate that urban landscapes expose wood mice to greater fragmentation in habitat quality than arable areas, leading to greater population isolation that is not mitigated by the presence of dispersal corridors.

Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus.

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

An approximately 247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous approximately 450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged approximately 10 million years ago. Comparisons of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated rice.

Genetic diversity of wild species and cultivated varieties of alstroemeria estimated through morphological descriptors and RAPD markers

In order to estimate the genetic diversity within the Alstroemeriaceae family, nine wild alstroemeria accessions, 10 commercial varieties and the monotype Leontochir ovallei were evaluated using two different methods, RAPD analysis and UPOVs morphological descriptors. DNA from leaves, roots and tepals were analyzed by RAPDs with eight primers that generated 236 RAPD bands. Dendrograms obtained allowed identification of five main clusters: A. garaventae alone , wild alstroemerias, commercial varieties, A. exserens and A. spathulata together , and L. ovallei. Twenty-five morphological descriptors related to stem, leaf and inflorescence characteristics were evaluated and a resulting dendrogram was analyzed containing two main clusters: one grouping all commercial varieties plus A. magnifica ssp. magnifica and the other one with the rest of the wild alstroemerias. With both methods, enough informative information data was obtained to place the wild alstroemerias and commercial varieties hierarchically in different clusters. In this respect, morphological analysis grouped all commercial varieties closer to each other. Also, morphological descriptors grouped all wild alstroemerias except A. magnifica ssp. magnifica, whereas RAPD markers grouped seven out of the nine wild alstroemerias, leaving in another cluster A. garaventae, A. exserens and A. spathulata. These results suggest that also in alstroemeria, RAPD markers are a useful tool for the protection of new releases from a breeding program.