A correction to this paper has been published: https://doi.org/10.1007/s12686-021-01211-w

Throughout Asian countries including India, water buffalo (Bubalus bubalis) plays a crucial role in socio-economic status of the farmers by providing nutritional security. The concept of genomic selection through genetic markers has been widely used in various livestock species and this is extended to buffalo species as well. Molecular markers have been extensively used in animal breeding for improvements

An eDNA assay for the detection of Pacific herring (Clupea pallasii) in water samples was developed using quantitative PCR (qPCR) technology. Species-specific primers and a minor groove binding (MGB) probe were designed based on the mitochondrial cytochrome b gene sequence. Upon conducting a cross-species test, the target species DNA was not only detected at low concentrations but also with high specificity

The original PumaPlex is a high-throughput assay developed to genotype 25 single nucleotide polymorphisms (SNPs) in pumas (Puma concolor). Here, we describe the development of PumaPlex100 – an expanded version of the original assay that now genotypes > 100 SNPs. We tested 142 candidate SNPs and developed a panel of 101 polymorphic loci, which are spread across four multiplexes and suitable for genotyping

Parrot egg seizure is frequent, and its impact on the population cannot be quantified due to difficulties in identifying the transportation of the eggs by traffickers. Morphological identification of species in eggs is difficult, especially when the embryos are not viable. In this context, DNA barcoding is an alternative for species identification. In May 2018, 31 eggs were seized at the Manaus/AM

For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species

We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically

Currently, the conservation of biodiversity is a pressing issue due to the extinction and endangerment of many species. There are multiple reasons for the extinction or endangerment of species including anthropogenic (poaching, hunting, and deforestation) and natural causes (forest fire, invasion of non-local species, climate change, and global warming). The somatic cell nuclear transfer (SCNT) is

We developed a reliable noninvasive PCR method for sex identification of the Gentoo penguin (Pygoscelis papua) based on the amplification of the chromobox-helicase DNA-binding (CHD) gene. Two sets of nested primers (F1/R1, F2/R2) were designed to amplify the introns of the CHD1W and CHD1Z genes. The fecal samples were lysed in an optimized lysis reagent containing PCR buffer. The fecal lysate was employed

This study provides the first standardized global microsatellite database for a shark species, the tiger shark (Galeocerdo cuvier). Genotyping of reference individuals was used to develop and apply a calibration key for data from eight microsatellite loci data produced by three different laboratories, thereby allowing merging of genotypes into a single dataset. The unified data helped to elucidate

Flyingfishes of the family Exocoetidae are sometimes difficult to identify solely based on morphology as members of certain genera share overlapping characteristics. Combining morphological and molecular analyses, the present study reports two specimens of stained flyingfish Cheilopogon spilonotopterus (Bleeker 1865) from the northern Bay of Bengal. As for COI gene sequences, nucleotide variations

Conservation genomics research often relies on accurate sex information to make inferences about species demography, dispersal, and population structure. However, field determined sex data are not always available and can be subject to human error, while laboratory sex assignment methods such as PCR assays can often be costly and challenging for non-model species. Conservation genomics programs increasingly

Coffee is one of the most economically important agricultural commodities in the world. Labeling accuracy and conservation efficiency are essential for coffee germplasm management and for the exchange and utilization in breeding new varieties. However, due to its homogenous genetic background, accurate identification of Coffea arabica germplasm has not been fully achieved. Specifically, data comparison

The Natterjack toad (Epidalea calamita) is the rarest amphibian species in Ireland, regionally Red-Listed as Endangered. We applied an eDNA approach to detect species presence in breeding pond water samples. We developed a species-specific qPCR assay targeting the cytochrome c oxidase subunit I (COI). The assay was tested in silico, in vitro (DNA extracted from tissue) and in vivo (DNA extracted from

The lack of available genetic resources for species of conservation concern is a significant barrier to assessments of their genetic diversity, which can provide unique insights into population health, demography, and resilience. Highly variable microsatellite markers are typically developed de novo as part of population genetic studies and are rarely tested systematically for their broader applicability

Due to the morphological similarity between some billfish species, the International Commission for the Conservation of Atlantic Tunas (ICCAT) recommends the use of molecular tools to identify billfish at the species level to properly manage this imperiled group. In this study, species-specific swordfish and billfish identification was carried out by using PCR-RFLP and multiplex PCR of the mitochondrial

The Atlantic goliath grouper, Epinephelus itajara (Lichtenstein, 1822), is considered a critically endangered species. In Brazil, the harvesting, transportation, and sale of E. itajara or it’s by products have been prohibited, but illegal harvesting still occurs. This study developed a simple, sensitive and accurate procedure for the safe identification of E. itajara by polymerase chain reaction (PCR)

The downstream section of the Jinsha River is a global biodiversity hotspot for fishes. However, cascade hydropower development has altered the original habitat and has had a huge impact on the area’s fish diversity. To assess the power of DNA barcoding and construct a DNA barcode library for Xiangjiaba reservoir area, 333 fish mitochondrial DNA barcodes (672 bp) employing a fragment of the mitochondrial

Over the last years, many studies have reported the challenge of precisely identifying shark and ray species from the fin trade. In Asia, the high demand for shark fin soup has resulted in correspondingly high prices for fins. This, in turn, has caused overexploitation of elasmobranch populations worldwide. Fin processing can cause the loss of morphological characteristics; therefore, species-specific

Genomic resources are under-developed for rodents, including well-studied species such as prairie dogs (Cynomys spp.). We conducted whole-genome resequencing on 10 Gunnison’s prairie dogs (C. gunnisoni, GUPD) and identified 12,842,055 high-quality SNPs, from which four sets of bait sequences were created. We designed two sets each (containing either 20k or 60k baits) for projects using contemporary

Existing molecular methods of sex identification have mixed success in different classes of birds. We report a new multiplex PCR method for sex identification based on CHD1gene using the P8/P2 and the 2550F/2718R primers. The new multiplex PCR approach successfully identified sex (two bands in female, single band in male) in edible-nest swiftlet (ENS) (Aerodramus fuciphagus inexpectatus) and plume-toed

Illegal and unsustainable logging of forests have contributed to deforestation and a massive loss of biodiversity, and despite the efforts to regulate the trade of plants and combat the commercialization of illegal logging, the problem continues. DNA analysis of plant tissues is an effective method in species identification, and it is important to dedicate efforts to obtain and amplify DNA from dry

Introduction Reproductive isolation by time can occur in fish populations composed of individuals with different reproductive schedules. Most studies have tested this phenomenon using mature fish rather than their offspring, which may mask signals of population relationships. Methods We directly sampled fish eggs from artificial fish nests at four different time instances and subsequently fed the eggs

Although genetic techniques are moving toward collecting massive amounts of genome-wide data through genome-scans, microsatellite markers (µsats) still provide a simple and cost-effective method for key applications such as parentage analyses, pedigree tracking, assessing likelihoods of disease conditions and DNA fingerprinting, among others. Newer laboratory protocols using high throughput sequencing

Microsatellites have been a staple of population genetics research for over three decades, and many large datasets have been generated with these markers. Microsatellites have been used, for example, to conduct genetic monitoring and construct large multigeneration pedigrees as well as genotype thousands of individuals from a given species to create high-resolution baselines of spatial genetic structure

The Dugong dugon (dugong) and Chelonia mydas (green sea turtle) are economically and culturally significant marine mega-herbivores whose populations are declining globally. Capture of these animals for study is challenging and stressful for the animals. Ecological questions can be answered using faeces, which can be collected floating on the water’s surface. However, green turtle and dugong faeces

American mink Neovison vison is a semi-aquatic mustelid that has been introduced throughout Europe. Several attempts to eradicate this invasive species have been carried out since its spread. In the Iberian Peninsula, an eradication program has started since 2001, as part of the national action plan for the conservation of European mink Mustela lutreola. Proper detection is crucial for management,

Rhinanthus major and R. minor are two annual plant species that are known to hybridize in nature and in which unilateral introgression is likely to occur. Here we used double-digest restriction site-associated DNA sequencing technology (ddRAD-seq) to detect 16,932 genome-wide SNPs in R. major and R. minor individuals from 9 populations. After screening these SNP markers across both species, we selected

The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed

Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for genetic analyses of pinnipeds. The present study evaluated

Rapid anthropogenic climate change and progressing habitat degradation are considered top threats to biodiversity. The employment of demanding umbrella species as indicators for ecosystem health is a popular and cost-effective strategy that facilitates continuous monitoring and evaluation within a long-term conservation management scheme. The Western Capercaillie (Tetrao urogallus) and the Black Grouse

Toll-like receptor (TLR) genes have recently been used to assess the adaptive genetic diversity under natural selection. Here, we newly developed a set of primer pairs for amplifying TLR genes (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7 and TLR15) in the vulnerable Chinese egret (Egretta eulophotes). The PCR products, ranged between 407 and 988 bp (an average of 762 bp), were successfully amplified by using

Aristeus antennatus is one of the most exploited and economically important resource for fisheries in the Western and Central Mediterranean Sea displaying low population differentiation with mitochondrial and microsatellite markers. The recent development of Genotyping-by-Sequencing (GBS) methods may contribute to the discovery of SNPs and the assessment of genetic differences between populations of

Accurate species identification is essential for the successful implementation of species conservation strategies and research. East Pacific horn sharks (genus Heterodontus) may be subject to overfishing and depletion in some areas, mandating an assessment of risk and vulnerability to exploitation. Unfortunately, morphological identification of the three eastern Pacific species can be challenging,

Single nucleotide polymorphisms (SNPs), known as the third-generation molecular markers, are becoming popular in molecular ecology studies. The rapid development of next generation sequencing technologies allow identifying large numbers of SNP markers that can be used in conservation genetics. Based on the genome resequencing dataset of Crested ibis (Nipponia nippon), we developed 31 polymorphic SNP

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low

Contamination and degradation are known challenges for reliable genotyping, since they can cause, among other problems, false microsatellite profiles. In this study we described a method to decrease the proportion of false microsatellite profiles from fish scale samples of endangered allis shads (Alosa alosa) from a reintroduction program, where cross-contamination with DNA from other individuals and

Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™

Habitat degradation and land-use change severely threaten the survival of fairy shrimp and the vernal pools in which they live. Limiting effective fairy shrimp conservation management efforts is the ability to readily identify species without the capture and sacrifice of individuals for microscopy. Here we demonstrate that eDNA metabarcoding is an effective non-invasive tool for monitoring fairy shrimp

Microsatellite DNA is among the several molecular tools used for determining genetic variability and inbreeding depression in threatened populations. It has been used extensively for population genetics studies in conservation of crocodilians. Even though single nucleotide polymorphisms have higher precision compared to microsatellite DNA markers, microsatellites offer a cost advantage which is particularly

We present a conservation genetics tool kit, which offers two ready-to-use workflows for the routine application of genetic methods in conservation management. The workflows were optimized for work load and costs and are accompanied by an easy-to-read and richly illustrated manual with guidelines regarding sampling design, sampling of genetic material, necessary permits, laboratory methods, statistical

Deer species has both scientific research and economic value, and half of these species, however, are listed as endangered animals. For the conservation purpose, we designed a novel universal deer-specific PCR primer pair based on an evolutionarily conservative coding sequence (i.e., CEP295NL gene) across some deer species. This primer pair was successfully amplified and sequenced, showing around ~ 540 bp

Dosidicus gigas (D. gigas) is a commercially important squid species in the Eastern Pacific Ocean. Due to the wide distribution of the species and its variable biological characteristics, there is a lack of reliable information regarding its genetic structure, which restricts the stock assessment and management of the D. gigas fishery resource. Therefore, there is an urgent need to develop sufficient

Analysis of wolves dietary is a currently important theme because of the discussion about wolves preying on livestock as sheep or goats. We developed molecular markers to especially amplify the DNA of the prey out of wolf scat. For this purpose, we used the mitochondrial D-Loop using public available sequences for wolf and seven potential prey species (even-toed ungulates). We developed special primers

After suffering a massive decline (~ 99%) in numbers caused by feeding on livestock carcasses containing the nephrotoxic drug diclofenac, critically endangered Gyps vultures now persist in low numbers in the Indian subcontinent. Most are concentrated near National Parks, likely due to availability of wild carcasses free from toxic veterinary drugs. Quantification of vulture diets is critical to test

The Smallmouth Bass (Micropterus dolomieu; SMB) is a widely distributed black bass species, but the southwestern edge of the species range within the Interior Highlands contains some of the most divergent ecotypes. The Neosho subspecies (M. d. velox) inhabits tributaries of the Arkansas River within the Ozark Mountains and a second lineage is reported from drainages of the Ouachita Mountains. We sought

We describe the development and testing of qPCR assays to detect four species of amphibians and reptiles of conservation concern in the South Central United States through environmental DNA (eDNA) samples. The target species include the Ringed Salamander (Ambystoma annulatum), Three-toed Amphiuma (Amphiuma tridactylum), Crawfish Frog (Rana areolata), and Chicken Turtle (Deirochelys reticularia). A

Although sex assignment is essential to study biology and ecology of an animal, in Xenarthra there is still no standardized assay for genetic sex identification. Here, we evaluate the potential of two nuclear fragments [Zinc finger (~ 400 bp) and Sex-determination region Y (~ 180 bp) genes] for sex identification of seven Xenarthra species. First, we amplified and sequenced both homologous segments

The hybrids of pimelodid catfish provide products of excellent genetic value for aquaculture due to their greater growth in size, resistance to diseases and adaptation to feed concentrate. However, this practice involves risks such as genetic contamination, the commercialization of hybrid products as pure species, the introduction of exotic species and escapes of fish farming products. Thus, the aim

Lined seahorse ( Hippocampus erectus ), an important economic and medicinal fish in China, exists widely in Atlantic Ocean. However, habitat destruction for its spawning and overfishing has led to profound decline the wild populations in recent years. Therefore, to improve the molecular-assisted selection (MAS) and resources conservation of H. erectus , the 100 novel single nucleotide polymorphism

A mini-barcoding system was developed to help identify endangered unionid mussels in the Lake Biwa system in Japan. A single primer set was designed to amplify a ca. 140-bp barcode fragment based on the published mitochondrial 16S rRNA gene sequences (ca. 350 bp) of Japanese unionids. The new primers successfully amplified genomic DNA from the foot tissues of 81 specimens of 12 target taxa from the

We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identified from Pacific walrus DNA. RADSeq was performed on

Rays (Batoidea) are among the most threatened groups of vertebrates. Slow growth and low fecundity make many species vulnerable to overfishing, but increased demand for gill rakers in traditional Chinese medicine and elasmobranch meat means exploitation continues. In response, protection has increased, with manta and devilrays (Mobulidae) and sawfishes (Pristidae) now listed on Convention on International

Green peafowl (Pavo muticus), a representative of the Southeast Asia Phasianidae, is assessed as globally endangered with populations that are declining. It is highly sensitive to human disturbance and habitat change, two threats that are unlikely to be removed soon in present range countries, and that increase the need for long-term continuous effort for in situ conservation. Captive breeding for

Chestnut species have large ecological, cultural and economic importance. Developing genetic markers for these species is of interest for conservation, breeding or evolutionary studies. We designed 192 primer pairs targeting microsatellites detected in the Castanea mollissima reference genome and tested them on C. sativa and C. crenata. We PCR amplified 3 × 50 microsatellites in 106 chestnut trees

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering

Brazilian elodea (Egeria densa) is an invasive freshwater plant that demonstrates widespread ecological impacts in freshwater ecosystems and causes substantial economic damage. Here, we developed an environmental DNA assay for detection of E. densa to provide resource managers with a tool for early detection, identification, and monitoring of invasive populations.

We developed single nucleotide polymorphism (SNP) markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) using restriction site-associated DNA sequencing (RAD-seq) genotyping on the Illumina HiSeq4000 platform. In total, we sequenced 44 individuals from seven populations occurring in the Caspian Sea basin. Of the 86 SNP loci, 43 loci were found to be polymorphic and bi-allelic

Identification of the species is a crucial step in many ecological studies. Sometimes, this could become a challenge, because of animal elusive behavior, low density population or for sympatric species leaving similar signs that are impossible to discriminate based only on their morphology. Here, we set up non-invasive molecular method to discern between the Italian hare (Lepus corsicanus) and the

Parrots (Psittaciformes) are among the most endangered groups of birds today and remain threatened by habitat loss and exploitation for the live bird trade. Under such conditions, reliable and non-invasive monitoring techniques are crucial for successful conservation measures. In this study, we developed a panel of 86 high quality SNPs for genotyping endangered sun parakeets (Aratinga solstitialis)