Genetic Diversity Of Wild Populations Research Articles

Population genomic analysis of the greater amberjack (Seriola dumerili) in the Mediterranean and the Northeast Atlantic, based on SNPs, microsatellites, and mitochondrial DNA sequences

The greater amberjack (Seriola dumerili) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a/TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.

A time-course transcriptome analysis revealing the potential molecular mechanism of early gonadal differentiation in the Chinese giant salamander

The Chinese giant salamander (CGS) Andrias davidianus is the largest extant amphibian and has recently become an important species for aquaculture with high economic value. Meanwhile, its wild populations and diversity are in urgent need of protection. Exploring the mechanism of its early gonadal differentiation will contribute to the development of CGS aquaculture and the recovery of its wild population. In this study, transcriptomic and phenotypic research was conducted on the critical time points of early gonadal differentiation of CGS. The results indicate that around 210 days post-hatching (dph) is the critical window for female CGS's gonadal differentiation, while 270 dph is that of male CGS. Besides, the TRPM1 gene may be the crucial gene among many candidates determining the sex of CGS. More importantly, in our study, key genes involved in CGS's gonadal differentiation and development are identified and their potential pathways and regulatory models at early stage are outlined. This is an initial exploration of the molecular mechanisms of CGS's early gonadal differentiation at multiple time points, providing essential theoretical foundations for its captive breeding and offering unique insights into the conservation of genetic diversity in wild populations from the perspective of sex development.

Best practices for genotype imputation from low-coverage sequencing data in natural populations.

Monitoring genetic diversity in wild populations is a central goal of ecological and evolutionary genetics and is critical for conservation biology. However, genetic studies of nonmodel organisms generally lack access to species-specific genotyping methods (e.g. array-based genotyping) and must instead use sequencing-based approaches. Although costs are decreasing, high-coverage whole-genome sequencing (WGS), which produces the highest confidence genotypes, remains expensive. More economical reduced representation sequencing approaches fail to capture much of the genome, which can hinder downstream inference. Low-coverage WGS combined with imputation using a high-confidence reference panel is a cost-effective alternative, but the accuracy of genotyping using low-coverage WGS and imputation in nonmodel populations is still largely uncharacterized. Here, we empirically tested the accuracy of low-coverage sequencing (0.1-10×) and imputation in two natural populations, one with a large (n = 741) reference panel, rhesus macaques (Macaca mulatta), and one with a smaller (n = 68) reference panel, gelada monkeys (Theropithecus gelada). Using samples sequenced to coverage as low as 0.5×, we could impute genotypes at >95% of the sites in the reference panel with high accuracy (median r2 ≥ 0.92). We show that low-coverage imputed genotypes can reliably calculate genetic relatedness and population structure. Based on these data, we also provide best practices and recommendations for researchers who wish to deploy this approach in other populations, with all code available on GitHub (https://github.com/mwatowich/LoCSI-for-non-model-species). Our results endorse accurate and effective genotype imputation from low-coverage sequencing, enabling the cost-effective generation of population-scale genetic datasets necessary for tackling many pressing challenges of wildlife conservation.

Whole-genome resequencing reveals genetic diversity and signatures of selection in mono-female grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is an important aquaculture species in China even in the world, and the production of mono-female population can effectively increase its yield as its females grow faster than males. Assessing the genetic basis of mono-female population is of great importance for breeding and culture, and the detection of signature of selection may shed light on genes and mutations associated with important phenotypic traits. In this study, whole-genome resequencing technology was employed to detect the genetic variation in wild populations of grass carp from the Yangtze River and the Pearl River, as well as in a mono-female population based on combining gynogenesis with sex-reversal breeding method. A total of 9,510,648 informative single nucleotide polymorphisms (SNPs) were identified across the three populations. The mean observed heterozygosity (Ho) and mean expected heterozygosity (He) of SNPs were calculated to be 0.2139 and 0.2894, 0.2313 and 0.2888, and 0.2523 and 0.2418 in the Yangtze River, Pearl River and mono-female population, respectively. The genetic distance between the mono-female population and the wild populations indicated that there was a moderate genetic differentiation between the three populations. Furthermore, analysis of run of homozygosity (ROH) revealed that the mono-female population exhibited a lower level of genomic inbreeding (inbreed coefficient = 0.075) compared to higher levels in the Yangtze River (inbreeding coefficient = 0.2410) and Pearl River populations (inbreed coefficient = 0.1894). Short ROHs were more frequently observed in the mono-female population, while long ROHs were more common in the Yangtze River and the Pearl River populations, providing insight into the population history of grass carp. Using the Yangtze River and Pearl River populations as references, 646 and 594 genes with hypothesized selection signature were identified by selective sweeps in the mono-female population, respectively. These genes were involved in 25 KEGG pathways associated with some important traits, such as growth (esm1 and zbed1), reproduction (ccnb1 and ptpn13), development (grin1a, mcc and brd2) and immune response (npr2, psmb9a, psmb8, tap2 and h2a). These results will be helpful for the molecular marker-assisted breeding and development conservation strategies of grass carp germplasm resources.

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing.

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Editorial

Editorial

Genetic Diversity and Structure of Latvian Trifolium fragiferum Populations, a Crop Wild Relative Legume Species, in the Context of the Baltic Sea Region

The aim of the present study was to investigate the genetic diversity and structure of eight Trifolium fragiferum populations in Latvia in the context of the Baltic Sea region. In addition, one wild population from Estonia and one from Denmark were analyzed, as well as the commercial cultivar ‘Palestine’. The genetic diversity of wild populations was low, compared to the higher diversity in the cultivar ‘Palestine’. The wild populations were differentiated into four clusters, separate from the cultivar ‘Palestine’. Three of the genetically similar Latvian populations were also geographically proximal, but the four populations geographically located near the capital, Riga, were genetically differentiated from each other. The genetic results were compared to previously published physiological studies of the same populations. The results from this study can be used as a basis for further studies of T. fragiferum populations in the Baltic Sea region, and to develop in situ and ex situ conservation strategies for this crop wild relative species.

Bryan Campbell Clarke. 24 June 1932—27 February 2014

Professor Bryan Clarke was a world-leading evolutionary geneticist. He combined theoretical understanding of the principles of evolutionary biology, an appreciation of the process of molecular evolution, and a love of fieldwork, through which he studied the genetic diversity of wild populations and the patterns of natural selection that operated on them. Bryan's primary interest was in studying evolution in the wild. In trying to observe evolution in action, geneticists focus on genetic polymorphisms, in which different genetic types (‘morphs’) coexist in the same wild population. In understanding how such variation is generated, and how it is maintained, we gain insight into the process of evolution as it has operated over the course of life on Earth.

Assessing Genetic Diversity of Wild Populations and Different Color Varieties for Genetic Improvement of Siamese Fighting Fish Betta splendens in Thailand.

To establish sustainable resources and founder populations for genetic improvement of the Siamese fighting fish Betta splendens, genetic diversity in wild and hatchery stocks was examined using mitochondrial (mt) DNA genes cytochrome b (cytb), 16S ribosomal DNA (16S rDNA), and cytochrome oxidase subunit I (COI), and eight microsatellite loci. Based on mtDNA sequences, restrictive levels of polymorphism (0, 3, and 1 substitutions) were observed in this study. For analysis of microsatellites, fluorescent multiplex PCR was developed, and subsequently identifying moderate levels of observed (Ho = 0.4488) and expected (He = 0.6627) heterozygosities and a high number of alleles per locus (15.125 alleles) for overall samples. Comparison of Siamese fighting fish from different sources revealed large genetic differences between pairs of farmed fish (eight groups) and between wild (three geographic locations) and farmed fish (P < 0.0031 following Bonferroni correction). This suggested limited exchanges of genetic resources between commercial farms. When different color varieties of B. splendens were compared, large genetic distances and significant FST estimates and genetic heterogeneity were found (P < 0.0031). Effective population sizes (Ne) were estimated and two farms (NP2-2BS and BK1-4BS) showed Ne greater than 10. Among color varieties, Multi-colors and Blue revealed reasonable Ne (large and 27.9), but lower Ne values (3.6-8.4) were found for the remaining color varieties. These results indicate an urgent need for the establishment of gene pool resources of B. splendens for effective genetic improvement of Siamese fighting fish in Thailand.

Effects of spawning success and rearing-environment on genome-wide variation of red drum in a large stock-enhancement program

Stock enhancement is an increasingly popular fisheries management strategy in which high mortality of early life history stages is circumvented by rearing juveniles in controlled or semi-controlled conditions. While the success of such programs is generally measured by the number of stocked individuals or individuals recruiting to the wild populations, an important consideration is minimizing impacts to the genetic diversity of wild populations by maximizing the number of breeders contributing to stocked progeny. The contribution of individual breeders is impacted both by variance in spawning success among adults and variance in mortality among families during grow-out. To disentangle the effects that these sources of variance have on parental contribution, red drum broodfish participating in three spawning events at the TWPD Marine Development Center were genotyped at several thousand SNP-containing loci along with their progeny. Progeny were sampled at three time points; shortly after introduction to grow-out ponds (T1), approximately midway through grow-out (T2), and as fingerlings during harvesting to be stocked in bays (T3). Using composite genotypes, progeny were assigned to parents to determine the reproductive success of individual broodfish at T1, T2, and T3 and to identify changes in the effective number of breeders (Nb) during rearing in grow-out ponds. Relationships between reproductive success and broodfish-specific parameters, including age and condition when introduced to the hatchery, time spent in the hatchery, and estimated age at spawning were assessed. Finally, associations between components of genomic variation in progeny from each sampling period and environmental parameters including salinity, pH, temperature, and dissolved oxygen present in the grow-out ponds, were identified. The results indicate that initial variance in reproductive success, including the failure of some individuals to spawn successfully, has the greatest impact on Nb. Mortality during growth had a relatively small impact on Nb and, in some cases, led to increases in Nb. Further, both family and environmental conditions in the outdoor rearing ponds significantly shaped the genetic diversity of stocked yearlings. Overall, these findings indicate that outdoor rearing in a semi-controlled environment exposes progeny to a range of environmental conditions across the season, which appears to play a role in maintaining and sometimes increasing Nb.

"Genetic variability and phylogenetic analysis of great snakehead Channa marulius based on mitochondrial cytochrome oxidase subunit I from River Sutlej in Punjab, India"

The present study was carried out to analyze the biodiversity of fish species under family Channidae and genetic diversity with special reference to Channa marulius from selected stretches of River Sutlej in Punjab. Total three species under family Channidae wererecorded i.e. Channa striata, C. marulius and C. punctata. In catch composition, among these three species, C. marulius was dominant (58%) followed by C. striata (37%) and C. punctata (5%). In C. marulius the Mean ± SE values of weight, total length and standard length were 1482.39±290.02 g, 57.70±3.74 cm and 49.94±3.27 cm, respectively. Length-weight relationship established a negative allometric growth pattern in C. marulius. The genetic variation in wild population of C. marulius was determined by using partial sequence of the Cytochrome oxidase subunit I of mitochondrial DNA. Three haplotypes were found in 14 Cytochrome Oxidase subunit I sequences of C. marulius at Sutlej River. The haplotype diversity (0.026) and nucleotide diversity were recorded low (0.045). The phylogenetic pattern of all the specimens of C. marulius were same barring two specimens which showed some variations. The intraspecific mean was 0.05 and pair-wise distance assorted from 0.00 to 0.192%, showed no significant difference. The nucleotidefrequency was A=23.1%, T=29.37%, G=17.33% and C=30.18% and G+C content was 0.475 (47.5%). Though no previous genetic diversity data of C. marulius from river Sutlej is available, the comparison of these diversity indices with C. striata stocks from other geographical locations indicates that C. marulius stocks in river Sutlej are less genetically diverse. The present study can be utilized as database for future policy framing and conservation measures.&nbsp;

Mismatches between Morphology and DNA in Italian Partridges May Not Be Explained Only by Recent Artificial Release of Farm-Reared Birds.

Simple SummaryOne of the major drivers of genetic pollution is artificial translocation, which causes hybridization and introgression. We analyzed genetic markers of Grey and Rock Partridges from collections, wild populations and farms, mostly in Italy. We documented a mismatch between morphology and DNA in the identification of some individuals, as well as hybridization between the two genera of the Grey and Rock Partridges: Perdix and Alectoris. Our results suggest that species of the two genera can hybridize in nature and that artificial translocations and releases of farm reared birds for restocking or reintroduction purposes may be only partially responsible for the DNA-morphology mismatches of Italian partridges.Translocations and releases of farm-reared birds are considered among the major drivers of genetic pollution with consequent loss of genetic diversity in wild populations. In this study, we aimed to assess the extent of hybridization and introgression in the Italian partridges as a consequence of translocation. We surveyed two mitochondrial markers and one nuclear marker of Alectoris and Perdix from collections (museums and private collections), extant wild populations and farms. Consistent with previous studies, we found haplotypes of allochthonous species within the same genus, likely due to introductions for hunting activities. In addition, we found hybrids between Perdix and Alectoris species with genetic markers from both genera in single individuals. Such introgression was bidirectional and in both mitochondrial and nuclear markers. Counterintuitively, most of the hybrid samples came from collections before the 1950s, when large-scale translocations started, from wild populations where Grey Partridge (Perdix perdix) and Rock Partridge (Alectoris graeca) overlap in their distribution, whereas only one hybrid occurred among the farmed birds. Our results suggest that Perdix and Alectoris species can hybridize in nature and that artificial translocations and releases of farm-reared birds for restocking or reintroduction purposes may be only partially responsible for the genomic mismatches of Italian partridges.

Conservation of genetic resources for sustainable aquaculture

Conservation of genetic resources for sustainable aquaculture

Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens

Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine regions in the Northern Territory, Australia. Additional samples were obtained from botanic garden plants that were originally collected in the Katherine region, Daly River and Spirit Hills in the Northern Territory, Australia. Using RADseq we recovered 2271 informative genome-wide SNPs, revealing low to moderate levels of gene diversity (uHe = 0.037 to 0.135), very low levels of gene flow, and significant levels of inbreeding (mean FIS = 0.491). Population structure and multivariate analysis showed that populations fall into two genetic groups (Katherine vs Litchfield + Daly River + Spirit Hills). Genetic differentiation was twice as high between populations of the Katherine and Litchfield regions (FST ~ 0.1) compared to within these two regions (FST ~ 0.05). Increasing population fragmentation together with high levels of inbreeding and very little gene flow are concerning for the future adaptability of this species. The results indicated that the ex-situ collections (1) had significantly lower genetic diversity than the wild populations, and (2) only partly capture the genetic diversity present, particularly because the Litchfield National Park populations are not represented. We recommend that ex-situ collections be expanded to incorporate the genetic diversity found in Litchfield National Park and to increase the number of representatives from Daly River/Spirit Hills, and that in-situ populations from the Katherine and Greater Litchfield regions be conserved as separate management units.

Genetic parentage reconstruction as a practical tool applied to aquaculture and restoration programs for the European flat oyster,Ostrea edulis

Preserving and maximizing genetic diversity in conservation programs, including for restocking, are of high importance. The threatened European flat oyster (Ostrea edulis) is currently the subject of several applied conservation and restocking programs, but concerns have been raised over potential negative side effects of these programs, for example due to our limited knowledge about the genetic effects in natural populations of releasing offspring of hatchery origin. Here, we developed an effective, easily applicable and highly reliable method to assess the genetic diversity and parental contributions in flat oyster hatchery production based on analyses of 17 microsatellite loci. We analysed four broodstocks and their hatchery-reared spat (totaln = 354) and compared diversity to that in wild samples of adults and spat from the broodstock source in the Limfjorden (totaln = 138). Based on four hatchery tank experiments with fully resolved parentage assignments, we found that five swarming events (larval releases) were characterized by a single maternal and multiple paternal contributions, and that the number of contributing parents varied greatly both among individual tanks, and between swarming events within tank. On average, the effective number of breeders was only one third of the actual broodstock size. Although the broodstock exhibited high genetic variation, the high reproductive skew resulted in produced offspring representing only a relatively small subset of this variation. The work demonstrates potential impact of hatchery reared offspring on decreasing genetic diversity in wild populations, but also that genetic monitoring can be integrated in conservation programs to minimize negative effects on restoration and supplementary restocking programs that utilize hatchery reared spats to support natural populations.

Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation.

PremiseMany cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century‐long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo.MethodsUsing 18 microsatellite markers, we studied the genetic composition of wild and backyard‐grown C. canephora shrubs in the Tshopo and Ituri provinces and multiple accessions from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations.ResultsGenetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi.ConclusionsMost C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes to increase the genetic resources available for breeding purposes and to support ex situ conservation.

A Significant Genetic Admixture in Farmed Populations of the Noble Scallop Chlamys nobilis Revealed by Microsatellite DNA Analysis in Southern China

The noble scallop, Chlamys nobilis, is an important bivalve mollusk with high commercial value and is usually farmed in the waters of southern China. To date, very little is known about the genetic diversity and population structure of C. nobilis. In this study, 10 microsatellite loci of four farmed C. nobilis populations were compared with one another and compared wild population in southern China. A total of 83 alleles were found. Surprisingly, the level of genetic diversity of the farmed C. nobilis populations was higher than that of the wild population. Although the population genetic of wild population was completely in the Hardy–Weinberg equilibrium, due to heterozygote deficiency, significant deviations from the Hardy–Weinberg equilibrium were found in all farmed populations, suggesting a genetic admixture caused by the mixing of seeds from various hatcheries. The Fst and AMOVA values showed significant genetic differences between wild and farmed populations. The Bayesian assignment also confirmed that genetic admixture was significant and widespread in artificial breeding of C. nobilis. Furthermore, the UPGMA tree topology and PCA demonstrated that the genetic diversity of wild population can be clearly distinguished from farmed populations. In a nutshell, the findings of this study not only fill the knowledge gaps in genetic diversity of wild and farmed C. nobilis populations, but also serve as a guide for maintaining the genetic diversity of C. nobilis in both farmed and wild populations.

Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations

Recent advances in mosquito genomics and genetic engineering technologies have fostered a need for quick and efficient methods for detecting targeted DNA sequence variation on a large scale. Specifically, detecting insertions and deletions (indels) at gene-edited sites generated by CRISPR guide RNA (gRNA)/Cas9-mediated non-homologous end-joining (NHEJ) is important for assessing the fidelity of the mutagenesis and the frequency of unintended changes. We describe here a protocol for digital-droplet PCR (ddPCR) that is well-suited for high-throughput NHEJ analysis. While this method does not produce data that identifies individual sequence variation, it provides a quantitative estimate of the sequence variation within a population. Additionally, with appropriate resources, this protocol can be implemented in a field-site laboratory setting more easily than next-generation or Sanger sequencing. ddPCR also has a faster turn-around time for results than either of those methods, which allows a more quick and complete analysis of genetic variation in wild populations during field trials of genetically-engineered organisms.

Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations.

Recent advances in mosquito genomics and genetic engineering technologies have fostered a need for quick and efficient methods for detecting targeted DNA sequence variation on a large scale. Specifically, detecting insertions and deletions (indels) at gene-edited sites generated by CRISPR guide RNA (gRNA)/Cas9-mediated non-homologous end-joining (NHEJ) is important for assessing the fidelity of the mutagenesis and the frequency of unintended changes. We describe here a protocol for digital-droplet PCR (ddPCR) that is well-suited for high-throughput NHEJ analysis. While this method does not produce data that identifies individual sequence variation, it provides a quantitative estimate of the sequence variation within a population. Additionally, with appropriate resources, this protocol can be implemented in a field-site laboratory setting more easily than next-generation or Sanger sequencing. ddPCR also has a faster turn-around time for results than either of those methods, which allows a more quick and complete analysis of genetic variation in wild populations during field trials of genetically-engineered organisms.

Developing a monitoring program of genetic diversity: what do stakeholders say?

Genetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and species. National and international legislation increasingly mandates a monitoring of genetic diversity. Examples are the United Nation’s Convention on Biological Diversity (CBD) Aichi target 13 and the current post-2020 negotiations to specify a new target for maintaining genetic diversity. To date, only a few pilot projects have been launched that systematically monitor genetic diversity over time in natural populations of a broad variety of wild species. The Swiss Federal Office for the Environment mandated a feasibility study in 2019 for implementing a national monitoring of genetic diversity in natural populations. To obtain information on whether stakeholders are interested in such a systematic monitoring, what they would expect from such a monitoring and where they see respective caveats, we conducted an online survey, which 138 (42% of those surveyed) Swiss stakeholders answered. We find that Swiss stakeholders are generally aware of the lacking evidence regarding the status of genetic diversity in wild populations and species. Accordingly, most stakeholders are interested in a monitoring of genetic diversity and see opportunities for the application of its results in their work. Nevertheless, stakeholders also expressed concerns regarding financial resources and that the results of a genetic diversity monitoring program would not benefit conservation practice. Our findings highlight the importance of stakeholder engagement and demonstrate the value of a detailed stakeholder analysis prior to developing and implementing a genetic diversity monitoring program. A powerful tool for examining the constellation and interactions of the different stakeholders are social network analyses (SNAs). Finally, it is particularly important to communicate transparently about the possibilities and limitations of a genetic diversity monitoring program as well as to closely involve stakeholders from the beginning to increase the acceptance of genetic diversity monitoring and facilitate its implementation.