Preservation Of Genetic Diversity Research Articles

Comprehensive Overview of Plant Germplasm Augmentation: Strategies, Techniques and Applications

Plant genetic resources (PGR) are fundamental for crop improvement and conservation, encompassing a wide range of genetic materials including land races, modern varieties, and wild relatives. Effective germplasm exploration is essential for advancing plant genetic resources and ensuring agricultural sustainability. Traditional germplasm collection faces challenges such as remote locations, limited material availability, and transport issues. This review explores various strategies to address these challenges, including coarse-grid and fine-grid survey methods, multi-species versus species-specific collecting missions, and the implications of breeding systems on germplasm collection. It highlights the benefits of Geographic Information Systems (GIS) in managing PGR, from incentivizing mapping strategies to optimizing conservation and evaluation processes. Additionally, the review emphasizes the role of in vitro techniques in overcoming limitations of traditional methods, detailing field and laboratory procedures for successful in vitro collection. By integrating these approaches, the review aims to enhance the efficiency and effectiveness of PGR management, ensuring the preservation of genetic diversity for future generations.

Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals

The primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, F IT and FIS value across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and − 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.

Morphological Characterization of Kage and Baruwal Sheep (Ovis aries Linnaeus, 1758) Breeds in Nepal

Sheep farming in Nepal is closely linked to its agricultural heritage and contributes to livelihoods and the socio-economic fabric. This study synthesizes the morphological characterization of Kage and Baruwal (Ovis aries Linnaeus, 1758) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. This study synthesizes the morphological characterization of Kage and Baruwal (O. aries) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. The analysis revealed a significant difference (P ≤ 0.01**) in quantitative traits between the two breeds. The Baruwal sheep exhibited higher mean values for tail length (12.96 ± 0.47 cm), ear length (10.67±0.20 cm), neck length (21.75±0.38 cm), chest girth (67.14±0.50), height at hip bone (64.78±0.44 cm), body weight (33.04±0.65 Kg), and height below withers (67.10±0.56). Additionally, correlation analysis of different quantitative traits was found to be significant at the 0.01 level on a two-tailed test. The study's results indicate significant quantitative variations, which suggest genetic adaptations and selective pressures. The analysis of qualitative traits highlights differences in horn presence, shape, fleece, head color, neckline, and tail shape, providing insights into genetic diversity and functional adaptations. The study concludes that comprehending such phenotypic traits helps with breed management, conservation, and sustainable agriculture. The preservation of genetic diversity and adaptability is underscored by indigenous sheep breeds, which requires further research to elucidate the genetic mechanisms underlying these traits.

Obtaining a culture of somatic cells using tissue material from the ear of dead sheep/snow sheep hybrid

Production and cryopreservation of somatic cells (SCs) from valuable and endangered animals allows a preservation of genetic diversity and ensuring their future reproduction. The aim of present work was to isolate SCs from the ear of unique hybrid sheep (Ovis aries) and snow sheep (Ovis nivicola borealis) post-mortem. In this purpose, enzymatic and mechanical methods of tissue preparation were compared.Materials and Methods. Ears from deceased animal were brought to the laboratory 12 hours after the death in a pasture, and biological material was thoroughly washed under running water. The hairs were removed from the part of the ear shell by the blade. Skin fragments were treated with 70% ethyl alcohol, washed three times in a saline solution with antibiotics and ground up to small pieces. The ear pieces were washed several times in phosphate buffer saline and divided into two parts. One part of the explants started in vitro culture without enzymatic treatment (group 1), whereas another part was pre-treated with a 0.25% trypsin/EDTA solution. After trypsinization, either tissue fragments (group 2), or cell complexes separated from cell suspension fraction (group 3) were taken for in vitro culture for 9 days. Monitoring of cell colony formation and growth was carried out daily. Results. In the group 3, cell colonies were formed on the second day of in vitro culture. In groups 1 and 2, cell growth was observed from tissue fragments after five days regardless of the treatment. On the 9th day, all the groups produced the primary cultures, represented by two types of SCs. In general, single cell complexes from the group 3 formed cell growth zones more quickly than tissue explants from the groups 1 and 2, however, final cultures of SCs and their morphological aspects were no different between the groups. Conclusion. Methodological protocols were proposed and successfully used to obtain in vitro cultures of SCs from the ear of dead sheep/snow sheep hybrid animal, 12 hours post-mortem that may allow further storage of valuable genetic material.

Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations (GS1, 2010, ex-situ; GS2, 2019, ex-situ; GS3, 2019, in-situ; XB1, 2010, in-situ; and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs (in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

ПОРОДНІ ОСОБЛИВОСТІ АЛЕЛЬНОГО ПРОФІЛЮ ГЕНІВ PIT1 ТА GH УКРАЇНСЬКОЇ АБОРИГЕННОЇ ЛЕБЕДИНСЬКОЇ ПОРОДИ КОРІВ

The preservation of genetic diversity is a paramount concern in addressing global challenges today. The foundation of biological diversity hinges on its genetic components, and the loss of species and genetic variability poses a genuine threat to the biosphere. This is because the sustainability of natural ecosystems and agroecosystems depends directly on their genetic adaptability to changing environmental conditions.
 In cattle, genes associated with milk yield play a crucial role, including genes related to milk proteins and hormones. Among these, the pituitary-specific transcription factor (PIT1) and growth hormone (GH) genes are of particular significance. In this study, we investigated the polymorphism of these genes in the Lebedyn breed of cattle.
 A total of 2 gene polymorphisms, PIT1 and GH, were examined through molecular and genetic research conducted at the genetics laboratory of the Institute of Animal Breeding and Genetics named after M. V. Zubets, part of the National Academy of Agrarian Science of Ukraine. The study utilized 32 DNA samples extracted from the venous blood of Lebedyn breed cows using the 'DNA Sorb-B' kit from AmpliSens. Genotyping was carried out through polymerase chain reaction (PCR-RFLP) analysis of restriction fragment length polymorphism, employing the “Tertsyk” amplifier for PCR. The resulting DNA restriction analysis products were assessed via electrophoresis in a 2–3% agarose gel containing ethidium bromide, with DNA fragment lengths determined using the GeneRuler TM 50 bp DNA Ladder and Thermo Scientific™ GeneRuler 1 kb Plus DNA Ladder markers.
 For the PIT1 gene analysis, a 451 bp amplified fragment was treated with the enzyme HinfI, yielding the following allele frequencies: A (0.38) and B (0.62). The heterozygous AB genotype was the most prevalent (0.45), while homozygotes for the A allele constituted 0.15 of the population. In the case of the GH gene fragment (223 bp), hydrolysis was performed using the restriction enzyme AluI. Analysis of allele frequency distribution indicated a high frequency of the L allele (0.85), with no animals exhibiting the homozygous GHVV genotype, and the GHLL genotype was present in 0.7 of the population.
 These findings reveal unique features of the allelic spectrum of the PIT1 (V-0.62) and GH (L-0.85) genes specific to the Ukrainian indigenous Lebedyn breed of cows. Selectionally significant genotypes include PIT1AA (15%) and GHLL (70%), while heterozygote carriers, which contribute to genetic diversity within the population, account for 45% and 30%, respectively.
 This study’s results hold particular value due to the alarming decline in the population of local indigenous breeds and the imminent threat to the preservation of agricultural genetic resources.

The Impact of Climate Change on Animal Health and Disease Patterns

Purpose: The aim of the study is to examine the impact of climate change on animal health and disease patterns
 Methodology: This study adopted a desktop methodology. This study used secondary data from which include review of existing literature from already published studies and reports that was easily accessed through online journals and libraries
 Findings: The study revealed that climate change has had a significant impact on animal health and disease patterns, with various negative consequences for biodiversity and ecosystems. Rising temperatures and changing rainfall patterns influence the distribution and abundance of disease vectors, such as mosquitoes and ticks and alter their geographic ranges. This can result in the spread of diseases like malaria, dengue fever, Lyme disease, and West Nile virus to new areas. Additionally, climate change enhance the replication and survival rates of pathogens, potentially leading to more frequent and severe disease outbreaks.
 Unique Contribution to Theory, Practice and Policy: The study was anchored on One Health theory and Stressor-response theory. The study recommends Incorporation of climate change considerations into wildlife conservation and management strategies. This involves protecting and restoring habitats, creating wildlife corridors to facilitate species movement, and implementing adaptive management practices that consider the potential impacts of climate change on disease dynamics. Conservation efforts should prioritize the preservation of genetic diversity and the enhancement of resilience in animal populations.

Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region.

Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole Myodes rufocanus was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35-20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16-24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. The genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.

Enhancing the Cryopreservation System of Larch Embryogenic Culture by Optimizing Pre-Culture, Osmoprotectants, and Rapid Thawing

Cryopreservation is considered the safe and efficient strategy for the long-term conservation of embryogenic cultures. The objective of this study was to cryopreserve the embryogenic tissues of hybrid larch to overcome the result raised by rapid growth rates of conifer embryogenic cultures necessitating frequent sub-culturing. We systematically evaluated several parameters, including the pre-culture method (liquid or solid), osmoprotectant type (DMSO, sucrose, or PEG6000), duration of cryoprotection (1–3 h), and thawing temperature (4 °C, 25 °C, or 40 °C). After one month of cryopreservation, we assessed the regeneration efficiency and maturation ability of both cryo-preserved and non-cryopreserved tissues. Our optimized protocol involves pre-culturing embryonic tissue on the solid medium with 0.4 M sorbitol for 48 h, followed by treatment with 10% DMSO, 0.4 M sucrose, and 15% PEG6000 for 1 h on ice, and immersion in liquid nitrogen with rapid thawing at 40 °C. Notably, the use of solid media during pre-culturing was crucial to enhancing the success rate of cryopreservation. Using protocol optimization, we achieved high embryogenic tissue survival rates of over 80% without affecting the ability of somatic embryogenesis. This work provides a comprehensive set of steps for routine cryopreservation of embryogenic tissues for long-term conservation in hybrid larch, along with sample protocols for cryopreservation of larch. The results demonstrate that vitrification is a reliable method for preserving embryogenic tissues of hybrid larch with broader implications for the cryopreservation of other plant species. Further optimization and standardization of protocols across different species would ensure the preservation of genetic diversity and facilitate future research in plant biotechnology that benefits human health, food security, and environmental sustainability.

Hope is the last thing lost: Colombian captive-bred population of the critically endangered Orinoco crocodile (Crocodylus intermedius) is a genetic reservoir that could help to save the species from extinction

A purpose of ex-situ populations is the preservation of genetic variation, but this is a challenging task since genetic diversity is commonly lost through each generation, and so the establishment of management guidelines should be a high priority. Fifty years ago, the National University of Colombia began a breeding program in the Roberto Franco Tropical Station (in Villavicencio, Meta) to conserve the critically endangered Orinoco crocodile Crocodylus intermedius. Despite the large number of individuals raised and kept in captivity, the Station has not been able to release individuals due to a lack of a complete genetic characterization that could determine whether the population is genetically viable. In this study we used a panel of 17 microsatellite loci to overcome this problem. We estimated from the founder animals and the live crocodiles the inbreeding, heterozygosities, the number of alleles, and their richness, and frequencies to understand the effects of managing a captive breeding program without considering genetic profiles. Our results revealed that the living population maintains much of its founder diversity with high levels of heterozygosity and low overall inbreeding, making it suitable for maintaining captive breeding and for implementing wild releases. We estimated the individual genetic diversity of the living crocodiles, as well as their relationships. This information, combined with the size, sex, and location, allowed us to propose combinations and to restructure the breeding groups. We demonstrated that molecular data could be used to improve the management of ex-situ conservation programs well beyond what could be achieved with pedigree information alone.

The unexplored effects of artificial selection on urban tree populations.

The unexplored effects of artificial selection on urban tree populations.

Biodiversity Genetic Conservation as a Key to Support Agro-Eco-Edu-Tourism Program in Southeast Asia

Biodiversity will be a long-term asset that needs to be studied sustainably for human welfare. Genetic diversity is the main pillar of species and ecosystem diversity. Genetic conservation is an effort to manage and conserve species using a molecular approach to understanding various aspects of species biology. The existence of biodiversity has various benefits. From a social perspective, biodiversity can be utilized for agro-edu education, recreation, and research facilities. Preservation of genetic diversity is an effort to support the agro-eco edu-tourism program, which has many benefits, including pleasure from tourism activities and visitors' education about biodiversity. Changes in land use cause forest degradation, habitat loss or damage, resulting in loss of biodiversity. Mitigation of biodiversity management is needed to maintain the balance of ecosystems and environmental functions.

Predicting Spruce Taiga Distribution in Northeast Asia Using Species Distribution Models: Glacial Refugia, Mid-Holocene Expansion and Future Predictions for Global Warming

Spruce taiga forests in Northeast Asia are of great economic and conservation importance. Continued climate warming may cause profound changes in their distribution. We use prognostic and retrospective species distribution models based on the Random Forest machine learning method to estimate the potential range change of the dominant taiga conifer Jezo spruce (Picea jezoensis (Siebold & Zucc.) Carrière) for the year 2070 climate warming scenarios and for past climate epochs–the Last Glacial Maximum (LGM) (~21,000 years before present) and the mid-Holocene Climatic Optimum (MHO) (~7000 years before the present) using the MIROC-ESM and CCSM4 climate models. The current suitable climatic conditions for P. jezoensis are estimated to be 500,000 km2. Both climatic models show similar trends in past and future ranges but provide different quantitative areal estimates. During the LGM, the main part of the species range was located much further south than today at 35–45° N. Projected climate warming will cause a greater change in the distributional range of P. jezoensis than has occurred since the MHO. Overlapping climatic ranges at different times show that the Changbai Mountains, the central parts of the Japanese Alps, Hokkaido, and the Sikhote-Alin Mountains will remain suitable refugia for Jezo spruce until 2070. The establishment of artificial forest stands of P. jezoensis and intraspecific taxa in the future climate-acceptable regions may be important for the preservation of genetic diversity.

Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China.

Clarifying the genetic structure can facilitate the understanding of a species evolution history. It is crucial for the management of germplasm resources and providing useful guidance for effective selective breeding. Bellamya is an economically and ecologically important freshwater snail for fish, birds and even humans. Population genetic structures of the Bellamya species, however, were unknown in previous studies. Population genomics approaches with tens to hundreds of thousands of single nucleotide polymorphisms (SNPs) make it possible to detect previously unidentified structures. The population genomic study of seven populations of B. aeruginosa across three river systems (Yellow River, Yangtze River and Pearl River) in China was conducted by SLAF-seq. SLAF-seq obtained a total of 4737 polymorphisms SLAF-tags and 25,999 high-consistency genome-wide SNPs. The population genetic structure showed a clear division among populations from the Yellow River basin (YH and WL) and the Pearl River basin (QSH and LB), as well as population YC from the Yangtze River basin using the SNPs data. However, there existed no distinct population structure using the mitochondrial DNA (mtDNA). The anthropogenic translocation from the Yangtze River basin to the Pearl River basin and the passive dispersion from the Yangtze River basin to the Yellow River basin by flooding have weakened the phylogeographic pattern of B. aeruginosa. The divergence of B. aeruginosa in the three river systems suggests that the anthropogenic dispersal for aquaculture and breeding requires serious consideration of the population structure for the preservation of genetic diversity and effective utilization of germplasm resources.

An evolutionary look into the history of lentil reveals unexpected diversity.

The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold‐season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty‐three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were “enzymes,” “Cell Wall Organization,” and “external stimuli response.” All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.

Uncovering haplotype diversity in cultivated Mexican vanilla species.

Although vanilla is one of the best-known spices, there is only a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. Using nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 ex situ accessions, we assessed species monophyly using phylogenetic analyses and genetic distances. Intraspecific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, Vanilla planifolia, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape. Three species (Vanilla planifolia, V. pompona, and V. insignis) and 13 haplotypes were identified among Mexican vanilla. Within V. planifolia haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes consisted exclusively of Mexican samples. The dominant V. planifolia haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and Chinantla. Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.

Recovering Ancient Grapevine Cultivars in the Balearic Islands: Sanitary Status Evaluation and Virus Elimination.

Recuperation and genetic diversity preservation of local cultivars have acquired a huge interest in viticulture areas worldwide. In the Balearic Islands, most of the old cultivars are only preserved in grapevine germplasm banks, and so far, the sanitary status of these local cultivars has remained unexplored. The aim of this study was to survey and detect the virus incidence of all conserved cultivars in the government Grapevine Germplasm Bank of the Balearic Islands and to promote the sanitary recovery of two important minor cultivars, Argamussa and Gorgollassa. Enzyme-linked immunosorbent assay (ELISA) screenings were performed on 315 vines of 33 local cultivars. It was shown that the local cultivars were highly infected with simple (39.7%) and mixed infections (52.1%) and only 8.25% of them were free from the viruses tested. Grapevine leafroll-associated virus 3 (GLRaV-3) infection was the most common (82%). Moreover, Grapevine fanleaf virus (GFLV) and Grapevine fleck virus (GFkV) were also present with considerable incidence (25.4% and 43.5%, respectively). In addition, two sanitation protocols were used: shoot tip culture (ST) and thermotherapy in combination with shoot tip culture (CT). Virus elimination using only ST was effective to obtain “healthy” vines of cvs. Argamussa and Gorgollassa. It is important to emphasize that the methods described in the current study were rapid and effective in eliminating both GLRaV-3 and GFLV, also in combination.

Effects of spawning group sex ratio and stocking density on the outcome of captive reproduction in golden cuttlefish Sepia esculenta

The supplemental release of hatchery-reared animals is important for maintaining or enhancing fishery resources. The golden cuttlefish, Sepia esculenta, is a commercially important cephalopod utilized in stock enhancement activities throughout East Asia. The long-term success of such activities requires proper breeding regimes to ensure the efficient use of resources and the preservation of genetic diversity in the offspring. For captive-bred cephalopods, information concerning the effects of different mating regimes on the paternity of offspring is scarce. However, it could be of particular importance for polyandric species such as golden cuttlefish. As previous studies have suggested that both the number and mating order of males are related to female fecundity, we investigated the effects of stocking density and sex ratio on female fecundity and determined the paternity of the offspring in golden cuttlefish. We used two experimental approaches. First, four different female (F): male (M) sex ratios (1F:1M, 1F:2.5 M, 1F:3M, 1F:6M) were set up to investigate the effects of operational sex ratio on mating behavior, female fecundity, and hatchling paternity. Next, we investigated female fecundity and hatchling paternity patterns under low and high stocking densities (5 or 10 individuals ∙ m−3), following a standard sex ratio setting that is widely employed in cuttlefish hatcheries (1F:2M). With an increasing proportion of males, the average fecundity of females and the participation rate of males in paternity decreased. With increasing stocking density, the females had lower average daily egg production, and the males had a high variance in reproductive success and decreased participation rate in spawning. The estimated effective number of breeders (Ne) was 19.29 (Ne/N ratio = 0.54) at high-density and 10.17 (Ne/N ratio = 0.57) at low density. To achieve high reproductive performance and assure genetic diversity of golden cuttlefish offspring, our study suggests that equal (1F:1M) or slightly male-biased (1F:2.5 M) sex ratios and a low stocking density may be useful when breeding golden cuttlefish in captivity.

Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii)

Combining population genetics with genomic data has transformed scientist’s ability and resolution of making ecological inferences, thus making it possible to detect previously unidentified structures and obtain more accurate estimates of demographic parameters in wild populations. Ark shell is an economically and ecologically important marine species for fisheries industry in China, but its habitats have been severely damaged due to overexploitation of natural resources. Recently, protection of the ark shell as a natural resource has attracted extensive attention. Here, we identified 10,108 single-nucleotide polymorphisms using Restriction-site Associated DNA Sequencing (2b-RAD) to explore the structure of seven populations of S. broughtonii from the Asian Pacific Northwest region (four sites in China, two in Korea, and one in North Korea). A high level of genetic diversity was detected in all seven S. broughtonii populations. Pairwise FST estimates and neighbor-joining (NJ) tree topologies showed a clear division between the populations from China and Korea, and Chinese populations exhibited low levels of divergence from one another. This significant genetic divergence of the Chinese population implies that translocation of individuals for aquaculture should be properly managed for the preservation of genetic diversity and eventual local adaptation in natural populations.

Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

BackgroundCurrently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos.ResultsRNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects.ConclusionsOur findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification.