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Which reproductive technologies are most relevant to studying, managing and conserving wildlife?

The advent of in vitro fertilisation (IVF) and embryo transfer in the 1970s led to speculation about the potential value of these and other 'reproductive technologies' to conserving endangered species. So far, and for the most part, assisted breeding techniques that are routine in domesticated species are not easily adapted to wildlife. Species differences in reproductive form (anatomy/morphology) and function (mechanisms regulating reproductive success) limit the practical applicability for offspring production. Thus, the limiting factor is the lack of basic knowledge about thousands of unstudied species, the foundation that is essential to allowing reproduction to be enhanced and/or controlled. There now is excellent evidence that reproductive technologies are most useful as tools for studying how different species reproduce, especially defining novel and unique mechanisms. The present paper reviews the status and relevance of various reproductive technologies that are useful or have potential for wildlife. Modern examples of progress are provided indicating how these tools are being used to understand ways that wildlife species reproduce and, in some cases, how such knowledge has been used for successful assisted breeding, improved management and conservation.

Animals↗

The monitoring of British breeding birds: a success story for conservation science?

For almost four decades the British Trust for Ornithology has monitored populations of the commoner 35-50% of species of British breeding birds. The monitoring involves surveillance of numbers, breeding output and survival rates across the whole of the United Kingdom. A formal alert system allows serious declines to be identified and brought to the attention not only of conservationists and those responsible for countryside policy but also the general public. Demographic modelling, the gathering of ancillary information and linked research programmes allow the causes of declines to be identified. The paper details the operation of the programme, illustrated by examples. The system has resulted in the widespread declines in farmland birds that occurred in the last quarter of the 20th century being brought to the attention of conservation scientists, campaigners, policy-makers, politicians and the public. From this (and from the associated understanding of the causes of the declines) have stemmed policies aimed at reducing the problems and a commitment by government to halt the declines. The success of the programme rests on scientifically rigorous design and analysis, on a partnership between volunteer birdwatchers (who do most of the fieldwork) and professional ecologists (responsible for design and analysis) and on effective interaction between scientists and policy makers.

Animals↗

Genomic insights into local adaptation of indigenous chickens.

Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1 022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.

Animals↗

Conservation of feline semen. Part I: cooling and freezing protocols.

There has been increased interest recently in the conservation of wild felids and preservation of valuable cat breeds. Assisted reproduction, by means of artificial insemination (AI), is an important tool for developing breeding programs for conservation. Optimal use of AI requires accurate data on semen conservation protocols and its long-term storage/survival. In this paper, semen cooling and freezing processes are described, with special emphasis on the results obtained in experiments performed in the domestic cat. Conception rates after AI in wild and domestic cats are also reported.

Animals↗

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers.

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F(ST)) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such a Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei's genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.

Animals↗

Effect of forage conservation (hay or silage) and cow breed on the coagulation properties of milks and on the characteristics of ripened cheeses.

Forty-two multiparous dairy cows of three different breeds (Holstein, Montbéliarde and Tarentaise) were fed on the same type of forage (natural grassland) preserved in the form of either hay (H) or silage (GS), according to a changeover design (two 4 week periods). The proportion of concentrate in the diet and the energy and nitrogen contents were similar in both treatments. The milk produced by these cows was used for the manufacture of Saint-Nectaire type cheeses, under controlled and identical cheesemaking technological conditions. More cheese was produced with the H treatment milk. The cheeses made with the GS treatment milk were more yellow and tended to be more bitter. The other chemical and sensory characteristics did not differ much between the two treatments. Of the 51 volatile compounds identified, four were in significantly higher proportion in the GS than in the H cheeses. Cheeses produced from Tarentaise cows' milk were more yellow and their pH was higher than those made with the milk of Holstein or Montbéliarde cows. The cheeses from Montbéliarde and Tarentaise cows' milk were firmer, more melting and tastier than those made with the milk of Holstein cows. Although some trends were apparent, there were no significant differences in cheese volatile compounds for different breeds.

Animal Feed↗

Aquatic Resource Conservation. The first Yangtze finless porpoise successfully born in captivity.

BACKGROUND: As the sole freshwater subspecies of finless porpoise (Neophocaena phocaenoides), the Yangtze finless porpoise (N. p. asiaeorientalis) lives only in the middle and lower reaches of the Yangtze River and its appended Poyang and Dongting Lakes. As a result of human activity on the river, including over and illegal fishing, pollution, transportation and dam construction, the population of Yangtze finless porpoises has been steadily and rapidly decreasing during the past several decades, which leads the animal to be endangered. METHODS: For saving this unique animal from extinction, three corresponding measures, in situ conservation, ex situ conservation, and intensifying breeding research in captivity, were proposed and have been implemented since the 1980s. RESULTS: After successfully rearing the animals in captivity for almost nine years, the first Yangtze finless porpoise was successfully born in captivity on July 5, 2005. The calf is male, with a body length of 69 cm. This is the first freshwater cetacean ever born in captivity. CONCLUSION: The successful birth of this calf confirms that it is possible to breed the Yangtze finless porpoise in captivity. Furthermore, this will greatly benefit the conservation efforts, and also greatly bolster our on-going efforts to study the reproductive biology of these animals. RECOMMENDATION: More studies and efforts are expected to establish a sustainable, captive colony of the Yangtze finless porpoise, which will not only greatly expand our knowledge about the reproduction biology of this animal, but also help to redeem the wild population through a careful yearly 'soft releasing' process.

Animal Husbandry↗

Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage.

A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of drug sensitivity to survey other purebred populations that might be genetically at risk. We found that the same allele, mdr1-1Delta, segregated in seven additional breeds, including two sighthounds that were not expected to share collie ancestry. A mutant haplotype that was conserved among affected breeds indicated that the allele was identical by descent. Based on breed histories and the extent of linkage disequilibrium, we conclude that all dogs carrying mdr1-1Delta are descendants of a dog that lived in Great Britain before the genetic isolation of breeds by registry (ca. 1873). The breed distribution and frequency of mdr1-1Delta have applications in veterinary medicine and selective breeding, whereas the allele's history recounts the emergence of formally recognized breeds from an admixed population of working sheepdogs.

Alleles↗

Genome-Wide SNP Characterisation of Three Kazakh Sheep Breeds: Kazakh Fat-Tailed Coarse-Wool, Degeres, and Etti Merino.

Kazakhstan's sheep portfolio underpins much of the country's mutton and wool production, yet several of its principal breeds remain genomically uncharacterised. The aim of this study was to characterise the genomic diversity, population structure, and global phylogenetic placement of three economically important Kazakh breeds and to determine whether they constitute separate gene pools requiring independent management. We present the first genome-wide SNP characterisation to include the Degeres (DE), the Etti Merino (EM), and the Kazakh fat-tailed coarse-wool (KKG) breeds simultaneously. A total of 1497 animals (DE = 354, EM = 642, KKG = 501) sampled across seven production households were genotyped and, after quality control, analysed at 42,279 SNPs, of which 22,766 LD-pruned markers were used for principal component analysis and AMOVA. We applied principal component analysis (PCA), pairwise FST, analysis of molecular variance (AMOVA), neighbour-joining phylogenetics, model-based ancestry estimation (ADMIXTURE), and Hill-number diversity profiling, and projected the breeds against the global Ovine SNP50 HapMap panel (74 reference breeds, 2819 animals; 37,685 shared SNPs). All three breeds retained uniformly high within-breed diversity (expected heterozygosity 0.413-0.417) with fixation indices at or near zero. AMOVA partitioned 94.03% of variance within breeds (&#x3a6;ST = 0.060, p < 0.001). PCA, phylogeny, and ADMIXTURE concordantly resolved three breed-specific clusters at K = 3, with a maximum interbreed FST of 0.038 within the study dataset. Against the global panel, EM was genetically closest to Merino and Merino-derived reference breeds (pooled FST = 0.017) and substantially more distant from Southwest Asian sheep (FST = 0.045), whereas DE and KKG showed the reciprocal pattern (FST = 0.027 and 0.020 to Southwest Asia, 0.052 to the Merino group). DE additionally displayed the heterozygote excess and partial admixture expected of an incompletely consolidated composite. These results delineate three distinct gene pools and carry direct implications for breed management and the conservation of genomic diversity in Kazakhstani sheep.

ADMIXTURE↗

Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data.

RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation.

Base Composition↗

The National Animal Germplasm Program: challenges and opportunities for poultry genetic resources.

In the United States, poultry genetic resources have consolidated because of economic pressures. Such consolidations can potentially jeopardize the poultry industry and the ability of research communities to respond to future challenges. To address the loss of genetic resources for all livestock and aquatic species, USDA established the National Animal Germplasm Program (NAGP) in 1999. Since the initiation of NAGP, population surveys have been conducted on nonindustrial chicken and turkey breeds. These surveys not only provide insight into breed status, but also serve as a benchmark for future comparisons. The survey results revealed that 20 chicken breeds and 9 turkey breeds were in various stages of being lost. The NAGP has initiated an ex situ repository for cryopreserved germplasm and tissue that already contains 59 chicken lines and 2,915 tissue samples. As the NAGP, along with its industry and university partners, continues developing the ex situ collection, there are research opportunities in cryopreserved tissue utilization and studies of genetic diversity. For cryopreserved tissues, several key research areas include improving the cryopreservation protocols for rooster and tom semen by using cryoprotectants other than glycerol and utilizing embryonic cells. Although surveys have been conducted on public research lines and rare breeds, there is a void in understanding the level of genetic diversity present in U.S. poultry populations. Therefore, an opportunity exists to perform a series of genetic diversity studies using molecular- based approaches. Such an evaluation can help clarify population differences between research lines and rare breeds and, thereby, facilitate conservation strategies. There appears to be growing consumer interest in poultry products derived from heritage breeds and/or poultry raised in nonindustrial production systems. Although the depth of such market trends is unknown, such an interest may provide an important niche for rare poultry breeds and, thereby, strengthen the genetic base.

Agriculture↗

[Significance of biotechnology in reproductive biology and veterinary medicine].

In the last decade a good number of biotechnical methods have been developed. They are available in medical, biological, and ecological fields of work as well as techniques that can replace animal experiments. These methods have been developed on the basis of researchwork in andrology (AI and cryoconservation of spermatozoa), endocrinology (hormonal control of reproduction) and the availability of industrial produced hormones and their analog. On the other hand practical clinical techniques for examination like the availability of sonography advice and clinical practical techniques for non-surgical recovery and transplantation of gamets and embryos have been the prerequisites for a successful work in this field of action. These fields of action are extended from breeding aspects (genetical progress) over the control of epidemics to the exportation of genetic material (especially developing countries to overcome hygienic and adaptation problems), the creation of gen-pools (conservation of breeds-species) and as well as the elimination of genetic defects like BLAD or DUMPS by help of PCR-techniques or the identification of positive characters like milk components and sexing of embryos. The industrial use of bioproducts produced by especially designed biosystems is in work but in Germany not possible by reasons of legislative restrictions. In the light of these developments the veterinary fields of work should be discussed and focussed towards an understanding that the veterinarian should be active and in a polposition in the processing of reproduction and production and presentation of food of animal origin by using these new technologies.

Animals↗

Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis.

Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

Base Sequence↗

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004.

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.

Analysis of Variance↗

Genomic prediction and genome-wide association studies of morphological traits and distraction index in Korean Sapsaree dogs.

The Korean Sapsaree dog is a native breed known for its distinctive appearance and historical significance in Korean culture. The accurate estimation of breeding values is essential for the genetic improvement and conservation of such indigenous breeds. This study aimed to evaluate the accuracy of breeding values for body height, body length, chest width, hair length, and distraction index (DI) traits in Korean Sapsaree dogs. Additionally, a genome-wide association study (GWAS) was conducted to identify the genomic regions and nearby candidate genes influencing these traits. Phenotypic data were collected from 378 Korean Sapsaree dogs, and of these, 234 individuals were genotyped using the 170k Illumina CanineHD BeadChip. The accuracy of genomic predictions was evaluated using the traditional BLUP method with phenotypes only on genotyped animals (PBLUP-G), another traditional BLUP method using a pedigree-based relationship matrix (PBLUP) for all individuals, a GBLUP method based on a genomic relationship matrix, and a single-step GBLUP (ssGBLUP) method. Heritability estimates for body height, body length, chest width, hair length, and DI were 0.45, 0.39, 0.32, 0.55, and 0.50, respectively. Accuracy values varied across methods, with ranges of 0.22 to 0.31 for PBLUP-G, 0.30 to 0.57 for PBLUP, 0.31 to 0.54 for GBLUP, and 0.39 to 0.67 for ssGBLUP. Through GWAS, 194 genome-wide significant SNPs associated with studied Sapsaree traits were identified. The selection of the most promising candidate genes was based on gene ontology (GO) terms and functions previously identified to influence traits. Notable genes included CCKAR and DCAF16 for body height, PDZRN3 and CNTN1 for body length, TRIM63, KDELR2, and SUPT3H for chest width, RSPO2, EIF3E, PKHD1L1, TRPS1, and EXT1 for hair length, and DDHD1, BMP4, SEMA3C, and FOXP1 for the DI. These findings suggest that significant QTL, combined with functional candidate genes, can be leveraged to improve the genetic quality of the Sapsaree population. This study provides a foundation for more effective breeding strategies aimed at preserving and enhancing the unique traits of this Korean dog breed.

Animals↗

Effect of semen collection method on pre- and post-thaw Guirra ram spermatozoa.

In this study, we evaluated the potential effect of the method of recovery (artificial vagina or electroejaculation) on the production and quality of Guirra ram spermatozoa cryopreserved for the possible constitution of a sperm bank. In order to address this question, we evaluated the effect of semen collection method on fresh semen quality parameters, including: volume, concentration, production, microscopic analysis (abnormal sperm and intact apical ridge) and sperm motility parameters determined by CASA system. For frozen-thawed semen, we evaluated motility parameters by CASA and intact apical ridge, acrosomal status, assessed by dual staining by IP and FITC-PNA and capacitation status, assessed by M540 and Yo-pro1, using flow cytometry. The main findings from this study were: (i) that electroejaculation resulted in a lower recovery efficiency (80% of the cases), as a consequence of contamination with urine or lack of response to the electrical stimulation; (ii) the fresh seminal quality was not significantly different between recovery methods, except for the concentration of spermatozoa, but total number of spermatozoa and the consequent number of possible seminal doses for artificial insemination were similar; and, (iii) a higher number of stable and functional spermatozoa (higher number of live non-capacitated cells, higher live acrosome intact cells and live acrosome reacted cells) were found for frozen-thawed spermatozoa collected by electro ejaculation than by artificial vagina. According to our results, we are able to develop both methodologies in the creation of the Guirra sperm bank. Assuming the advantages and limitations of both methodologies, in Guirra breed, would enable the rapid constitution of a sperm bank including samples from a large number of non-trained rams in a short period of time, which will increase the genetic variability, and so guarantee the conservation of this breed.

Acrosome↗

Dynamics of Antibiotic Resistance Gene Profiles in Captive Forest Musk Deer (Moschus berezovskii) Along a Breeding Duration Gradient.

BACKGROUND: To conserve wild populations and ensure a sustainable supply of musk, China initiated the captive breeding of forest musk deer. The temporal dynamics of gut antibiotic resistance gene (ARG) profiles in captive forest musk deer along a breeding duration gradient remain poorly characterized. METHODS: In this study, we employed metagenomic sequencing to systematically characterize the profiles and potential mobility of ARGs. Samples were divided into short-term, medium-term and long-term groups according to breeding durations. RESULTS: A total of 331 ARG subtypes and 71 mobile genetic element (MGE) subtypes were annotated across all samples. ARG Shannon diversity differed overall across groups (Kruskal-Wallis, p = 0.03); Bonferroni-adjusted Dunn's test showed no significant pairwise differences. PCoA (Bray-Curtis) demonstrated distinct separation of the ST group (p = 0.002), and shared core ARG subtypes gradually increased with extended breeding years. A strong positive correlation between ARG and MGE abundances was identified (r = 0.85, p = 0.0001). In total, 63 contigs carrying co-localized ARG-MGE complexes were recovered. The ST group contained the highest proportion of such contigs. The ST group displayed tight physical ARG-MGE linkage within 1-3 kb genomic intervals. CONCLUSIONS: Our results reveal that breeding duration is associated with the gut ARG characteristics of captive forest musk deer. Short-term captivity has higher ARG-MGE co-localization, suggesting a higher possibility of mobilization.

One Health↗

Stabilizing selection on genomic divergence in a wild fish population.

Conservation programs use breeding protocols to increase genomic divergence (by mating genetically dissimilar individuals) in an attempt to circumvent population declines resulting from inbreeding depression. However, disruption of either beneficial gene complexes or local genetic adaptations can lead to outbreeding depression, and thus, there should be a reduction in fitness of individuals at either end of the genomic divergence continuum. Although such simultaneous inbreeding and outbreeding depression has been observed in plant populations, it rarely has been demonstrated in animal populations. Here, I use both genetic and phenotypic measures to show that there is stabilizing selection on genomic divergence in a wild population of bluegill sunfish (Lepomis macrochirus). I also show that breeding individuals that exercise mate choice produce offspring that are closer to the optimal level of genomic divergence than random mating alone would predict.

Animals↗