Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “conservation breeding”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed2026

Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Epinephelus itajara), Islas del Rosario, Colombia.

Epinephelus itajara, commonly known as the Atlantic Goliath grouper, is the largest species among the western North Atlantic groupers and is critically endangered. This species plays a crucial ecological, cultural, and economic role and has been the focus of captive breeding efforts at the Oceanario of the Rosario Islands, Colombia. However, despite its ecological and conservation importance, genomic resources and population genomic data for E. itajara remain scarce, particularly in the Colombian Caribbean. This study presents a reference-guided chromosome-scale genome assembly and an analysis of the population genomic structure of E. itajara using PacBio HiFi sequencing and Illumina technologies. The assembled genome has a total size of 1.12 Gb, with a contig N50 of 42.69 Mb and a scaffold N50 of 46.30 Mb. A total of 22,692 protein-coding genes were identified after masking 46% of the genome, which consists of repetitive elements. Comparative genomic analyses revealed a high degree of collinearity with closely related Epinephelus species and identified E. lanceolatus as the closest relative, supporting recent divergence and conserved genome architecture within the genus. Additionally, a population genomics analysis was conducted using 7706 high-quality SNPs to assess the genomic structure of captive populations. The results revealed four distinct genomic lineages, with moderate genetic differentiation among the sampled individuals. In the Colombian Caribbean, two unique lineages were identified, associated with the localities of Bahía Cispatá and Bahía Barbacoas, suggesting possible geographic isolation. These genomic resources provide valuable tools and new opportunities to better understand the genomic diversity, evolutionary history, and reproductive mechanisms of E. itajara. Moreover, they serve as a foundation for conservation strategies, including selective breeding programs aimed at increasing genomic diversity in captive populations and guiding restoration efforts in its natural habitat.

Epinephelus itajara↗
PubMed1992

Numerical variation of nucleolar organizer regions after silver staining in domestic and wild Suidae (Mammalia).

Selective silver staining was used to investigate the cellular distribution of numbers of nucleolar organizer regions (NORs) in domestic pigs (Sus scrofa) of eight different breeds, the European wild boar (S. scrofa scrofa), Indonesian wild boar (S. scrofa vittatus), Javan warty pig (S. verrucosus), Sulawesi warty pig (S. celebensis), and pigmy hog (S. salvanius). In the domestic pig as well as in the wild (sub)species of Sus, actively transcribing ribosomal RNA genes were found to be present in the secondary constrictions of chromosome pairs 10 and 8. Chromosomes 10 were consistently Ag-positive. Chromosomes 8 less frequently showed Ag-NORs, resulting in different mean numbers of Ag-NORs per individual animal. Mean Ag-NOR numbers per breed or (sub)species were generally higher in the wild representatives of Sus than in the domestic breeds. The highest mean numbers of Ag-NORs were observed in the Meishan breed and in S. celebensis and S. salvanius. The Meishan breed appears to be conservative in Ag-NOR staining pattern, being more comparable to the Asian wild Suidae than to the European breeds.

Animals↗
PubMed2001

The canine homeobox gene MSX2: sequence, chromosome assignment and genetic analysis in dogs of different breeds.

The MSX2 gene encodes a homeodomain transcription factor important for normal head and face morphogenesis. MSX2 is expressed in key craniofacial structures during development and mutations in the human gene give rise to various craniofacial abnormalities. We are interested in the genetic basis of non-pathogenic variation in skull and face shape. As part of this study we have analysed DNA from a panel of different dog breeds, selected for the differences they show in these traits and investigated MSX2 as a candidate gene. In this paper we describe the cloning of the canine homologue of MSX2, the determination of its structure, sequence and localization of the gene to dog chromosome 4q23. The DNAs from 11 individual domestic dogs belonging to 10 different breeds were sequenced in a search for genetic variation. Our studies show that variation in MSX2 does not contribute to the diversity of face shape observed in these domestic dogs and that the MSX2 sequence is strongly conserved between different dog breeds. The proximal promoter shows a high level of interspecies sequence conservation and several conserved transcription factor binding motifs have been identified and their significance discussed.

Amino Acid Sequence↗
PubMed2005

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms.

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.

Animals↗
PubMed2004

Ex situ population management in the absence of pedigree information.

For captive breeding to play a significant role in conservation, ex situ populations must be scientifically managed to meet objective goals for retaining representative genetic variation. Imperfect genealogical information requires fundamental assumptions to be made that may bias downstream measures of genetic importance, upon which management decisions are based. The impacts of such assumptions are most pronounced within breeding programmes characterized by a high proportion of individuals of unknown ancestry, as exemplified by the large captive population of the St Vincent parrot (Amazona guildingii). The degree to which microsatellite-based estimates of relatedness may improve upon the assumptions of conventional pedigree-based management was investigated using genotypic data collected at eight microsatellite loci and two marker-based relatedness estimators. The measure, rxyLR, was found to explain the highest amount of variation in true relatedness. Integration of pairwise estimates of founder relatedness with studbook data transformed current understanding of the relatedness structure of the A. guildingii population from two subgroups characterized by a high and low degree of relatedness, respectively, to a situation where all 72 individuals are prioritized for breeding according to their estimated mean kinships. Furthermore, the discovery of opposing, directional bias exhibited by rxyLR and rxyQG in assigning dyads to a given relationship category suggests that an approach that utilizes a combination of pairwise relatedness estimators may provide the most genetic information for balancing the dual considerations of maximizing gene diversity and minimizing inbreeding in developing breeding recommendations.

Animals↗
PubMed2003

Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding.

Selection and mating principles in a closed breeding population (BP) were studied by computer simulation. The BP was advanced, either by random assortment of mates (RAM), or by positive assortative mating (PAM). Selection was done with high precision using clonal testing. Selection considered both genetic gain and gene diversity by "group-merit selection", i.e. selection for breeding value weighted by group coancestry of the selected individuals. A range of weights on group coancestry was applied during selection to vary parent contributions and thereby adjust the balance between gain and diversity. This resulted in a series of scenarios with low to high effective population sizes measured by status effective number. Production populations (PP) were selected only for gain, as a subset of the BP. PAM improved gain in the PP substantially, by increasing the additive variance (i.e. the gain potential) of the BP. This effect was more pronounced under restricted selection when parent contributions to the next generation were more balanced with within-family selection as the extreme, i.e. when a higher status effective number was maintained in the BP. In that case, the additional gain over the BP mean for the clone PP and seed PPs was 32 and 84% higher, respectively, for PAM than for RAM in generation 5. PAM did not reduce gene diversity of the BP but increased inbreeding, and in that way caused a departure from Hardy-Weinberg equilibrium. The effect of inbreeding was eliminated by recombination during the production of seed orchard progeny. Also, for a given level of inbreeding in the seed orchard progeny or in a mixture of genotypes selected for clonal deployment, gain was higher for PAM than for RAM. After including inbreeding depression in the simulation, inbreeding was counteracted by selection, and the enhancement of PAM on production population gain was slightly reduced. In the presence of inbreeding depression the greatest PP gain was achieved at still higher levels of status effective number, i.e. when more gene diversity was conserved in the BP. Thus, the combination of precise selection and PAM resulted in close to maximal short-term PP gain, while conserving maximal gene diversity in the BP.

Computer Simulation↗
PubMed1999

Comparison of milk protein allele frequencies in Nordic cattle breeds.

Allele frequencies at four milk protein loci were studied in five modern and 17 old Nordic cattle breeds in order to reveal variants that are characteristic for these populations. The B allele of CSN3, which has been associated with improved manufacturing properties of milk, showed significantly lower frequencies in modern production breeds than in old breeds of interest for conservation purposes. Characteristic frequencies of CSN1S1 (C), CSN2 (A2) and CSN3 (B) were found in Icelandic cattle, Swedish Mountain cattle, Northern Finncattle and Western Fjord cattle, which indicate a common origin of these populations. Further comparisons of allele frequencies in old Nordic breeds suggest sorting of these breeds into two groups with a northern and southern geographic location.

Alleles↗
PubMed2006

Effects of breed on kinetics of ovine FSH and ovarian response in superovulated sheep.

Embryo production is a useful tool for ex situ conservation of endangered species and breeds, despite a high variability in the ovarian response to superovulatory treatments. The current study evaluated the incidence and mechanisms of genetic factors in such variability, by determining the pharmacokinetics and pharmacodynamics of a standard treatment with ovine FSH (oFSH) in two endangered Spanish sheep breeds (Rubia del Molar, R, and Negra de Colmenar, N) in comparison to Manchega ewes (M, control group). In the first experiment, pharmacokinetics of an i.m. single dose of 1.32 mg of oFSH was evaluated in seven animals of each breed. Plasma FSH concentrations reached their maximum at 4h post-administration in all the ewes, but several of the kinetic parameters (plasma FSH concentration at 4h post-administration, maximum plasma FSH concentration, C(max), and both the area under the plasma concentration-time curve extrapolated to the infinite, AUC(inf), and to the last moment of sampling, AUC(last)) were higher in the N group. In the second trial, 10 animals of each breed were superovulated using eight decreasing doses of oFSH (3 x 1.32 mg, 2 x 1.10 mg, and 3 x 0.88 mg). The R group, when compared to N and M, showed both a higher number of corpora lutea (13.7+/-0.6 versus 10.0+/-0.4 in N and 9.8+/-0.6 in M, P<0.05 for both) and embryos (7.9+/-0.8 versus 4.3+/-0.4 in N, P<0.05, and 6.7+/-0.5 in M, n.s.). Evaluation of pharmacokinetic and dynamic parameters showed that, although there was a trend for a higher hormone availability in R sheep, mean FSH plasma concentrations were similar between breeds (0.54+/-0.08 ng/ml for R, 0.45+/-0.05 ng/ml for N and 0.35+/-0.05 ng/ml for M). However, differences were found in the number of preovulatory follicles growing in response to the FSH treatment between R (24.4+/-2.2), M (18.9+/-1.5, n.s.) and N sheep (14.1+/-1.4; P<0.01). Thus, differences in embryo yields between breeds would be related to differences in the pattern of follicular growth in response to FSH treatment.

Animals↗
PubMed2005

Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population.

Chimpanzees are presently classified into three subspecies: Pan troglodytes verus from west Africa, P.t. troglodytes from central Africa, and P.t. schweinfurthii from east Africa. A fourth subspecies (P.t. vellerosus), from Cameroon and northern Nigeria, has been proposed. These taxonomic designations are based on geographical origins and are reflected in sequence variation in the first hypervariable region (HVR-I) of the mtDNA D-loop. Although advances have been made in our understanding of chimpanzee phylogenetics, little has been known regarding the subspecies composition of captive chimpanzees. We sequenced part of the mtDNA HVR-I region in 218 African-born population founders and performed a phylogenetic analysis with previously characterized African sequences of known provenance to infer subspecies affiliations. Most founders were P.t. verus (95.0%), distantly followed by the troglodytes schweinfurthii clade (4.6%), and a single P.t. vellerosus (0.4%). Pedigree-based estimates of genomic representation in the descendant population revealed that troglodytes schweinfurthii founder representation was reduced in captivity, vellerosus representation increased due to prolific breeding by a single male, and reproductive variance resulted in uneven representation among male P.t.verus founders. No increase in mortality was evident from between-subspecies interbreeding, indicating a lack of outbreeding depression. Knowledge of subspecies and their genomic representation can form the basis for phylogenetically informed genetic management of extant chimpanzees to preserve rare genetic variation for research, conservation, or possible future breeding.

Africa↗
PubMed1994

Pandas, people and policy.

Panda conservation in China has been plagued by controversy and cultural and political differences. But international cooperation, together with new studies identifying the main threats, offer renewed hope for the species' survival.

Animals↗
PubMed2004

Analysis of the genetic structure of endangered bovine breeds from the Western Pyrenees using DNA microsatellite markers.

In the Western Pyrenees, three out of four native cattle breeds are in grave danger of extinction. Genetic variation of all four breeds was assessed by analyzing 478 animals using 11 microsatellite markers. A moderate/high within-breed variability was found, a favorable factor to consider when planning conservation and improvement programs. Interestingly, the only selected commercial breed, the Pirenaica, showed depressed heterozygosity levels and a low average number of alleles, perhaps explainable by intensive human selection exacerbated by a bottleneck effect. The Pirenaica also exhibited pronounced genetic differences and was the largest contributor of diversity among the breeds from the Western Pyrenees. Among endangered cattle breeds from this region, our results highlight the singularity of the Betizu. Geographic isolation among herds may be responsible for the large F(IS) value found in the Betizu breed. Lastly, our study suggests that the use of highly selected breeds may be one of the causes of distortion in phylogenetic analyses.

Alleles↗
PubMed1994

Zoo animal welfare.

The history of zoo animal welfare legislation extends back to 1876, and is often tied to general animal welfare regulations. As knowledge and societal values have changed, so have the focus of zoos and the regulations governing them. Today, the issues involved in zoo animal welfare are complex and broad-based. Building on the basic welfare tenets of adequate feed, water, shelter, sanitation and veterinary care, current issues include the following: handling and training of captive animals, psychological well-being and environmental enrichment, enclosure design, species preservation, environmental and conservation issues, captive-breeding programmes. Complicating the matter further, government regulations try to assimilate all aspects of zoo animal welfare into the laws to provide humane care and handling for all species concerned. Zoo animal welfare will remain a challenging area, as increasing demands are placed on zoos and regulatory agencies to manage this diminishing resource.

Animal Husbandry↗
PubMed1996

Juridical and sociocultural problems on the definition of a law concerning property, usage and access to genetic resources in Colombia.

The property, usage, and access to genetic resources, is today one of the primary topics in international business, as a result of the strategic importance of the resources for the biotechnology industry. Internationally, the sovereignty that each country has over its natural patrimony is recognized. However, the new laws of international marketing have obligated countries in the process of development, such as Colombia, to adopt and copy a concept of intellectual property on living resources that does not have anything to do with the country's sociocultural identity, and sometimes even does not take into account its material enjoyment. The new juridical movement that treats genetic resources as private property produces a cultural conflict between indigenous populations, Afro-Americans and peasants, because for them the genetic resources are an element of community life. In these communities, knowledge is freely transmitted; it is an understanding that they have to conserve their agricultural customs and the relationship that they have with the environment. They do not recognize the term "property' according to patenting laws. These elements have to be considered, respected, and guaranteed in the laws that recognize the genetic resources in the country. On the other hand, not even countries that are pioneers in biotechnological development can adopt a concept about patents that is in agreement with the particularities that the living materials possess. This is obviously the reason for the numerous discussions on the legal interpretation, as well as complicated debates in court. Confronting that situation, there are countries rich in biodiversity, such as Colombia, but which do not have a proper concept and are not economically strong in the international context. These countries have to copy inadequate protection policies that do not take into account all their rights. This paper describes some of the technical, juridical, and sociocultural difficulties which Colombia has to confront, in order to set a guideline on patenting living organisms, and on the access and usage of the genetic resources.

Breeding↗
PubMed2006

Mating system in a low-density natural population of the dioecious wind-pollinated Patagonian cypress.

The mating system of a species is an essential factor that determines the genotypic frequencies of its populations in each generation. Thus, knowledge in this regard is important in the application of practical measures in conservation and forest tree breeding. Austrocedrus chilensis (D.DON) PIC. SER. ET BIZZARRI: is a member of the Cupressaceae native to the Andean-Patagonian Forest of Argentina and Chile with regional economic importance. It is a dioecious tree with pollen and seeds distributed by wind. Isozyme markers were utilized to study the mating system of this species through the survey of individual effective pollen clouds in a natural low-density population. If random mating occurs, effective pollen clouds that pollinate single seed trees are expected to be genetically homogeneous. The classical HardyWeinberg test of panmixia was also performed. Although it failed to reject random mating, the analysis of the pollen clouds showed that this mating pattern does not occur. Evidence of locally distributed heterogeneous pollen clouds is presented. The two methods are critically compared.

Alleles↗
PubMed2005

Cadaveric sperm induces intergeneric androgenesis in the fish, Hemigrammus caudovittatus.

Intergeneric androgenetic golden Buenos Aires tetra (BT), Hemigrammus caudovittatus was generated using sperm drawn from post-mortem males preserved at -20 degrees C for 10, 20, 30 and 40 days or fresh sperm to activate the UV-irradiated oocytes of black widow tetra (WT), Gymnocorymbus ternetzi. UV-irradiation (4.2 W/m(2)) of the oocytes for 3 min inactivated their nuclear genome. Fry hatched out from these activated oocytes were haploids; suffering haploid syndrome, they died before or within 48 h after hatching. Fresh BT sperm activated 95% oocytes; however, the sperm drawn from post-mortem males preserved at -20 degrees C for 60 (within glycerol packing) and 30 days (without glycerol packing) activated only 24 and 19% oocytes, respectively. Following activation, diploidy was restored by shocking the 25-min-old embryos at 41 degrees C for 2 min. Nuclear genomic inactivation of the oocytes was confirmed by (i) production of 100% haploids, (ii) karyotype and erythrocyte measurements, (iii) phenotypic markers, (iv) progeny testing and (v) species-specific marker. At hatching, survival of androgenotes decreased from 11% for those induced with fresh sperm to 4% for those generated using sperm from 30-day-old post-mortem males. Reproductive performance of the 'fresh' and 'cadaveric' F(0) and F(1) androgenetic males (Y(2)Y(2)) was superior to the control (X(1)Y(2)). Crosses involving homozygous (Y(2)Y(2)) 'fresh' F(0) androgenetic males with heterozygous females (X(1)X(2)) and F(0) homozygous males (Y(2)Y(2)) with females (X(2)X(2)) produced 2-4% unexpected female progenies. Paternal autosomes, inherited by the homozygous androgenetic female (X(2)X(2)), induced the production of female progenies in significantly less number of crosses than the crosses with heterozygous females (X(1)X(2)), which carried equal number of paternal and maternal autosomes. PCR analyses of the genomic DNA of normal male and unexpected F(1) and F(2) female progenies amplified by DMRT 1 specific primer produced bands of 237 and 300 bp length, and thereby confirmed that these unexpected females were genetic males. RAPD analyses of the androgenetic progenies showed that their genome was not contaminated with maternal genome.

Animals↗
PubMed2002

Enhancing the crops to feed the poor.

Solutions to the problem of how the developing world will meet its future food needs are broader than producing more food, although the successes of the 'Green Revolution' demonstrate the importance of technology in generating the growth in food output in the past. Despite these successes, the world still faces continuing vulnerability to food shortages. Given the necessary funding, it seems likely that conventional crop breeding, as well as emerging technologies based on molecular biology, genetic engineering and natural resource management, will continue to improve productivity in the coming decades.

Agriculture↗
PubMed2002

Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers.

The genetic structure of five types of Taihu pig (Erhualian, Middle Meishan, Small Meishan, Mizhu and Shawutou), Jiangquhai and Dongchuan pigs in China were investigated, by means of 27 microsatellite markers proposed by the Food and Agriculture Organisation, International Society for Animal Genetics (FAO-ISAG). The Hardy-Weinberg equilibrium test indicated that genetic drift had occurred in these populations, which may be caused by founder effects, intensive selection and close breeding. Genetic heterozygosity and the effective number of alleles per population were calculated, and showed that the genetic variability of the Jiangquhai pig was the largest, while the Small Meishan had the lowest. Genetic differentiation was within each population as shown by the fixation index (F(ST)=0.18). Both a neighbour-joining (NJ) tree constructed from Nei's standard genetic distance and principal component analysis based on allele frequencies can distinguish types of Taihu pig from the other two breeds. Among Taihu pig populations, Erhualian and Mizhu grouped into one branch, while Middle Meishan, Small Meishan and Shawutou clustered as another branch. By including previously published data on European pigs reported, we confirmed that Chinese indigenous pigs and European pigs have diverged into two distinct groups.

Alleles↗
PubMed2004

Breeding for high water-use efficiency.

There is a pressing need to improve the water-use efficiency of rain-fed and irrigated crop production. Breeding crop varieties with higher water-use efficiency is seen as providing part of the solution. Three key processes can be exploited in breeding for high water-use efficiency: (i) moving more of the available water through the crop rather than it being wasted as evaporation from the soil surface or drainage beyond the root zone or being left behind in the root zone at harvest; (ii) acquiring more carbon (biomass) in exchange for the water transpired by the crop, i.e. improving crop transpiration efficiency; (iii) partitioning more of the achieved biomass into the harvested product. The relative importance of any one of these processes will vary depending on how water availability varies during the crop cycle. However, these three processes are not independent. Targeting specific traits to improve one process may have detrimental effects on the other two, but there may also be positive interactions. Progress in breeding for improved water-use efficiency of rain-fed wheat is reviewed to illustrate the nature of some of these interactions and to highlight opportunities that may be exploited in other crops as well as potential pitfalls. For C3 species, measuring carbon isotope discrimination provides a powerful means of improving water-use efficiency of leaf gas exchange, but experience has shown that improvements in leaf-level water-use efficiency may not always translate into higher crop water-use efficiency or yield. In fact, the reverse has frequently been observed. Reasons for this are explored in some detail. Crop simulation modelling can be used to assess the likely impact on water-use efficiency and yield of changing the expression of traits of interest. Results of such simulations indicate that greater progress may be achieved by pyramiding traits so that potential negative effects of individual traits are neutralized. DNA-based selection techniques may assist in such a strategy.

Agriculture↗