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PubMed2003

Biodiversity of domestic livestock in the Republic of Yemen.

This paper describes the domestic livestock of the Republic of Yemen and aspires to complement earlier sources listing or partially describing 'breeds'. It attempts to cover all species and provide indications of production parameters through a literature review and via field observations made by the author in 1999. Information is provided on livestock numbers and the economic importance of animal production. Most animals are kept in sedentary mixed crop-livestock production systems; transhumant systems have the next greatest number of stock; with nomadic systems being of least and declining importance. Yemen's livestock appear to comprise at least 11 breeds of sheep, 5 breeds of goat, 2 breeds of cattle, 4 breeds of camel, 2 breeds of donkey and 1 breed of horse. There are no data on breeds of poultry but domestic fowl (where clearly considerable diversity exists) and pigeons are kept. There is little formal information on the history and relationships of most breeds. Some appear to be of ancient local origin, whereas others show affinities with those of neighbouring and other countries. None of the identified types is considered endangered, so conservation would be premature. A more formal and detailed genetic characterization, to add to the largely morphological and traditional classification, may, however, reveal such a need.

Agriculture↗
PubMed2004

Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags.

The polyploid nature of wheat is a key characteristic of the plant. Full-length complementary DNAs (cDNAs) provide essential information that can be used to annotate the genes and provide a functional analysis of these genes and their products. We constructed a full-length cDNA library derived from young spikelets of common wheat, and obtained 24056 expressed sequence tags (ESTs) from both ends of the cDNA clones. These ESTs were grouped into 3605 contigs using the phrap method, representing expressed loci from each of the three genomes. Using BLAST, 3605 contigs were grouped into 1902 gene clusters, showing that loci of the three genomes are not always expressed. A homology search of these gene clusters against a wheat EST database (15964 gene clusters) and a rice full-length cDNA database (21447 gene clusters) revealed that a quarter of the wheat full-length cDNAs were novel. A protein database of Arabidopsis was used to examine the functional classification of these gene clusters. The GC-content in the 5 -UTR region of wheat cDNAs was compared to that of rice. Forty-three genes (3.5% of wheat cDNAs homologous to those of rice) possessed distinct GC-content in the 5 -UTR region, suggesting different breeding behaviors of wheat and rice.

5' Untranslated Regions↗
PubMed1991

Juvenile-onset polyarthritis syndrome in Akitas.

Two young Akitas were examined because of manifestation of a juvenile-onset form of polyarthritis. A search of medical records at the New York State College of Veterinary Medicine found 6 more similarly affected Akitas. The clinical manifestations were marked by cyclic febrile illness and signs of profound joint-related pain. Two dogs had concurrent aseptic meningitis. The syndrome resembles juvenile rheumatoid arthritis in human beings, although it shares features with systemic lupus erythematosus. Pedigree analysis of affected Akitas supported a heritable component to the syndrome. Treatment with immunosuppressive drugs was effective in 2 dogs that achieved complete remission, and in 2 dogs that achieved only partial remission. Classification of this syndrome is difficult and may represent an "overlap" syndrome commonly described in human beings.

Animals↗
PubMed2026

Uncovering hub genes and key pathways responsive to drought stress in rice via meta-analysis of transcriptomic data.

Drought stress presents a formidable threat to global rice cultivation, triggering complex molecular responses that impact plant growth and productivity. To decipher the underlying gene expression dynamics, we performed a comprehensive meta-analysis of transcriptomic datasets derived from drought-tolerant rice genotypes. Via microarray data from three independent studies, we identified a set of consistently expressed differentially expressed genes (DEGs) under drought conditions. Integration of functional annotation tools, including GO and KEGG pathway enrichment, revealed key biological processes and signaling cascades involved in stress mitigation, such as ABA signaling, protein folding, and photosynthesis suppression. Protein-protein interaction (PPI) network construction, followed by hub gene identification via maximal clique centrality (MCC), highlighted pivotal regulators including LEA proteins, dehydrins, HSP70, and several transcription factors. Machine learning approaches further prioritize potential biomarkers, with Random Forest models achieving high classification accuracy and pinpointing key predictive genes. Chromosomal localization analysis provided spatial insights into the distribution of these hub genes, whose expression patterns were further compared against qRT-PCR data from previously published studies. This integrative approach identifies candidate genomic markers and mechanistic insights that may support future breeding strategies for drought-tolerant rice, pending experimental validation.

Cytoscape↗
PubMed2004

Stages and duration of spermatogenesis in the domestic ferret (Mustela putorius furo).

Classification of seminiferous tubules is the basis for understanding normal and abnormal spermatogenesis. The aim of the present study was to determine spermatogenic stages and the duration of the cycle in the domestic ferret using bromodeoxyuridine (BrdU) as a tracer. Eleven adult male ferrets that were maintained in a breeding condition were used. Testicular sections were stained with the periodic acid-Schiff reaction for light microscopy. To determine the cycle duration, six ferrets were injected intraperitoneally with BrdU, and testes were collected 3h later and 10 days and 3h later. BrdU was detected by immunohistochemistry. Seminiferous tubules were classified into eight stages, and frequencies of stages I-VIII were 10.6, 2.2, 7.9, 13.1, 22.3, 21.9, 14.0 and 8.0%, respectively. The most advanced BrdU-labeled cells at 3h post-injection were leptotene spermatocytes in stage VI and those at 10 days and 3h were pachytene spermatocytes in stage V. From differences in stage frequency and BrdU staining frequency between two time points, the duration of one cycle was estimated to be 13.0 days. The present observations indicate that stages and the cycle duration of the ferret spermatogenesis are similar to those reported in other carnivores.

Animals↗
PubMed2005

Spatial, temporal, and dietary determinants of organic contaminants in nestling tree swallows in Point Pelee National Park, Ontario, Canada.

Point Pelee National Park of Canada in southwestern Ontario, an important migratory route and vital breeding area for many birds, has localized areas of organochlorine (OC) pesticide contamination from agricultural production during the 1950s and 1960s. During 2001 and 2002, we investigated movement of persistent contaminants through the food web with the insectivorous tree swallow (Tachycineta bicolor) as a sentinel. The a priori site classifications, contaminated or reference, were based on soil residues of dichlorodiphenyltrichloroethane (DDT) and its breakdown products (sigmaDDT), dieldrin, and other OC pesticides. In 2001, all nestling tissue samples were pooled by site, and residue levels did not reflect the soil contaminant status. To improve sampling accuracy in 2002, tissue residues were determined from birds in individual nests. This showed OC pesticides to be higher in samples from contaminated sites compared with reference sites (p = 0.031). Polychlorinated biphenyls (PCBs), which were not detected in soil samples, were present in the nestlings and were not related to site of origin (p = 0.422). In 2002, dietary samples were collected from nestlings and identified to taxon, and representative insects collected from nesting sites were analyzed for PCBs and other OCs. Consumption of terrestrial prey was positively correlated with tissue residues of sigmaDDT (p = 0.006), whereas PCBs came from aquatic prey, Hexagenia mayflies (p = 0.003). Dietary details proved valuable in this study of contaminant transfer in insectivorous vertebrates.

Animals↗
PubMedDate not supplied

A review of canine inherited bleeding disorders: biochemical and molecular strategies for disease characterization and carrier detection.

Many different inherited bleeding disorders have been identified in dogs, defined on the basis of quantitative, functional, or structural defects in specific hemostatic proteins or pathways. Most of these disorders are caused by single-gene defects and biochemical assays provide an accurate measure of disease phenotype. Phenotypic disease classifications, however, are often genetically heterogeneous. Protein-based carrier detection assays are fast, inexpensive, and do not require specific identification of causative mutations. The limitations of these tests arise from variable "overlap" regions between carrier and clear dogs, influencing positive and negative predictive values of carrier detection tests within breed populations. Molecular diagnostic techniques enhance the accuracy of carrier detection, providing their clinical application takes into account the molecular heterogeneity underlying naturally occurring hemostatic defects in dogs.

Animals↗
PubMed2005

Developing indicators for European birds.

The global pledge to deliver 'a significant reduction in the current rate of biodiversity loss by 2010' is echoed in a number of regional and national level targets. There is broad consensus, however, that in the absence of conservation action, biodiversity will continue to be lost at a rate unprecedented in the recent era. Remarkably, we lack a basic system to measure progress towards these targets and, in particular, we lack standard measures of biodiversity and procedures to construct and assess summary statistics. Here, we develop a simple classification of biodiversity indicators to assist their development and clarify purpose. We use European birds, as example taxa, to show how robust indicators can be constructed and how they can be interpreted. We have developed statistical methods to calculate supranational, multi-species indices using population data from national annual breeding bird surveys in Europe. Skilled volunteers using standardized field methods undertake data collection where methods and survey designs differ slightly across countries. Survey plots tend to be widely distributed at a national level, covering many bird species and habitats with reasonable representation. National species' indices are calculated using log-linear regression, which allows for plot turnover. Supranational species' indices are constructed by combining the national species' indices weighted by national population sizes of each species. Supranational, multi-species indicators are calculated by averaging the resulting indices. We show that common farmland birds in Europe have declined steeply over the last two decades, whereas woodland birds have not. Evidence elsewhere shows that the main driver of farmland bird declines is increased agricultural intensification. We argue that the farmland bird indicator is a useful surrogate for trends in other elements of biodiversity in this habitat.

Animals↗
PubMed1990

Genetic analysis of population structure in marine teleosts around Japan.

Genetic differentiation and genetic variability were estimated from data on electrophoretically detectable isozymic loci in 12 species of marine teleosts belonging to 10 families of six orders, this study permitted conclusions concerning population structures within the species of marine teleosts. As a result the 12 species could be grouped into two classes, one of which showed higher genetic diversity and included the species inhabiting coastal areas; the other showed lower genetic diversity and included the species inhabiting offshore areas and spawning free pelagic eggs. Class I and Class II could be further divided into two groups (I-1 and I-2, and II-1 and II-2) on the basis of the level of average heterozygosity. Based on the above classification and ecological characteristics, the degree of genetic differentiation may be defined mainly by the level of mixing of eggs and by fry migration, and only to a small extent by adult migration between localities. The degree of average heterozygosity should be a measure of effective population size of the breeding units within the species but not of the whole species. Putting together the above facts, six types of population structure have been proposed for marine teleosts as follows: Species in type I-1 have formed some large populations with large breeding units in offshore areas; Type I-2-1, species have formed a large number of breeding populations with relatively large effective sizes of breeding units in the coastal areas or rivers where they were hatched, even though the species may have migrated over a wide pelagic area during their juvenile to adult stages. The species in type I-2-2 would have formed a number of local subpopulations with large to intermediate breeding units in the coastal areas they inhabit. Type I-2-3 species have formed two or more completely isolated local races (or subspecies) with relatively large breeding units, but with a low level of genetic differentiation within each local race. The species in Type II-1 would have formed a single large population consisting of a few breeding units with large effective sizes in offshore areas around Japan. Type II-2 species would have formed one large population consisting of a large number of breeding units with small effective sizes in wide offshore areas around Japan.

Alleles↗
PubMed1989

[Dermatophilus congolensis bovine dermatophilosis in the French West Indies. III. A comparison between infected and non-infected cattle].

The determination of the distinctive features between infected and uninfected cattle by Dermatophilus has been performed among 93 bovine stock in La Martinique, and 120 in La Guadeloupe and Saint-Martin Islands. Nearly half of the herds had been or were infected. Morbidity rates reach 33 per cent in La Martinique and 29 per cent in La Guadeloupe with a mortality ratio of 15 per cent and 5 per cent respectively. No frequency difference could be observed with respect to the season or the geographical area. Similarly, differences are little or nil as regards animal exposure toward aggressive factors such as sun, soil moisture, thorns, etc. On the other hand, the presence of Amblyomma variegatum is a determining factor considering the prevailing situation in La Martinique, where all breeds of cattle are sensitive to the disease. In this case, 63 per cent of the tick infested cattle develops dermatophilosis versus 2.5 per cent for the still uninfected animals. Conversely, in La Guadeloupe were Creole zebus are highly resistant (as a consequence of their natural selection), only 27 per cent of the infected stock suffers from this illness. In these two islands, regular dipping measures have proved to be beneficial in that it reduces the disease frequency. The study also reveals an underlying typology of the various rearing systems, thus allowing their classification as for their behaviour and response when meeting illness. In La Martinique, whatever they may be, quite none of them is infected in the tick free area. In the tick infested zones, the traditional small breeders rearing a sensitive cattle and who do not care with prophylactic rules, are mostly stricken, while more structured ones have succeeded in controlling the disease, owning to some appropriate measures together with a fair animal management. On the other hand, in La Guadeloupe where this tick is cosmopolitan, the small breeders who run a resistant Creole cattle, are not concerned, despite a rudimentary prophylactic behaviour. Conversely, the intensive rearing system, based upon improved imported breeds, meets great difficulties to master the infection.

Actinomycetales Infections↗
PubMed2006

Individual variation in the pup attraction call produced by female Australian fur seals during early lactation.

Otariid seals (fur seals and sea lions) are colonial breeders with large numbers of females giving birth on land during a synchronous breeding period. Once pups are born, females alternate between feeding their young ashore and foraging at sea. Upon return, both mother and pup must relocate each other and it is thought to be primarily facilitated by vocal recognition. Vocalizations of thirteen female Australian fur seals (Arctocephalus pusillus doriferus) were recorded during the breeding seasons of December 2000 and 2001, when pups are aged from newborns to one month. The pup attraction call was examined to determine whether females produce individually distinct calls which could be used by pups as a basis for vocal recognition. Potential for individual coding, discriminant function analysis (DFA), and classification and regression tree analysis were used to determine which call features were important in separating individuals. Using the results from all three analyses: F0, MIN F and DUR were considered important in separating individuals. In 76% of cases, the PAC was classified to the correct caller, using DFA, suggesting that there is sufficient stereotypy within individual calls, and sufficient variation between them, to enable vocal recognition by pups of this species.

Acoustics↗
PubMed2025

Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production.

Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.

Solanum tuberosum↗
PubMed1984

Helminth fauna of sandhill crane populations in Texas.

Three species of trematode [Orchipedium jolliei Schell, 1967; Prohyptiamus grusi Kocan, Waldrup, Ramakka, and Iverson, 1982; Echinostoma revolutum (Froelich, 1802)], three species of nematode (Tetrameres grusi Shumakovich, 1946; Synhimanthus sp.; Contracaecum sp.), and one species of cestode (Anomotaenia sp.) were recovered from 146 sandhill cranes, Grus canadensis (Linnaeus), collected in Alaska, Canada, and two areas in Texas. The only common and abundant species were O. jolliei and T grusi. Of cranes collected in Texas, those that came from the Canadian breeding grounds had significantly greater abundances of O. jolliei and T. grusi than those from Alaska. However, cluster analysis using rank abundances of helminth species across the four geographic regions and stepwise multiple discriminant analysis using the grouping variable of the presence or absence of a subspecies-specific pancreatic protein indicated that classification of cranes into populations based on helminth abundances was impractical as a management technique.

Alaska↗
PubMed2002

Repeat breeding in dairy heifers: follicular dynamics and estrous cycle characteristics in relation to sexual hormone patterns.

Repeat breeding occurs at an incidence of 10% in the Swedish dairy cow population. Evidence is available for a hormonal asynchrony around estrus in repeat-breeder heifers (RBH). This asynchrony seems to be the underlying cause for a series of dysfunctions such as prolonged standing estrus and delayed ovulation, leading to fertilization failure. For further determinations of repeat-breeder estrous cycle characteristics, seven strictly selected RBH and six virgin heifers (VH) were studied during 3-7 consecutive cycles, with particular attention paid to the estrous period. Follicular dynamics were studied by ultrasonography and related to estrous behavior and pattern of sexual hormones (progesterone, estradiol-17beta, and LH) in peripheral circulation. Mean group data were compared and a classification model was designed. The most prominent findings for RBH were prolonged duration of estrus, delayed LH peak, prolonged lifespan of the preovulatory follicle, and a late postovulatory rise in plasma progesterone. There was also a strong tendency for peri-ovulatory suprabasal progesterone levels in RBH. It is suspected that these deviations cause changes in the microenvironment of the preovulatory follicle, negatively affecting the final maturation of the oocyte. The heterogeneity of the RBH group underlines the multifactorial cause of the repeat-breeder syndrome. The VH formed a homogenous group with data varying within physiological limits. A classification model based on three characteristic variables managed to identify 81% of the VH and 79% of the RBH correctly. Results from this study propose that some heifers have general, consistent problems in synchronizing estrous events, displayed as varying symptoms in the course of consecutive estrous cycles. These subfertile animals could be classified as repeat-breeders.

Animals↗
PubMed2003

Simulation study of teat score in first-parity Gelbvieh cows: parameter estimation.

Teat scores from 9,598 first-parity Gelbvieh cows were used to investigate the adequacy of grouping approaches to decrease score misclassifications or inconsistencies as well as to simplify the data collection process. The procedure was tested using simulated data and then validated using teat score records of Gelbvieh cattle. First-parity cows were considered to be 4 yr of age or younger at first calving, did not have multiple records within 280 d, and were at least 50% Gelbvieh. Producers scored cows within 24 h of parturition. Teat score, a subjective measure of teat size, ranged from 0 (very large) to 50 (very small). A linear mixed model that included herd-year, month of calving, and age at calving as systematic effects; regression on the percentage of Gelbvieh; and additive breeding values (BV) and residual as random effects was used to generate the data. Simulated data were analyzed using one of three scoring methods: all values (S50), 10 classes (S10), and five classes (S5). The 10 classes were formed by subdividing every five scores into a single class starting at score zero. Similarly, the five classes were formed by combining every 10 scores into one class. The average Pearson correlations, based on five replicates, between the true and estimated BV (systematic effects) were 0.36 (0.85), 0.35 (0.89), and 0.32 (0.87) using S50, S10, and S5, respectively. Average correlations between estimated BV (systematic effects) were 0.97 (0.95), 0.89 (0.92), and 0.92 (0.97) based on S50 and S10, S50 and S5, and S10 and S5, respectively. Field data were used to validate the simulation procedure. The field data were categorized into 10 classes (F10) and five classes (F5) as described for the simulated data. Pearson correlations between estimated BV (systematic effects) were 0.99 (0.93), 0.93 (0.88), and 0.93 (0.96), based on F50 with F10, F50 with F5, and F10 with F5, respectively. The extremely high correlations between predicted BV based on S50, S10, S5, F50, F10, with F5 suggest that a simplified score classification method could be adopted without compromising the expected genetic progress for the trait under consideration. Furthermore, the difference in corresponding Pearson correlations across the field and simulated data might suggest the presence of some inconsistencies or misclassifications of the actual scoring system.

Animals↗
PubMed2002

Morphological, cytological and BSA-based testing on limited segregation population AFLPs.

Cytoplasmic male sterility (cms) in rye (Secale cereale L.), especially cytoplasma PAMPA, is used commercially in hybrid breeding programmes. The development of molecular markers that are tightly linked to the numerous genes coding for pollen fertility is expected to have great impact in the field. Morphological and cytological analyses of plants from a three-way cross C394: [(S67P/94 x S38/94) x CHD296] indicated the presence of at least several genes acting at different stages of pollen grain development, and proved the concurrence of both approaches in plant classification. The AFLP technique combined with the Bulk Segregant Analysis (BSA) were applied to identify DNA fragments linked to the genes of interest. All the 256 possible primer pair combinations based on the MseI and EcoRI restriction sites generated distinct band patterns allowing the identification of 31143 DNA fragments, visualised using the isotopic method. On average, any given primer combination generated 122 fragments. Among 1111 and 431 potential genetic markers respectively identified in the restorer form and the maternal lines, 775 and 295 were present in the F2 population. These numbers were then reduced to 109 and 51. The identified DNA fragments were tested on a limited segregating population, C394-F2, in order to eliminate false signals and to select markers for a future marker-assisted selection programme. Twenty-five markers were selected. Four of these markers were not identified via the BSA approach, indicating that if a highly polymorphic component is used for a cross, or a polygenic trait is studied, then the use of a limited population may be required.

Breeding↗
PubMed2005

Errors in development of fetuses and placentas from in vitro-produced bovine embryos.

In vitro systems for oocyte maturation, fertilization and embryo culture [in vitro production (IVP)] have the potential for more wide-spread use in creative breeding programs for dairy and beef cattle. However, one negative consequence of both IVP and somatic cell nuclear transfer (SCNT) in cattle and other species is that embryos, fetuses, placentas, and offspring can differ significantly in morphology and developmental competence compared with those from embryos produced in vivo. Fetuses and placentas derived from IVP and SCNT embryos may fall within the normal range of development, may have obvious abnormalities such as increased fetal and placental weights, or may have subtle abnormalities such as aberrant development of fetal skeletal muscle, placental blood vessels, and altered metabolism. Failures in physiologic and/or genetic mechanisms essential for proper fetal growth and survival outside of the uterus contribute significantly to pregnancy and neonatal losses. Oversized fetuses are at increased risk of death during parturition and the adverse consequences of severe dystocia may compromise the dam. Collectively, these abnormalities have been referred to as 'large offspring syndrome' or 'large calf syndrome'. Abnormal phenotypes resulting from IVP and SCNT embryos are stochastic in occurrence and they have not been consistently linked to aberrant expression of single genes or specific pathophysiology. Thus, reliable methods of early diagnosis of the condition are not yet available. The objective of this paper is to examine abnormal development of fetuses and placentas resulting from embryos produced using in vitro systems. The term 'abnormal offspring syndrome (AOS)' is introduced and a classification system of developmental outcomes is proposed to facilitate research efforts on the mechanisms of the various abnormal phenotypes. We also discuss potential genetic and physiologic mechanisms that may contribute to abnormal phenotypes following transfer of IVP and SCNT embryos.

Animals↗
PubMed2006

Success at first insemination in Australian Angus cattle: analysis of uncertain binary responses.

Field data from Australian Angus herds were used to investigate 2 methods of analyzing uncertain binary responses for success or failure at first insemination. A linear mixed model that included herd, year, and month of mating as fixed effects; unrelated service sire, additive animal, and residual as random effects; and linear and quadratic effects of age at mating as covariates was used to analyze binary data. An average gestation length (GL) derived from artificial insemination data was used to assign an insemination date to females mated to natural service sires. Females that deviated from this average GL led to uncertain binary responses. Two analyses were carried out: 1) a threshold model fitted to uncertain binary data, ignoring uncertainty (M1); and 2) a threshold model fitted to uncertain binary data, accounting for uncertainty via fuzzy logic classification (M2). There was practically no difference between point estimates obtained from M1 and M2 for service sire and herd variance; however, when uncertain binary data were analyzed ignoring uncertainty (M1), additive variance and heritability estimates were greater than with M2. Pearson correlations indicated that no major reranking would be expected for service sire effects and animal breeding values using M1 and M2. Given the results of the current study, a threshold model contemplating uncertainty is suggested for noisy binary data to avoid bias when estimating genetic parameters.

Animals↗