Search

Objective: The main objective of this study was to develop a pipeline to detect phenogenomic introgression across different multivariety breeds and to validate such classification focusing on external egg and hatchability-related traits using a discriminant canonical analysis approach. Methods: For this, 1,368 eggs belonging a flock of 94 endangered Spanish autochthonous breed breeding hens (Andalusian Tufted, Blue Andalusian, Spanish White-Faced, and Utrerana) and a control outgroup comprising 32 eggs belonging to 4 Araucana hens were considered. Multicollinearity analysis of hatchability-related traits revealed embryonic mortality, embryonic mortality in the second stage of incubation, viable hatching chick, major diameter, and minor diameter should be discarded from the analysis (variance inflation factor =5) given they did not significantly contribute to variability explanation potential of the discriminant model. Results: A stepwise discriminant canonical analysis was developed and egg weight, shape index, hatchability, and fertility variables reported the highest discriminant power (Wilks' Lambda values of 0.7861, 0.7871, 0.8076, and 0.9457, respectively). The first two functions explained 85.25% intergroup variability. Interbreed and varieties proximity was evaluated using Mahalanobis distances representation and data mining cross-validation allowed to detect genetic introgression between different genotypes. Conclusion: Easily collectable traits as egg weight and shape index must be considered for the development of breeding programs as a measure to ensure breed protection. The model may be translatable to other endangered breeds to optimize avian breeds conservation plans worldwide. [ABSTRACT FROM AUTHOR]

This study is aimed to define the effect of season on internal turkey eggs produced in backyard systems. To this goal, a total of 197 turkey eggs from Andalusian hens were continuously collected throughout 15 months to study internal quality attributes. A discriminant canonical analysis was performed considering season as the dependent variable and these quality attributes as independent variables. Yolk weight was discarded from analysis due to multicollinearity problems (VIF > 5), and then, statistically explanatory variables were obtained (p <.05). All colour yolk traits, including yolk colorimetric (lightness, redness and yellowness axes) and DSM® fan performed as discriminating variables. Moreover, the yield of egg components (yolk diameter and albumen weight) and almost every shell trait (shell strength, thickness and resistance area) were powerful explanatory variables as well. Albumen height and pH were reported explanatory variables, but possibly due to the effect of the environment from laying to egg collection. Results obtained show a great adaptation of this genotype to its traditional environment and rearing conditions. This study provides the first description of the effect of season on internal food quality attributes of turkey eggs and would provide a better understanding of egg production in organic-like systems. Moreover, the results of this study represent a step forward in the procedures for the institutional recognition of the breed. Highlights: Internal egg quality attributes in turkey species vary throughout seasons and serve as explanatory variables in the discriminant canonical analysis. Eggs laid in different seasons can be successfully classified attending to the variance of their internal egg characteristics. Yolk colour attributes, particularly yolk yellowness (b*), showed great explanatory properties, which evidences different trends in pasture availability and consumption during the year. General internal quality did not decline during the summer, which evidences the great adaptation of the Andalusian turkey breed to its environment. Effects of climate change are visible in egg quality in organic-like rearing systems. [ABSTRACT FROM AUTHOR]

Extant diversity for phenotypic traits is an essential criterion to be considered when ordering priorities for conservation and improvement of animal genetic resources. Concretely, the characterisation of the distinctive body morphometry of a particular group of animals can aid in the design of selective breeding programs, given the strong correlation between body morphology and productive function. The present research aims to characterise an endangered autochthonous camel breed (Canarian camel), mainly relegated to leisure riding, for its body morphology, with a double objective: to explore the phenotypic diversity and structure of the breed for zoometric traits and assess the zoometric profile of this genetic resource that supports its differentiation from other camel breeds. Overall, the results highlight the existence of a high degree of diversity, which may be linked to genetic factors for zoometric traits in an endangered autochthonous breed with traditional in situ breeding schemes, which predicts the success of the implementation of genetic improvement schemes for such functional characteristics. This phenotypic diversity in body morphology could also be a tool for the evaluation of new functional niches within the efforts of functional valorisation of this camel breed for its sustainable conservation. Body morphology traits in the studied camel breed are significantly influenced by sex, physiological status and coat colour. [ABSTRACT FROM AUTHOR]

This study aimed to develop a tool for predicting the potential impact of research studies involving the effect of antioxidants in rooster semen freezing diluent, depending on the variables that have been studied. To achieve this, a comprehensive meta-analysis of fifty-eight research documents was performed. Sixty-two traits were sorted into four major categories: study demographics, study design-related parameters, rooster semen quality-related parameters, and fertility level indicators. The quartile determination of each research document was collected from the Journal Citation Reports database. After twenty-five testing rounds, all variables that showed multicollinearity problems were discarded from further analyses (VIF < 5). HOST, pellet volume, mass motility, light hours, and sperm concentration were the most influential traits for the classification of papers in different quartiles (Wilks' lambda: 0.797, 0.891, 0.895, 0.896, and 0.904, respectively). The research was validated as reported in the cross-validation analysis, with 93.60% of papers being correctly classified within their group. The present research assists researchers not only in the decision-making process for journals in which to publish the outcomes of their studies, but also to seek for the inclusion of parameters which attract a wider interest for the matter from scientific readers. This leads to the optimisation of resources in studies evaluating the effect of antioxidants in poultry reproduction by identifying the most scientifically relevant variables and those which in trun will lead toa greater impact on research publications. HIGHLIGHTS: Using the discriminant canonical analysis, the scientific community can know which variables to take into account to achieve a greater impact in the cryopreservation studies of rooster sperm. The study of membrane functionality (HOST) could be a surrogate for in vivo fertility assessment as it predicts the survival rate of spermatozoa in the female reproductive tract. Pellet volume, mass motility, light hours for sperm-donor animals, and semen concentration have a higher discriminatory capacity for studies in different quartiles of the JCR database. [ABSTRACT FROM AUTHOR]

Simple Summary: The standardization of the poultry semen cryopreservation technique is necessary for the conservation of genetic resources; however, during this process, a series of cellular lesions are generated as a consequence of the increase in reactive oxygen species (ROS). The objective of the present study is to determine which antioxidants are most commonly used in roosters to mitigate this effect after their addition to the cryopreservation diluent by studying different characteristics of seminal quality. A discriminant canonical analysis (DCA) was performed, and the variables hypo-osmotic swelling test (HOST), viability, and total motility were reported to be the ones that provided the most information, as they were the most discriminant variables between groups. According to the descriptive statistics, antioxidants catalase and serine were the ones that gave the best results in most of the variables studied. In conclusion, given that catalase had the most beneficial effects on the seminal quality parameters that proved to have the greatest discriminating power, this antioxidant could be the one of choice. The standardization of the semen cryopreservation technique could be an effective tool in poultry for the conservation of genetic resources. During this process, the production of reactive oxygen species increases, leading to oxidative stress that causes damage to the spermatozoa. To reduce this effect, the addition of exogenous antioxidants in the cryopreservation diluent has been reported to be effective. Multiple antioxidants such as catalase, vitamin E, cysteamine, ergothioneine, and serine have been studied in roosters. Therefore, the present investigation aims to perform a meta-analysis to determine if the use of the aforementioned antioxidants added to the cryopreservation extender produces an improvement in semen quality parameters in roosters after thawing. After collecting the data, a discriminant canonical analysis was performed to determine which of the selected semen quality traits provided the most information, with hypo-osmotic swelling test (HOST), viability, and total motility variables showing the highest discriminatory power. However, according to the descriptive statistics, catalase and serine are the antioxidants that improve a greater number of seminal quality parameters, and since catalase gives the most favorable results for most of the discriminating variables, it could be the antioxidant of choice. [ABSTRACT FROM AUTHOR]

Sperm cryopreservation is a fundamental tool for the conservation of avian genetic resources; however, avian spermatozoa are susceptible to this process. To cope with the high production of reactive oxygen species (ROS), the addition of exogenous antioxidants is beneficial. Pectoliv30 is a substance derived from alperujo, and in this study, its effect was analyzed on seminal quality after its addition to the cryopreservation extender of roosters at different concentrations. For this purpose, 16 Utrerana breed roosters were used, and seminal collection was performed in six replicates, creating a pool for each working day with ejaculates of quality. After cryopreservation, one sample per treatment and replicate was thawed, and several seminal quality parameters were evaluated. Statistical analysis revealed numerous correlations between these variables, both positive and negative according to the correlation matrix obtained. Furthermore, the chi-squared automatic interaction detection (CHAID) decision tree (DT) reported significant differences in the hypo-osmotic swelling test (HOST) variable between groups. Moreover, results for this parameter were more desirable at high concentrations of Pectoliv30. The application of this substance extracted from the by-product alperujo as an antioxidant allows the improvement of the post-thawing seminal quality in roosters and facilitates optimization of the cryopreservation process as a way to improve the conservation programs of different endangered poultry breeds. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: Currently, research on livestock production suffers from isolation from other disciplines and a generalist nature, which makes publishing in top-tier journals a very difficult task. This situation is even more drastic when it comes to turkey meat research, which is an underdeveloped area that has historically suffered from a lack of resources compared to other species. For this reason, the aim of the present study is to develop a tool that allows researchers to determine which carcass and meat quality traits are related to increased interest by the scientific community and the quality standards of the journals in which studies are published. Variables improving journal standards include carcass dressing traits, muscle fibers properties, pH, colorimetry, some texture and water captivity traits, and chemical composition. Contrarily, carcass or piece yield is not a recommended variable to be performed in studies, as this parameter did not show a clear impact on publication quality. Finally, measures after 72 h are contraindicated since they showed a correlation with poor journal quality standards. Thus, this work can be used as a guideline for designing turkey carcass and meat quality studies, describing parameters to prioritize in order to maximize the impact quality of publication in the scientific community. The present research aims to describe how turkey meat and carcass quality traits define the interest of the scientific community through the quality standards of journals in which studies are published. To this end, an analysis of 92 research documents addressing the study of turkey carcass and meat quality over the last 57 years was performed. Meat and carcass quality attributes were dependent variables and included traits related to carcass dressing, muscle fiber, pH, colorimetry, water-holding capacity, texture, and chemical composition. The independent variables comprised publication quality traits, including journal indexation, database, journal impact factor (JIF), quartile, publication area, and JIF percentage. For each dependent variable, a data-mining chi-squared automatic interaction detection (CHAID) decision tree was developed. Carcass or piece yield was the only variable that did not show an impact on the publication quality. Moreover, color and pH measurements taken at 72 h postmortem showed a negative impact on publication interest. On the other hand, variables including water-retaining attributes, colorimetry, pH, chemical composition, and shear force traits stood out among the quality-enhancing variables due to their low inclusion in papers, while high standards improved power. [ABSTRACT FROM AUTHOR]

Introduction: Various climatological and lunar cycle parameters have a direct impact on animal reproduction, and in the case of the avian species, spermatozoa are extremely sensitive to heat stress. These parameters could influence sperm freezability, which will ultimately affect post-thawing semen quality, being sperm motility in roosters a relevant indicator of this quality as it is highly related to fertility. Therefore, the objective of the present study is to determine which are the climatological and lunar cycle parameters that have a greater effect on sperm freezability in roosters. Methods: Sperm was obtained from 16 Utrerana breed roosters and a total of 27 replicates were performed. A pool was made with those ejaculates that met the minimum quality criteria for each replicate, and four freezing-thawing samples per replicate were analyzed. The straws were thawed, and sperm motility was evaluated, classifying the results obtained into four seminal quality groups according to the guidelines of the Food and Agriculture Organization of the United Nations (Group 1: Good, Group 2: Satisfactory, Group 3: Acceptable but undesirable and Group 4: Unsatisfactory). The following traits were recorded for each day of semen collection: maximum temperature, minimum temperature, maximum barometric pressure, minimum barometric pressure, maximum gust, wind direction, mean wind speed, sunshine hours, rainfall, moon phase, and percentage of illuminated lunar surface over the total area. Results: A discriminant canonical analysis was performed to determine which of these parameters offered the most information when classifying an ejaculate in each quality group, with minimum temperature, the new moon as moon phase, minimum barometric pressure, and rainfall being the most significant variables. Discussion: According to the results obtained, semen quality decreases when temperature and precipitation are lower, pressure is higher, and when there is a new moon phase. Therefore, these environmental conditions should be avoided for sperm collection and processing. [ABSTRACT FROM AUTHOR]

Simple Summary: This study reveals a significant decline in the Black Andalusian cattle breed population due to agricultural changes and foreign breed introductions, leading to smaller herds and a shift in the male-to-female ratio. Although inbreeding rates are low, there is concern over assortative mating. Key ancestors influence genetic diversity, with variations in population size and geographic subpopulations. Historical transhumance routes, notably the Cañadas Reales, impact genetic connections. Conservation efforts, including breed association initiatives, have increased registrations, but challenges persist, requiring genealogical registration, targeted breeding, and collaborative efforts. Monitoring and adjusting selection practices are crucial to maintaining genetic diversity. Continued proactive measures are essential for conserving the Black Andalusian breed's genetic viability, acknowledging historical factors, and addressing contemporary challenges. This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity. [ABSTRACT FROM AUTHOR]

The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy–Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied. [ABSTRACT FROM AUTHOR]

Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, with 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with nongame chickens. Particularly noteworthy is a variant in an intron of the isoprenoid synthase domain containing gene (ISPD), an extreme outlier present at a frequency of 89% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.