In this paper the genetic relationships between major reproductive traits in beef cattle (Calving... more In this paper the genetic relationships between major reproductive traits in beef cattle (Calving Date, Calving Interval and Age at First Calving) and type traits have been estimated to evaluate the usefulness of type classification in predicting reproductive performance in beef cattle. We estimated favourable genetic correlations between Calving Interval and type traits ranging from 2 0.027 to 2 0.297. However, type traits and Calving Date appear to be genetically independent and the genetic relationships between Age at First Calving and type traits are, in general, non-favourable. Genetic correlations between type traits and Calving Date ranged from 0.0 to -0.125. Genetic correlations between Age at First Calving and Final Score, Body Depth and Tight Development were, respectively, 0.399, 0.445 and 0.447. Our results suggest that the possibility of using type classification to construct an index to improve reproductive performance is little. The more reliable possibility to build a possible selection index comprising type classification and reproductive performance would be based on Age at First Calving. Type classification at first calving could help to increase the information to select dams to stay on the farm in subsequent calvings on the basis of their expected performance.
In this paper a methodology is developed to improve the design and implementation of a linear mor... more In this paper a methodology is developed to improve the design and implementation of a linear morphological system in beef cattle using artificial intelligence. The proposed process involves an iterative mechanism where type traits are successively defined and computationally represented using knowledge engineering methodologies, scored by a set of trained human experts and finally, analysed by means of four reputed machine learning algorithms. The results thus achieved serve as feed back to the next iteration in order to improve the accuracy and efficacy of the proposed assessment system. A sample of 260 conformation records of the Asturiana de los Valles beef cattle breed is shown to illustrate the methodology. Three sources of inconsistency were detected: (a) the existence of different interpretations of the trait's definition, increasing the subjectivity of the assessment; (b) the narrow range of variation of some of the anatomical traits assessed; (c) the inclusion of some complex traits in the assessment system. In this sense, the reopening of the evaluated Asturiana de los Valles assessment system is recommended. In spite of the difficulty of collecting data from live animals, further implications of the artificial intelligence systems on morphological assessment are pointed out.
Despite a number of recent studies that have focused on the origin of domestic horses, genetic re... more Despite a number of recent studies that have focused on the origin of domestic horses, genetic relationships between major geographical clusters still remain poorly understood. In this study we analyzed a 296 bp mtDNA fragment from the HVI region of 171 horses representing 11 native Iberian, Barb, and Exmoor breeds to assess the maternal phylogeography of Iberian horses. The mtDNA haplogroup with a CCG motif (nucleotide position 15,494 to 15,496) was the most frequent in Iberian and Barb breeds (0.42 and 0.57, respectively), regardless of geographic location or group of breeds. This finding supports the close genetic relationship between the ancestral mare populations of the Iberian Peninsula and Northern Africa. Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Our results also suggest that Northern Iberian ponies-which are phenotypically close to British ponies, especially Exmoor-are the result of an introgression rather than population replacement.
The validity of the official SEUROP bovine carcass classification to grade light carcasses by mea... more The validity of the official SEUROP bovine carcass classification to grade light carcasses by means of three well reputed Artificial Intelligence algorithms has been tested to assess possible differences in the behavior of the classifiers in affecting the repeatability of grading. We used two training sets consisting of 65 and 162 examples respectively of light and standard carcass classifications, including up to 28 different attributes describing carcass conformation. We found that the behavior of the classifiers is different when they are dealing with a light or a standard carcass. Classifiers follow SEUROP rules more rigorously when they grade standard carcasses using attributes characterizing carcass profiles and muscular development. However, when they grade light carcasses, they include attributes characterizing body size or skeletal development. A reconsideration of the SEUROP classification system for light carcasses may be recommended to clarify and standardize this specific beef market in the European Union. In addition, since conformation of light and standard carcasses can be considered different traits, this could affect sire evaluation programs to improve carcass conformation scores from data from markets presenting a great variety of ages and weights of slaughtered animals. #
Although many research papers have studied diversity and differentiation within livestock species... more Although many research papers have studied diversity and differentiation within livestock species, genetic relationships among neighboring populations remain poorly understood. Here we apply recent methodologies to analyze the polymorphism of 14 microsatellites in 238 unrelated individuals belonging to six sheep breeds from Northern Spain to ascertain their historical relationships and the relative genetic contributions existing between populations. Individual genotypes were analyzed to assess the existence of an underlying genetic structure. Long-term and recent migration rates were estimated to identify patterns of relative genetic contribution among breeds. The complete data
Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic... more Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic variability and as a useful tool for conservation purposes. Using simulated data, molecular coancestry has been shown to become constant very quickly after separation of populations, leading to population diversity remaining constant. However, the use of molecular coancestry information to study the genetic relationships between breeds has not yet been widely explored. Here we analyze the polymorphism of 14 microsatellites in 222 unrelated individuals belonging to seven native Spanish breeds to ascertain the usefulness of molecular coancestry-based methodologies in providing information on their genetic relationships. Average kinship distance (D k ) and average molecular coancestry coefficients (f ij ) were compared with well-known genetic dis-
The aim of this work is to highlight the need of monitoring small populations to conserve their g... more The aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under-represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices.
In this paper the genetic relationships between major reproductive traits in beef cattle (Calving... more In this paper the genetic relationships between major reproductive traits in beef cattle (Calving Date, Calving Interval and Age at First Calving) and type traits have been estimated to evaluate the usefulness of type classification in predicting reproductive performance in beef cattle. We estimated favourable genetic correlations between Calving Interval and type traits ranging from 2 0.027 to 2 0.297. However, type traits and Calving Date appear to be genetically independent and the genetic relationships between Age at First Calving and type traits are, in general, non-favourable. Genetic correlations between type traits and Calving Date ranged from 0.0 to -0.125. Genetic correlations between Age at First Calving and Final Score, Body Depth and Tight Development were, respectively, 0.399, 0.445 and 0.447. Our results suggest that the possibility of using type classification to construct an index to improve reproductive performance is little. The more reliable possibility to build a possible selection index comprising type classification and reproductive performance would be based on Age at First Calving. Type classification at first calving could help to increase the information to select dams to stay on the farm in subsequent calvings on the basis of their expected performance.
In this paper a methodology is developed to improve the design and implementation of a linear mor... more In this paper a methodology is developed to improve the design and implementation of a linear morphological system in beef cattle using artificial intelligence. The proposed process involves an iterative mechanism where type traits are successively defined and computationally represented using knowledge engineering methodologies, scored by a set of trained human experts and finally, analysed by means of four reputed machine learning algorithms. The results thus achieved serve as feed back to the next iteration in order to improve the accuracy and efficacy of the proposed assessment system. A sample of 260 conformation records of the Asturiana de los Valles beef cattle breed is shown to illustrate the methodology. Three sources of inconsistency were detected: (a) the existence of different interpretations of the trait's definition, increasing the subjectivity of the assessment; (b) the narrow range of variation of some of the anatomical traits assessed; (c) the inclusion of some complex traits in the assessment system. In this sense, the reopening of the evaluated Asturiana de los Valles assessment system is recommended. In spite of the difficulty of collecting data from live animals, further implications of the artificial intelligence systems on morphological assessment are pointed out.
Despite a number of recent studies that have focused on the origin of domestic horses, genetic re... more Despite a number of recent studies that have focused on the origin of domestic horses, genetic relationships between major geographical clusters still remain poorly understood. In this study we analyzed a 296 bp mtDNA fragment from the HVI region of 171 horses representing 11 native Iberian, Barb, and Exmoor breeds to assess the maternal phylogeography of Iberian horses. The mtDNA haplogroup with a CCG motif (nucleotide position 15,494 to 15,496) was the most frequent in Iberian and Barb breeds (0.42 and 0.57, respectively), regardless of geographic location or group of breeds. This finding supports the close genetic relationship between the ancestral mare populations of the Iberian Peninsula and Northern Africa. Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Our results also suggest that Northern Iberian ponies-which are phenotypically close to British ponies, especially Exmoor-are the result of an introgression rather than population replacement.
The validity of the official SEUROP bovine carcass classification to grade light carcasses by mea... more The validity of the official SEUROP bovine carcass classification to grade light carcasses by means of three well reputed Artificial Intelligence algorithms has been tested to assess possible differences in the behavior of the classifiers in affecting the repeatability of grading. We used two training sets consisting of 65 and 162 examples respectively of light and standard carcass classifications, including up to 28 different attributes describing carcass conformation. We found that the behavior of the classifiers is different when they are dealing with a light or a standard carcass. Classifiers follow SEUROP rules more rigorously when they grade standard carcasses using attributes characterizing carcass profiles and muscular development. However, when they grade light carcasses, they include attributes characterizing body size or skeletal development. A reconsideration of the SEUROP classification system for light carcasses may be recommended to clarify and standardize this specific beef market in the European Union. In addition, since conformation of light and standard carcasses can be considered different traits, this could affect sire evaluation programs to improve carcass conformation scores from data from markets presenting a great variety of ages and weights of slaughtered animals. #
Although many research papers have studied diversity and differentiation within livestock species... more Although many research papers have studied diversity and differentiation within livestock species, genetic relationships among neighboring populations remain poorly understood. Here we apply recent methodologies to analyze the polymorphism of 14 microsatellites in 238 unrelated individuals belonging to six sheep breeds from Northern Spain to ascertain their historical relationships and the relative genetic contributions existing between populations. Individual genotypes were analyzed to assess the existence of an underlying genetic structure. Long-term and recent migration rates were estimated to identify patterns of relative genetic contribution among breeds. The complete data
Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic... more Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic variability and as a useful tool for conservation purposes. Using simulated data, molecular coancestry has been shown to become constant very quickly after separation of populations, leading to population diversity remaining constant. However, the use of molecular coancestry information to study the genetic relationships between breeds has not yet been widely explored. Here we analyze the polymorphism of 14 microsatellites in 222 unrelated individuals belonging to seven native Spanish breeds to ascertain the usefulness of molecular coancestry-based methodologies in providing information on their genetic relationships. Average kinship distance (D k ) and average molecular coancestry coefficients (f ij ) were compared with well-known genetic dis-
The aim of this work is to highlight the need of monitoring small populations to conserve their g... more The aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under-represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices.
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Papers by Isabel Alvarez