I. Álvarez

Genetic relationships between calving date, calving interval, age at first calving and type traits in beef cattle

Abstract 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 −0.027 to −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.

Differences in the expression of the ASIP gene are involved in the recessive black coat colour pattern in sheep: evidence from the rare Xalda sheep breed

Here we have tested the hypothesis of association between different levels of agouti signalling peptide (ASIP) mRNA and the recessive black coat colour in the rare Xalda breed of sheep. To deal with this task, we first tested the possible action of both the dominant black extension allele (E(D)) and a 5-bp deletion (X99692:c.100_104del; A(del)) in the ovine ASIP coding sequence on the black coat colour pattern in 188 Xalda individuals. The E(D) allele was not present in the sample and only 11 individuals were homozygous for the A(del)ASIP allele. All Xalda individuals carrying the A(del)/A(del) genotype were phenotypically black. However, most black-coated individuals (109 out of 120) were not homozygous for the 5-bp deletion, thus rejecting the A(del)/A(del) genotype as the sole cause of recessive black coat colour in sheep. Differences in expression of ASIP mRNA were assessed via RT-PCR in 14 black-coated and 10 white-coated Xalda individuals showing different ASIP genotypes (A(wt)/A(wt), A(wt)/A(del) and A(del)/A(del)). Levels of expression in black animals were significantly (P < 0.0001) lower than those assessed for white-coated individuals. However, the ASIP genotype did not influence the ASIP mRNA level of expression. The consistency of these findings with those recently reported in humans is discussed, and the need to isolate the promoter region of ovine ASIP to obtain further evidence for a role of ASIP in recessive black ovine pigmentation is pointed out.

Genetic analysis of calf survival at different preweaning ages in beef cattle

a ´´ SERIDA-CENSYRA-Somio, C/Camino de los Claveles 604, E-33203 Gijon, Asturias, Spain b ´ Abstract The aim of this paper is to assess the suitability of including calf survival traits in the breeding objective of beef cattle improvement programs. To do so, we analysed the genetic parameters affecting calf survival during the perinatal period (PS), between the perinatal period and weaning (LM) and at weaning (WS) using Asturiana de los Valles breed field data. Up to 36 125 calf survival records were used in the analysis. Heritabilities estimated for the direct effect ranged from 0.033 to 0.084 for PS, from 0.011 to 0.112 for LM and from 0.039 to 0.142 for WS. Our results suggest that LM is not affected by a maternal genetic component, whereas its effect is slight and similar in magnitude for both PS and WS. In general, the analysed traits are affected by a slight maternal permanent environmental effect ranging from 1 to 2%. PS and WS seem to be consistently determined by the same genes, presenting genetic correlations between the respective direct or maternal genetic effects of 0.95 and 1.0. Genetic correlation between the direct effects affecting PS and LM was 0.745. Current analyses show that WS has a higher genetic variability than would justify the inclusion of calf survival at weaning in the beef cattle breeding objective.  2003 Elsevier B.V. All rights reserved.

The usefulness of artificial intelligence techniques to assess subjective quality of products in the food industry

In this paper we advocate the application of Artificial Intelligence techniques to quality assessment of food products. Machine Learning algorithms can help us to: (a) extract operative human knowledge from a set of examples; (b) conclude interpretable rules for classifying samples regardless of the non-linearity of the human behaviour or process; and (c) help us to ascertain the degree of influence of each objective attribute of the assessed food on the final decision of an expert. We illustrate these topics with an example of how it is possible to clone the behaviour of bovine carcass classifiers, leading to possible further industrial applications.

Microsatellite analysis characterizes Burkina Faso as a genetic contact zone between Sahelian and Djallonke sheep.

A total of 123 sheep belonging to the Djallonké, Mossi, and Burkina-Sahel breeds, along with 41 Spanish Xalda sheep were genotyped for 27 microsatellites. The pair Djallonké-Mossi had the highest between breeds molecular coancestry. Admixture analysis informed on the parental role of the Burkina-Sahel and Djallonké breeds. The Mossi breed was a hybrid population nearer to the Djallonké breed. Only half of the Mossi individuals were correctly assigned to their breed. The Burkina-Sahel and Djallonké breeds can be considered ancestrally different genetic entities. Differentiation between the Djallonké and Mossi breeds may be due to introgression of Sahelian sheep.

Artificial intelligence techniques point out differences in classification performance between light and standard bovine carcasses

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.

Using artificial intelligence to design and implement a morphological assessment system in beef cattle

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.

Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goat.

To date, no comprehensive study has been performed on mitochondrial genetic diversity of the West African goat. Here, we analysed a 481-bp fragment of the HVI region of 111 goats representing four native West African populations, namely the three main Burkina Faso breeds, zoo-farm kept Dwarf goats and endangered Spanish goat breeds used as the outgroup. Analyses gave 83 different haplotypes with 102 variable sites. Most haplotypes (65) were unique. Only three haplotypes were shared between populations. Haplotypes were assigned to cluster A except for H45 (belonging to the Spanish Bermeya goat) which was assigned to cluster C. amova analysis showed that divergence between groups (Phi(CT)) was not statistically significant regardless of whether the partition in two hierarchical levels that was fitted included Spanish samples or not. The West African goat scenario shown here is consistent with that previously reported for the species: haplogroup A is predominant and has a very high haplotype diversity regardless of the geographic area or sampled breed. The large phenotypic differences observable between the West African Dwarf and Sahelian long-legged goat populations are not detectable with mitochondrial markers. Moreover, a previously suggested introgression of Sahelian goat southwards because of desertification could not be assessed using mtDNA information.

Quantifying diversity losses due to selection for scrapie resistance in three endangered Spanish sheep breeds using microsatellite information.

The effect of selection for scrapie resistance on genetic variability in three endangered Spanish sheep breeds (Colmenareña, Mallorquina and Rubia de El Molar) was studied using two different criteria for quantifying contributions to genetic variability: (a) molecular coancestry or genetic identity; and (b) average number of alleles per locus or allelic richness. A total of 236 (81 Colmenareña, 76 Mallorquina and 79 Rubia de El Molar) individuals were genotyped for the PrP gene and for 22 microsatellite markers. The analyses assumed a selective policy aimed at the elimination of the VRQ allele and the reduction of the frequency of the ARQ/ARQ genotype. These goals are approached by rejecting for breeding those individuals with the highest susceptibility for scrapie (risk groups R4 and R5) in a genetic scenario with no previous selection programmes considering the PrP gene polymorphism carried out. When all the individuals classified into risk groups R4 and R5 were removed from the dataset, the total molecular coancestry slightly increased in the Colmenareña breed illustrating that the carriers of undesirable PrP genotypes are not essential to maintain its overall gene diversity. When the allelic richness was considered, the removal of the R4 and R5 individuals gave high losses in the Rubia de El Molar breed. The analyses carried out considering the sex of the individuals informed that most increases in genetic identity in the Colmenareña breed resulted from the removal of the R4 and R5 males while in the Mallorquina breed resulted from the removal of the undesirable females. Losses of diversity in the Rubia de El Molar breed were basically independent of the sex of the individuals due to the balanced contributions to diversity of both sexes. As a general recommendation, not all the individuals of undesirable risk groups should be rejected for reproduction at the same time to avoid irretrievable loses of genetic diversity but according to the sex of the individuals.

Ascertaining gene flow patterns in livestock populations of developing countries: a case study in Burkina Faso goat

BackgroundIntrogression of Sahel livestock genes southwards in West Africa may be favoured by human activity and the increase of the duration of the dry seasons since the 1970’s. The aim of this study is to assess the gene flow patterns in Burkina Faso goat and to ascertain the most likely factors influencing geographic patterns of genetic variation in the Burkina Faso goat population.ResultsA total of 520 goat were sampled in 23 different locations of Burkina Faso and genotyped for a set of 19 microsatellites. Data deposited in the Dryad repository: http://dx.doi.org/10.5061/dryad.41h46j37. Although overall differentiation is poor (FST = 0.067 ± 0.003), the goat population of Burkina Faso is far from being homogeneous. Barrier analysis pointed out the existence of: a) genetic discontinuities in the Central and Southeast Burkina Faso; and b) genetic differences within the goat sampled in the Sahel or the Sudan areas of Burkina Faso. Principal component analysis and admixture proportion scores were computed for each population sampled and used to construct interpolation maps. Furthermore, Population Graph analysis revealed that the Sahel and the Sudan environmental areas of Burkina Faso were connected through a significant number of extended edges, which would be consistent with the hypothesis of long-distance dispersal. Genetic variation of Burkina Faso goat followed a geographic-related pattern. This pattern of variation is likely to be related to the presence of vectors of African animal trypanosomosis. Partial Mantel test identified the present Northern limit of trypanosome vectors as the most significant landscape boundary influencing the genetic variability of Burkina Faso goat (p = 0.008). The contribution of Sahel goat genes to the goat populations in the Northern and Eastern parts of the Sudan-Sahel area of Burkina Faso was substantial. The presence of perennial streams explains the existence of trypanosome vectors. The South half of the Nakambé river (Southern Ouagadougou) and the Mouhoun river loop determined, respectively, the Eastern and Northern limits for the expansion of Sahelian goat genes. Furthermore, results from partial Mantel test suggest that the introgression of Sahelian goat genes into Djallonké goat using human-influenced genetic corridors has a limited influence when compared to the biological boundary defined by the northern limits for the distribution of the tsetse fly. However, the genetic differences found between the goat sampled in Bobo Dioulasso and the other populations located in the Sudan area of Burkina Faso may be explained by the broad goat trade favoured by the main road of the country.ConclusionsThe current analysis clearly suggests that genetic variation in Burkina Faso goat: a) follows a North to South clinal; and b) is affected by the distribution of the tsetse fly that imposes a limit to the Sahelian goat expansion due to their trypanosusceptibility. Here we show how extensive surveys on livestock populations can be useful to indirectly assess the consequences of climate change and human action in developing countries.