Person:
Gutiérrez García, Juan Pablo

First Name

Juan Pablo

Last Name

Gutiérrez García

URI

https://hdl.handle.net/20.500.14352/80469

Affiliation

Universidad Complutense de Madrid

Faculty / Institute

Veterinaria

Department

Producción Animal

Area

Producción Animal

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Now showing 1 - 10 of 23

Combining Threshold, Thurstonian and Classical Linear Models in Horse Genetic Evaluations for Endurance Competitions
(Animals, 2020) Cervantes Navarro, Isabel; Gutiérrez García, Juan Pablo; García-Ballesteros, Silvia; Varona, Luis
The racing time and rank at finish traits are commonly used for endurance horse breeding programs as a measure of their performance. Even so, given the nature of endurance competitions, many horses do not finish the race. However, the exclusion of non placed horses from the dataset could have an influence on the prediction of individual breeding values. The objective of the present paper was to develop a multitrait model including race time (T), rank (R) and placing (P), with different methodologies, to improve the genetic evaluation in endurance competitions in Spain. The database contained 6135 records from 1419 horses, with 35% of the records not placed. Horse pedigree included 10868 animals, with 52% Arab Horses. All models included gender, age and race effect as systematic effects and combined different random effects beside the animal and residual effects: rider, permanent environmental effect, and interaction horse-rider. The kilometers per race was included as a covariate for T. Heritabilities were estimated as moderately low, ranging from 0.06 to 0.14 for T, 0.09 to 0.15 for P, and 0.07 to 0.17 for R, depending on the model. T and R appeared mostly as inverse measures of the same trait due to their high genetic correlation, suggesting that T can be ignored in future genetic evaluations. P was the most independent trait from the genetic correlations. The possibility of simultaneously processing the threshold, Thurstonian and continuous traits has opened new opportunities for genetic evaluation in horse populations, and much more practical genetic evaluations can be done to help a proper genetic selection.
Modulating birth weight heritability in mice
(Journal of Animal Science, 2017) Ibáñez-Escriche, Noelia; Gutiérrez García, Juan Pablo; Cervantes Navarro, Isabel; Formoso-Rafferty Castilla, Nora
Expected genetic response is proportional to the heritability of the trait, and this parameter is considered inherent of a specific trait in a particular population. However, models assuming heterogeneity in residual variance lead to different estimates of heritability across combinations of systematic (environmental) effects. Modifying the residual variance of the birth weight by artificial selection was shown to be feasible in a divergent selection experiment in mice. The objectives of this work were to 1) estimate the evolution of the heritability of birth weight in mice in the mentioned experiment, and 2) estimate different heritability regarding systematic effects. Data came from eleven generations of a divergent selection experiment to modify the residual variability of birth weight in mice. A total of 15,431 birth weight records from 959 females and 1,641 litters in combination with 14,786 pedigree records were used. The model used for analysis included generation, litter size, sex, and parity number as systematic effects. Each record of birth weight was assigned to the mother of the pup in the model which assumes that the residual variance is heterogeneous and partially under genetic control. Differences in heritability between lines reached values of 0.06 in the last generations. Choosing the most extreme values of systematic effects, the birth weight heritability ranged from 0.04 to 0.22. From these results, the possibility of modulating the heritability for this trait could be explored in 1 of 2 ways: selecting to decrease the residual variability, or choosing the specific levels of the systematic effects.
Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance
(Frontiers in Genetics, 2023) Ojeda Marín, Candela; Cervantes Navarro, Isabel; Formoso-Rafferty Castilla, Nora; Gutiérrez García, Juan Pablo
This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (FNEJ), Li and Horvitz (FL&H), Van Raden method 1 (FVR1) and method 2 (FVR2), and Yang (FYAN). Inbreeding based on runs of homozygosity (FROH) and pedigree inbreeding (FPED) were also computed. FROH, FNEJ, and FL&H were also adjusted for their average values in the first generation of selection and named FROH0, FNEJ0, and FL&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆FPEDt) and individual increases in inbreeding (∆FPEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆FNEJ0, ∆FL&H, ∆FL&H0, ∆FVR1, ∆FVR2, ∆FYAN, and ∆FROH0). The Ne was obtained from different ∆F, such as NePEDt, NePEDi, NeNEJ0, NeL&H, NeL&H0, NeVR1, NeVR2, NeYAN, and NeROH0. Comparing with FPED, FROH, FNEJ and FVR2 overestimated inbreeding while FNEJ0, FL&H, FL&H0, FVR1 and FYAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. FROH had the highest correlation with FPED (0.89); FYAN had correlations >0.95 with all the other molecular inbreeding coefficients. NePEDi was more reliable than NePEDt and presented similar behaviour to NeL&H0 and NeNEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation NePEDi was 42.20, NeL&H0 was 45.04 and NeNEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively FROH presented the highest correlation with FPED, which addresses the identity by descent probability (IBD). The evolution of NeL&H0 and NeNEJ0 was the most similar to that of NePEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.
Métodos de estimación de parámetros genéticos en el vacuno frisón español
(2019) Gutiérrez García, Juan Pablo; Rico Gutiérrez, Marcos; Cañón Ferreras, Francisco Javier
En este trabajo se propuso una metodología a seguir para obtener estimaciones lo menos costosas posibles a la vez que suficientemente precisas, de los principales parámetros genéticos de interés en las poblaciones de animales domésticos, utilizando como ejemplo una muestra española de ganado vacuno de raza Frisona. En primer lugar se obtuvieron los coeficientes de endogamia de los animales con el objeto de, por un lado, conocer el valor de este parámetro en la población y, por otro, saber si era necesario incluir su valor en la matriz de relaciones aditivas para realizar las estimaciones correspondientes en la segunda parte. El coeficiente de consanguinidad medio resultó ser de 4,03x10(-4). Posteriormente, se obtuvieron estimaciones de los componentes de varianza de la población en los caracteres producción de leche y producción de grasa...
Feed and reproductive efficiency differences between divergently selected lines for birthweight environmental variability in mice
(Journal Animal Breeding and Genetics, 2018) Flor, Miguel de la; Formoso-Rafferty Castilla, Nora; Gutiérrez García, Juan Pablo; Cervantes Navarro, Isabel
Sustainability has come to play an important role in agricultural production. A way to combine efficiency with sustainability might be by searching for robust animals that can be selected for the homogeneity of certain traits. Furthermore, the optimization of feed efficiency is one of the challenges to improve livestock genetics programmes, but this might compromise reproductive efficiency. Animals from two divergent mouse lines, regarding variability of birthweight, were used to check whether homogeneity was also related to both feed and reproductive efficiency. The objective of this study was to use these divergent lines of mice to compare them with their feed efficiency and the reproductive capacity. Animal weight, weight gain, feed intake, relative intake and cumulated transformation index were considered as feed efficiency traits. Animals from the low line had both lower weight and feed intake from 21 to 56 days. They had a worse transforming index in the three last weeks when litter size was fitted as an effect of the model, but the lines become similar if the higher litter size of the low line was not included. Reproductively, the low line performed better considering the number of females having parturitions, the number of parturitions, and with higher litter size and survival in both parturitions. Hence, the low variability line was preferred because of reproductive efficiency without seriously affecting its feed efficiency. Homogeneity seemed to be related to robustness with similar feed efficiency but higher reproductive efficiency.
Genetic and phenotypic analysis of reproductive traits in the Murciano-Granadina does: Predictive ability of the statistical models and estimation of genetic parameters
(Small Rumiants Research, 2024) Mokhtari, Morteza; Esmailizadeh, Ali; Mirmahmoudi, Rouhollah; Roudbari, Zahra; Barazandeh, Arsalan; Gutiérrez García, Juan Pablo; Mohebbinejad, Ehsan
In the present study, data collected between 2016 and 2022 from a private dairy farm of the Murciano-Granadina goat breed, in Ghale-Ganj city, located in the southern area of Kerman province, Iran was used for model comparison and estimation of genetic parameters for reproductive performance. Studied reproductive traits included litter size at birth per doe kidding (LSB), litter size at weaning per doe kidding (LSW), total litter weight at birth per doe kidding (TLWB), and total litter weight at weaning per doe kidding (TLWW). Four univariate animal models comprising various combinations of direct additive genetic, animal permanent environmental, and service sires effects were fitted for each trait. The predictive ability of models was evaluated by applying the predictive ability measure including the mean square of error (MSE) and the Pearson's correlation coefficient between observed and predicted values (r(y,y ̂)) through a two-fold cross-validation study. For LSW, TLWB, and TLWW, the model with direct additive genetic, animal permanent environmental, and service sires effects had the lowest MSE and the highest values for r(y,y ̂) than other models. For LSB, the model included direct additive genetic and animal permanent environmental was identified as the best model among the tested models. The posterior means for heritability estimates of the studied traits were low values of 0.02 ± 0.01, 0.07 ± 0.01, 0.02 ± 0.01, and 0.03 ± 0.01 for LSB, LSW, TLWB, and TLWW, respectively. The posterior means for repeatability estimates were 0.04 ± 0.01, 0.08 ± 0.02, 0.03 ± 0.01, and 0.04 ± 0.01 for LSB, LSW, TLWB, and TLWW, respectively. The posterior means for the ratio of service sires variance to phenotypic variance (S2) for LSW, TLWB, and TLWW were 0.09 ± 0.02, 0.02 ± 0.01, and 0.02 ± 0.01, respectively. Genetic correlation estimates were high in magnitude and ranged from 0.69 ± 0.09 (LSB-TLWW) to 0.97 ± 0.02 (LSB-LSW). Phenotypic correlations were low to medium estimates and ranged from 0.17 ± 0.01 (TLWB-TLWW) to 0.55 ± 0.02 (LSB-LSW). Because of low heritability estimates for the studied reproductive traits in the Murciano-Granadina goat breed genetic progress resulting from direct genetic selection for these traits is likely to be slow and improvement in environmental conditions is of great importance for improving the reproductive performance. No genetic and phenotypic antagonism were found among the studied traits. Therefore, it should be possible to simultaneously improve these traits.
Ascertaining the genetic background of the Celtic-Iberian pig strain: A signatures of selection approach
(Journal of Animal Breeding and Genetics, 2023) Arias, Katherine D.; Lee, Hanboreum; Bozzi, Riccardo; Álvarez, Isabel; Gutiérrez García, Juan Pablo; Fernández, Iván; Menéndez, Juan; Beja Pereira, Albano; Goyache Goñi, Félix
Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, FST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.
Embryo survival and fertility differ in lines divergently selected for birth weight homogeneity in mice
(Journal of Animal Breeding and Genetics, 2023) Formoso-Rafferty Castilla, Nora; El‐Ouazizi El‐Kahia, Laila; Arias Álvarez, María; Gutiérrez García, Juan Pablo; Cervantes Navarro, Isabel
The selection of animals for lower environment sensitivity around the optimum trait value can also provide benefits in productivity and welfare. A divergent selection experiment for birth weight environmental variability in mice was successfully conducted over 17 generations. Animals from low variability selected line (L-line) were more robust by having a higher litter size and survival at weaning in a common breeding environment, than those from high variability line (H-line). The objective of this study was to analyze the differences between those divergently selected lines for embryo and fetal survival and for fertility and prolificacy rate. To study embryo survival and ovulation rate, a total of 98 females (34 H-line and 50 L-line) were studied in four generations of the divergent experiment. To analyze fetal survival and fertility rate, 378 female mice (138 H-line and 240 L-line) in 10 generations or the divergent experiment were studied. Ultrasound scans were performed at day 14 of gestation to establish the number of total fetal and the embryo absorptions. Mortality was addressed as the difference between litter size at birth and the number of fetuses at 14 days of gestation. The number of pregnant females in the first 3 days after mating was used to measure fertility. A linear model was also fitted to analyze embryo mortality, litter size, and the number of embryos at 14 days of gestation. A categorical model was then used to study fertility, including line, generation, and its interaction as effects. Despite the fact that there were no significant differences in the ovulation rate, litter size at birth was significantly higher in the L-line than in the H-line (9.82 vs. 8.36 pups, p < 0.001). Moreover, embryo mortality was significantly lower in the L-line than in the H-line (1.39 vs. 2.87 fetuses, p < 0.001). L-line females were more fertile (53.49% vs. 23.26% for the H-line). According to these results, the line selected for low environmental variance would be preferable for robustness and animal welfare.
Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs
(Genetics Selection Evolution, 2023) Arias, Katherine D.; Gutiérrez García, Juan Pablo; Fernández, Iván; Álvarez, Isabel; Goyache Goñi, Félix
Background: In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz’s, FLH; and Yang and colleague’s FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents’ mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons. Results: The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors. Conclusions: Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.
Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight
(Journal of Animal Breeding and Genetics, 2023) Ojeda Marín, Candela; Gutiérrez García, Juan Pablo; Formoso-Rafferty Castilla, Nora; Goyache Goñi, Félix; Cervantes Navarro, Isabel
Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED) information, on ROH identified using the SW method (FROHSW) and on ROH identified using the CR method (FROHCR). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW. Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED. Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.