Person: Alfonso Ruiz, Leopoldo
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Alfonso Ruiz
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Leopoldo
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Agronomía, Biotecnología y Alimentación
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IS-FOOD. Research Institute on Innovation & Sustainable Development in Food Chain
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0000-0002-5662-9997
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1974
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Publication Open Access Mipob: un programa de simulación para el aprendizaje en mejora genética animal(Universidad de Córdoba, 2014) Alfonso Ruiz, Leopoldo; Producción Agraria; Nekazaritza EkoizpenaSe ha desarrollado un programa de simulación de apoyo a la docencia de los cursos introductorios a la Mejora genética animal. El programa surgió ante la ausencia de este tipo de herramientas docentes orientadas a estudiantes de primeros cursos de grado universitario, especialmente en lengua española. El programa simula una población animal cerrada de censo reducido en la que los estudiantes deben de ir tomando las decisiones de elección de futuros reproductores y cómo aparearlos. De esta forma se facilita la introducción de los conceptos básicos sobre selección y evaluación genética, y conservación y genética de poblaciones. El programa considera el caso particular del vacuno de carne y se pueden realizar hasta un total de diez generaciones de selección. Tras haber sido probado durante dos cursos consecutivos en enseñanza reglada universitaria, está disponible de forma gratuita para su libre utilización y distribución.Publication Open Access Textile characteristics of fiber from Huacaya alpacas (Vicugna pacos)(Universidad Nacional de Trujillo (Perú). Facultad de Ciencias Agropecuarias, 2019) Paucar Chanca, Rufino; Alfonso Ruiz, Leopoldo; Soret Lafraya, Beatriz; Mendoza Ordóñez, G.; Alvarado Quezada, F.; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta ElikaduraFiber from alpacas represents a substantial component of economic output for South American countries. In this study it determined the textile characteristics of fibers obtained from Huacaya alpacas raised at the South American Camelids Research and Development Center-Lachocc (CRDC-Lachocc) located at The National University of Huancavelica (UNH). Fleece samples were obtained from the mid-side rib area of 74 white alpacas (42 females and 32 males) of varying ages. The Average Fiber Diameter (AFD), Standard Deviation of the Average Fiber Diameter (SDAFD), Fiber Diameter Coefficient of Variation (FDCV), Comfort Factor (CF) and Staple Length (SL) were measured as textile characteristics and related to sex and age group. Most of the fleece samples could be classified as baby alpaca fleece according to the Peruvian Technical Standard classification (231.301.2014). Sex had no influence on any textile characteristic (p > 0.05). Meanwhile, age affected only AFD and CF (p < 0.05). Together the results indicated that alpacas farmed at CRDC-Lachocc had good potential to produce high quality fibers.Publication Open Access Molecular traceability of beef from synthetic Mexican bovine breeds(FUNPEC-RP, 2011) Rodríguez Ramírez, R.; Arana Navarro, Ana; Alfonso Ruiz, Leopoldo; González Córdova, A. F.; Torrescano, G.; Guerrero Legarreta, I.; Vallejo Córdoba, B.; Producción Agraria; Nekazaritza EkoizpenaTraceability ensures a link between carcass, quarters or cuts of beef and the individual animal or the group of animals from which they are derived. Meat traceability is an essential tool for successful identification and recall of contaminated products from the market during a food crisis. Meat traceability is also extremely important for protection and value enhancement of good-quality brands. Molecular meat traceability would allow verification of conventional methods used for beef tracing in synthetic Mexican bovine breeds. We evaluated a set of 11 microsatellites for their ability to identify animals belonging to these synthetic breeds, Brangus and Charolais/Brahman (78 animals). Seven microsatellite markers allowed sample discrimination with a match probability, defined as the probability of finding two individuals sharing by chance the same genotypic profile, of 10-8. The practical application of the marker set was evaluated by testing eight samples from carcasses and pieces of meat at the slaughterhouse and at the point of sale. The DNA profiles of the two samples obtained at these two different points in the productioncommercialization chain always proved that they came from the same animal.Publication Open Access Ayuda a las decisiones de apareamiento en poblaciones animales con información genealógica incompleta(Asociación Interprofesional para el Desarrollo Agrario, 2018) Alfonso Ruiz, Leopoldo; Institute on Innovation and Sustainable Development in Food Chain - ISFOODLos coeficientes de parentesco y de relación media de parentesco son dos herramientas útiles para determinar apareamientos con el objetivo de controlar, de forma práctica, el aumento de la consanguinidad en poblaciones animales. No obstante, su utilidad se ve condicionada por la cantidad de información genealógica disponible, pues ésta determina, en ausencia de información genómica, la precisión con que podemos estimarlos. Cuando la información genealógica sea incompleta, afectando de forma distinta a los animales, la precisión de las estimaciones de los coeficientes variará entre animales, comprometiendo el resultado de las decisiones de apareamiento. El objetivo del trabajo es calcular algunas medidas de la fiabilidad de la estimación de los coeficientes de parentesco y de relación media de parentesco. Se plantea la utilización de dos medidas basadas en la proporción de antecesores conocidos en las cinco generaciones anteriores de un animal y en la incorporación de información conocida, pero no contenida en la genealogía, a través del concepto de grupos genéticos. Los resultados muestran que estas medidas pueden ayudar a mejorar las decisiones de elección de reproductores y de acoplamiento.Publication Open Access DNA extraction procedures and validation parameters of a real-time PCR method to control milk containing only A2 β-casein(Elsevier, 2022) Jiménez Montenegro, Lucía; Mendizábal Aizpuru, José Antonio; Alfonso Ruiz, Leopoldo; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD; Gobierno de Navarra / Nafarroako Gobernua; Universidad Pública de Navarra / Nafarroako Unibertsitate PublikoaBovine milk mainly contains two types of β-casein: A1 and A2 variants. In recent years, a new variety of cows’ milk has emerged in the dairy sector called “A2 milk”. This novel product is characterised by the absence of A1 β-casein, which has been associated with possible gastrointestinal discomfort due to β-casomorphin-7 (BCM-7) release during gastrointestinal digestion. In this context, methods to verify the A1 allele absence in A2 milk are required as a quality control in the A2 milk commercialisation. Therefore, the aim of the present study was to develop a locked nucleic acid (LNA) probe-based duplex real-time PCR (qPCR) assay for A1 allele detection in A2 milk samples. Firstly, four DNA isolation methods from milk somatic cells were optimised and evaluated. The results suggests that the commercial kit NucleoSpin Tissue was the most suitable method in terms of DNA quality and amplificability for downstream applications. Then, optimisation and validation of the qPCR assay were carried out. For both A1 and A2 alleles, the absolute limits of detection of this qPCR assay were 7.3 DNA copies/reaction (2 x 10−5 ng DNA) and 30.4 DNA copies/reaction (0.1 ng DNA) at a 95% confidence level with synthetic reference DNA samples and heterozygous genotyped DNA sample, respectively. The relative limits of detection were 2% (15 copies) and 5% (152 copies) for the A1 allele in A2 samples at 95% confidence with synthetic reference and genotyped DNA samples, respectively. The qPCR assay was robust, with intra- and inter-assay variability below 4.3%, and specific, differentiating between A1 and A2 alleles with 100% genotyping accuracy. In conclusion, this cost-effective and fast method could be used to discriminate A1 allele in A2 samples and, consequently, to verify the A1 allele absence in “A2 milk” by screening commercial products on the market.Publication Open Access An expression of mixed animal model equations to account for different means and variances in the base population(Editions Scientifiques Medicales Elsevier, 1999) Alfonso Ruiz, Leopoldo; Estany Illa, Joan; Producción Agraria; Nekazaritza EkoizpenaThis paper presents a general expression to predict breeding values using animal models when the base population is selected, i.e. the means and variances of breeding values in the base generation differ among individuals. Rules for forming the mixed model equations are also presented. A numerical example illustrates the procedure.Publication Open Access Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection(Springer Nature, 2022) Jiménez Montenegro, Lucía; Mendizábal Aizpuru, José Antonio; Alfonso Ruiz, Leopoldo; Azparren Domínguez, Leire; Urrutia Vera, Olaia; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute on Innovation and Sustainable Development in Food Chain - ISFOODMilk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.Publication Open Access Impact of incorporating greenhouse gas emission intensities in selection indexes for sow productivity traits(Elsevier, 2019) Alfonso Ruiz, Leopoldo; Institute on Innovation and Sustainable Development in Food Chain - ISFOODGenetic improvement programmes should incorporate emerging challenges about environmental concerns into breeding goals. The large volume of pig meat production implies important greenhouse gas (GHG) emissions despite its lower carbon footprint per animal in front of ruminant productions. The different breeding goals considered by swine industry depending on different purebred lines, or line crosses adapted to different market demands and production constraints, could mask the effect of incorporating GHG emissions into selection indexes for improving sow productivity traits in nucleus populations. This paper analysed this effect following a methodological approach consisting in augmenting existing selection indexes derived from profit functions. An index previously described in the literature including litter size at birth, piglet perinatal survival, piglet survival to weaning, age at first conception and weaning to conception interval, was employed. This index was expanded to include GHG emissions calculating the emission intensities per litter, assuming a finished pig market and different scenarios and financial costs of GHG emissions. Results indicated that the inclusion of GHG emissions diminished the economic weight of litter size and piglet survival vs. the age at first conception and the interval weaning to conception, but did not affect significantly the contributions of these traits in the selection indexes. The improvement of sow productivity traits diluted relevantly the GHG emissions per piglet produced, and so, per kg of pork produced. The approach used in this study, despite its limitations in front of bio-economic models, has shown to be a simple and flexible way to analyse the effect of incorporating GHG emissions into existing selection indexes.Publication Open Access Comparative description of growth, fat deposition, carcass and meat quality characteristics of Basque and Large White pigs(EDP Sciences, 2005) Alfonso Ruiz, Leopoldo; Mourot, Jacques; Insausti Barrenetxea, Kizkitza; Mendizábal Aizpuru, José Antonio; Arana Navarro, Ana; Producción Agraria; Nekazaritza Ekoizpena; Gobierno de Navarra / Nafarroako GobernuaCharacteristics of growth, fat deposition, carcass and meat quality of pigs from the Basque Black Pied breed were described and compared with those of Large White pigs. Four pens, two per breed, of eleven pigs born during the same two week period, were simultaneously fattened and slaughtered, under the same conditions. The experiment was carried out over a fixed duration (124 days) and slaughter was carried out at a fixed average age (202 days). Basque pigs showed lower growth and feed efficiency and higher backfat depth (2.6 vs. 1.7 cm, P < 0.001) than Large White pigs. The difference was especially noticeable in the middle subcutaneous fat layer (0.5 cm, P < 0.001). The meat of Basque pigs was darker, redder, more marbled, and with higher pH values than in Large White pigs. Differences in fatty acid composition were observed between breeds but they were not statistically significant (P > 0.05) because of high variability observed between animals. The Basque breed exhibited an early and higher adipose development and a higher activity of enzymes responsible for lipid synthesis than the Large White. The diameter of intramuscular adipose cells was larger in Basque (40.2 vs. 33.0 μm, P < 0.001) than in Large White pigs. The results show the particular characteristics of the Basque breed as compared to pig lines highly selected for lean growth efficiency.Publication Open Access Adiposity and adipogenic gene expression in four different muscles in beef cattle(Public Library of Science, 2017) Martínez del Pino, Lara; Arana Navarro, Ana; Alfonso Ruiz, Leopoldo; Mendizábal Aizpuru, José Antonio; Soret Lafraya, Beatriz; Producción Agraria; Nekazaritza EkoizpenaAnatomical site and divergent functionalities of muscles can be related to differences in IMF content, metabolism and adipogenic gene expression. Then, potential differences in different muscles in beef cattle were studied. As a second objective, the main sources of experimental variability associated to RT-qPCR results were analyzed following a nested design in order to implement appropriate experimental designs minimizing gene expression variability. To perform the study Longissimus thoracis (LT), Semitendinosus (SM), Masseter (MS), Sternomandibularis (ST) and subcutaneous adipose tissue (SAT) samples of Pirenaica young bulls (n = 4) were collected for IMF, collagen and protein quantification, analysis of adipocyte size distribution and gene expression (PPARG, CEBPA, FAPB4 and WNT10B). A greater IMF content was observed in MS and SM muscles, which had a bimodal adipocyte size distribution while it was unimodal in the muscles LT and ST. This suggest that the different IMF accretion in the muscles studied might be related to different rates of hyperplasia and hypertrophy and that IMF might develop later in LT and ST muscles. The former differences were not mirrored by the expression of the genes analyzed, which might be related to the different contribution of mature and non-mature adipocytes to the total gene expression. When comparing IMF and SAT gene expression, late and early developing tissues respectively, expression of PPARG, CEBPA and FABP4 was higher in the SAT, in agreement with bigger cell size and numbers. The variability study indicates that the analytical factors that add higher variability to the gene expression are the sampling and RT and therefore, it would be appropriate to include those replicates in the design of future experiments. Based on the results, the use of MS and SM muscles could allow less expensive experimental designs and bigger sample size that could permit the detection of lower relevant differences in gene expression.