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 Gobernua
Characteristics 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.
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 - ISFOOD
Genetic 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.
Open Access
Adipose tissue modification through feeding strategies and their implication on adipogenesis and adipose tissue metabolism in ruminants
(MDPI, 2020) Urrutia Vera, Olaia; Mendizábal Aizpuru, José Antonio; Alfonso Ruiz, Leopoldo; Soret Lafraya, Beatriz; Insausti Barrenetxea, Kizkitza; Arana Navarro, Ana; Agronomia, Bioteknologia eta Elikadura; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD; Agronomía, Biotecnología y Alimentación; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Dietary recommendations by health authorities have been advising of the importance of diminishing saturated fatty acids (SFA) consumption and replacing them by polyunsaturated fatty acids (PUFA), particularly omega-3. Therefore, there have been efforts to enhance food fatty acid profiles, helping them to meet human nutritional recommendations. Ruminant meat is the major dietary conjugated linoleic acid (CLA) source, but it also contains SFA at relatively high proportions, deriving from ruminal biohydrogenation of PUFA. Additionally, lipid metabolism in ruminants may differ from other species. Recent research has aimed to modify the fatty acid profile of meat, and other animal products. This review summarizes dietary strategies based on the n-3 PUFA supplementation of ruminant diets and their effects on meat fatty acid composition. Additionally, the role of n-3 PUFA in adipose tissue (AT) development and in the expression of key genes involved in adipogenesis and lipid metabolism is discussed. It has been demonstrated that linseed supplementation leads to an increase in alpha-linolenic acid (ALA) and eicosapentaenoic acid (EPA), but not in docosahexaenoic acid (DHA), whilst fish oil and algae increase DHA content. Dietary PUFA can alter AT adiposity and modulate lipid metabolism genes expression, although further research is required to clarify the underlying mechanism.
Open Access
Worldwide research trends on milk containing only A2 β-casein: a bibliometric study
(MDPI, 2022) Jiménez Montenegro, Lucía; Alfonso Ruiz, Leopoldo; Mendizábal Aizpuru, José Antonio; Urrutia Vera, Olaia; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD
The protein fraction of β-casein may play a key role in the manifestation of a new intolerance: milk protein intolerance. The most common forms of β-casein among dairy cattle breeds are A1 and A2 β-casein. During gastrointestinal digestion of A1 β-casein, an opioid called peptide β-casomorphin-7 (BCM-7) is more frequently released, which can lead to adverse health outcomes. For that reason, novel products labelled as "A2 milk"or "A1-free dairy products" have appeared on the market. In this context, a bibliometric analysis on A2 β-casein research was carried out through the Web of Science (WoS) database. The main objective of this work was to provide an overview of the state of the art in the field of β-casein A2 by analyzing the number of publications per year, trends in thematic content, the most frequently used terms, and the most important institutions and countries in the field. This bibliometric study showed that a greater effort is needed to determine the possible implications of this novel product for human health and the market.
Open Access
Preservation of milk in liquid nitrogen during sample collection does not affect the RNA quality for RNA-seq analysis
(BMC, 2025-05-24) Jiménez Montenegro, Lucía; Alfonso Ruiz, Leopoldo; Soret Lafraya, Beatriz; Mendizábal Aizpuru, José Antonio; Urrutia Vera, Olaia; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa; Gobierno de Navarra / Nafarroako Gobernua
Background. Standard procedures for milk sample collection for transcriptome analysis use ice as preservation method, which can afect the RNA stability and requires immediate sample processing. These problems would be eased if the milk samples could be snap-frozen in liquid nitrogen. This study describes the applicability of a new method for milk sample collection and subsequent RNA extraction from milk fat globules, determining whether the quality, integrity and quantity of the RNA extracts met the minimum requirements for downstream RNA-seq. Results. The quality of the extracts measured by A260/280 ratio and the Integrity and Quality (IQ) values obtained fulflled the reference values of 1.9 - 2.1 (P10.05) and failed to meet the RIN≥7 benchmark for RNA-seq (P>0.05). Milk fat globules contain low molecular-weight RNA fragments and minimal 18S and 28S rRNA, suggesting low RIN values were inherent to sample type. Likewise, the RNA concentration from milk fat globules were generally low (120.43±22.27 ng/µL, 102.87±15.64 ng/µL and 109.43±22.69 ng/µL, measured by Nanodrop, Qubit HS and QuanTI Ribogreen, respectively). Nevertheless, RNA-seq yielded 52.7 million paired-end reads per sample. The raw reads passed all quality control parameters having the same sequence-read lengths (151 bp), 100% base-coverage, 49% GC base content, and base quality scores of 36, enabling successful transcriptome profling. Moreover, milk proteins were identifed as the most abundant transcripts in MFG in the analysis of the most expressed genes, indicating that the sequenced reads would accurately refect the transcriptome of this milk fraction. Conclusions. Milk preservation in liquid nitrogen is a suitable sample collection method that overcomes the limitations of immediate sample processing required if ice is used. Thus, this procedure, together with the subsequent RNA isolation from milk fat globules and its sequencing by RNA-seq, would provide a practical and a non-invasive method for measuring the mammary epithelial cell transcriptome, improving the feasibility of conducting studies related to mammary gland and lactation physiology.
Open Access
Conversión de las explotaciones de vacuno de leche a la producción de leche A2 ante una posible demanda del mercado: posibilidades e implicaciones
(Asociación Interprofesional para el Desarrollo Agrario, 2019) Alfonso Ruiz, Leopoldo; Urrutia Vera, Olaia; Mendizábal Aizpuru, José Antonio; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD
El mercado de la leche de vaca, tras la desaparición de las cuotas lácteas, está provocando una importante restructuración en el sector. Una de las alternativas que están desarrollando, fundamentalmente las pequeñas explotaciones familiares, es la diferenciación de sus productos. En ese contexto, ha aparecido un tipo diferenciado de leche conocida como leche A2. Esta se caracteriza por estar libre de la variante A1 de la proteína β-caseína que, debido a una mayor producción de β-casomorfina-7 tras la digestión, puede dar lugar a intolerancias y afecciones gastrointestinales. En este trabajo se analizan las posibilidades e implicaciones de una selección a favor de la β-caseína A2 en el caso concreto de las explotaciones familiares de Guipúzcoa. Los resultados obtenidos a partir de 1868 hembras genotipadas muestran que la frecuencia del alelo que codifica la proteína A2 es 0,55, y no se han encontrado asociaciones desfavorables entre el alelo A2 y el valor genético para caracteres productivos, funcionales y morfológicos, ni con otros genes ni haplotipos. Bajo esta situación de partida, y empleando exclusivamente toros A2A2, la utilización o no de semen sexado, junto con las diferentes ratios de reposición que se apliquen, determinarán el periodo y el coste económico de la conversión de los rebaños a la producción de leche A2. En un escenario de costes razonables esta se estima entre los 8 y los 15 años, pudiendo llegar a suponer a una explotación de 150 vacas unos costes de unos 6.000 y 1.000 €/año, respectivamente.
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 Ekoizpena
Traceability 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.
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 - ISFOOD
Milk 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.
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 Ekoizpena
This 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.
Open Access
The effects of selective breeding against scrapie susceptibility on the genetic variability of the latxa black-faced sheep breed
(EDP Sciences, 2006) Alfonso Ruiz, Leopoldo; Parada Rey, Analia; Legarra, Andrés; Ugarte, Eva; Arana Navarro, Ana; Producción Agraria; Nekazaritza Ekoizpena
Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites). The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent) and low frequency alleles (30 percent) in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.