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3. Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study

Author

European Commission, Fabbri, Maria Chiara [0000-0002-3224-745X], Lozada-Soto, Emmanuel [0000-0001-8381-7988], Tiezzi, Francesco [0000-0002-4358-9236], Čandek-Potokar, M. [0000-0003-0231-126X], Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Fontanesi, Luca [0000-0001-7050-3760], Óvilo Martín, Cristina [0000-0002-5738-8435], Bozzi, Riccardo [0000-0001-8854-0834], Fabbri, Maria Chiara, Lozada-Soto, Emmanuel, Tiezzi, Francesco, Čandek-Potokar, M., Bovo, Samuele, Schiavo, Giuseppina, Fontanesi, Luca, Muñoz, María, Óvilo Martín, Cristina, Bozzi, Riccardo, European Commission, Fabbri, Maria Chiara [0000-0002-3224-745X], Lozada-Soto, Emmanuel [0000-0001-8381-7988], Tiezzi, Francesco [0000-0002-4358-9236], Čandek-Potokar, M. [0000-0003-0231-126X], Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Fontanesi, Luca [0000-0001-7050-3760], Óvilo Martín, Cristina [0000-0002-5738-8435], Bozzi, Riccardo [0000-0001-8854-0834], Fabbri, Maria Chiara, Lozada-Soto, Emmanuel, Tiezzi, Francesco, Čandek-Potokar, M., Bovo, Samuele, Schiavo, Giuseppina, Fontanesi, Luca, Muñoz, María, Óvilo Martín, Cristina, and Bozzi, Riccardo

Abstract

Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbree

Published
2024

4. Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds

Author

Università di Bologna, European Commission, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Schiavo, Giuseppina [0000-0002-3497-1337], Bertolini, F. [0000-0003-4181-3895], Bovo, Samuele [0000-0002-5712-8211], Galimberti, Giuliano [0000-0002-9161-9671], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Schiavo, Giuseppina, Bertolini, F., Bovo, Samuele, Galimberti, Giuliano, Muñoz, María, Bozzi, Riccardo, Čandek-Potokar, M., Óvilo Martín, Cristina, Fontanesi, Luca, Università di Bologna, European Commission, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Schiavo, Giuseppina [0000-0002-3497-1337], Bertolini, F. [0000-0003-4181-3895], Bovo, Samuele [0000-0002-5712-8211], Galimberti, Giuliano [0000-0002-9161-9671], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Schiavo, Giuseppina, Bertolini, F., Bovo, Samuele, Galimberti, Giuliano, Muñoz, María, Bozzi, Riccardo, Čandek-Potokar, M., Óvilo Martín, Cristina, and Fontanesi, Luca

Abstract

Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied the Boruta algorithm, a wrapper of the machine learning random forest algorithm, on a database of 23 European pig breeds (20 autochthonous and three cosmopolitan breeds) genotyped with a 70k SNP chip, to pre-select informative SNPs. To identify different sets of SNPs, these pre-selected markers were then ranked with random forest based on their mean decrease accuracy and mean decrease gene indexes. We evaluated the efficiency of these subsets for breed classification and the usefulness of this approach to detect candidate genes affecting breed-specific phenotypes and relevant production traits that might differ among breeds. The lowest overall classification error (2.3%) was reached with a subpanel including only 398 SNPs (ranked based on their mean decrease accuracy), with no classification error in seven breeds using up to 49 SNPs. Several SNPs of these selected subpanels were in genomic regions in which previous studies had identified signatures of selection or genes associated with morphological or production traits that distinguish the analysed breeds. Therefore, even if these approaches have not been originally designed to identify signatures of selection, the obtained results showed that they could potentially be useful for this purpose.

Published
2024

8. A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

Author

European Commission, Slovenian Research Agency, Poklukar, Klavdija [0000-0001-5360-1860], Škrlep, Martin [0000-0002-8252-8022], Čandek-Potokar, M. [0000-0003-0231-126X], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Riquet, Juliette [0000-0001-7787-031X], Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Ribani, Anisa [0000-0001-6778-1938], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Kušec, Goran [0000-0002-2900-4019], Mercat, Marie-José [0000-0002-3087-082X], Razmaite, Violeta [0000-0001-9006-5761], Araújo, José Pedro [0000-0002-1232-3160], Radović, Čedomir [0000-0002-1800-2448], Savić, Radomir [0000-0003-2131-5303], Karolyi, Danijel [0000-0003-0409-9071], Servin, Bertrand [0000-0001-5141-0913], Poklukar, Klavdija, Mestre, Camille, Škrlep, Martin, Čandek-Potokar, M., Óvilo Martín, Cristina, Fontanesi, Luca, Riquet, Juliette, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Muñoz, María, Gallo, Maurizio, Bozzi, Riccardo, Charneca, Rui, Quintanilla, Raquel, Kušec, Goran, Mercat, Marie-José, Zimmer, Christoph, Razmaite, Violeta, Araújo, José Pedro, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Servin, Bertrand, European Commission, Slovenian Research Agency, Poklukar, Klavdija [0000-0001-5360-1860], Škrlep, Martin [0000-0002-8252-8022], Čandek-Potokar, M. [0000-0003-0231-126X], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Riquet, Juliette [0000-0001-7787-031X], Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Ribani, Anisa [0000-0001-6778-1938], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Kušec, Goran [0000-0002-2900-4019], Mercat, Marie-José [0000-0002-3087-082X], Razmaite, Violeta [0000-0001-9006-5761], Araújo, José Pedro [0000-0002-1232-3160], Radović, Čedomir [0000-0002-1800-2448], Savić, Radomir [0000-0003-2131-5303], Karolyi, Danijel [0000-0003-0409-9071], Servin, Bertrand [0000-0001-5141-0913], Poklukar, Klavdija, Mestre, Camille, Škrlep, Martin, Čandek-Potokar, M., Óvilo Martín, Cristina, Fontanesi, Luca, Riquet, Juliette, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Muñoz, María, Gallo, Maurizio, Bozzi, Riccardo, Charneca, Rui, Quintanilla, Raquel, Kušec, Goran, Mercat, Marie-José, Zimmer, Christoph, Razmaite, Violeta, Araújo, José Pedro, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, and Servin, Bertrand

Abstract

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

Published
2023

14. 87. Perceptions of stakeholders involved in preserving local breeds – A survey by the GEroNIMO project

Author

Mercat, M.J., primary, Amaral, A., additional, Bozzi, R., additional, Čandek-Potokar, M., additional, Fernandes, P., additional, Gutierrez Vallejos, J., additional, Karolyi, D., additional, Laloë, D., additional, Luković, Z., additional, Lenoir, H., additional, Restoux, G., additional, Vicente, A., additional, Ribeiro, V., additional, Rodríguez Silva, T., additional, Rouger, R., additional, Škorput, D., additional, and Škrlep, M., additional

Published
2023
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15. Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia

Author

European Commission, Slovenian Research Agency, University of Zagreb, Josip Juraj Strossmayer University of Osijek, Zorc, Minja [0000-0003-3330-7909], Škorput, Dubravko [0000-0002-1217-8901], Gvozdanović, Kristina [0000-0002-1989-2630], Margeta, Polona [0000-0002-6264-2864], Karolyi, Danijel [0000-0003-0409-9071], Luković, Zoran [0000-0001-5447-3637], Salajpal, Krešimir [0000-0002-9005-8091], Savić, Radomir [0000-0003-2131-5303], Bovo, Samuele [0000-0002-5712-8211], Djurkin Kušec, Ivona [0000-0002-1363-8447], Radović, Čedomir [0000-0002-1800-2448], Kušec, Goran [0000-0002-2900-4019], Čandek-Potokar, M. [0000-0003-0231-126X], Dovč, Peter [0000-0002-7418-0054], Zorc, Minja, Škorput, Dubravko, Gvozdanović, Kristina, Margeta, Polona, Karolyi, Danijel, Luković, Zoran, Salajpal, Krešimir, Savić, Radomir, Muñoz, María, Bovo, Samuele, Djurkin Kušec, Ivona, Radović, Čedomir, Kušec, Goran, Čandek-Potokar, M., Dovč, Peter, European Commission, Slovenian Research Agency, University of Zagreb, Josip Juraj Strossmayer University of Osijek, Zorc, Minja [0000-0003-3330-7909], Škorput, Dubravko [0000-0002-1217-8901], Gvozdanović, Kristina [0000-0002-1989-2630], Margeta, Polona [0000-0002-6264-2864], Karolyi, Danijel [0000-0003-0409-9071], Luković, Zoran [0000-0001-5447-3637], Salajpal, Krešimir [0000-0002-9005-8091], Savić, Radomir [0000-0003-2131-5303], Bovo, Samuele [0000-0002-5712-8211], Djurkin Kušec, Ivona [0000-0002-1363-8447], Radović, Čedomir [0000-0002-1800-2448], Kušec, Goran [0000-0002-2900-4019], Čandek-Potokar, M. [0000-0003-0231-126X], Dovč, Peter [0000-0002-7418-0054], Zorc, Minja, Škorput, Dubravko, Gvozdanović, Kristina, Margeta, Polona, Karolyi, Danijel, Luković, Zoran, Salajpal, Krešimir, Savić, Radomir, Muñoz, María, Bovo, Samuele, Djurkin Kušec, Ivona, Radović, Čedomir, Kušec, Goran, Čandek-Potokar, M., and Dovč, Peter

Abstract

The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).

Published
2022

17. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Author

Muñoz, M., Bozzi, R., García-Casco, J., Núñez, Y., Ribani, A., Franci, O., García, F., Škrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kušec, I., Mercat, M. J., Riquet, J., Estellé, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fernández, A. I., Fontanesi, L., and Óvilo, C.

Published
2019
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19. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Università di Bologna, European Commission, Schiavo, Giampietro [0000-0002-3497-1337], Bovo, S. [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, J.P. [0000-0002-1232-3160], Bozzi, R. [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Fernández, Ana Isabel [0000-0002-1509-5191], Kušec, Goran [0000-0002-2900-4019], Campos Martín, José Miguel [0000-0002-7913-9851], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, V. [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Schiavo, Giampietro, Bovo, Samuele, Muñoz, María, Ribani, Anisa, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Fernández, Ana Isabel, Gallo, Maurizio, García, Fabián, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, Università di Bologna, European Commission, Schiavo, Giampietro [0000-0002-3497-1337], Bovo, S. [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, J.P. [0000-0002-1232-3160], Bozzi, R. [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Fernández, Ana Isabel [0000-0002-1509-5191], Kušec, Goran [0000-0002-2900-4019], Campos Martín, José Miguel [0000-0002-7913-9851], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, V. [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Schiavo, Giampietro, Bovo, Samuele, Muñoz, María, Ribani, Anisa, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Fernández, Ana Isabel, Gallo, Maurizio, García, Fabián, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

Abstract

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Published
2021

20. Muscle Transcriptome Analysis Reveals Molecular Pathways Related to Oxidative Phosphorylation, Antioxidant Defense, Fatness and Growth in Mangalitsa and Moravka Pigs

Author

European Commission, Slovenian Research Agency, Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Savić, Radomir [0000-0003-2131-5303], García-Casco, Juan M [0000-0003-0851-608X], Čandek-Potokar, M. [0000-0003-0231-126X], Benítez, Rita [0000-0001-7459-2836], Radojković, Dragan [0000-0002-7743-4726], Lukić, Miloš [0000-0002-8560-3956], Gogić, Marija [0000-0001-8121-4649], Muñoz, María [0000-0002-7018-6977], Fontanesi, Luca [0000-0001-7050-3760], Óvilo, Cristina [0000-0002-5738-8435], Núñez, Yolanda, Radović, Čedomir, Savić, Radomir, García Casco, Juan María, Čandek-Potokar, M., Benítez Yáñez, Rita María, Radojković, Dragan, Lukić, Miloš, Gogić, Marija, Muñoz, María, Fontanesi, Luca, Óvilo Martín, Cristina, European Commission, Slovenian Research Agency, Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Savić, Radomir [0000-0003-2131-5303], García-Casco, Juan M [0000-0003-0851-608X], Čandek-Potokar, M. [0000-0003-0231-126X], Benítez, Rita [0000-0001-7459-2836], Radojković, Dragan [0000-0002-7743-4726], Lukić, Miloš [0000-0002-8560-3956], Gogić, Marija [0000-0001-8121-4649], Muñoz, María [0000-0002-7018-6977], Fontanesi, Luca [0000-0001-7050-3760], Óvilo, Cristina [0000-0002-5738-8435], Núñez, Yolanda, Radović, Čedomir, Savić, Radomir, García Casco, Juan María, Čandek-Potokar, M., Benítez Yáñez, Rita María, Radojković, Dragan, Lukić, Miloš, Gogić, Marija, Muñoz, María, Fontanesi, Luca, and Óvilo Martín, Cristina

Abstract

This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin-supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT-NDs, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate ge

Published
2021

25. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Author

European Commission, Università di Bologna, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Suárez García, Fabián [0000-0002-1970-293X], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gallo, Maurizio [0000-0002-9801-2856], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Moscatelli, Giulia [0000-0002-6284-2911], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie-José, Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, European Commission, Università di Bologna, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Suárez García, Fabián [0000-0002-1970-293X], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gallo, Maurizio [0000-0002-9801-2856], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Moscatelli, Giulia [0000-0002-6284-2911], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie-José, Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

Abstract

Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Published
2020

26. Potential use of near-infrared spectroscopy to predict fatty acid profile of meat from different European autochthonous pig breeds

Author

European Commission, Ortiz, Alberto [0000-0003-2432-2373], Parrini, Silvia [0000-0001-8068-2475], Tejerina, David [0000-0001-6409-3865], de Araújo, José Pedro Pinto [0000-0002-1232-3160], Čandek-Potokar, M. [0000-0003-0231-126X], Crovetti, Alessandro [0000-0002-4052-0794], García Casco, Juan María [0000-0003-0851-608X], González, Joel [0000-0002-5693-0528], Hernández-García, Francisco I. [0000-0003-2313-2762], Karolyi, Danijel [0000-0003-0409-9071], Martins, José Manuel [0000-0003-3616-8406], Nieto, Rosa M. [0000-0002-8330-2471], Petig, M. [0000-0001-9821-7213], Razmaite, Violeta [0000-0001-9006-5761], Sirtori, Francesco [0000-0002-7443-0156], Lebret, B. [0000-0001-5435-0389], Bozzi, Riccardo [0000-0001-8854-0834], Ortiz, Alberto, Parrini, Silvia, Tejerina, David, de Araújo, José Pedro Pinto, Čandek-Potokar, M., Crovetti, Alessandro, García Casco, Juan María, González, Joel, Hernández-García, Francisco I., Karolyi, Danijel, Margeta, Vladimir, Martins, José Manuel, Nieto, Rosa M., Petig, M., Razmaite, Violeta, Sirtori, Francesco, Lebret, B., Bozzi, Riccardo, European Commission, Ortiz, Alberto [0000-0003-2432-2373], Parrini, Silvia [0000-0001-8068-2475], Tejerina, David [0000-0001-6409-3865], de Araújo, José Pedro Pinto [0000-0002-1232-3160], Čandek-Potokar, M. [0000-0003-0231-126X], Crovetti, Alessandro [0000-0002-4052-0794], García Casco, Juan María [0000-0003-0851-608X], González, Joel [0000-0002-5693-0528], Hernández-García, Francisco I. [0000-0003-2313-2762], Karolyi, Danijel [0000-0003-0409-9071], Martins, José Manuel [0000-0003-3616-8406], Nieto, Rosa M. [0000-0002-8330-2471], Petig, M. [0000-0001-9821-7213], Razmaite, Violeta [0000-0001-9006-5761], Sirtori, Francesco [0000-0002-7443-0156], Lebret, B. [0000-0001-5435-0389], Bozzi, Riccardo [0000-0001-8854-0834], Ortiz, Alberto, Parrini, Silvia, Tejerina, David, de Araújo, José Pedro Pinto, Čandek-Potokar, M., Crovetti, Alessandro, García Casco, Juan María, González, Joel, Hernández-García, Francisco I., Karolyi, Danijel, Margeta, Vladimir, Martins, José Manuel, Nieto, Rosa M., Petig, M., Razmaite, Violeta, Sirtori, Francesco, Lebret, B., and Bozzi, Riccardo

Abstract

Autochthonous pig breeds provide products of differentiated quality, among which quality control is difficult to perform and insufficient for current market requirements. The present research evaluates the predictive ability of near-infrared (NIR) spectroscopy, combined with chemometric methods as a rapid and affordable tool to assure traceability and quality control. Thus, NIR technology was assessed for intact and minced muscle Longissimus thoracis et lumborum samples collected from 12 European autochthonous pig breeds for the quantification of lipid content and fatty acid composition. Different tests were performed using different numbers of samples for calibration and validation. The best predictive ability was found using minced presentation and set with 80% of the samples for the calibration and the remaining 20% for the external validation test for the following traits: lipid content and saturated and polyunsaturated fatty acids, which attained both the highest determination coefficients (0.89, 0.61, and 0.65, respectively) and the lowest root mean square errors in external validation (0.62, 1.82, and 1.36, respectively). Lower predictive ability was observed for intact muscles. These results could contribute to improve the management of autochthonous breeds and to ensure quality of their products by traditional meat industry chains.

Published
2020

29. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Schiavo, G., Schiavo, G., Bovo, S., Munoz, M., Ribani, A., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A. I., Gallo, M., Garcia, F., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M.-J., Nunez, Y., Quintanilla, R., Radović, C., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C., Fontanesi, L., Schiavo, G., Schiavo, G., Bovo, S., Munoz, M., Ribani, A., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A. I., Gallo, M., Garcia, F., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M.-J., Nunez, Y., Quintanilla, R., Radović, C., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C., and Fontanesi, L.

Abstract

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent commonROHs withinthe samepopulationdefineROHislandsand indicatehotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP PorcineHDGenomic Profiler. PLINK software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via overrepresentation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n=32), Cinta Senese (n=26) and LithuanianWhite Old Type (n=22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of

Published
2021

30. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Schiavo, G., primary, Bovo, S., additional, Muñoz, M., additional, Ribani, A., additional, Alves, E., additional, Araújo, J. P., additional, Bozzi, R., additional, Čandek‐Potokar, M., additional, Charneca, R., additional, Fernandez, A. I., additional, Gallo, M., additional, García, F., additional, Karolyi, D., additional, Kušec, G., additional, Martins, J. M., additional, Mercat, M.‐J., additional, Núñez, Y., additional, Quintanilla, R., additional, Radović, Č., additional, Razmaite, V., additional, Riquet, J., additional, Savić, R., additional, Usai, G., additional, Utzeri, V. J., additional, Zimmer, C., additional, Ovilo, C., additional, and Fontanesi, L., additional

Published
2021
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31. Genetic structure of autochthonous and commercial pig breeds using a high-density SNP chip

Author

Muñoz, M, García-Casco, JM, Fernández, AI, García, F, Geraci, C, Fontanesi, L, Čandek- Potokar, M, and Óvilo, C

Abstract

One of the main objectives in TREASURE project is the genetic characterisation of European autochthonous pig breeds through genetic and genomic tools. The aim of the current pilot study was to evaluate the usefulness of the GeneSeek Genomic Profiler porcine SNP chip to describe genetic diversity of five Mediterranean autochthonous and three commercial pig breeds. 44 animals from Iberian (12), Krskopolje (4), Casertana (5), Cinta Senese (5), Apulo Calabrese (5), Duroc (5), Large White (4) and Landrace (4) breeds were genotyped. All DNA samples were successfully genotyped (call rates ≥0.98). A total of 59,193 SNPs were used in the genetic analyses after QC filtering. Observed (Ho) and expected (He) heterozygosities, FIS statistic and genetic distances (DS and FST) were computed. The overall FST value was 0.15. Ho and Hs values per breed ranged from 0.25 to 0.36 (Ho) and from 0.26 to 0.40 (Hs). Calabrese and Duroc were the breeds with the highest (0.16) and lowest (-0.01) FIS values, respectively. DS and FST genetic distances were very similar. Duroc and Large-White were the closest breeds, since DS and FST were 0.09 and 0.19, respectively and Landrace and Duroc the furthest ones, being DS and FST values equal to 0.22 and 0.34. Distribution of minor allele frequencies (MAF) showed that Iberian is the breed with the highest number of monomorphic SNPs (25.3%) and Landrace and Krskopolje have more alleles at intermediate frequencies. These results provide insights on the genetic diversity and relationships among the investigated breeds. This study will be enlarged to characterize the structure of European autochthonous pig populations using the same SNP chip. Funded by European Union’s H2020 RIA program (grant agreement no. 634476).

Published
2018
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33. Growth of Krškopolje piglets during lactation and first rearing period

Author

Tomažin, U, Batorek Lukač, N, Škrlep, M, Prevolnik Povše, M, Mežan, A, and Čandek-Potokar, M

Subjects
Pre- and post-weaning growth, Krškopolje breed growth rate
Abstract

The only Slovenian autochthonous pig breed (Krškopolje) is reared in very diverse conditions resulting in variable growth rates. As literature data on this breed is scarce, different growth phases were assessed within the TREASURE project. Growth in the pre-weaning period (n=156) was recorded on the farms of their origin (7 organic and 11 conventional), whereas the post-weaning period data originated from a subsample (n=42; piglets from 5 organic and 9 conventional farms). transferred to the experimental farm. There the piglets were assigned within litter to three pens; one pen (ECO; n=14) received organic feed mixture (12.8 MJ metabolizable energy, 17% crude proteins), while two pens (CON, n=28) received a conventional starter for 10 days (14 MJ metabolizable energy, 17.8% crude proteins) and thereafter a grower diet (13.6 MJ metabolizable energy, 16.8% crude proteins). Piglets were fed ad libitum and weighed at the average age of 38, 54 and 113 days. Prior to weaning, the piglets grew faster on conventional (app. 20%) than on organic farms (209±16 vs. 173±19 g/day, respectively), but the difference was not significant (P=0.17). Post-weaning, CON group had only 8% higher daily gain than ECO (391±31 vs. 361±41 g/day, respectively; P=0.60). The results suggest that no differences in between the systems are expected within similar rearing and feeding conditions.

Published
2018

34. Productive performance of Krškopolje pig breed – Review of preliminary results

Author

Batorek Lukač, N, Tomažin, U, Škrlep, M, Prevolnik Povše, M, and Čandek-Potokar, M

Subjects
Carcass quality, Autochthonous breed, General Medicine, Growth, Meat quality
Abstract

As raças suínas locais estão adaptadas a ambientes locais específicos e são alimentadas com vários alimentos disponíveis localmente. Para além do seu interesse genético da óptica da agro-biodiversidade, elas representam uma base para fileiras suínas locais sustentáveis. O objetivo do presente trabalho é resumir os dados já disponíveis na literatura sobre a performance produtiva da raça autóctone Eslovena, a raça Krškopolje, que é uma das raças estudadas no âmbito do projeto TREASURE. Foi realizada uma pesquisa e revisão da literatura disponível sobre parâmetros produtivos (crescimento, qualidade de carcaça e da carne) de suínos Krškopolje. A revisão da literatura indica que o crescimento do nascimento ao abate é, em média, de 492 g/dia (339-637 g/dia, n=6). O abate é feito, em média, aos 293 dias de idade (230-360 dias; n=9) e a 118kg de peso vivo (90-145 kg; n=7). O rendimento de carcaça é, em média, de 77,3% (71,7 – 80,2%; n=9) e o teor em tecido magro de 43,5% (37,5–47,8%; n=7). A espessura da gordura dorsal medida ao nível da última costela é, em média, 38mm (28-53mm; n=11), enquanto que a área do lombo e a área da gordura do lombo são, em média, 32,6 e 33,0 cm2, respetivamente (23,2-41,7; n=5 e 27,7-42,2; n=4, respetivamente). Nos estudos que reportam a qualidade da carne de porcos Krškopolje, o pH 24h post-mortem no músculo Longissimus dorsi é, em média, 5,46 (5,28-5,60; n=7), a perda por gotejamento “drip loss” 48h post-mortem atinge 5,1% (3,9-6,7%; n=4) e o teor em gordura intramuscular é de 3,5% (2,7-4,6%; n=6). Embora havendo poucos estudos sobre o porco Krškopolje, a presente revisão dá uma primeira visão sobre a performances produtivas desta raça local.

Published
2018

35. An online phenotype database: first step towards breeding programs in local pig breeds

Author

Mercat, MJ, Zahlan, E, Petig, M, Lenoir, H, Cheval, P, Čandek-Potokar, M, Škrlep, M, Kastelic, A, Lukić, B, Nunes, J, Pires, P, and Lebret, B

Subjects
race porcine locale, base de données, viande, Database, local breeds, pigs, breeding program, phenotype, carcasse, indicateur de qualité, porc
Abstract

In order to further allow implementation of breeding programs in local pig breeds, with selection objectives defined for each local breed, we aimed at developing a standardised recording of carcass and meat quality traits. These data have to be connected with herdbooks to estimate genetic parameters of the traits (heritabilities and genetic correlations) which are necessary to define breeding objectives. Today the situation is very different from one local breed to another. No or very few phenotypes are recorded in some of them, while breeding programs already exist for a few breeds. To promote phenotyping, a dedicated database and a website were developed in the frame of the TREASURE project. First, the required variables have been collected for six local breeds: Basque (FR), Bísaro (PT), Crna slavonska (HR), Gascon (FR), Krškopoljski (SI) and Schwäbisch-Hällisches (DE). In total 74 variables have been identified dealing with animal herdbook information (10), rearing and growth (22), carcass (22) and meat quality (20) attributes. The database is compatible with the various identifiers used in the different countries: animal IDs, breed, farm… codifications. Major attention has been paid to the description of measurement methods of traits. Thus, each carcass and meat quality phenotype is associated to a method description representing 35 additional variables. The website can be easily translated into several languages. The website and database are currently on test until the end of the TREASURE project. All the breeds studied in TREASURE are free to use these tools. The database can be duplicated so that each partner can host its own data. Funded by European Union H2020 RIA program (grant agreement no. 634476).

Published
2018

37. Structural differences among pig genomes illustrate genetic uniqueness of breeds

Author

Zorc, M., Ogorevc, J., Škrlep, M., Bozzi, R., Petig, M., Fontanesi, L., Ovilo, C., Radović, C., Kušec, G., ČANDEK-POTOKAR, M., and Dovč, P.

Subjects
local pig, whole genome sequencing, KIT gene, MC1R gene, pig, dataset, NGS, WGS
Abstract

pig breed genomes opened a new area of genomic research focused on variation caused by single nucleotide polymorphisms (SNP), small scale variation and structural variants which may all contribute to phenotypic variation among pig breeds. In our study (performed within TREASURE project) we re-analysed WGS-based data sets from more than 20 breeds, including commercial and local breeds as well as some wild boar genomes, deposited in publicly available databases. This bioinformatics tool enables discovery of new SNPs, estimation of allele frequencies (genotyping by sequencing) at candidate loci and identification of structural variation in a wide range of pig breeds. The analysis underlined the relevance of structural differences at KIT and MC1R locus involved in colour pattern formation, as well as LEPR locus associated with fatness, fatty acid metabolism and intramuscular fat composition. This approach allows discovery of important genomic differences between commercial breeds and local breeds which are analysed in the frame of the TREASURE project. Extensive mining of publicly available genomic data can together with the newly generated genomic information from local breeds, significantly contribute to the detailed characterisation of animal genetic resources present in local pig breeds. Funded by European Union’s H2020 RIA program (grant agreement No. 634476).

Published
2018

38. Environmental impacts of pig production systems relying on European local breeds

Author

Monteiro, Alessandra, Wilfart, Aurélie, Utzeri, V.J., Lukač, Nina Batorek, Tomazin, Urska, Nanni-Costa, L., Čandek-Potokar, M, Fontanesi, L., Faure, Justine, and Garcia-Launay, Florence

Subjects
race porcine locale, séquestration du carbone, acidification, digestibilité, élevage extensif, aliment, impact environnemental, élevage extérieur, eutrophisation, porc, phosphore
Abstract

Traditional pig productions systems, relying mainly on local pig breeds and outdoor rearing, have been poorly investigated so far in terms of environmental impacts. The few existing studies did not account for possible sequestration of carbon and emissions consecutive to grazing. Twenty-five farms of Gascon breed in France (FR), 8 with Mora Romagnola breed in Italy (IT), and 15 of Krškopolje breed in Slovenia (SI) were evaluated while accounting for the emissions from pasture intake and the potential for carbon sequestration. Pig production system in SI presented the lowest impacts per kg of live weight, due to better feed conversion ratio caused by indoor production and due to lower impacts of feeds – most diets were based on grains, vegetables, tubers and roots produced on farm. Among the systems, acidification potential (AP) was 13% higher in IT than the average for FR and SI, due to higher dietary crude protein content (+9% than the average), while the eutrophication potential (EP) was 27% higher in FR system than the average, as a result of higher phosphorus content of feeds (+28% than the average). When the potential of carbon sequestration was taken into account, the GWP impact was reduced 4% on average. Conversely, when accounting for the emissions from pasture intake the GWP was increased by 2%, mainly when a high digestible grass was considered. The use of high digestible grass provided lower AP and EP impacts than low digestible grass. The large variability between farms in terms of environmental impacts suggests that the margins for improvement of local breeds’ production rely on improvement of feed composition and supply, and origin of feed ingredients. There is a great need for better estimation of digestibility of grasses and of carbon sequestration, in order to reduce the uncertainties associated with the environmental impacts evaluated of outdoor pigs’ systems. Funded by European Union’s H2020 RIA program (grant agreement no. 634476).

Published
2018

39. Signatures of de‐domestication in autochthonous pig breeds and of domestication in wild boar populations fromMC1RandNR6A1allele distribution

Author

Ribani, A., primary, Utzeri, V. J., additional, Geraci, C., additional, Tinarelli, S., additional, Djan, M., additional, Veličković, N., additional, Doneva, R., additional, Dall'Olio, S., additional, Nanni Costa, L., additional, Schiavo, G., additional, Bovo, S., additional, Usai, G., additional, Gallo, M., additional, Radović, Č., additional, Savić, R., additional, Karolyi, D., additional, Salajpal, K., additional, Gvozdanović, K., additional, Djurkin‐Kušec, I., additional, Škrlep, M., additional, Čandek‐Potokar, M., additional, Ovilo, C., additional, and Fontanesi, L., additional

Published
2019
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40. Diversity across major and candidate genes in European local pig breeds

Author

Kušec, Goran [0000-0002-2900-4019], Estellé, Jordi [0000-0002-6241-1732], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Riquet, Juliette [0000-0001-7787-031X], Djurkin Kušec, Ivona [0000-0002-1363-8447], Fernández, Ana Isabel [0000-0002-1509-5191], Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Muñoz Muñoz, María, Bozzi, Riccardo, García, Fabián, Núñez, Yolanda, Geraci, C., Crovetti, Alessandro, García Casco, Juan María, Alves, Estefania, Škrlep, Martin, Charneca, Rui, Martins, José Manuel, Quintanilla, Raquel, Tibau, J., Kušec, Goran, Djurkin Kušec, Ivona, Mercat, Marie-José, Riquet, Juliette, Estellé, Jordi, Zimmer, Christoph, Razmaite, Violeta, Araújo, José Pedro, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, M., Fontanesi, Luca, Fernández, Ana Isabel, Óvilo Martín, Cristina, Kušec, Goran [0000-0002-2900-4019], Estellé, Jordi [0000-0002-6241-1732], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Riquet, Juliette [0000-0001-7787-031X], Djurkin Kušec, Ivona [0000-0002-1363-8447], Fernández, Ana Isabel [0000-0002-1509-5191], Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Muñoz Muñoz, María, Bozzi, Riccardo, García, Fabián, Núñez, Yolanda, Geraci, C., Crovetti, Alessandro, García Casco, Juan María, Alves, Estefania, Škrlep, Martin, Charneca, Rui, Martins, José Manuel, Quintanilla, Raquel, Tibau, J., Kušec, Goran, Djurkin Kušec, Ivona, Mercat, Marie-José, Riquet, Juliette, Estellé, Jordi, Zimmer, Christoph, Razmaite, Violeta, Araújo, José Pedro, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, M., Fontanesi, Luca, Fernández, Ana Isabel, and Óvilo Martín, Cristina

Abstract

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and

Published
2018

41. Local pig breeds Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE

Author

Čandek-Potokar, M., Nieto Martínez, Raquel, Pugliese, C., Araujo, J. P., Charneca, R., García Casco, Juan María, González Sánchez, E., Hernández-García, F. I., Izquierdo, M., Karolyi, D., Kušec, G., Lebret, B., Mercat, M. J., Petig, M., and Radović, Č and Savić, R.

Subjects
Nutritional requirements, Pig, Local pig breeds, Feeding resources, Management innovations
Abstract

TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereafter shortly presented. Their concepts and main objectives with some highlights on already available results are described. © 2017, University of Zagreb. All rights reserved.

Published
2017

42. Effect of production system (organic vs. conventional) and roughage supplementation in diet on performance of growing-finishing krškopolje pigs

Author

Batorek Lukač, N, Tomažin, U, Prevolnik Povše, M, Škrlep, M, and Čandek-Potokar, M

Subjects
2. Zero hunger, Autochthonous breed, feed intake, growth rate, backfat, Krškopolje pig
Abstract

Performance of Krškopolje pigs in conventional and organic production system was investigated in project TREASURE. Thirty-six castrates were assigned (at app. 70 kg) to 3 treatment groups (TG): organic (ECO), conventional (CON) and conventional with lucerne supplementation (CON+L). CON (n=12) and CON+L (n=12) were housed indoors, while ECO (n=12) pigs were housed in a pen with an outdoor access. Two barley based diets were composed; organic for ECO (12.4 MJ ME, 12.9% CP, 0.7% Lys) and conventional (12.7 MJ ME, 13.6% CP, 1.2 % Lys) for CON and CON+L and distributed in equal quantities (app. 3.4 kg per pig) to CON and ECO whereas CON+L were offered 10% less feed. ECO and CON+L were supplemented with lucerne hay or pellets, respectively. After 73 days on trial, CON+L pigs had 11% lower (P=0.148) average daily gain (ADG) and ECO had 13% higher (P= 0.097) ADG than CON pigs. ECO pigs had less variation in body weight at the end of the trial. Backfat thickness gain was 0.28 vs. 0.32 and 0.36 mm/day for CON+L, CON and ECO, respectively (P=0.083). Feed conversion ratio was comparable in CON and CON+L (4.90 vs. 4.91 kg feed/kg gain).

Published
2016
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43. Improving Sustainability Of Local Pig Breeds Using Quality Labels – Case Review And Trademark Development In Project Treasure

Author

Čandek-Potokar, M, Giusto, A, Conti, C, Cosola, C, and Fontanesi, L

Subjects
Branding strategy, Pork value chain, local pig breeds, trademark, intellectual property, commercial exploitation, sustainability, Genetic resources
Abstract

The interest for traditional genetic resources, here comprised local pig breeds, has been increased in the last decades. Yet, at the time being, majority of local pig breeds still need to be supported with subsidies to ensure their conservation. However, the best strategy is if breeds could reach self-sustainability which is possible by an efficient marketing strategy of their products. The majority of studied breeds in project TREASURE are untapped, so the ambition is to develop an “umbrella” collective trademark that would gather together all breeds and that would create added values for their products. Major socio-economic aspects related to the implementation of the collective trademark include rights, responsibilities and expected added value for end-users. Based on the results obtained by an internal survey conducted in TREASURE, we have identified the main features of the collaborative trademark: 1) it should attract end-users such as farmers, breeders associations and meat processors; 2) it should be developed and promoted by an operational committee of end-users, under the coordination and supervision of TREASURE Consortium; 3) it should emphasize local pig genetic resources as the key common point, considering also production systems and nutrition; 4) it should explore possible collaboration or conflict with existing EU protected products (PDO, PGI, TSG) in order to optimally promote local products. An overview of intellectual property rights (IPR) in the context of pork value chains existing in the European Union is presented and prospects for TREASURE trademark analysed.

Published
2016
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48. Characterization and diversity analysis of European local pig breeds and production systems under Treasure project framework

Author

Fernández, A.I., Fontanesi, L, Bozzi, R, Estellé, J, Óvilo, C, Nieto, RM, García-Casco, JM, Pugliese, C, Gil, JM, Lebret, B, Oliver. MA, and Čandek- Potokar, M

Subjects
transcriptomics, metagenomics, Treasure, European local pig breeds, genomics, transcriptomics, metagenomics, genomics, Treasure, European local pig breeds
Abstract

Treasure is a multidisciplinary European Union H2020 funded project focused on the research and development of activities for the benefit of sustainable pork chains based on European local pig breeds and their production systems. One of the main objectives of the project is to demonstrate singularity of about 20 untapped local pig populations from nine European countries (Portugal, Spain, France, Italy, Slovenia, Croatia, Serbia, Germany and Lithuania) through phenotypic, genomic and transcriptomic activities. Genomic approaches include the use of high density SNP data, candidate gene analyses and whole genome sequencing (WGS). Untapped breeds are first characterized at the production system level through a specific survey addressed to collect census data, breed distribution and phenotypic traits and information on breed organizations and production chains. Genomic data analyses bring the possibility for the estimation of different population genetics and population genomics indicators, such as relative homozygosity and observed and expected genetic diversity of the studied local pig breeds, as well as the definition of the structure of meta-populations through the proportion of shared alleles/haplotypes among animals and population admixture parameters. Comparative analyses including commercial pig populations in Europe identify genome regions with evidence of selective sweeps or signatures of demographic events across breeds. WGS analyses are focused on population adaptation and resilience signatures. To complete the local pig breed characterization, identification of population-specific biological processes responsible for specific production traits and product quality will be achieved through transcriptomic and metagenomic assays under specific production systems and management conditions. Together all these analyses are expected to provide useful methods and DNA markers for authentication and traceability of mono-breed products, conservation of local pig genetic resources and development of specific breeding programs for sustainable pork production chains in Europe. The Treasure project is funded under European Union’s Horizon 2020 research and innovation program, Grant. No. 634476.

Published
2016

50. Local pig breeds Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE

Author

Kušec, Goran [0000-0002-2900-4019], Karolyi, Danijel [0000-0003-0409-9071], Radović, Čedomir [0000-0002-1800-2448], Čandek-Potokar, M., Nieto Martínez, Raquel, Pugliese, Carolina, Araújo, José Pedro, Charneca, Rui, García Casco, Juan María, González-Sánchez, Elena, Hernández-García, Francisco I., Izquierdo, Mercedes, Karolyi, Danijel, Kušec, Goran, Lebret, B., Mercat, Marie-José, Petig, M., Radović, Čedomir, Savić, Radomir, Kušec, Goran [0000-0002-2900-4019], Karolyi, Danijel [0000-0003-0409-9071], Radović, Čedomir [0000-0002-1800-2448], Čandek-Potokar, M., Nieto Martínez, Raquel, Pugliese, Carolina, Araújo, José Pedro, Charneca, Rui, García Casco, Juan María, González-Sánchez, Elena, Hernández-García, Francisco I., Izquierdo, Mercedes, Karolyi, Danijel, Kušec, Goran, Lebret, B., Mercat, Marie-José, Petig, M., Radović, Čedomir, and Savić, Radomir

Abstract

TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereaft er shortly presented. Th eir concepts and main objectives with some highlights on already available results are described.

Published
2017

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