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1. A compendium of genetic regulatory effects across pig tissues

Author

Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, Maria, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., Zhang, Zhe, and Fang, Lingzhao

Published
2024
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7. The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird

Author

Spurgin, Lewis G., primary, Bosse, Mirte, additional, Adriaensen, Frank, additional, Albayrak, Tamer, additional, Barboutis, Christos, additional, Belda, Eduardo, additional, Bushuev, Andrey, additional, Cecere, Jacopo G., additional, Charmantier, Anne, additional, Cichon, Mariusz, additional, Dingemanse, Niels J., additional, Doligez, Blandine, additional, Eeva, Tapio, additional, Erikstad, Kjell Einar, additional, Fedorov, Vyacheslav, additional, Griggio, Matteo, additional, Heylen, Dieter, additional, Hille, Sabine, additional, Hinde, Camilla A., additional, Ivankina, Elena, additional, Kempenaers, Bart, additional, Kerimov, Anvar, additional, Krist, Milos, additional, Kvist, Laura, additional, Laine, Veronika N., additional, Mänd, Raivo, additional, Matthysen, Erik, additional, Nager, Ruedi, additional, Nikolov, Boris P., additional, Norte, Ana Claudia, additional, Orell, Markku, additional, Ouyang, Jenny, additional, Petrova‐Dinkova, Gergana, additional, Richner, Heinz, additional, Rubolini, Diego, additional, Slagsvold, Tore, additional, Tilgar, Vallo, additional, Török, János, additional, Tschirren, Barbara, additional, Vágási, Csongor I., additional, Yuta, Teru, additional, Groenen, Martien A. M., additional, Visser, Marcel E., additional, van Oers, Kees, additional, Sheldon, Ben C., additional, and Slate, Jon, additional

Published
2024
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8. A compendium of genetic regulatory effects across pig tissues

Author

National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., Fang, Lingzhao, National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., and Fang, Lingzhao

Abstract

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Published
2024

9. Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

Author

Raluca Mateescu, García-Contreras, Consolación, Madsen, Ole, Groenen, Martien A. M., López-García,Adrián, Astiz, Susana, Núñez, Yolanda, Benítez, Rita, Fernández, Almudena, González-Bulnes, Antonio, Óvilo, Cristina, Rey Muñoz, Ana Isabel, Isabel Redondo, Beatriz, Vázquez Gómez, Marta, Raluca Mateescu, García-Contreras, Consolación, Madsen, Ole, Groenen, Martien A. M., López-García,Adrián, Astiz, Susana, Núñez, Yolanda, Benítez, Rita, Fernández, Almudena, González-Bulnes, Antonio, Óvilo, Cristina, Rey Muñoz, Ana Isabel, Isabel Redondo, Beatriz, and Vázquez Gómez, Marta

Abstract

Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype∗weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development., MINECO, FEDER, Depto. de Producción Animal, Fac. de Veterinaria, TRUE, pub

Published
2024

20. Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs

Author

Yang, Bin, Cui, Leilei, Perez-Enciso, Miguel, Traspov, Aleksei, Crooijmans, Richard P. M. A., Zinovieva, Natalia, Schook, Lawrence B., Archibald, Alan, Gatphayak, Kesinee, Knorr, Christophe, Triantafyllidis, Alex, Alexandri, Panoraia, Semiadi, Gono, Hanotte, Olivier, Dias, Deodália, Dovč, Peter, Uimari, Pekka, Iacolina, Laura, Scandura, Massimo, Groenen, Martien A. M., Huang, Lusheng, and Megens, Hendrik-Jan

Published
2020
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25. The genomics of adaptation to climate in European great tit (Parus major) populations.

Author

Stonehouse, Joanne C, Spurgin, Lewis G, Laine, Veronika N, Bosse, Mirte, Consortium, The Great Tit HapMap, Groenen, Martien A M, Oers, Kees van, Sheldon, Ben C, Visser, Marcel E, and Slate, Jon

Subjects
GREAT tit, GENOMICS, SINGLE nucleotide polymorphisms, GENETIC variation, GLACIAL Epoch
Abstract

The recognition that climate change is occurring at an unprecedented rate means that there is increased urgency in understanding how organisms can adapt to a changing environment. Wild great tit (Parus major) populations represent an attractive ecological model system to understand the genomics of climate adaptation. They are widely distributed across Eurasia and they have been documented to respond to climate change. We performed a Bayesian genome-environment analysis, by combining local climate data with single nucleotide polymorphisms genotype data from 20 European populations (broadly spanning the species' continental range). We found 36 genes putatively linked to adaptation to climate. Following an enrichment analysis of biological process Gene Ontology (GO) terms, we identified over-represented terms and pathways among the candidate genes. Because many different genes and GO terms are associated with climate variables, it seems likely that climate adaptation is polygenic and genetically complex. Our findings also suggest that geographical climate adaptation has been occurring since great tits left their Southern European refugia at the end of the last ice age. Finally, we show that substantial climate-associated genetic variation remains, which will be essential for adaptation to future changes. [ABSTRACT FROM AUTHOR]

Published
2024
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26. A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwar?sm in Chicken.

Author

Zhou Wu, Derks, Martijn F. L., Dibbits, Bert, Megens, Hendrik-Jan, Groenen, Martien A. M., and Crooijmans, Richard P. M. A.

Subjects
MEMBRANE proteins, CHICKENS, NONSENSE mutation, WHOLE genome sequencing, GENETIC variation, SOMATOTROPIN receptors
Abstract

Autosomal dwarfism (adw) in chickens is a growth deficiency caused by a recessive mutation. Characteristic for adw is an approximately 30% growth reduction with short shank. The adw variant was first recognized in the Cornell K-strain of White Leghorns, but the genetic causal variant remained unknown. To identify the causal variant underlying the adw phenotype, fine mapping was conducted on chromosome 1, within 52--56 Mb. This region was known to harbor the causal variant from previous linkage studies.We compared whole-genome sequence data of this region from normal-sized and adw chickens in order to find the unique causal variant. We identified a novel nonsense mutation NP_001006244.1:p.(Trp59*), in the transmembrane protein 263 gene (TMEM263), completely associated with adw. The nonsense mutation truncates the transmembrane protein within the membrane-spanning domain, expected to cause a dysfunctional protein. TMEM263 is reported to be associated with bone mineral deposition in humans, and the protein shows interaction with growth hormone 1 (GH1). Our study presents molecular genetic evidence for a novel loss-of-function variant, which likely alters body growth and development in autosomal dwarf chicken. [ABSTRACT FROM AUTHOR]

Published
2024
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28. The genomics of adaptation to climate in European great tit (Parus major) populations

Author

Stonehouse, Joanne C., Spurgin, Lewis G., Laine, Veronika N., Bosse, Mirte, Groenen, Martien A. M., van Oers, Kees, Sheldon, Ben C., Visser, Marcel E., Slate, Jon, Stonehouse, Joanne C., Spurgin, Lewis G., Laine, Veronika N., Bosse, Mirte, Groenen, Martien A. M., van Oers, Kees, Sheldon, Ben C., Visser, Marcel E., and Slate, Jon

Abstract

The recognition that climate change is occurring at an unprecedented rate means that there is increased urgency in understanding how organisms can adapt to a changing environment. Wild great tit (Parus major) populations represent an attractive ecological model system to understand the genomics of climate adaptation. They are widely distributed across Eurasia and they have been documented to respond to climate change. We performed a Bayesian genome-environment analysis, by combining local climate data with single nucleotide polymorphisms genotype data from 20 European populations (broadly spanning the species’ continental range). We found 36 genes putatively linked to adaptation to climate. Following an enrichment analysis of biological process Gene Ontology (GO) terms, we identified over-represented terms and pathways among the candidate genes. Because many different genes and GO terms are associated with climate variables, it seems likely that climate adaptation is polygenic and genetically complex. Our findings also suggest that geographical climate adaptation has been occurring since great tits left their Southern European refugia at the end of the last ice age. Finally, we show that substantial climate-associated genetic variation remains, which will be essential for adaptation to future changes.

Published
2023

29. Assessing the relationship between the in silico predicted consequences of 97 missense mutations mapping to 68 genes related to lipid metabolism and their association with porcine fatness traits

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, González-Prendes, Rayner, Derks, Martijn F. L., Groenen, Martien A. M., Quintanilla, Raquel, Amills, Marcel, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, González-Prendes, Rayner, Derks, Martijn F. L., Groenen, Martien A. M., Quintanilla, Raquel, and Amills, Marcel

Abstract

In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene. Although the lack of endophenotypes and the limited sample size of certain genotypic classes might have limited to some extent the reach of the current study, our data indicate that present-day bioinformatic tools have a modest ability to predict the impact of missense mutations on complex phenotypes.

Published
2023

34. Additional file 2 of Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry

Author

Wu, Zhou, Bosse, Mirte, Rochus, Christina M., Groenen, Martien A. M., and Crooijmans, Richard P. M. A.

Abstract

Additional file 2: Figure S1. Unrooted Neighbor-Joining Tree (NJ-tree) illustrates the Reynold’s distance between breeds. Figure S2. Manhattan plot of hapFLK results. Figure S3. Distribution of shared identity-by-descent blocks identified between breeds. Figure S4. Distribution of regions of rIBD across the genome, showing the relative fraction of the haplotype sharing between DrFwB and DB and that between DrFwB and DrFw. Figure S5. Correlation of assignments of individuals based on the two clustering approaches. Figure S6. Demonstration of two CNV detected by signatures of selection in the SOX5 and SOX10 genes. Figure S7. Distribution of relative identity-by-descent (rIBD)on chromosome 1, showing the relative fraction of haplotype blocks shared between GrMwB and DB (positive rIBD) and GrMwB and GrMw (negative rIBD).

Published
2023
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35. Additional file 1 of High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data

Author

Lee, Young-Lim, Bosse, Mirte, Takeda, Haruko, Moreira, Gabriel Costa Monteiro, Karim, Latifa, Druet, Tom, Oget-Ebrad, Claire, Coppieters, Wouter, Veerkamp, Roel F., Groenen, Martien A. M., Georges, Michel, Bouwman, Aniek C., and Charlier, Carole

Abstract

Additional file 1: Figure S1. Number of discovered SVs depending on mean sequencing depth. Figure S2. Distinctive RD distribution discerning mCNVs from biallelic duplications. Figure S3. Size distribution of overall CNVs. Figure S4. Canonical and non-canonical copy number variants. Figure S5. Number of variants before and after filtering steps. Figure S6. Mendelian error fraction obtained from the effective number of trios. Figure S7. Minor allele frequency between the discovery and validation cohort. Figure S8. Maximum LD (r2) between CNV-SNP pairs in WGS data set. Figure S9. Underlying WGS data for a 16-kb mCNV inspected in IGV. Figure S10. Underlying WGS data for two copy gain duplication events. Figure S11. Manual correction of ORM1 duplication genotypes.

Published
2023
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38. High-resolution structural variation catalogue in a large-scale whole genome sequenced bovine family cohort data

Author

Lee, Young-Lim, primary, Bosse, Mirte, additional, Takeda, Haruko, additional, Moreira, Gabriel Costa Monteiro, additional, Karim, Latifa, additional, Druet, Tom, additional, Oget-Ebrad, Claire, additional, Coppieters, Wouter, additional, Veerkamp, Roel F., additional, Groenen, Martien A. M., additional, Georges, Michel, additional, Bouwman, Aniek C., additional, and Charlier, Carole, additional

Published
2022
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45. Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

Author

Ministerio de Economía y Competitividad (España), European Commission, Garcia-Contreras, Consolacion [0000-0003-4624-2585], Groenen, Martien A. M. [0000-0003-0484-4545], López-García, Adrián [0000-0002-8649-750X], Vázquez-Gómez, M. [0000-0002-8916-2086], Astiz, Susana [0000-0002-9718-0903], Núñez, Yolanda [0000-0001-5988-7628], Benítez Yáñez, Rita María [0000-0001-7459-2836], Fernández, Almudena [0000-0002-4495-9366], Isabel, Beatriz [0000-0001-6192-6411], Rey, Ana I. [0000-0003-4403-9225], González De Bulnes, Antonio [0000-0002-0917-4475], Óvilo Martín, Cristina [0000-0002-5738-8435], Garcia-Contreras, Consolacion, Madsen, Ole, Groenen, Martien A. M., López-García, Adrián, Vázquez-Gómez, M., Astiz, Susana, Núñez, Yolanda, Benítez Yáñez, Rita María, Fernández, Almudena, Isabel, Beatriz, Rey, Ana I., González De Bulnes, Antonio, Óvilo Martín, Cristina, Ministerio de Economía y Competitividad (España), European Commission, Garcia-Contreras, Consolacion [0000-0003-4624-2585], Groenen, Martien A. M. [0000-0003-0484-4545], López-García, Adrián [0000-0002-8649-750X], Vázquez-Gómez, M. [0000-0002-8916-2086], Astiz, Susana [0000-0002-9718-0903], Núñez, Yolanda [0000-0001-5988-7628], Benítez Yáñez, Rita María [0000-0001-7459-2836], Fernández, Almudena [0000-0002-4495-9366], Isabel, Beatriz [0000-0001-6192-6411], Rey, Ana I. [0000-0003-4403-9225], González De Bulnes, Antonio [0000-0002-0917-4475], Óvilo Martín, Cristina [0000-0002-5738-8435], Garcia-Contreras, Consolacion, Madsen, Ole, Groenen, Martien A. M., López-García, Adrián, Vázquez-Gómez, M., Astiz, Susana, Núñez, Yolanda, Benítez Yáñez, Rita María, Fernández, Almudena, Isabel, Beatriz, Rey, Ana I., González De Bulnes, Antonio, and Óvilo Martín, Cristina

Abstract

Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

Published
2020

46. Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene

Author

Oliveira, Haniel C., Derks, Martijn F. L., Lopes, Marcos S., Madsen, Ole, Harlizius, Barbara, van Son, Maren, Grindflek, Eli H., Gòdia, Marta, Gjuvsland, Arne B., Otto, Pamela Itajara, Groenen, Martien A. M., and Guimaraes, Simone E. F.

Subjects
pig genomics, finemapping, WIAS, Genetics, GWAS, Molecular Medicine, backfat, Fokkerij en Genomica, animal breeding, Animal Breeding and Genomics, Genetics (clinical)
Abstract

Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.

Published
2022

47. Familial follicular cell thyroid carcinomas in a large number of Dutch German Longhaired Pointers

Author

Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, Crooijmans, Richard P M A, Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, and Crooijmans, Richard P M A

Abstract

Thyroid carcinomas (TCs) originating from follicular cells of the thyroid gland occur in both humans and dogs, and they have highly similar histomorphologic patterns. In dogs, TCs have not been extensively investigated, especially concerning the familial origin of TCs. Here, we report familial thyroid follicular cell carcinomas (FCCs) confirmed by histology in 54 Dutch origin German longhaired pointers. From the pedigree, 45 of 54 histopathologically confirmed cases are closely related to a pair of first-half cousins in the past, indicating a familial disease. In addition, genetics contributed more to the thyroid FCC than other factors by an estimated heritability of 0.62 based on pedigree. The age of diagnosis ranged between 4.5 and 13.5 years, and 76% of cases were diagnosed before 10 years of age, implying an early onset of disease. We observed a significant higher pedigree-based inbreeding coefficient in the affected dogs (mean F, 0.23) compared to unaffected dogs (mean F, 0.14), suggesting the contribution of inbreeding to tumour development. The unique occurrence of familial thyroid FCC in this dog population and the large number of affected dogs make this population an important model to identify the genetic basis of familial thyroid FCC in this breed and may contribute to the research into pathogenesis, prevention and treatment in humans.

Published
2022

49. Familial follicular cell thyroid carcinomas in a large number of Dutch German Longhaired Pointers

Author

Veterinair Pathologisch Diagnostisch Cnt, VPDC pathologie, dPB CR, VP pathologie, Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, Crooijmans, Richard P M A, Veterinair Pathologisch Diagnostisch Cnt, VPDC pathologie, dPB CR, VP pathologie, Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, and Crooijmans, Richard P M A

Published
2022

50. Strong signatures of selection in the domestic pig genome

Author

Rubin, Carl-Johan, Megens, Hendrik-Jan, Barrio, Alvaro Martinez, Maqbool, Khurram, Sayyab, Shumaila, Schwochow, Doreen, Wang, Chao, Carlborg, Örjan, Jern, Patric, Jørgensen, Claus B., Archibald, Alan L., Fredholm, Merete, Groenen, Martien A. M., and Andersson, Leif

Published
2012

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