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3. Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

Wang, Ming-Shan, Zhang, Jin-Jin, Guo, Xing, Li, Ming, Meyer, Rachel, Ashari, Hidayat, Zheng, Zhu-Qing, Wang, Sheng, Peng, Min-Sheng, Jiang, Yu, Thakur, Mukesh, Suwannapoom, Chatmongkon, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Kharrati-Koopaee, Hamed, Zeng, Lin, Wang, Yun-Mei, Yin, Ting-Ting, Yang, Min-Min, Li, Ming-Li, Lu, Xue-Mei, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasig, Thilina Madusanka, Feng, Shao-Hong, Zhang, Hao, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Thuy, Le Thi, Mwai, Okeyo A, Ibrahim, Mohamed Nawaz Mohamed, Zhang, Guojie, Qu, Kai-Xing, Hanotte, Olivier, Shapiro, Beth, Bosse, Mirte, Wu, Dong-Dong, Han, Jian-Lin, and Zhang, Ya-Ping

Subjects
Biotechnology, Genetics, Human Genome, Animals, Animals, Domestic, Chickens, Domestication, Genome, Genomics, Humans, Bottleneck, Genetic load, Deleterious mutation, Domestic chicken, Developmental Biology
Abstract

BackgroundSpecies domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.ResultsWe analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.ConclusionThis study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Published
2021

5. A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds

Author

Ceccobelli, Simone, Landi, Vincenzo, Senczuk, Gabriele, Mastrangelo, Salvatore, Sardina, Maria Teresa, Ben-Jemaa, Slim, Persichilli, Christian, Karsli, Taki, Bâlteanu, Valentin-Adrian, Raschia, María Agustina, Poli, Mario Andrés, Ciappesoni, Gabriel, Muchadeyi, Farai Catherine, Dzomba, Edgar Farai, Kunene, Nokuthula Winfred, Lühken, Gesine, Deniskova, Tatiana Evgenievna, Dotsev, Arsen Vladimirovich, Zinovieva, Natalia Anatolievna, Zsolnai, Attila, Anton, István, Kusza, Szilvia, Carolino, Nuno, Santos-Silva, Fátima, Kawęcka, Aldona, Świątek, Marcin, Niżnikowski, Roman, Špehar, Marija, Anaya, Gabriel, Granero, Antonio, Perloiro, Tiago, Cardoso, Pedro, Grande, Silverio, de los Santos, Beatriz López, Danchin-Burge, Coralie, Pasquini, Marina, Martínez Martínez, Amparo, Delgado Bermejo, Juan Vicente, Lasagna, Emiliano, Ciani, Elena, Sarti, Francesca Maria, and Pilla, Fabio

Published
2023
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7. Author Correction: 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Biochemistry and Cell Biology, Biological Sciences, Clinical Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

8. 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Genetics, Animal Distribution, Animals, Animals, Domestic, Asia, Chickens, Domestication, Gene Pool, Genome, Geography, Likelihood Functions, Phylogeny, Poultry, Selection, Genetic, Biochemistry and Cell Biology, Clinical Sciences, Developmental Biology
Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Published
2020

10. Genomic responses to climatic challenges in beef cattle: A review.

Author

Colombi, Daniele, Perini, Francesco, Bettini, Stefano, Mastrangelo, Salvatore, Abeni, Fabio, Conte, Giuseppe, Marletta, Donata, Cassandro, Martino, Bernabucci, Umberto, Ciampolini, Roberta, and Lasagna, Emiliano

Subjects
BEEF cattle breeds, CLIMATE change adaptation, GREENHOUSE gases, LIVESTOCK breeding, CLIMATE extremes, PHYSIOLOGICAL effects of cold temperatures
Abstract

Climate change is a major concern for the near future and for livestock breeding. Cattle breeding, due to its greenhouse gas emissions, is one of the most implicated industries. Consequently, the main future goals are to breed animals resilient to climate change, with the aim of lowering the livestock impact on the environment and selecting animals that will be able to resist different, unsuitable, and changing climates. The aim of this literature review is to compare the most recent studies on the response and adaptation of beef cattle breeds to extreme environments, in terms of genes and pathways involved. Beef breeding is just starting to implement genomics in its selection plans, and shedding light on the genomic responses to extreme climates could speed up and simplify the adaptation of these breeds to climate change. This review discusses the genes involved in climatic stress responses, including those related to extremely cold climates, in beef and dual‐purpose cattle breeds. Genes were associated with productive traits, coat and skin structure and development, thermotolerance, cellular physiology and DNA repair mechanisms, immune system, and fertility traits. The knowledge of genes and pathways involved in climate resilience should be taken into consideration for further selection in beef cattle breeding and could promote the valorization of local breeds adapted to extreme environmental conditions. The use of local or resilient breeds could enhance the environmental and social sustainability, animal welfare, and production, compared with the introduction of cosmopolitan breeds with uncertain adaptation in uncontrolled environmental areas. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Understanding the genetic variation and structure of the Rustipollos chicken synthetic population locally adapted to Paraguay : opportunities for a sustainable chicken productivity

Author

Universidad Nacional de Asunción. Facultad de Ciencias Veterinarias, Castro Rojas, Liz Aurora, Ceccobelli, Simone, Gayozo Melgarejo, Elvio, Méndez Morán, Natalia, Marchegiani, Sara, Martínez Martínez, Amparo, Camacho Vallejo, María Esperanza, Toalombo Vargas, Paula Alexandra, Araújo de Carvalho, Débora, Pons Barro, Agueda Laura, Quirõz, Jorge, Fernández Barriocanal, José, Torres Ñumbay, Miguel Wenceslao, Lasagna, Emiliano, Universidad Nacional de Asunción. Facultad de Ciencias Veterinarias, Castro Rojas, Liz Aurora, Ceccobelli, Simone, Gayozo Melgarejo, Elvio, Méndez Morán, Natalia, Marchegiani, Sara, Martínez Martínez, Amparo, Camacho Vallejo, María Esperanza, Toalombo Vargas, Paula Alexandra, Araújo de Carvalho, Débora, Pons Barro, Agueda Laura, Quirõz, Jorge, Fernández Barriocanal, José, Torres Ñumbay, Miguel Wenceslao, and Lasagna, Emiliano

Abstract

The production of backyard chickens is an activity of great importance in the economy of rural families in Paraguay. The Rustipollos population was created through directed crosses between a commercial meat line and a local population belonging to non-specific breeds but phenotypically assimilated to Creole breeds. The aim of this study was to evaluate the genetic diversity, relationship, and structure of Rustipollos using 29 microsatellite markers. Analysis was performed on 50 Rustipollos animals and 926 other individuals as reference breeds/populations from Europe, Africa, South, and North America. A total of 318 alleles were detected, with a mean of 10.97 per locus. The polymorphic information content indicated that 80% of all loci were highly to moderately informative. Only two breeds/populations showed loci that did not deviate from the Hardy–Weinberg equilibrium. The results of genetic diversity indexes suggested moderate levels of genetic variability in Rustipollos population and low inbreeding level. The genetic differentiation index indicates a high genetic differentiation between populations. The results of the Neighbor-Net tree and STRUCTURE analyses indicate the existence of distinct gene pools, with some genetic relationships between Rustipollos, the commercial chicken strain, and south Spanish breeds. The Discriminant Analysis of Principal Components confirmed the observed genetic distances between breeds/populations. The results will be useful for sustainable use and official recognition of this population.

Published
2024

13. Understanding the Genetic Variation and Structure of the Rustipollos Chicken Synthetic Population Locally Adapted to Paraguay: Opportunities for a Sustainable Chicken Productivity.

Author

Castro Rojas, Liz Aurora, Ceccobelli, Simone, Gayozo, Elvio, Méndez Morán, Natalia, Marchegiani, Sara, Martínez Martínez, Amparo, Camacho Vallejo, María Esperanza, Toalombo Vargas, Paula Alexandra, de Carvalho, Débora Araújo, Pons Barro, Agueda Laura, Quirõz, Jorge, Barriocanal, José Fernández, Ñumbay, Miguel Torres, and Lasagna, Emiliano

Subjects
CHICKEN breeds, SUSTAINABILITY, POULTRY genetics
Abstract

The production of backyard chickens is an activity of great importance in the economy of rural families in Paraguay. The Rustipollos population was created through directed crosses between a commercial meat line and a local population belonging to non-specific breeds but phenotypically assimilated to Creole breeds. The aim of this study was to evaluate the genetic diversity, relationship, and structure of Rustipollos using 29 microsatellite markers. Analysis was performed on 50 Rustipollos animals and 926 other individuals as reference breeds/populations from Europe, Africa, South, and North America. A total of 318 alleles were detected, with a mean of 10.97 per locus. The polymorphic information content indicated that 80% of all loci were highly to moderately informative. Only two breeds/populations showed loci that did not deviate from the Hardy–Weinberg equilibrium. The results of genetic diversity indexes suggested moderate levels of genetic variability in Rustipollos population and low inbreeding level. The genetic differentiation index indicates a high genetic differentiation between populations. The results of the Neighbor-Net tree and STRUCTURE analyses indicate the existence of distinct gene pools, with some genetic relationships between Rustipollos, the commercial chicken strain, and south Spanish breeds. The Discriminant Analysis of Principal Components confirmed the observed genetic distances between breeds/populations. The results will be useful for sustainable use and official recognition of this population. [ABSTRACT FROM AUTHOR]

Published
2024
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15. The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Author

Cortellari, Matteo, Barbato, Mario, Talenti, Andrea, Bionda, Arianna, Carta, Antonello, Ciampolini, Roberta, Ciani, Elena, Crisà, Alessandra, Frattini, Stefano, Lasagna, Emiliano, Marletta, Donata, Mastrangelo, Salvatore, Negro, Alessio, Randi, Ettore, Sarti, Francesca M., Sartore, Stefano, Soglia, Dominga, Liotta, Luigi, Stella, Alessandra, Ajmone-Marsan, Paolo, Pilla, Fabio, Colli, Licia, and Crepaldi, Paola

Published
2021
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17. Author Correction: The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Author

Cortellari, Matteo, Barbato, Mario, Talenti, Andrea, Bionda, Arianna, Carta, Antonello, Ciampolini, Roberta, Ciani, Elena, Crisà, Alessandra, Frattini, Stefano, Lasagna, Emiliano, Marletta, Donata, Mastrangelo, Salvatore, Negro, Alessio, Randi, Ettore, Sarti, Francesca M., Sartore, Stefano, Soglia, Dominga, Liotta, Luigi, Stella, Alessandra, Ajmone‑Marsan, Paolo, Pilla, Fabio, Colli, Licia, and Crepaldi, Paola

Published
2021
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19. Genomics of Dwarfism in Italian Local Chicken Breeds

Author

Perini, Francesco, Cendron, Filippo, Wu, Zhou, Sevane Fernández, Natalia, Li, Zhiqiang, Huang, Chunhua, Smith, Jacqueline, Lasagna, Emiliano, Cassandro, Martino, Penasa, Mauro, Perini, Francesco, Cendron, Filippo, Wu, Zhou, Sevane Fernández, Natalia, Li, Zhiqiang, Huang, Chunhua, Smith, Jacqueline, Lasagna, Emiliano, Cassandro, Martino, and Penasa, Mauro

Abstract

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed., Ministry of Agricultural, Food and Forestry Policies (Italy), China Scholarship Council, Depto. de Producción Animal, Fac. de Veterinaria, TRUE, pub

Published
2023

21. Genomics of Dwarfism in Italian Local Chicken Breeds

Author

Perini, Francesco, primary, Cendron, Filippo, additional, Wu, Zhou, additional, Sevane, Natalia, additional, Li, Zhiqiang, additional, Huang, Chunhua, additional, Smith, Jacqueline, additional, Lasagna, Emiliano, additional, Cassandro, Martino, additional, and Penasa, Mauro, additional

Published
2023
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23. Nutrigenomics in Animal Feeding: Digital Gene Expression Analysis in Poultry Fed Tenebrio molitor Larvae Meal

Author

Soglia, Dominga, primary, Viola, Irene, additional, Nery, Joana, additional, Maione, Sandra, additional, Sartore, Stefano, additional, Lasagna, Emiliano, additional, Perini, Francesco, additional, Gariglio, Marta, additional, Bongiorno, Valentina, additional, Moretti, Riccardo, additional, Chessa, Stefania, additional, Sacchi, Paola, additional, Bergero, Domenico, additional, Biasato, Ilaria, additional, Gasco, Laura, additional, and Schiavone, Achille, additional

Published
2022
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25. Author Correction:The climatic and genetic heritage of Italian goat breeds with genomic SNP data (Scientific Reports, (2021), 11, 1, (10986), 10.1038/s41598-021-89900-2)

Author

Cortellari, Matteo, Barbato, Mario, Talenti, Andrea, Bionda, Arianna, Carta, Antonello, Ciampolini, Roberta, Ciani, Elena, Crisà, Alessandra, Frattini, Stefano, Lasagna, Emiliano, Marletta, Donata, Mastrangelo, Salvatore, Negro, Alessio, Randi, Ettore, Sarti, Francesca M., Sartore, Stefano, Soglia, Dominga, Liotta, Luigi, Stella, Alessandra, Ajmone‑Marsan, Paolo, Pilla, Fabio, Colli, Licia, and Crepaldi, Paola

Abstract

The Data Availability section in the original version of this Article was omitted. It now appears as below: “The genotyping data for the Italian goat considered in this study are deposited and publicly available on Mendeley Data (DOI: 10.17632/hnd59x6gmg.1; URL: https:// data. mende ley. com/ datas ets/ hnd59 x6gmg/1).” The original Article has been corrected.

Published
2021
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29. Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

Author

Soglia, Dominga, primary, Sartore, Stefano, additional, Lasagna, Emiliano, additional, Castellini, Cesare, additional, Cendron, Filippo, additional, Perini, Francesco, additional, Cassandro, Martino, additional, Marzoni, Margherita, additional, Iaffaldano, Nicolaia, additional, Buccioni, Arianna, additional, Dabbou, Sihem, additional, Castillo, Annelisse, additional, Maione, Sandra, additional, Bianchi, Chiara, additional, Profiti, Margherita, additional, Sacchi, Paola, additional, Cerolini, Silvia, additional, and Schiavone, Achille, additional

Published
2021
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30. Additional file 1 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Author

Cortellari, Matteo, Bionda, Arianna, Negro, Alessio, Frattini, Stefano, Mastrangelo, Salvatore, Somenzi, Elisa, Lasagna, Emiliano, Sarti, Francesca M., Ciani, Elena, Ciampolini, Roberta, Marletta, Donata, Liotta, Luigi, Ajmone Marsan, Paolo, Pilla, Fabio, Colli, Licia, Talenti, Andrea, and Crepaldi, Paola

Abstract

Additional file 1: Figure S1. Geographic distribution (a), phylogeny tree (b), and multidimensional scaling analysis (c) of all the Italian goat breeds included in the study.

Published
2021
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31. Additional file 2 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Author

Cortellari, Matteo, Bionda, Arianna, Negro, Alessio, Frattini, Stefano, Mastrangelo, Salvatore, Somenzi, Elisa, Lasagna, Emiliano, Sarti, Francesca M., Ciani, Elena, Ciampolini, Roberta, Marletta, Donata, Liotta, Luigi, Ajmone Marsan, Paolo, Pilla, Fabio, Colli, Licia, Talenti, Andrea, and Crepaldi, Paola

Abstract

Additional file 2: Figure S2. Manhattan plots representing the signals of signatures of selection in the two population groups (CSD and NRD), of the ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.

Published
2021
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32. Additional file 1 of Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

Wang, Ming-Shan, Zhang, Jin-Jin, Guo, Xing, Li, Ming, Meyer, Rachel, Ashari, Hidayat, Zheng, Zhu-Qing, Wang, Sheng, Peng, Min-Sheng, Jiang, Yu, Thakur, Mukesh, Suwannapoom, Chatmongkon, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Kharrati-Koopaee, Hamed, Zeng, Lin, Wang, Yun-Mei, Yin, Ting-Ting, Yang, Min-Min, Li, Ming-Li, Lu, Xue-Mei, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasig, Thilina Madusanka, Feng, Shao-Hong, Zhang, Hao, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Thuy, Le Thi, Mwai, Okeyo A., Ibrahim, Mohamed Nawaz Mohamed, Zhang, Guojie, Qu, Kai-Xing, Hanotte, Olivier, Shapiro, Beth, Bosse, Mirte, Wu, Dong-Dong, Han, Jian-Lin, and Zhang, Ya-Ping

Abstract

Additional file 1: Figure S1. Nucleotide diversity for G. g. spadiceus and chicken populations (grouped by samling locations and breeds). Figure S2. Demographic histories for G. g. spadiceus and diverse chicken groups by PSMC. A total of 18 chicken populations were included in this analysis. Figure S3. Four tested demographic models for dadi analysis. Nanc, ancestral population size before the split; T, timepoints; m, migrations; Napop, ancestral population size after split. Ncpop, current population size. Arrows depict migration directions. Figure S4. Comparing observed data and model allele frequency spectrum for the best model (Model 3). Figure S5. Provean-scores for nonsynonymous mutations (for all mutations, left; and for mutations with Provean-scores ≤ –2.5, right) in microchromosomes, macrochromosomes, and intermediate chromosomes. Figure S6. Pipeline for constructing the mouse model with a mutation at the mouse TSHR locus (p. Gly559Arg; c.1675G>A). Figure S7. Photograph showing TSHR-559Arg knock-in homozygous (HO) and wild-type mice at 10 months old. Figure S8. Gly558Arg knock-in mice consumed less food than wild-type. *, P

Published
2021
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33. Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Author

Senczuk, Gabriele, Mastrangelo, Salvatore, Ajmone-Marsan, Paolo, Becskei, Zsolt, Colangelo, Paolo, Colli, Licia, Ferretti, Luca, Karsli, Taki, Lancioni, Hovirag, Lasagna, Emiliano, Marletta, Donata, Persichilli, Christian, Portolano, Baldassare, Sarti, Francesca M., Ciani, Elena, and Pilla, Fabio

Abstract

Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.

Published
2021
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34. Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Author

Senczuk, Gabriele, Mastrangelo, Salvatore, Ajmone-Marsan, Paolo, Becskei, Zsolt, Colangelo, Paolo, Colli, Licia, Ferretti, Luca, Karsli, Taki, Lancioni, Hovirag, Lasagna, Emiliano, Marletta, Donata, Persichilli, Christian, Portolano, Baldassare, Sarti, Francesca M., Ciani, Elena, and Pilla, Fabio

Abstract

Additional file 10: Figure S8. Projection on a single LDA axis in the model-grouping approach (a) and on the first two LDA axes in the six scenarios separately (b).

Published
2021
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35. Evolution of inbreeding: A gaze into the history of 5 Italian beef cattle breeds

Author

Rovelli, Giacomo, Luigi-Sierra, Maria Gracia, Guan, Dailu, Sbarra, Fiorella, Quaglia, Andrea, Amills, Marcel, and Lasagna, Emiliano

Abstract

Resumen del póster presentado a la 38th International Conference on Animal Genetics (ISAG), celebrada virtualmente del 26 al 30 de julio de 2021., Inbreeding is the main consequence of mating individuals related through common ancestry, to a higher degree than the average relatedness of this population. Minimizing inbreeding is a key point in cattle breeding to avoid the phenotypic expression of detrimental alleles in the offspring as well as to ensure the maintenance of genetic diversity. In the current work, we aimed to characterize the historical evolution of inbreeding in 5 Italian beef cattle breeds (Chianina, 909; Marchigiana, 879; Romagnola, 904; Maremmana, 334; and Podolica, 555) between 2002 and 2019 by using both molecular and genealogical estimates of inbreeding coefficients. PLINK v1.9 software was used to compute inbreeding coefficient Fhat2, while Endog v4.8 was used to calculate the pedigree inbreeding coefficient (Fped), defined as the probability that an individual has 2 “identical-by-descent” alleles. Arlequin software v3.5.2.2 was used to estimate within-population diversity, by calculating observed (Ho) and expected (He) heterozygosities, and historical trends in effective population size (Ne) were estimated with the SNeP software using default settings. The average estimates of Ho, He, Fhat2, and Fped across years (2002–2019) fluctuated between 0.340 and 0.401, 0.348 and 0.392, –0.121 and 0.072, and 0.000 and 0.068, respectively. Despite the fact that we detected fluctuations in the magnitudes of Fhat2 and Fped during the last 20 years, these oscillations were not very important. Changes in homozygosity and inbreeding coefficients across time might be partly explained by the fact that the number of breeders, and particularly sires, is not constant across years. We also observed a slight augment of Fhat2 in the 5 breeds during 2002–2019 increasing 0.01–0.02% per year, while Fped remained quite stable, with an annual increase rate of 0.003–0.004%. The use of a high number of bulls combined with strategies implemented by National Association of Italian Beef Cattle Breeders (ANABIC) to minimize inbreeding might explain these results. Moreover, we detected a sustained decrease of the population effective size (Ne) of these 5 breeds; such results should be interpreted with caution due to the inherent difficulty of estimating Ne from SNPs data in a reliable manner.

Published
2021

36. Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

Wang, Ming Shan, Zhang, Jin Jin, Guo, Xing, Li, Ming, Meyer, Rachel, Ashari, Hidayat, Zheng, Zhu Qing, Wang, Sheng, Peng, Min Sheng, Jiang, Yu, Thakur, Mukesh, Suwannapoom, Chatmongkon, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Kharrati-Koopaee, Hamed, Zeng, Lin, Wang, Yun Mei, Yin, Ting Ting, Yang, Min Min, Li, Ming Li, Lu, Xue Mei, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasig, Thilina Madusanka, Feng, Shao Hong, Zhang, Hao, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Thuy, Le Thi, Mwai, Okeyo A., Ibrahim, Mohamed Nawaz Mohamed, Zhang, Guojie, Qu, Kai Xing, Hanotte, Olivier, Shapiro, Beth, Bosse, Mirte, Wu, Dong Dong, Han, Jian Lin, Zhang, Ya Ping, Wang, Ming Shan, Zhang, Jin Jin, Guo, Xing, Li, Ming, Meyer, Rachel, Ashari, Hidayat, Zheng, Zhu Qing, Wang, Sheng, Peng, Min Sheng, Jiang, Yu, Thakur, Mukesh, Suwannapoom, Chatmongkon, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Kharrati-Koopaee, Hamed, Zeng, Lin, Wang, Yun Mei, Yin, Ting Ting, Yang, Min Min, Li, Ming Li, Lu, Xue Mei, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasig, Thilina Madusanka, Feng, Shao Hong, Zhang, Hao, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Thuy, Le Thi, Mwai, Okeyo A., Ibrahim, Mohamed Nawaz Mohamed, Zhang, Guojie, Qu, Kai Xing, Hanotte, Olivier, Shapiro, Beth, Bosse, Mirte, Wu, Dong Dong, Han, Jian Lin, and Zhang, Ya Ping

Abstract

Background: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. Results: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the “cost of domestication” hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. Conclusion: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Published
2021

37. Evolution of inbreeding: a gaze into five Italian beef cattle breeds history

Author

Rovelli, Giacomo, Luigi-Sierra, Maria Gracia, Guan, Dailu, Sbarra, Fiorella, Quaglia, Andrea, Sarti, Francesca Maria, Amills, Marcel, Lasagna, Emiliano, Rovelli, Giacomo, Luigi-Sierra, Maria Gracia, Guan, Dailu, Sbarra, Fiorella, Quaglia, Andrea, Sarti, Francesca Maria, Amills, Marcel, and Lasagna, Emiliano

Abstract

In the last decades, intensive selection programs have led to sustained increases of inbreeding in dairy cattle, a feature that might have adverse consequences on the viability and phenotypic performance of their offspring. This study aimed to determine the evolution of inbreeding of five Italian beef cattle breeds (Marchigiana, Chianina, Romagnola, Maremmana, and Podolica) during a period of almost 20 years (2002– 2019). The estimates of Ho, He, Fhat2, and Fped averaged across years (2002–2019) in the studied breeds fluctuated between 0.340–0.401, 0.348–0.392, –0.121–0.072, and 0.000–0.068, respectively. Moreover, annual rates of increase of the estimated inbreeding coefficients have been very low (Fhat2 = 0.01–0.02%; Fped = 0.003–0.004%). The use of a high number of bulls combined with strategies implemented by the Association of Italian Beef Cattle Breeders ANABIC to minimize inbreeding might explain these results. Despite the fact that diversity and inbreeding have remained quite stable during the last two decades, we have detected a sustained decrease of the population effective size of these five breeds. Such results should be interpreted with caution due to the inherent difficulty of estimating Ne from SNPs data in a reliable manner.

Published
2021

38. 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, Zhang, Ya-Ping, Wang, Ming Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world’s most numerous domestic animal.

Published
2020

39. PRNP Polymorphisms in Eight Local Goat Populations/Breeds from Central and Southern Italy

Author

Torricelli, Martina, primary, Sebastiani, Carla, additional, Ciullo, Marcella, additional, Ceccobelli, Simone, additional, Chiappini, Barbara, additional, Vaccari, Gabriele, additional, Capocefalo, Antonio, additional, Conte, Michela, additional, Giovannini, Samira, additional, Lasagna, Emiliano, additional, Sarti, Francesca Maria, additional, and Biagetti, Massimo, additional

Published
2021
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43. Into the origin and diversification of Podolian cattle breeds by testing Neolithic scenarios of European colonization using genome-wide SNP data

Author

Senczuk, Gabriele, primary, MASTRANGELO, Salvatore, additional, Marsan, Paolo Ajmone, additional, Becskei, Zsolt, additional, Colangelo, Paolo, additional, Colli, Licia, additional, Ferretti, Luca, additional, Karsli, Taki, additional, Lancioni, Hovirag, additional, Lasagna, Emiliano, additional, Marletta, Donata, additional, Persichilli, Christian, additional, PORTOLANO, Baldassare, additional, Sarti, Francesca, additional, Ciani, Elena, additional, and Pilla, Fabio, additional

Published
2020
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44. The genetics of phenotypic plasticity in livestock in the era of climate change: a review

Author

Rovelli, Giacomo, primary, Ceccobelli, Simone, additional, Perini, Francesco, additional, Demir, Eymen, additional, Mastrangelo, Salvatore, additional, Conte, Giuseppe, additional, Abeni, Fabio, additional, Marletta, Donata, additional, Ciampolini, Roberta, additional, Cassandro, Martino, additional, Bernabucci, Umberto, additional, and Lasagna, Emiliano, additional

Published
2020
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45. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Author

Cendron, Filippo, primary, Perini, Francesco, additional, Mastrangelo, Salvatore, additional, Tolone, Marco, additional, Criscione, Andrea, additional, Bordonaro, Salvatore, additional, Iaffaldano, Nicolaia, additional, Castellini, Cesare, additional, Marzoni, Margherita, additional, Buccioni, Arianna, additional, Soglia, Dominga, additional, Schiavone, Achille, additional, Cerolini, Silvia, additional, Lasagna, Emiliano, additional, and Cassandro, Martino, additional

Published
2020
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47. Genetic variability assessment in different Mediterranean canine breeds using microsatellite markers

Author

Lasagna, Emiliano, Ceccobelli, Simone, Martinez Martinez, Amparo, Lancioni, Hovirag, Landi, Vincenzo, Cosenza, Mario, Gruppetta, Anthony, Sarti, Francesca Maria, Chiofalo, Vincenzo, San Jose, Carlos, Monteagudo Ibanez, Luis, Liotta, Luigi, Attard, George, and 23rd Congress of Animal Science and Production Association

Subjects
Microsatellites (Genetics), Dog breeds -- Mediterranean Region, Genetics, Pharaoh hound -- Malta
Abstract

The domestic dog (Canis familiaris) was the first species to be domesticated. Today, the ‘Fédération Cynologique Internationale’ distinguishes and recognises 360 canine breeds, classified in 10 ethnological groups. Group 5 ‘Spitz and primitive type’ is subdivided into 7 sections. The Kelb tal Fenech (KTF) is allocated in section 6, while section 7 includes the Italian breed Cirneco dell’Etna (CIE) and different breeds (Valenciano, Ibicenco, Canario, Andaluz) of the Spanish Podenco (POD)., peer-reviewed

Published
2019

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