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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024; 141:531-549. [PMID: 38520124 DOI: 10.1111/jbg.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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Qi L, Xiao L, Fu R, Nie Q, Zhang X, Luo W. Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens. Poult Sci 2024; 103:103863. [PMID: 38810566 PMCID: PMC11166977 DOI: 10.1016/j.psj.2024.103863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.
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Affiliation(s)
- Lin Qi
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Liangchao Xiao
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Rong Fu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China.
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Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats. Sci Rep 2024; 14:14908. [PMID: 38942813 PMCID: PMC11213886 DOI: 10.1038/s41598-024-65303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Ethiopia.
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Abdulfatai Tijjani
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology (IoB), Addis Ababa University, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Siobhan Mor
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Palaeogenomics and Bioarchaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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Danso F, Iddrisu L, Lungu SE, Zhou G, Ju X. Effects of Heat Stress on Goat Production and Mitigating Strategies: A Review. Animals (Basel) 2024; 14:1793. [PMID: 38929412 PMCID: PMC11200645 DOI: 10.3390/ani14121793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Goats, versatile creatures selectively bred for various purposes, have become pivotal in shaping the socioeconomic landscape, particularly in rural and economically challenged areas. Their remarkable ability to withstand and adapt to extreme heat has proven invaluable, allowing them to flourish and reproduce in even the harshest climates on Earth. Goat farming has emerged as a reliable and sustainable solution for securing food resources. However, despite its significance, the goat-producing industry has received less attention than other ruminants. Despite goats' inherent resilience to heat, their productivity and reproductive performance suffer under high ambient temperatures, leading to heat stress. This presents a significant challenge for goat production, necessitating a comprehensive multidisciplinary approach to mitigating the adverse effects of heat stress. This review aims to explore the diverse impacts of heat stress on goats and propose effective measures to address the sector's challenges. By understanding and addressing these issues, we can enhance the resilience and sustainability of goat farming, ensuring its continued contribution to food security and socioeconomic development.
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Affiliation(s)
- Felix Danso
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (F.D.); (S.E.L.)
- Department of Veterinary Medicine, Guangdong Ocean University, Zhanjiang 524088, China
| | - Lukman Iddrisu
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Shera Elizabeth Lungu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (F.D.); (S.E.L.)
| | - Guangxian Zhou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (F.D.); (S.E.L.)
| | - Xianghong Ju
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (F.D.); (S.E.L.)
- Department of Veterinary Medicine, Guangdong Ocean University, Zhanjiang 524088, China
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Kichamu N, Astuti PK, Wanjala G, Strausz P, Bagi Z, Kusza S. A Review on Indigenous Goats of East Africa: A Case for Conservation and Management. BIOLOGY 2024; 13:419. [PMID: 38927299 PMCID: PMC11200369 DOI: 10.3390/biology13060419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa.
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Affiliation(s)
- Nelly Kichamu
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (N.K.); (P.K.A.); (G.W.); (Z.B.)
- Doctoral School of Animal Science, University of Debrecen, Böszözrményi út 138, H-4032 Debrecen, Hungary
| | - Putri Kusuma Astuti
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (N.K.); (P.K.A.); (G.W.); (Z.B.)
- Doctoral School of Animal Science, University of Debrecen, Böszözrményi út 138, H-4032 Debrecen, Hungary
| | - George Wanjala
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (N.K.); (P.K.A.); (G.W.); (Z.B.)
- Doctoral School of Animal Science, University of Debrecen, Böszözrményi út 138, H-4032 Debrecen, Hungary
- Institute of Animal Sciences and Wildlife Management, University of Szeged, Andrássy út 15., H-6800 Hódmezővásárhely, Hungary
| | - Péter Strausz
- Department of Management, Institute of Strategy and Management, Corvinus University of Budapest, Fővám tér 8., H-1093 Budapest, Hungary;
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (N.K.); (P.K.A.); (G.W.); (Z.B.)
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (N.K.); (P.K.A.); (G.W.); (Z.B.)
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Sheriff O, Ahbara AM, Haile A, Alemayehu K, Han JL, Mwacharo JM. Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Front Genet 2024; 15:1353026. [PMID: 38854428 PMCID: PMC11156998 DOI: 10.3389/fgene.2024.1353026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.
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Affiliation(s)
- Oumer Sheriff
- Department of Animal Science, Assosa University, Assosa, Ethiopia
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abulgasim M. Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
| | - Aynalem Haile
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Kefyalew Alemayehu
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
- Ethiopian Agricultural Transformation Institute, Amhara Agricultural Transformation Center, Bahir Dar, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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Zhang C, Asadollahpour Nanaei H, Jafarpour Negari N, Amiri Roudbar M, Amiri Ghanatsaman Z, Niyazbekova Z, Yang X. Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats. BMC Genomics 2024; 25:477. [PMID: 38745140 PMCID: PMC11094986 DOI: 10.1186/s12864-024-10387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. RESULTS To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (- 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. CONCLUSIONS The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.
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Affiliation(s)
- Chenxi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hojjat Asadollahpour Nanaei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | | | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Farahvashi MA, Mousavi SF, Banabazi MH, Asadi Fozi M. High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep. Trop Anim Health Prod 2024; 56:150. [PMID: 38691202 DOI: 10.1007/s11250-024-04002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Mohammad Ali Farahvashi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran
| | - Seyedeh Fatemeh Mousavi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI) Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
- Department of Animal Biosciences (HBIO), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
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Ojeda-Marín C, Gutiérrez JP, Formoso-Rafferty N, Goyache F, Cervantes I. Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight. J Anim Breed Genet 2024; 141:193-206. [PMID: 37990938 DOI: 10.1111/jbg.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/11/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED ) information, on ROH identified using the SW method (FROHSW ) and on ROH identified using the CR method (FROHCR ). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW . Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED . Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.
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Affiliation(s)
- Candela Ojeda-Marín
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Félix Goyache
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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10
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Huang C, Zhao Q, Chen Q, Su Y, Ma Y, Ye S, Zhao Q. Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China. Genes (Basel) 2024; 15:313. [PMID: 38540373 PMCID: PMC10970279 DOI: 10.3390/genes15030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 06/14/2024] Open
Abstract
Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.
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Affiliation(s)
- Chang Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yinxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
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11
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Selionova M, Trukhachev V, Aibazov M, Sermyagin A, Belous A, Gladkikh M, Zinovieva N. Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals (Basel) 2024; 14:327. [PMID: 38275787 PMCID: PMC10812594 DOI: 10.3390/ani14020327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number-only 1 SNP-for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Vladimir Trukhachev
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Magomet Aibazov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Marianna Gladkikh
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
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12
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Gebreselase HB, Nigussie H, Wang C, Luo C. Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing. Animals (Basel) 2024; 14:307. [PMID: 38254476 PMCID: PMC10812714 DOI: 10.3390/ani14020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.
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Affiliation(s)
- Haile Berihulay Gebreselase
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Department of Biotechnology, College of Natural and Computational Science, Aksum University, Aksum 1010, Tigray, Ethiopia
| | | | - Changfa Wang
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China;
| | - Chenglong Luo
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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13
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Senczuk G, Macrì M, Di Civita M, Mastrangelo S, Del Rosario Fresno M, Capote J, Pilla F, Delgado JV, Amills M, Martínez A. The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data. Genet Sel Evol 2024; 56:2. [PMID: 38172652 PMCID: PMC10763158 DOI: 10.1186/s12711-023-00869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. RESULTS The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. CONCLUSIONS This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Martina Macrì
- Animal Breeding Consulting S.L., 14014, Córdoba, Spain
- Universidad de Córdoba, 14071, Córdoba, Spain
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | | | - Juan Capote
- Instituto Canario de Investigaciones Científicas, 38260, Tenerife, Spain
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | | | - Marcel Amills
- CRAG, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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14
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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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16
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Masembe C, Benda KK, Opoola O, Francis MJ, Ndinawe RP, Beine P, Mukiibi R. A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle. Vet Med Sci 2023; 9:2844-2851. [PMID: 37725326 PMCID: PMC10650367 DOI: 10.1002/vms3.1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The cattle industry contributes to Uganda's agricultural output. It faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent molecular genomics and bioinformatics technologies. OBJECTIVES We employed genomic analyses to establish potential ownership of a group of nine cattle that were being claimed by two farmers in Uganda. We investigated the genetic relationship of Ugandan cattle with regional indigenous breeds as well as exotic breeds that are currently present in Uganda. In addition, we investigated regions that are likely to be under selection in the Ugandan cattle. METHODS Hair samples were collected from seven and two animals from farmers A and B, respectively. They were genotyped for 53,218 Single Nucleotide Polymorphism markers. To establish genetic relationships between the sampled animals, we performed genomic analyses including, principal component analysis (PCA), hierarchical clustering analysis and identity by state/descent. We also performed admixture and runs of homozygosity analyses to assess the ancestry composition and identify regions potentially under selection in Ugandan cattle, respectively. RESULTS The seven animals from Farmer A were genetically close to each other but showed minimal relationship with the disputed animals. The two animals from Farmer B were genetically distant from each other but showed greater similarity to four of the disputed animals. Four of the disputed animals showed great dissimilarity from the animals of both farmers. Comparison of these with the reference breeds revealed minimal European exotic genetic introgression into these animals, but rather high similarity to the Sheko. Results also revealed high homozygosity in the major histocompatibility complex regions. CONCLUSIONS Our results demonstrate the use of currently available genomic tools to empirically establish the ownership of cattle; these could be scaled up as a resourceful and viable tool that could be employed to support conflict resolution where reliable livestock identification is unavailable.
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Affiliation(s)
- Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Kirungi Katali Benda
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Oluyinka Opoola
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
- Centre for Tropical Livestock Genetics and Health (CTLGH)University of EdinburghEdinburghUK
| | - Mayega Johnson Francis
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Ruth Pamela Ndinawe
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Peter Beine
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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17
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Ayalew W, Wu X, Tarekegn GM, Sisay Tessema T, Naboulsi R, Van Damme R, Bongcam-Rudloff E, Edea Z, Enquahone S, Yan P. Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation. Animals (Basel) 2023; 13:3269. [PMID: 37893993 PMCID: PMC10603685 DOI: 10.3390/ani13203269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.
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Affiliation(s)
- Wondossen Ayalew
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Getinet Mekuriaw Tarekegn
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
- Scotland’s Rural College (SRUC), Roslin Institute Building, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Rakan Naboulsi
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
| | - Renaud Van Damme
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Zewdu Edea
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia;
| | - Solomon Enquahone
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
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18
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Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
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Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
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19
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Pallotti S, Picciolini M, Antonini M, Renieri C, Napolioni V. Genome-wide scan for runs of homozygosity in South American Camelids. BMC Genomics 2023; 24:470. [PMID: 37605116 PMCID: PMC10440933 DOI: 10.1186/s12864-023-09547-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. RESULTS A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. CONCLUSIONS The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
| | | | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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20
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Amiri Ghanatsaman Z, Ayatolahi Mehrgardi A, Asadollahpour Nanaei H, Esmailizadeh A. Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds. Sci Rep 2023; 13:8722. [PMID: 37253766 DOI: 10.1038/s41598-023-35973-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/26/2023] [Indexed: 06/01/2023] Open
Abstract
During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Ahmad Ayatolahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
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Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds. Animals (Basel) 2023; 13:ani13040753. [PMID: 36830540 PMCID: PMC9952073 DOI: 10.3390/ani13040753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
There are five indigenous chicken breeds in Henan Province, China. These breeds have their own unique phenotypic characteristics in terms of morphology, behavior, skin and feather color, and productive performance, but their genetic basis is not well understood. Therefore, we analyzed the genetic structure, genomic diversity, and migration history of Henan indigenous chicken populations and the selection signals and genes responsible for Henan gamecock unique phenotypes using whole genome resequencing. The results indicate that Henan native chickens clustered most closely with the chicken populations in neighboring provinces. Compared to other breeds, Henan gamecock's inbreeding and selection intensity were more stringent. TreeMix analysis revealed the gene flow from southern chicken breeds into the Zhengyang sanhuang chicken and from the Xichuan black-bone chicken into the Gushi chicken. Selective sweep analysis identified several genes and biological processes/pathways that were related to body size, head control, muscle development, reproduction, and aggression control. Additionally, we confirmed the association between genotypes of SNPs in the strong selective gene LCORL and body size and muscle development in the Gushi-Anka F2 resource population. These findings made it easier to understand the traits of the germplasm and the potential for using the Henan indigenous chicken.
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22
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Taheri S, Saedi N, Zerehdaran S, Javadmanesh A. Identification of selection signatures in Capra hircus and Capra aegagrus in Iran. Anim Sci J 2023; 94:e13864. [PMID: 37560768 DOI: 10.1111/asj.13864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 04/09/2023] [Accepted: 05/17/2023] [Indexed: 08/11/2023]
Abstract
Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.
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Affiliation(s)
- Sadegh Taheri
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Naghmeh Saedi
- Centre for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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23
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Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs. Vet Sci 2022; 10:vetsci10010003. [PMID: 36669004 PMCID: PMC9862740 DOI: 10.3390/vetsci10010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.
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Magoro AM, Mtileni B, Hadebe K, Zwane A. Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review. Animals (Basel) 2022; 12:ani12233353. [PMID: 36496874 PMCID: PMC9735466 DOI: 10.3390/ani12233353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.
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Affiliation(s)
- Aletta Matshidiso Magoro
- Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
- Agricultural Research Council, Animal Production, Irene 0062, South Africa
- Correspondence:
| | - Bohani Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
| | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Onderstepoort 0110, South Africa
| | - Avhashoni Zwane
- Agricultural Research Council, Animal Production, Irene 0062, South Africa
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25
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Genomic Selection in Chinese Holsteins Using Regularized Regression Models for Feature Selection of Whole Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182419. [PMID: 36139283 PMCID: PMC9495168 DOI: 10.3390/ani12182419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Genomic selection (GS) is increasingly widely used in animal breeding, owing to its high efficiency in the genetic improvement of economic traits. In China, GS has been implemented for genetic evaluation of young bulls in dairy cattle breeding programs since 2012. GS is commonly based on single nucleotide polymorphism (SNP) chips. The cost of whole genome sequencing (WGS) has decreased tremendously in recent years, allowing increased studies of WGS-based GS. In this study, based on the imputed WGS data of approximately 8000 Chinese Holsteins, we investigated the performance of GS of milk production traits using the feature selection method of regularized regression. The results showed that WGS-based GS using regularized regression models and the commonly used linear mixed models achieved comparable prediction accuracies. For milk and protein yields, GS using a combination of SNPs selected with a regularized regression model and 50K SNP chip data achieved the best prediction performance, and GS using SNPs selected with a linear mixed model combined with 50K SNP chip data performed best for fat yield. The proposed method of GS based on WGS data, i.e., feature selection using regularization regression models, provides a valuable novel strategy for genomic selection. Abstract Genomic selection (GS) is an efficient method to improve genetically economic traits. Feature selection is an important method for GS based on whole-genome sequencing (WGS) data. We investigated the prediction performance of GS of milk production traits using imputed WGS data on 7957 Chinese Holsteins. We used two regularized regression models, least absolute shrinkage and selection operator (LASSO) and elastic net (EN) for feature selection. For comparison, we performed genome-wide association studies based on a linear mixed model (LMM), and the N single nucleotide polymorphisms (SNPs) with the lowest p-values were selected (LMMLASSO and LMMEN), where N was the number of non-zero effect SNPs selected by LASSO or EN. GS was conducted using a genomic best linear unbiased prediction (GBLUP) model and several sets of SNPs: (1) selected WGS SNPs; (2) 50K SNP chip data; (3) WGS data; and (4) a combined set of selected WGS SNPs and 50K SNP chip data. The results showed that the prediction accuracies of GS with features selected using LASSO or EN were comparable to those using features selected with LMMLASSO or LMMEN. For milk and protein yields, GS using a combination of SNPs selected with LASSO and 50K SNP chip data achieved the best prediction performance, and GS using SNPs selected with LMMLASSO combined with 50K SNP chip data performed best for fat yield. The proposed method, feature selection using regularization regression models, provides a valuable novel strategy for WGS-based GS.
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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
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27
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McManus CM, Lucci CM, Maranhão AQ, Pimentel D, Pimentel F, Rezende Paiva S. Response to heat stress for small ruminants: Physiological and genetic aspects. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Chokoe TC, Hadebe K, Muchadeyi FC, Nephawe KA, Dzomba EF, Mphahlele TD, Matelele TC, Mtileni BJ. Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker. Front Genet 2022; 13:909472. [PMID: 36017496 PMCID: PMC9395594 DOI: 10.3389/fgene.2022.909472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.
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Affiliation(s)
- T. C. Chokoe
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
- School of Agriculture & Environmental Sciences, University of Limpopo, Polokwane, South Africa
- *Correspondence: T. C. Chokoe,
| | - K. Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - K. A. Nephawe
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of Kwazulu-Natal, Scottsville, South African
| | - T. D. Mphahlele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - T. C. Matelele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - B. J. Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
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Torres-Hernández G, Maldonado-Jáquez JA, Granados-Rivera LD, Salinas-González H, Castillo-Hernández G. Status quo of genetic improvement in local goats: a review. Arch Anim Breed 2022; 65:207-221. [PMID: 35693297 PMCID: PMC9176210 DOI: 10.5194/aab-65-207-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/14/2022] [Indexed: 11/26/2022] Open
Abstract
This review aims to summarize and synthesize the
fragmented information available on the genetic improvement of local goats
(criollo, indigenous, native) on the American and other continents, where
populations with these goats have an important role in food security and the
economy of rural communities, as well as in conservation of biodiversity and
productivity improvement. Topics such as the current state of goat
production globally, conservation programs, resistance to parasites and
diseases, use of phenotypical characteristics and genomic information, and
molecular markers for genetic improvement are addressed. The main
challenges, opportunities, and limitations described in recent literature
concerning local goats in the immediate future are discussed.
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Affiliation(s)
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados-Campus Montecillo, 56230 Montecillo, Estado
de México, México
- Instituto Nacional de Investigaciones Forestales, Agrícolas y
Pecuarias, Centro de Investigación Regional Norte Centro, Campo
Experimental La Laguna, 27440 Matamoros, Coahuila, México
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y
Pecuarias, Centro de Investigación Regional Noreste, Campo Experimental
General Terán, 67400 General Terán, Nuevo León, México
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados-Campus Montecillo, 56230 Montecillo, Estado
de México, México
- Facultad de Estudios
Superiores Cuautitlán, Universidad Nacional Autónoma de México, 54714 Cuautitlán Izcalli, Estado de
México, México
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30
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Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
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Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
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Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
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Berton MP, da Silva RP, Banchero G, Mourão GB, Ferraz JBS, Schenkel FS, Baldi F. Genomic integration to identify molecular biomarkers associated with indicator traits of gastrointestinal nematode resistance in sheep. J Anim Breed Genet 2022; 139:502-516. [PMID: 35535437 DOI: 10.1111/jbg.12682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/21/2022] [Indexed: 12/19/2022]
Abstract
This study aimed to integrate GWAS and structural variants to propose possible molecular biomarkers related to gastrointestinal nematode resistance traits in Santa Inês sheep. The phenotypic records FAMACHA, haematocrit, white blood cell count, red blood cell count, haemoglobin, platelets and egg counts per gram of faeces were collected from 700 naturally infected animals, belonging to four Brazilian flocks. A total of 576 animals were genotyped using the Ovine SNP12k BeadChip and were imputed using a reference population with Ovine SNP50 BeadChip. The GWAS approaches were based on SNPs, haplotypes, CNVs and ROH. The overlapping between the significant genomic regions detected from all approaches was investigated, and the results were integrated using a network analysis. Genes related to the immune system were found, such as ABCB1, IL6, WNT5A and IRF5. Genomic regions containing candidate genes and metabolic pathways involved in immune responses, inflammatory processes and immune cells affecting parasite resistance traits were identified. The genomic regions, biological processes and candidate genes uncovered could lead to biomarkers for selecting more resilient sheep and improving herd welfare and productivity. The results obtained are the start point to identify molecular biomarkers related to indicator traits of gastrointestinal nematode resistance in Santa Inês sheep.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Rosiane Pereira da Silva
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Georgget Banchero
- Instituto Nacional de Investigación Agropecuária (INIA), Colonia, Uruguay
| | - Gerson Barreto Mourão
- Departamento de Zootecnia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo/ESALQ, Piracicaba, Brazil
| | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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Serranito B, Cavalazzi M, Vidal P, Taurisson-Mouret D, Ciani E, Bal M, Rouvellac E, Servin B, Moreno-Romieux C, Tosser-Klopp G, Hall SJG, Lenstra JA, Pompanon F, Benjelloun B, Da Silva A. Local adaptations of Mediterranean sheep and goats through an integrative approach. Sci Rep 2021; 11:21363. [PMID: 34725398 PMCID: PMC8560853 DOI: 10.1038/s41598-021-00682-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.
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Affiliation(s)
- Bruno Serranito
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France
- CRESCO, Museum National d'Histoire Naturelle (MNHN), 35800, Dinard, France
| | | | - Pablo Vidal
- Universidad Catolica de Valencia, Valencia, Spain
| | - Dominique Taurisson-Mouret
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
- CNRS, UMR 5815, Dynamiques du droit, Université de Montpellier, Montpellier, France
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Marie Bal
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
| | | | - Bertrand Servin
- GenPhySE, INRAE, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | | | - Stephen J G Hall
- Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
- National Institute of Agronomic Research (INRA), Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Anne Da Silva
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France.
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Liu D, Chen Z, Zhao W, Guo L, Sun H, Zhu K, Liu G, Shen X, Zhao X, Wang Q, Ma P, Pan Y. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC Genomics 2021; 22:747. [PMID: 34654366 PMCID: PMC8520274 DOI: 10.1186/s12864-021-08042-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08042-x.
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Affiliation(s)
- Dengying Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Zhenliang Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Wei Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Longyu Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Xiuping Shen
- Shanghai Agricultural Development Promotion Center, 200335, Shanghai, PR China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China.
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China.
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Yuan J, Ni A, Li Y, Bian S, Liu Y, Wang P, Shi L, Isa AM, Ge P, Sun Y, Ma H, Chen J. Transcriptome Analysis Revealed Potential Mechanisms of Resistance to Trichomoniasis gallinae Infection in Pigeon ( Columba livia). Front Vet Sci 2021; 8:672270. [PMID: 34595226 PMCID: PMC8477972 DOI: 10.3389/fvets.2021.672270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Trichomoniasis gallinae (T. gallinae) is one of the most pathogenic parasites in pigeon, particularly in squabs. Oral cavity is the main site for the host-parasite interaction. Herein, we used RNA-sequencing technology to characterize lncRNA and mRNA profiles and compared transcriptomic dynamics of squabs, including four susceptible birds (S) from infected group, four tolerant birds (T) without parasites after T. gallinae infection, and three birds from uninfected group (N), to understand molecular mechanisms underlying host resistance to this parasite. We identified 29,809 putative lncRNAs and characterized their genomic features subsequently. Differentially expressed (DE) genes, DE-lncRNAs and cis/trans target genes of DE-lncRNAs were further compared among the three groups. The KEGG analysis indicated that specific intergroup DEGs were involved in carbon metabolism (S vs. T), metabolic pathways (N vs. T) and focal adhesion pathway (N vs. S), respectively. Whereas, the cis/trans genes of DE-lncRNAs were enriched in cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, p53 signaling pathway and insulin signaling pathway, which play crucial roles in immune system of the host animal. This suggests T. gallinae invasion in pigeon mouth may modulate lncRNAs expression and their target genes. Moreover, co-expression analysis identified crucial lncRNA-mRNA interaction networks. Several DE-lncRNAs including MSTRG.82272.3, MSTRG.114849.42, MSTRG.39405.36, MSTRG.3338.5, and MSTRG.105872.2 targeted methylation and immune-related genes, such as JCHAIN, IL18BP, ANGPT1, TMRT10C, SAMD9L, and SOCS3. This implied that DE-lncRNAs exert critical influence on T. gallinae infections. The quantitative exploration of host transcriptome changes induced by T. gallinae infection broaden both transcriptomic and epigenetic insights into T. gallinae resistance and its pathological mechanism.
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Affiliation(s)
- Jingwei Yuan
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Aixin Ni
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yunlei Li
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Shixiong Bian
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yunjie Liu
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Panlin Wang
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Lei Shi
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Adamu Mani Isa
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China.,Department of Animal Science, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Pingzhuang Ge
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yanyan Sun
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Hui Ma
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Jilan Chen
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
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37
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Rostamzadeh Mahdabi E, Esmailizadeh A, Ayatollahi Mehrgardi A, Asadi Fozi M. A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes. Genet Sel Evol 2021; 53:72. [PMID: 34503452 PMCID: PMC8428137 DOI: 10.1186/s12711-021-00664-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. Results Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). Conclusions Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00664-9.
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Affiliation(s)
- Elaheh Rostamzadeh Mahdabi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran.
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Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
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Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
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Deniskova TE, Dotsev AV, Selionova MI, Reyer H, Sölkner J, Fornara MS, Aybazov AMM, Wimmers K, Brem G, Zinovieva NA. SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats. Front Genet 2021; 12:708740. [PMID: 34276802 PMCID: PMC8282346 DOI: 10.3389/fgene.2021.708740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.
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Affiliation(s)
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Marina I Selionova
- Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | - Ali-Magomed M Aybazov
- All-Russian Research Institute of Sheep and Goat Breeding - Branch of the Federal State Budgetary Scientific Institution, North Caucasian Agrarian Center, Stavropol, Russia
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations. Animals (Basel) 2021; 11:ani11061510. [PMID: 34071004 PMCID: PMC8224610 DOI: 10.3390/ani11061510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs. Abstract The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.
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Fang Y, Hao X, Xu Z, Sun H, Zhao Q, Cao R, Zhang Z, Ma P, Sun Y, Qi Z, Wei Q, Wang Q, Pan Y. Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data. Front Genet 2021; 12:629966. [PMID: 33995477 PMCID: PMC8116706 DOI: 10.3389/fgene.2021.629966] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Laiwu pigs, distinguished by their high intramuscular fat of 7-9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1-5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.
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Affiliation(s)
- Yifei Fang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Hao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Cao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | | | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
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Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Nascimento AV, Santos DJA, Stefani G, Brito LF. Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models. J Dairy Sci 2021; 104:5768-5793. [PMID: 33685677 DOI: 10.3168/jds.2020-19534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/02/2021] [Indexed: 01/14/2023]
Abstract
Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from -0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies.
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Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daniel J A Santos
- Department of Animal and Avian Science, University of Maryland, College Park 20742
| | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Saravanan K, Panigrahi M, Kumar H, Bhushan B, Dutt T, Mishra B. Genome-wide analysis of genetic diversity and selection signatures in three Indian sheep breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Cortellari M, Bionda A, Talenti A, Ceccobelli S, Attard G, Lasagna E, Crepaldi P, Liotta L. Genomic variability of Cirneco dell’Etna and the genetic distance with other dog breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1873076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Andrea Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - George Attard
- Department of Rural Sciences and Food Systems, University of Malta, Msida, Malta
- Ministry for Agriculture, Fisheries and Animal Rights, Agency for the Governance of Agricultural Bio-Resources, Marsa, Malta
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
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Abstract
Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear in a homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n = 25), brown layer (BL, n = 25), broiler line A (BRA, n = 20), broiler line B (BRB, n = 20) and Red Junglefowl (RJF, n = 25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (±18.7) per bird, despite carrying it in short segments (0.3-1 Mb). Population-wise inbreeding measures based on Wright's (Fis) and genomic (FROH) metrics revealed highly inbred genome of layer lines relative to the broilers and Red Junglefowl. We further revealed the ROH islands, among commercial lines overlapped with QTL related to limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response to Newcastle virus (ROBO2), and feather pecking. Comparison of ROH landscape in sequencing resolution demonstrated that a sizable portion of genome of commercial lines segregates in homozygote state, reflecting many generations of assortative mating and intensive selection in their recent history. In contrary, wild birds carry shorter ROH segments, likely suggestive of older evolutionary events.
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Moscarelli A, Sardina MT, Cassandro M, Ciani E, Pilla F, Senczuk G, Portolano B, Mastrangelo S. Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations. Anim Genet 2020; 52:21-31. [PMID: 33174276 DOI: 10.1111/age.13019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The FST -outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual-purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.
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Affiliation(s)
- A Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, 35020, Italy
| | - E Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, Bari, 70124, Italy
| | - F Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - G Senczuk
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
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Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer ( Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool 2020; 17:31. [PMID: 33072165 PMCID: PMC7565370 DOI: 10.1186/s12983-020-00379-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
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Affiliation(s)
- Buweihailiqiemu Ababaikeri
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China.,College of Xinjiang Uyghur Medicine, Hoten, 848000 Xinjiang China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China.,Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Yilamujiang Tohetahong
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Tayerjan Mamat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Adil Ahmat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Mahmut Halik
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
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