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Álvarez Cecco P, Balbi M, Bonamy M, Rogberg Muñoz A, Olivera H, Giovambattista G, Fernández ME. Skin transcriptome analysis in Brangus cattle under heat stress. J Therm Biol 2024; 121:103852. [PMID: 38615495 DOI: 10.1016/j.jtherbio.2024.103852] [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: 10/04/2023] [Revised: 02/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N = 5) and non-stressed (N = 5) groups. Skin transcriptomics was performed and correlations between breed composition, phenotypic and skin histological traits were evaluated. Results showed 4309 differentially expressed genes (P < 0.01), 2113 downregulated and 2196 upregulated. Enrichment and ontology analyses revealed 132 GO terms and 67 pathways (P < 0.01), including thermogenesis, glycolysis, gluconeogenesis, mitochondrial activity, antioxidant and immune response, and apoptosis. The identity of the terms and pathways indicated the diversity of mechanisms directed to relieve the animals' suffering, acting from simple passive mechanisms (conduction, convection and radiation) to more complex active ones (behavioural changes, evaporation, vasodilation and wheezing). Furthermore, significant differences between phenotypic and skin histological traits and correlations between pairs of traits suggested a direction towards heat dissipation processes. In this sense, number of vessels was positively correlated with number of sweat glands (P < 0.001) and both were positively correlated with zebuine genetic content (P < 0.05 and P < 0.01, respectively), gland size was positively correlated with epidermal thickness and negatively with hair length (P < 0.05), and epidermal thickness was negatively correlated with gland-epidermis distance (P < 0.0005). These results support the notion that response to heat stress is physiologically complex, producing significant changes in the expression of genes involved in several biological pathways, while the animal's ability to face it depends greatly on their skin features.
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Affiliation(s)
- Paulo Álvarez Cecco
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Marianela Balbi
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Martín Bonamy
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ, Buenos Aires, Argentina
| | - Hernán Olivera
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Guillermo Giovambattista
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - María Elena Fernández
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina.
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2
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Hwang YH, Lee EY, Lim HT, Joo ST. Multi-Omics Approaches to Improve Meat Quality and Taste Characteristics. Food Sci Anim Resour 2023; 43:1067-1086. [PMID: 37969318 PMCID: PMC10636221 DOI: 10.5851/kosfa.2023.e63] [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: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 11/17/2023] Open
Abstract
With rapid advances in meat science in recent decades, changes in meat quality during the pre-slaughter phase of muscle growth and the post-slaughter process from muscle to meat have been investigated. Commonly used techniques have evolved from early physicochemical indicators such as meat color, tenderness, water holding capacity, flavor, and pH to various omic tools such as genomics, transcriptomics, proteomics, and metabolomics to explore fundamental molecular mechanisms and screen biomarkers related to meat quality and taste characteristics. This review highlights the application of omics and integrated multi-omics in meat quality and taste characteristics studies. It also discusses challenges and future perspectives of multi-omics technology to improve meat quality and taste. Consequently, multi-omics techniques can elucidate the molecular mechanisms responsible for changes of meat quality at transcriptome, proteome, and metabolome levels. In addition, the application of multi-omics technology has great potential for exploring and identifying biomarkers for meat quality and quality control that can make it easier to optimize production processes in the meat industry.
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Affiliation(s)
- Young-Hwa Hwang
- Institute of Agriculture & Life
Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Eun-Yeong Lee
- Division of Applied Life Science (BK21
Four), Gyeongsang National University, Jinju 52828,
Korea
| | - Hyen-Tae Lim
- Institute of Agriculture & Life
Science, Gyeongsang National University, Jinju 52828,
Korea
- Division of Animal Science, Gyeongsang
National University, Jinju 52828, Korea
| | - Seon-Tea Joo
- Institute of Agriculture & Life
Science, Gyeongsang National University, Jinju 52828,
Korea
- Division of Applied Life Science (BK21
Four), Gyeongsang National University, Jinju 52828,
Korea
- Division of Animal Science, Gyeongsang
National University, Jinju 52828, Korea
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3
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Habimana V, Nguluma AS, Nziku ZC, Ekine-Dzivenu CC, Morota G, Mrode R, Chenyambuga SW. Heat stress effects on milk yield traits and metabolites and mitigation strategies for dairy cattle breeds reared in tropical and sub-tropical countries. Front Vet Sci 2023; 10:1121499. [PMID: 37483284 PMCID: PMC10361820 DOI: 10.3389/fvets.2023.1121499] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Heat stress is an important problem for dairy industry in many parts of the world owing to its adverse effects on productivity and profitability. Heat stress in dairy cattle is caused by an increase in core body temperature, which affects the fat production in the mammary gland. It reduces milk yield, dry matter intake, and alters the milk composition, such as fat, protein, lactose, and solids-not-fats percentages among others. Understanding the biological mechanisms of climatic adaptation, identifying and exploring signatures of selection, genomic diversity and identification of candidate genes for heat tolerance within indicine and taurine dairy breeds is an important progression toward breeding better dairy cattle adapted to changing climatic conditions of the tropics. Identifying breeds that are heat tolerant and their use in genetic improvement programs is crucial for improving dairy cattle productivity and profitability in the tropics. Genetic improvement for heat tolerance requires availability of genetic parameters, but these genetic parameters are currently missing in many tropical countries. In this article, we reviewed the HS effects on dairy cattle with regard to (1) physiological parameters; (2) milk yield and composition traits; and (3) milk and blood metabolites for dairy cattle reared in tropical countries. In addition, mitigation strategies such as physical modification of environment, nutritional, and genetic development of heat tolerant dairy cattle to prevent the adverse effects of HS on dairy cattle are discussed. In tropical climates, a more and cost-effective strategy to overcome HS effects is to genetically select more adaptable and heat tolerant breeds, use of crossbred animals for milk production, i.e., crosses between indicine breeds such as Gir, white fulani, N'Dama, Sahiwal or Boran to taurine breeds such as Holstein-Friesian, Jersey or Brown Swiss. The results of this review will contribute to policy formulations with regard to strategies for mitigating the effects of HS on dairy cattle in tropical countries.
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Affiliation(s)
- Vincent Habimana
- Department of Animal, Aquaculture, and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Athumani Shabani Nguluma
- Department of Animal, Aquaculture, and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | | | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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4
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Mullakkalparambil Velayudhan S, Sejian V, Devaraj C, Manjunathareddy GB, Ruban W, Kadam V, König S, Bhatta R. Novel Insights to Assess Climate Resilience in Goats Using a Holistic Approach of Skin-Based Advanced NGS Technologies. Int J Mol Sci 2023; 24:10319. [PMID: 37373465 DOI: 10.3390/ijms241210319] [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: 05/30/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
A novel study was conducted to elucidate heat-stress responses on a number of hair- and skin-based traits in two indigenous goat breeds using a holistic approach that considered a number of phenotypic and genomic variables. The two goat breeds, Kanni Aadu and Kodi Aadu, were subjected to a simulated heat-stress study using the climate chambers. Four groups consisting of six goats each (KAC, Kaani Aadu control; KAH, Kanni Aadu heat stress; KOC, Kodi Aadu control; and KOH, Kodi Aadu heat stress) were considered for the study. The impact of heat stress on caprine skin tissue along with a comparative assessment of the thermal resilience of the two goat breeds was assessed. The variables considered were hair characteristics, hair cortisol, hair follicle quantitative PCR (qPCR), sweating (sweating rate and active sweat gland measurement), skin histometry, skin-surface infrared thermography (IRT), skin 16S rRNA V3-V4 metagenomics, skin transcriptomics, and skin bisulfite sequencing. Heat stress significantly influenced the hair fiber characteristics (fiber length) and hair follicle qPCR profile (Heat-shock protein 70 (HSP70), HSP90, and HSP110). Significantly higher sweating rate, activated sweat gland number, skin epithelium, and sweat gland number (histometry) were observed in heat stressed goats. The skin microbiota was also observed to be significantly altered due to heat stress, with a relatively higher alteration being noticed in Kanni Aadu goats than in Kodi Aadi goats. Furthermore, the transcriptomics and epigenetics analysis also pointed towards the significant impact of heat stress at the cellular and molecular levels in caprine skin tissue. The higher proportion of differentially expressed genes (DEGs) along with higher differentially methylated regions (DMRs) in Kanni Aadu goats due to heat stress when compared to Kodi Aadu goats pointed towards the better resilience of the latter breed. A number of established skin, adaptation, and immune-response genes were also observed to be significantly expressed/methylated. Additionally, the influence of heat stress at the genomic level was also predicted to result in significant functional alterations. This novel study thereby highlights the impact of heat stress on the caprine skin tissue and also the difference in thermal resilience exhibited by the two indigenous goat breeds, with Kodi Aadu goats being more resilient.
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Affiliation(s)
| | - Veerasamy Sejian
- Rajiv Gandhi Institute of Veterinary Education and Research, Kurumbapet, Pondicherry 605008, India
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | - Chinnasamy Devaraj
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
| | | | - Wilfred Ruban
- Department of Livestock Product Technology, Hebbal Veterinary College, Karnataka Veterinary Animal and Fishery Sciences University, Hebbal, Bangalore 560024, India
| | - Vinod Kadam
- Textile Manufacturing and Textile Chemistry Division, Central Sheep and Wool Research Institute, Avikanagar, Malpura 304501, India
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstr. 21b, 35390 Giessen, Germany
| | - Raghavendra Bhatta
- Centre for Climate Resilient Animal Adaptation Studies, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, India
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5
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Sosa F, Carmickle AT, Oliveira LJ, Sagheer M, Saleem M, Yu FH, Altman MD, Dikmen S, Denicol AC, Sonstegard TS, Larson CC, Hansen PJ. Effects of the bovine SLICK1 mutation in PRLR on sweat gland area, FOXA1 abundance, and global gene expression in skin. J Dairy Sci 2022; 105:9206-9215. [PMID: 36085108 DOI: 10.3168/jds.2022-22272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022]
Abstract
The SLICK1 mutation in the prolactin receptor (PRLR) results in a short-hair coat and increased ability to regulate body temperature during heat stress. It is unclear whether the mutation affects capacity for sweating. The objective of this observational study was to evaluate whether the SLICK1 mutation in PRLR alters characteristics of skin related to sweat gland abundance or function. Skin biopsies from 31 Holstein heifers, including 14 wild-type (SL-/-) and 17 heterozygous slick (SL+/-), were subjected to histological analysis to determine the percent of the surface area of skin sections that are occupied by sweat glands. We detected no effect of genotype on this variable. Immunohistochemical analysis of the forkhead transcription factor A1 (FOXA1), a protein essential for sweating in mice, from 6 SL-/- and 6 SL+/- heifers indicated twice as much FOXA1 in sweat glandular epithelia of SL+/- heifers as in SL-/- heifers. Results from RNA sequencing of skin biopsies from 5 SL-/- and 7 SL+/- heifers revealed few genes that were differentially expressed and none that have been associated with sweat gland development or function. In conclusion, results do not support the idea that the SLICK1 mutation changes the abundance of sweat glands in skin, but do show that functional properties of sweat glands, as indicated by increased abundance of immunoreactive FOXA1, are modified by inheritance of the mutation in PRLR.
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Affiliation(s)
- F Sosa
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville 32611-0910
| | - A T Carmickle
- Department of Animal Science, University of California-Davis, Davis 95616
| | - L J Oliveira
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens 30602
| | - M Sagheer
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville 32611-0910
| | - M Saleem
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville 32611-0910; Department of Theriogenology, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - F H Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville 32610
| | - M D Altman
- Department of Animal Science, University of California-Davis, Davis 95616
| | - S Dikmen
- Faculty of Veterinary Medicine, Department of Animal Science, University of Uludag, Bursa, 16059, Turkey
| | - A C Denicol
- Department of Animal Science, University of California-Davis, Davis 95616
| | | | - C C Larson
- Okeechobee County Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida, Okeechobee 34972
| | - P J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville 32611-0910.
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6
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Kang D, Shin D, Choe H, Hwang D, Bugenyi AW, Na CS, Lee HK, Heo J, Shim K. Transcriptome-wide analysis reveals gluten-induced suppression of
small intestine development in young chickens. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:752-769. [PMID: 35969701 PMCID: PMC9353357 DOI: 10.5187/jast.2022.e42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/15/2022] [Accepted: 05/22/2022] [Indexed: 11/20/2022]
Abstract
Wheat gluten is an increasingly common ingredient in poultry diets but its impact
on the small intestine in chicken is not fully understood. This study aimed to
identify effects of high-gluten diets on chicken small intestines and the
variation of their associated transcriptional responses by age. A total of 120
broilers (Ross Strain) were used to perform two animal experiments consisting of
two gluten inclusion levels (0% or 25%) by bird’s age (1
week or 4 weeks). Transcriptomics and histochemical techniques were employed to
study the effect of gluten on their duodenal mucosa using randomly selected 12
broilers (3 chicks per group). A reduction in feed intake and body weight gain
was found in the broilers fed a high-gluten containing diet at both ages.
Histochemical photomicrographs showed a reduced villus height to crypt depth
ratio in the duodenum of gluten-fed broilers at 1 week. We found mainly a
significant effect on the gene expression of duodenal mucosa in gluten-fed
broilers at 1 week (289 differentially expressed genes [DEGs]). Pathway analyses
revealed that the significant DEGs were mainly involved in ribosome, oxidative
phosphorylation, and peroxisome proliferator-activated receptor (PPAR) signaling
pathways. These pathways are involved in ribosome protein biogenesis, oxidative
phosphorylation and fatty acid metabolism, respectively. Our results suggest a
pattern of differential gene expression in these pathways that can be linked to
chronic inflammation, suppression of cell proliferation, cell cycle arrest and
apoptosis. And via such a mode of action, high-gluten inclusion levels in
poultry diets could lead to the observed retardation of villi development in the
duodenal mucosa of young broiler chicken.
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Affiliation(s)
- Darae Kang
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence
Technology, Jeonbuk National University, Jeonju 54896,
Korea
| | - Hosung Choe
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Doyon Hwang
- Institute for Animal Products Quality
Evaluation, Sejong 339011, Korea
| | - Andrew Wange Bugenyi
- Department of Agricultural Convergence
Technology, Jeonbuk National University, Jeonju 54896,
Korea
- National Agricultural Research
Organization, Entebbe 295, Uganda
| | - Chong-Sam Na
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Jaeyoung Heo
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
- Corresponding author: Jaeyoung Heo,
Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896,
Korea. Tel: +82-63-270-2549, E-mail:
| | - Kwanseob Shim
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
- Corresponding author: Kwanseob Shim,
Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896,
Korea. Tel: +82-63-270-2609, E-mail:
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7
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Wang M, Li H, Zhang X, Yang L, Liu Y, Liu S, Sun Y, Zhao C. An analysis of skin thickness in the Dezhou donkey population and identification of candidate genes by RNA-seq. Anim Genet 2022; 53:368-379. [PMID: 35307856 DOI: 10.1111/age.13196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/20/2022] [Accepted: 03/11/2022] [Indexed: 12/17/2022]
Abstract
The aim of the present study was to analyze the main factors that have a significant impact on skin thickness, and to further identify the genes and signaling pathways regulating skin growth by RNA-seq in Dezhou donkeys. Skin samples from different body regions of 15 slaughtered donkeys were obtained to study variations in skin thickness over the bodies. Skin thickness data for another 514 donkeys was obtained by minimally invasive skin sampling from the back, and measurements of the donkeys' body size traits and pedigree data were also collected. These data were used to analyze changes in skin thickness and estimate genetic parameters. In addition, transcriptomic analysis was conducted on the skin tissues of individuals from two groups with significant differences in skin thickness. Our results showed that skin thickness over the bodies ranged from 1.08 to 4.36 mm. The skin from the back was the thickest and had the highest correlation with that of other regions of the body. The skin thickness decreased from the back to the side of the ventral abdomen, and the skin thickness on the limbs increased from the proximal end to the distal end. The results also showed that the skin from the same body regions of jacks was thicker than that of jennies in the same age group. The skin thickness of jennies increased from birth to the age of 2 and then clearly decreased after 2 years of age. The estimated heritability of skin thickness was 0.15, and the genetic correlations between skin thickness and body size traits were negligible. Transcriptome analysis showed that the thick-skin group had 65 up-regulated genes and 38 down-regulated genes compared with the thin-skin group. The differentially expressed genes were highly enriched in epidermal development and cell adhesion molecule signaling pathways. We identified the candidate genes responsible for variations in skin thickness in the Dezhou donkey, including KRT10, KRT1, CLDN9, MHCII and MMP28. These results contribute to a better understanding of the growth and development of donkey skin, reveal the molecular mechanism responsible for donkey skin thickness and suggest directions for genetic selection in the Dezhou donkey population.
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Affiliation(s)
- Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Laboratory of Animal Genetics Resource and Molecular Breeding, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-E E-Jiao Co. Ltd, Liaocheng, China
| | - Xinhao Zhang
- National Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-E E-Jiao Co. Ltd, Liaocheng, China
| | - Li Yang
- National Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-E E-Jiao Co. Ltd, Liaocheng, China
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Laboratory of Animal Genetics Resource and Molecular Breeding, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Laboratory of Animal Genetics Resource and Molecular Breeding, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China
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8
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Cao YH, Xu SS, Shen M, Chen ZH, Gao L, Lv FH, Xie XL, Wang XH, Yang H, Liu CB, Zhou P, Wan PC, Zhang YS, Yang JQ, Pi WH, Hehua EE, Berry DP, Barbato M, Esmailizadeh A, Nosrati M, Salehian-Dehkordi H, Dehghani-Qanatqestani M, Dotsev AV, Deniskova TE, Zinovieva NA, Brem G, Štěpánek O, Ciani E, Weimann C, Erhardt G, Mwacharo JM, Ahbara A, Han JL, Hanotte O, Miller JM, Sim Z, Coltman D, Kantanen J, Bruford MW, Lenstra JA, Kijas J, Li MH. Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol 2021; 38:838-855. [PMID: 32941615 PMCID: PMC7947771 DOI: 10.1093/molbev/msaa236] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.
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Affiliation(s)
- Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - EEr Hehua
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Hui Autonomous Region, Yinchuan, Ningxia, China
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24, Moro, Bari, Italy
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Abeba, Ethiopia
- Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Fish and Wildlife Enforcement Branch Forensic Unit, Government of Alberta, Edmonton, AB, Canada
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, QLD, Australia
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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