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Kebede FG, Derks MFL, Dessie T, Hanotte O, Barros CP, Crooijmans RPMA, Komen H, Bastiaansen JWM. Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens. BMC Genomics 2024; 25:284. [PMID: 38500079 PMCID: PMC10946127 DOI: 10.1186/s12864-024-10193-6] [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: 10/03/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.
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Affiliation(s)
- Fasil Getachew Kebede
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands.
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Tadelle Dessie
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
- School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Carolina Pita Barros
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - Hans Komen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
| | - John W M Bastiaansen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB-6708, The Netherlands
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University of Alabama at Birmingham Nathan Shock Center: comparative energetics of aging. GeroScience 2021; 43:2149-2160. [PMID: 34304389 DOI: 10.1007/s11357-021-00414-1] [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: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/09/2022] Open
Abstract
The UAB Nathan Shock Center focuses on comparative energetics and aging. Energetics, as defined for this purpose, encompasses the causes, mechanisms, and consequences of the acquisition, storage, and use of metabolizable energy. Comparative energetics is the study of metabolic processes at multiple scales and across multiple species as it relates to health and aging. The link between energetics and aging is increasingly understood in terms of dysregulated mitochondrial function, altered metabolic signaling, and aberrant nutrient responsiveness with increasing age. The center offers world-class expertise in comprehensive, integrated energetic assessment and analysis from the level of the organelle to the organism and across species from the size of worms to rats as well as state-of-the-art data analytics. The range of services offered by our three research cores, (1) The Organismal Energetics Core, (2) Mitometabolism Core, and (3) Data Analytics Core, is described herein.
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Guo L, Sun H, Zhao Q, Xu Z, Zhang Z, Liu D, Qadri QR, Ma P, Wang Q, Pan Y. Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data. Anim Genet 2021; 52:143-154. [PMID: 33458851 DOI: 10.1111/age.13034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.
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Affiliation(s)
- L Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - D Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q R Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
| | - Y Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
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Aguilar-Jimenez W, Zapata W, Rivero-Juárez A, Pineda JA, Laplana M, Taborda NA, Biasin M, Clerici M, Caruz A, Fibla J, Rugeles MT. Genetic associations of the vitamin D and antiviral pathways with natural resistance to HIV-1 infection are influenced by interpopulation variability. INFECTION GENETICS AND EVOLUTION 2019; 73:276-286. [PMID: 31103723 DOI: 10.1016/j.meegid.2019.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 01/06/2023]
Abstract
Vitamin D (VitD) may modulate anti-HIV-1 responses modifying the risk to acquire the HIV-1-infection. We performed a nested case-control exploratory study involving 413 individuals; HIV-1-exposed seropositives (cases) and seronegatives (HESN) (controls) from three cohorts: sexually-exposed from Colombia and Italy and parenterally-exposed from Spain. The association and interactions of 139 variants in 9 VitD pathway genes, and in 14 antiviral genes with resistance/susceptibility (R/S) to HIV-1 infection was evaluated. Associations between variants and mRNA levels were also analyzed in the Colombian samples. Variants and haplotypes in genes of VitD and antiviral pathways were associated with R/S, but specific associations were not reproduced in all cohorts. Allelic heterogeneity could explain such inconsistency since the associations found in all cohorts were consistently in the same genes: VDR and RXRA of the VitD pathway genes and in TLR2 and RNASE4. Remarkably, the multi-locus genotypes (interacting variants) observed in genes of VitD and antiviral pathways were present in most HESNs of all cohorts. Finally, HESNs carrying resistance-associated variants had higher levels of VitD in plasma, of VDR mRNA in blood cells, and of ELAFIN and defensins mRNA in the oral mucosa. In conclusion, despite allelic heterogeneity, most likely due to differences in the genetic history of the populations, the associations were locus dependent suggesting that genes of the VitD pathway might act in concert with antiviral genes modulating the resistance phenotype of the HESNs. Although these associations were significant after permutation test, only haplotype results remained statistically significant after Bonferroni test, requiring further replications in larger cohorts and functional analyzes to validate these conclusions.
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Affiliation(s)
- Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, 050010 Medellín, Colombia.
| | - Wildeman Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, 050010 Medellín, Colombia; Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, 050012 Medellín, Colombia
| | - Antonio Rivero-Juárez
- Unidad Clínica de Enfermedades Infecciosas, Instituto Maimonides para la Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofia, 14004 Córdoba, Spain
| | - Juan A Pineda
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, 41014 Seville, Spain
| | - Marina Laplana
- Unitat de Genètica Humana, Departament de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Natalia A Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, 050010 Medellín, Colombia; Grupo de Investigaciones Biomédicas UniRemington, Facultad de Medicina, Corporación Universitaria Remington, 050010 Medellín, Colombia
| | - Mara Biasin
- Dipartimento di Scienze Biomediche e Cliniche-L. Sacco, Università Degli Studi di Milano, 20157 Milan, Italy.
| | - Mario Clerici
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, 20100 Milan, Italy; Fondazione Don C, Gnocchi IRCCS, 20100 Milan, Italy.
| | - Antonio Caruz
- Unidad de Inmunogenética, Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071 Jaén, Spain.
| | - Joan Fibla
- Unitat de Genètica Humana, Departament de Ciències Mèdiques Bàsiques, IRBLleida, Universitat de Lleida, 25198 Lleida, Spain.
| | - María T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, 050010 Medellín, Colombia.
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Novembre J, Han E. Human population structure and the adaptive response to pathogen-induced selection pressures. Philos Trans R Soc Lond B Biol Sci 2012; 367:878-86. [PMID: 22312055 DOI: 10.1098/rstb.2011.0305] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The past few years of research in human evolutionary genetics have provided novel insights and questions regarding how human adaptations to recent selective pressures have taken place. Here, we review the advances most relevant to understanding human evolution in response to pathogen-induced selective pressures. Key insights come from theoretical models of adaptive evolution, particularly those that consider spatially structured populations, and from empirical population genomic studies of adaptive evolution in humans. We also review the CCR5-Δ32 HIV resistance allele as a case study of pathogen resistance in humans. Taken together, the results make clear that the human response to pathogen-induced selection pressures depends on a complex interplay between the age of the pathogen, the genetic basis of potential resistance phenotypes, and how population structure impacts the adaptive process in humans.
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Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
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