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Okandeji ME, Lijoka AD, Olude MA, Atiba F, Olopade JO. Permanent Tooth Eruption Patterns in Nigerian Local Pigs. J Vet Dent 2023; 40:236-242. [PMID: 36721364 DOI: 10.1177/08987564231152390] [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] [Indexed: 02/02/2023]
Abstract
Pigs are diphyodonts with heterodont dentition and have been used in studies involving teeth and jawbone regeneration, and dental implants. Patterns of tooth eruption are used to age animals and determine the effects of environmental and genetic influences on occurrence of variations. As with other species, variations exist in the tooth eruption pattern in pigs. The aim of this study was to determine the permanent teeth eruption patterns of Nigerian local pigs. Twenty-six healthy pigs were observed throughout the study period. Pigs were firmly held in dorsal or lateral recumbency and their mouths gently held open to visually examine all quadrants of the dental arches (right and left maxillary, right and left mandibular). Observations were recorded from 16 weeks of age, until the last permanent tooth erupted. Results obtained from the study showed that males had lower mean values for eruption time (54%) of examined teeth in comparison to females. The mean values of eruption time for the maxillary third incisor, the mandibular and maxillary canines, and the mandibular fourth premolar teeth were statistically significant in the males (P = .0017, P = .0088, P = .0002 and P = .0244, respectively). Sixty-nine percent of the adult pigs did not have eruption of the mandibular first premolar, while polydontia was observed in the maxillary and mandibular incisors. These results show that intra-breed and inter-breed variations exist in the dental eruption pattern in pigs. The data obtained from this study can be used for comparative dental studies and can aid further research on the developmental anatomy of Nigerian local pigs.
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Affiliation(s)
- Michael Efeturi Okandeji
- Department of Veterinary Anatomy, Federal University of Abeokuta, Abeokuta, Nigeria
- Department of Veterinary Anatomy, University of Ibadan, Ibadan, Nigeria
| | | | | | - Folusho Atiba
- Department of Anatomy, University of Ibadan, Ibadan, Nigeria
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Zhang K, Wang G, Wang L, Wen B, Fu X, Liu N, Yu Z, Jian W, Guo X, Liu H, Chen SY. A genome-wide association study of coat color in Chinese Rex rabbits. Front Vet Sci 2023; 10:1184764. [PMID: 37655262 PMCID: PMC10467280 DOI: 10.3389/fvets.2023.1184764] [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: 03/12/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Coat color is an important phenotypic characteristic of the domestic rabbit (Oryctolagus cuniculus) and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, p = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, p = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein (ASIP) gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that ASIP is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
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Affiliation(s)
- Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Bin Wen
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Ning Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Zhiju Yu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Wensu Jian
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiaolin Guo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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Wu X, Zhang H, Long H, Zhang D, Yang X, Liu D, E G. Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig. Animals (Basel) 2023; 13:2158. [PMID: 37443955 DOI: 10.3390/ani13132158] [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: 05/25/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of INPP5B and TRAK2 were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs.
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Affiliation(s)
- Xinming Wu
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China
| | - Haoyuan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China
| | - Haoyuan Long
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China
| | - Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Cui J, Jiang Z, Wang Z, Shao J, Dong C, Wang L, Li X, Du J, Li S, Qiao Z, Zhang M. Eight single nucleotide polymorphisms and their association with food habit domestication traits and growth traits in largemouth bass fry ( Micropterus salmoides) based on PCR-RFLP method. PeerJ 2023; 11:e14588. [PMID: 36643624 PMCID: PMC9835702 DOI: 10.7717/peerj.14588] [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: 08/12/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023] Open
Abstract
Background The largemouth bass (Micropterus salmoides), an economically important freshwater fish species widely farmed in China, is traditionally cultured using a diet of forage fish. However, given the global decline in forage fish fisheries and increasing rates of waterbody pollution and disease outbreaks during traditional culturing, there is a growing trend of replacing forage fish with formulated feed in the largemouth bass breeding industry. The specific molecular mechanisms associated with such dietary transition in this fish are, nevertheless, poorly understood. Methods To identify single nucleotide polymorphisms (SNPs) related to food habit domestication traits and growth traits in largemouth bass fry, we initially genotyped fry using eight candidate SNPs based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with genetic parameters being determined using Popgen32 and Cervus 3.0. Subsequently, we assessed the associations between food habit domestication traits of largemouth bass fry and these SNPs using the Chi-square test or Fisher's exact test. Furthermore, we used a general linear model to assess the relationships between the growth traits of largemouth bass fry and these SNPs. The Pearson correlation coefficient between growth traits and the SNPs was also determined using bivariate correlation analysis in IBM SPSS Statistics 22. Finally, the phenotypic variation explained (PVE) by the SNPs was calculated by regression analysis in Microsoft Excel. Results The genotyping results obtained based on PCR-RFLP analysis were consistent with those of direct sequencing. Five SNPs (SNP01, SNP02, SNP04, SNP05, and SNP06) were found to be significantly correlated with the food habit domestication traits of fry (P < 0.05); SNP01 (P = 0.0011) and SNP04 (P = 0.0055) particularly, had showed highly significant associations. With respect to growth traits, we detected significant correlations with the two SNPs (SNP01 and SNP07) (P < 0.05), with SNP01 being significantly correlated with body length, and height (P < 0.05), and SNP07 being significantly correlated with body height only (P < 0.05). Conclusions Our findings indicated that the PCR-RFLP can be used as a low-cost genotyping method to identify SNPs related to food habit domestication and growth traits in largemouth bass, and that these trait-related SNPs might provide a molecular basis for the future breeding of new varieties of largemouth bass.
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Affiliation(s)
- Jiao Cui
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zhou Jiang
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zerui Wang
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Jiaqi Shao
- College of Fisheries, Henan Normal University, Xinxiang, China,Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, China
| | - Chuanju Dong
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Lei Wang
- College of Fisheries, Henan Normal University, Xinxiang, China,Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Xinxiang, China
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang, China,Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Xinxiang, China
| | - Jinxing Du
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, China
| | - Shengjie Li
- College of Fisheries, Henan Normal University, Xinxiang, China,Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, China
| | - Zhigang Qiao
- College of Fisheries, Henan Normal University, Xinxiang, China,Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Xinxiang, China
| | - Meng Zhang
- College of Fisheries, Henan Normal University, Xinxiang, China,Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Xinxiang, China
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Bull JK, Stanford BCM, Bokvist JK, Josephson MP, Rogers SM. Environment and genotype predict the genomic nature of domestication of salmonids as revealed by gene expression. Proc Biol Sci 2022; 289:20222124. [PMID: 36475438 PMCID: PMC9727666 DOI: 10.1098/rspb.2022.2124] [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] [Indexed: 12/12/2022] Open
Abstract
Billions of salmonids are produced annually by artificial reproduction for harvest and conservation. Morphologically, behaviourally and physiologically these fish differ from wild-born fish, including in ways consistent with domestication. Unlike most studied domesticates, which diverged from wild ancestors millennia ago, salmonids offer a tractable model for early-stage domestication. Here, we review a fundamental mechanism for domestication-driven differences in early-stage domestication, differentially expressed genes (DEGs), in salmonids. We found 34 publications examining DEGs under domestication driven by environment and genotype, covering six species, over a range of life-history stages and tissues. Three trends emerged. First, domesticated genotypes have increased expression of growth hormone and related metabolic genes, with differences magnified under artificial environments with increased food. Regulatory consequences of these DEGs potentially drive overall DEG patterns. Second, immune genes are often DEGs under domestication and not simply owing to release from growth-immune trade-offs under increased food. Third, domesticated genotypes exhibit reduced gene expression plasticity, with plasticity further reduced in low-complexity environments typical of production systems. Recommendations for experimental design improvements, coupled with tissue-specific expression and emerging analytical approaches for DEGs present tractable avenues to understand the evolution of domestication in salmonids and other species.
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Affiliation(s)
- James K. Bull
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4
| | | | - Jessy K. Bokvist
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4,Fisheries and Oceans Canada, South Coast Area Office, Nanaimo, British Columbia, Canada V9T 1K3
| | - Matthew P. Josephson
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4
| | - Sean M. Rogers
- Department of Biological Sciences, University of Calgary, Alberta, Canada T2N 1N4,Bamfield Marine Sciences Centre, Bamfield, British Columbia, Canada V0R 1B0
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Inbreeding is associated with shorter early-life telomere length in a wild passerine. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01441-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractInbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows (Passer domesticus) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows (n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres (n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.
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Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
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Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
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González Ariza A, Arando Arbulu A, León Jurado JM, Navas González FJ, Delgado Bermejo JV, Camacho Vallejo ME. Discriminant Canonical Tool for Differential Biometric Characterization of Multivariety Endangered Hen Breeds. Animals (Basel) 2021; 11:ani11082211. [PMID: 34438669 PMCID: PMC8388411 DOI: 10.3390/ani11082211] [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: 06/16/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Breed undefinition boosts the risk of irreversible breed loss due to its substitution by dominant breeds. Breed loss results detrimental for the fraction of the genetic pool which is linked to the value of livestock as perfectly adapted elements of domestic ecosystems among other desirable features. In turn, this ensures and maximizes population sustainability. The present study aimed to design a biometric characterization tool in autochthonous avian breeds and their varieties in Andalusia (south of Spain): Utrerana and Sureña breeds. For this, different quantitative and qualitative measurements were collected in 473 females and 135 roosters belonging to these breeds. Even though both genotypes belong to a common original trunk, discriminant canonical analysis (DCA) revealed clear differences between both breeds and within the varieties that they comprise. In particular, certain variables such as ocular ratio and phaneroptic characteristics, which may be intrinsically related to the capacity of the breeds to adapt to the environmental conditions in which they thrive, could allow breeders to develop breeding programs focused on the enhancement productive potential of individuals. Abstract This study aimed to develop a tool to perform the morphological characterization of Sureña and Utrerana breeds, two endangered autochthonous breeds ascribed to the Mediterranean trunk of Spanish autochthonous hens and their varieties (n = 608; 473 females and 135 males). Kruskal–Wallis H test reported sex dimorphism pieces of evidence (p < 0.05 at least). Multicollinearity analysis reported (variance inflation factor (VIF) >5 variables were discarded) white nails, ocular ratio, and back length (Wilks’ lambda values of 0.191, 0.357, and 0.429, respectively) to have the highest discriminant power in female morphological characterization. For males, ocular ratio and black/corneous and white beak colors (Wilks’ lambda values of 0.180, 0.210, and 0.349, respectively) displayed the greatest discriminant potential. The first two functions explained around 90% intergroup variability. A stepwise discriminant canonical analysis (DCA) was used to determine genotype clustering patterns. Interbreed and varieties proximity was evaluated through Mahalanobis distances. Despite the adaptability capacity to alternative production systems ascribed to both avian breeds, Sureña and Utrerana morphologically differ. Breed dimorphism may evidence differential adaptability mechanisms linked to their aptitude (dual purpose/egg production). The present tool may serve as a model for the first stages of breed protection to be applicable in other endangered avian breeds worldwide.
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Affiliation(s)
- Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
| | - Ander Arando Arbulu
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
- Animal Breeding Consulting S.L., 14014 Córdoba, Spain
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain;
- Correspondence: ; Tel.: +34-651-679-262
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (A.G.A.); (A.A.A.); (J.V.D.B.)
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Hua G, Chen J, Wang J, Li J, Deng X. Genetic basis of chicken plumage color in artificial population of complex epistasis. Anim Genet 2021; 52:656-666. [PMID: 34224160 DOI: 10.1111/age.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/18/2022]
Abstract
Chicken plumage color, the genetic basis of which is often affected by epistasis, has long interested scientists. In the current study, a population of complex epistasis was constructed by crossing dominant White Leghorn chickens with recessive white feather chickens. Through a genome-wide association study, we identified single nucleotide polymorphisms and genes significantly associated with white and colored plumage in hens at different developmental stages. Interestingly, white plumage in adulthood was associated with the recessive white feather gene (TYR), whereas white feathers at birth stage were associated with the dominant white feather gene (PMEL), indicating age-related roles for these genes. TYR was shown to exert an epistatic effect on PMEL in adult hens. Additionally, TYR had an epistatic effect on barred plumage, while barred plumage had an epistatic effect on black plumage. TYR had no epistatic effect on the yellow plumage. We confirmed that the barred plumage gene is CDKN2A, as reported in previous studies. Golgb1 and REEP3, which play important roles in the Golgi network and affect the formation of feather pigments, are important candidate genes for yellow plumage. The candidate genes for black plumage are CAMKK1 and IFT22. Further research is warranted to elucidate the molecular mechanisms underlying these traits.
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Affiliation(s)
- Guoying Hua
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
| | - Jianfei Chen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
| | - Jiankui Wang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
| | - Xuemei Deng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
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Kaya C, Generalovic TN, Ståhls G, Hauser M, Samayoa AC, Nunes-Silva CG, Roxburgh H, Wohlfahrt J, Ewusie EA, Kenis M, Hanboonsong Y, Orozco J, Carrejo N, Nakamura S, Gasco L, Rojo S, Tanga CM, Meier R, Rhode C, Picard CJ, Jiggins CD, Leiber F, Tomberlin JK, Hasselmann M, Blanckenhorn WU, Kapun M, Sandrock C. Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens. BMC Biol 2021; 19:94. [PMID: 33952283 PMCID: PMC8101212 DOI: 10.1186/s12915-021-01029-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Background The black soldier fly (Hermetia illucens) is the most promising insect candidate for nutrient-recycling through bioconversion of organic waste into biomass, thereby improving sustainability of protein supplies for animal feed and facilitating transition to a circular economy. Contrary to conventional livestock, genetic resources of farmed insects remain poorly characterised. We present the first comprehensive population genetic characterisation of H. illucens. Based on 15 novel microsatellite markers, we genotyped and analysed 2862 individuals from 150 wild and captive populations originating from 57 countries on seven subcontinents. Results We identified 16 well-distinguished genetic clusters indicating substantial global population structure. The data revealed genetic hotspots in central South America and successive northwards range expansions within the indigenous ranges of the Americas. Colonisations and naturalisations of largely unique genetic profiles occurred on all non-native continents, either preceded by demographically independent founder events from various single sources or involving admixture scenarios. A decisive primarily admixed Polynesian bridgehead population serially colonised the entire Australasian region and its secondarily admixed descendants successively mediated invasions into Africa and Europe. Conversely, captive populations from several continents traced back to a single North American origin and exhibit considerably reduced genetic diversity, although some farmed strains carry distinct genetic signatures. We highlight genetic footprints characteristic of progressing domestication due to increasing socio-economic importance of H. illucens, and ongoing introgression between domesticated strains globally traded for large-scale farming and wild populations in some regions. Conclusions We document the dynamic population genetic history of a cosmopolitan dipteran of South American origin shaped by striking geographic patterns. These reflect both ancient dispersal routes, and stochastic and heterogeneous anthropogenic introductions during the last century leading to pronounced diversification of worldwide structure of H. illucens. Upon the recent advent of its agronomic commercialisation, however, current human-mediated translocations of the black soldier fly largely involve genetically highly uniform domesticated strains, which meanwhile threaten the genetic integrity of differentiated unique local resources through introgression. Our in-depth reconstruction of the contemporary and historical demographic trajectories of H. illucens emphasises benchmarking potential for applied future research on this emerging model of the prospering insect-livestock sector. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01029-w.
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Affiliation(s)
- Cengiz Kaya
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.,Department of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland
| | | | - Gunilla Ståhls
- Zoology unit, Finnish Museum of Natural History, Helsinki, Finland
| | - Martin Hauser
- California Department of Food and Agriculture, Plant Pest Diagnostics Branch, Sacramento, USA
| | - Ana C Samayoa
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan
| | - Carlos G Nunes-Silva
- Department of Genetics and Biotechnology Graduate Program, Federal University of Amazonas, Manaus, Brazil
| | - Heather Roxburgh
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jens Wohlfahrt
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Ebenezer A Ewusie
- Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, Accra, Ghana
| | | | - Yupa Hanboonsong
- Department of Entomology, Khon Kaen University, Khon Kaen, Thailand
| | - Jesus Orozco
- Department of Agricultural Sciences and Production, Zamorano University, Zamorano, Honduras
| | - Nancy Carrejo
- Department of Biology, Universidad del Valle, Santiago de Cali, Colombia
| | - Satoshi Nakamura
- Crop, Livestock and Environmental Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Santos Rojo
- Department of Environmental Sciences and Natural Resources, University of Alicante, Alicante, Spain
| | - Chrysantus M Tanga
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, Republic of South Africa
| | - Christine J Picard
- Department of Biology, Indiana University - Purdue University Indianapolis, Indianapolis, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Florian Leiber
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | | | - Martin Hasselmann
- Department of Livestock Population Genomics, University of Hohenheim, Stuttgart, Germany
| | - Wolf U Blanckenhorn
- Department of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland.,Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Christoph Sandrock
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
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12
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Yan H, Liu Q, Wen F, Bai B, Wen Y, Chen W, Lu W, Lin Y, Xia Q, Wang G. Characterization and potential application of an α-amylase (BmAmy1) selected during silkworm domestication. Int J Biol Macromol 2020; 167:1102-1112. [PMID: 33188814 DOI: 10.1016/j.ijbiomac.2020.11.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Efficient resource utilization plays a central role in the high productivity of domesticated plants and animals. Whether artificial selection acts on digestive enzymes in the domesticated silkworm (Bombyx mori), which is larger than its wild ancestor, Bombyx mandarina (B. mandarina), remains unknown. In this study, we present the characteristics of a novel alpha-amylase, BmAmy1, in B. mori. The activity of recombinant BmAmy1 was maximal at 35 °C and pH 9.0, and could be suppressed by amylase inhibitors from mulberry, the exclusive food source of silkworms. Three different transposable element fragments, which were independently inserted in the 5'-upstream regulatory region, might be responsible for the enhanced expression of BmAmy1 in different domesticated silkworm strains as revealed by dual-luciferase reporter assay. The BmAmy1 overexpression increased the weight of female and male B. mori by 11.9% and 6.8%, respectively, compared with non-transgenic controls. Our results emphasize that, by exploring the genetic mechanisms of human-selected traits, the domestication process could be further accelerated through genetic engineering and targeted breeding.
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Affiliation(s)
- Hao Yan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingsong Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Feng Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Bingchuan Bai
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Yuchan Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wenwen Chen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China.
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13
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Ren T, Yang Y, Lin W, Li W, Xian M, Fu R, Zhang Z, Mo G, Luo W, Zhang X. A 31-bp indel in the 5' UTR region of GNB1L is significantly associated with chicken body weight and carcass traits. BMC Genet 2020; 21:91. [PMID: 32847500 PMCID: PMC7450547 DOI: 10.1186/s12863-020-00900-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND G-protein subunit beta 1 like (GNB1L) encodes a G-protein beta-subunit-like polypeptide. Chicken GNB1L is upregulated in the breast muscle of high feed efficiency chickens, and its expression is 1.52-fold that in low feed efficiency chickens. However, no report has described the effects of GNB1L indels on the chicken carcass and growth traits. RESULTS This study identified a 31-bp indel in the 5' untranslated region (UTR) of GNB1L and elucidated the effect of this gene mutation on the carcass and growth traits in chickens. The 31-bp indel showed a highly significant association with the body weight at 8 different stages and was significantly correlated with daily gains at 0 to 4 weeks and 4 to 8 weeks. Similarly, the mutation was significantly associated with small intestine length, breast width, breast depth and breast muscle weight. Moreover, DD and ID were superior genotypes for chicken growth and carcass traits. CONCLUSIONS These results show that the 31-bp indel of GNB1L significantly affects chicken body weight and carcass traits and can serve as a candidate molecular marker for chicken genetics and breeding programs.
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Affiliation(s)
- Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,College of Life Science, Foshan University, Foshan, 528231, Guangdong, China
| | - Ying Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Wujian Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Mingjian Xian
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Zihao Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Guodong Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.
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14
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Ren T, Zhang Z, Fu R, Yang Y, Li W, Liang J, Mo G, Luo W, Zhang X. A 51 bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits. Anim Genet 2020; 51:568-578. [PMID: 32400914 DOI: 10.1111/age.12942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2020] [Indexed: 01/04/2023]
Abstract
Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G-protein-coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4-8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding.
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Affiliation(s)
- T Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Z Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - R Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Y Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - W Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - J Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - G Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - W Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - X Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
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15
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Hou Y, Qi F, Bai X, Ren T, Shen X, Chu Q, Zhang X, Lu X. Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals. BMC Genomics 2020; 21:204. [PMID: 32131728 PMCID: PMC7057487 DOI: 10.1186/s12864-020-6613-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
Background In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection. Results First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild. Conclusions After a comprehensive investigation on genomic diversity and evolutionary trajectories in chickens, we revealed basis, pattern and evolutionary significance of molecular convergence in domesticated bird and mammals, highlighted the genetic basis of a compromise on utmost adaptation to the lives with human at the cost of high risk of neurophysiological changes affecting animals’ fitness in wild.
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Affiliation(s)
- Yali Hou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,China National Center for Bioinformation, Beijing, People's Republic of China.
| | - Furong Qi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xue Bai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China
| | - Tong Ren
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xu Shen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Xiquan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, People's Republic of China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China.
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16
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Poklukar K, Čandek-Potokar M, Batorek Lukač N, Tomažin U, Škrlep M. Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review. Animals (Basel) 2020; 10:E424. [PMID: 32138208 PMCID: PMC7142902 DOI: 10.3390/ani10030424] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022] Open
Abstract
Modern pig breeds, which have been genetically improved to achieve fast growth and a lean meat deposition, differ from local pig breeds with respect to fat deposition, fat specific metabolic characteristics and various other properties. The present review aimed to elucidate the mechanisms underlying the differences between fatty local and modern lean pig breeds in adipose tissue deposition and lipid metabolism, taking into consideration morphological, cellular, biochemical, transcriptomic and proteomic perspectives. Compared to modern breeds, local pig breeds accumulate larger amounts of fat, which generally contains more monounsaturated and saturated fatty acids; they exhibit a higher adipocyte size and higher activity of lipogenic enzymes. Studies using transcriptomic and proteomic approaches highlighted several processes like immune response, fatty-acid turn-over, oxidoreductase activity, mitochondrial function, etc. which differ between local and modern pig breeds.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
- University of Maribor, Faculty of Agriculture and Life Sciences, Hoče SI-2311, Slovenia
| | - Nina Batorek Lukač
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Urška Tomažin
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
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17
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The Temporal Dynamics of Background Selection in Nonequilibrium Populations. Genetics 2020; 214:1019-1030. [PMID: 32071195 DOI: 10.1534/genetics.119.302892] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/30/2020] [Indexed: 01/06/2023] Open
Abstract
Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.
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18
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Wang X, Wei C, Zhang Z, Liu D, Guo Y, Sun G, Wang Y, Li H, Tian Y, Kang X, Han R, Li Z. Association of growth traits with a structural variation downstream of the KCNJ11 gene: a large population-based study in chickens. Br Poult Sci 2020; 61:320-327. [PMID: 32008360 DOI: 10.1080/00071668.2020.1724878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. The potassium voltage-gated channel subfamily J member 11 gene (KCNJ11) is involved in the insulin secretion pathway. Studies have shown that mutation in this gene is associated with muscle weakness. The objective of the present study was to establish the association between KCNJ11 gene polymorphism and chicken growth performance and to analyse its expression pattern. 2. A novel 163-bp insertion/deletion (indel) polymorphism was identified in the region downstream of the KCNJ11 gene in 2330 individuals from ten populations by polymerase chain reaction (PCR). An F2 resource population was used to investigate the genetic effects of the chicken KCNJ11 gene. Association analysis showed that the indel was significantly associated with chicken growth traits and that the phenotypic value of the ins-ins (II) genotype is higher than that of the ins-del (ID) and del-del (DD) genotypes. 3. Gene expression for different genotypes showed that birds carrying the II allele had a higher expression level than the DD genotypes. Analysis of tissue and spatiotemporal expression patterns indicated that the KCNJ11 gene was highly expressed in muscle tissues, with the highest levels in muscle tissue at one week of age, and that a 10% crude protein diet reduced the expression of this gene, average daily gain and muscle fibre diameter. 4. The results suggested that this novel 163-bp indel has the potential to become a new target for marker-assisted selection.
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Affiliation(s)
- X Wang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - C Wei
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Z Zhang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - D Liu
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Guo
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - G Sun
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Wang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - H Li
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Tian
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - X Kang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - R Han
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Z Li
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
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19
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Solberg MF, Robertsen G, Sundt-Hansen LE, Hindar K, Glover KA. Domestication leads to increased predation susceptibility. Sci Rep 2020; 10:1929. [PMID: 32029847 PMCID: PMC7005312 DOI: 10.1038/s41598-020-58661-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2020] [Indexed: 12/18/2022] Open
Abstract
Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.
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Affiliation(s)
- Monica F Solberg
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.
| | - Grethe Robertsen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Line E Sundt-Hansen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kevin A Glover
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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20
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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21
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Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L. Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples. Genetics 2019; 212:587-614. [PMID: 31088861 PMCID: PMC6614887 DOI: 10.1534/genetics.119.302057] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/01/2019] [Indexed: 11/18/2022] Open
Abstract
Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.
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Affiliation(s)
- Gabriel Renaud
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
| | - Kristian Hanghøj
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Department of Zoology, University of Cambridge, CB2 3EJ, UK
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- The Danish Institute for Advanced Study at The University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France
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22
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Steensels J, Gallone B, Voordeckers K, Verstrepen KJ. Domestication of Industrial Microbes. Curr Biol 2019; 29:R381-R393. [DOI: 10.1016/j.cub.2019.04.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Karimi K, Sargolzaei M, Plastow GS, Wang Z, Miar Y. Opportunities for genomic selection in American mink: A simulation study. PLoS One 2019; 14:e0213873. [PMID: 30870528 PMCID: PMC6417779 DOI: 10.1371/journal.pone.0213873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/01/2019] [Indexed: 12/25/2022] Open
Abstract
Genomic selection can be considered as an effective tool for developing breeding programs in American mink. However, the genetic gains for economically important traits can be influenced by the accuracy of genomic predictions. The objective of this study was to investigate the prediction accuracies of traditional best linear unbiased prediction (BLUP), multi-step genomic BLUP (GBLUP) and single-step GBLUP (ssGBLUP) methods in American mink using simulated data with different levels of heritability, marker density, training set (TS) sizes and selection designs based on either phenotypic performance or estimated breeding values (EBVs). Under EBV selection design, the accuracy of BLUP predictions was increased by 38% and 44% for h2 = 0.10, 27% and 29% for h2 = 0.20, and 5.8% and 6% for h2 = 0.50 using GBLUP and ssGBLUP methods, respectively. Under phenotypic selection design, the accuracies of prediction by ssGBLUP method were 11.8% and 15.4% higher than those obtained by GBLUP for heritability of 0.10 and 0.20, respectively. However, the efficiency of ssGBLUP and GBLUP was not influenced by selection design at higher level of heritability (h2 = 0.50). Furthermore, higher selection intensity increased the bias of predictions in both pedigree-based and genomic evaluations. Regardless of selection design, TS sizes for GBLUP and ssGBLUP methods should be at least 3000 to achieve more accuracy than using BLUP for heritability of 0.50 and marker density of 10k and 50k. Overall, more accurate predictions were obtained using ssGBLUP method particularly for lowly heritable traits and low density of markers. Our results indicated that TS sizes should be optimized in accordance with heritability level, marker density, selection design and prediction method for genomic selection in American mink. The results provided an initial framework for designing genomic selection in mink breeding programs.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- Select Sires Inc., Plain City, Ohio, United States of America
| | - Graham Stuart Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
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24
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Zhu YN, Wang LZ, Li CC, Cui Y, Wang M, Lin YJ, Zhao RP, Wang W, Xiang H. Artificial selection on storage protein 1 possibly contributes to increase of hatchability during silkworm domestication. PLoS Genet 2019; 15:e1007616. [PMID: 30668559 PMCID: PMC6358105 DOI: 10.1371/journal.pgen.1007616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/01/2019] [Accepted: 12/16/2018] [Indexed: 11/19/2022] Open
Abstract
Like other domesticates, the efficient utilization of nitrogen resources is also important for the only fully domesticated insect, the silkworm. Deciphering the way in which artificial selection acts on the silkworm genome to improve the utilization of nitrogen resources and to advance human-favored domestication traits, will provide clues from a unique insect model for understanding the general rules of Darwin's evolutionary theory on domestication. Storage proteins (SPs), which belong to a hemocyanin superfamily, basically serve as a source of amino acids and nitrogen during metamorphosis and reproduction in insects. In this study, through blast searching on the silkworm genome and further screening of the artificial selection signature on silkworm SPs, we discovered a candidate domestication gene, i.e., the methionine-rich storage protein 1 (SP1), which is clearly divergent from other storage proteins and exhibits increased expression in the ova of domestic silkworms. Knockout of SP1 via the CRISPR/Cas9 technique resulted in a dramatic decrease in egg hatchability, without obvious impact on egg production, which was similar to the effect in the wild silkworm compared with the domestic type. Larval development and metamorphosis were not affected by SP1 knockout. Comprehensive ova comparative transcriptomes indicated significant higher expression of genes encoding vitellogenin, chorions, and structural components in the extracellular matrix (ECM)-interaction pathway, enzymes in folate biosynthesis, and notably hormone synthesis in the domestic silkworm, compared to both the SP1 mutant and the wild silkworm. Moreover, compared with the wild silkworms, the domestic one also showed generally up-regulated expression of genes enriched in the structural constituent of ribosome and amide, as well as peptide biosynthesis. This study exemplified a novel case in which artificial selection could act directly on nitrogen resource proteins, further affecting egg nutrients and eggshell formation possibly through a hormone signaling mediated regulatory network and the activation of ribosomes, resulting in improved biosynthesis and increased hatchability during domestication. These findings shed new light on both the understanding of artificial selection and silkworm breeding from the perspective of nitrogen and amino acid resources. Like other domesticates, nitrogen resources are also important for the only fully domesticated insect, the silkworm. Deciphering the way in which artificial selection acts on the silkworm genome to improve the utilization of nitrogen resources, thereby advancing human-favored domestication traits, will provide clues from a unique insect model for understanding the general rules of Darwin's theory on artificial selection. However, the mechanisms of domestication in the silkworm remain largely unknown. In this study, we focused on one important nitrogen resource, the storage protein (SP). We discovered that the methionine-rich storage protein 1 (SP1), which is divergent from other SPs, is the only target of artificial selection. Based on functional evidence, together with key findings from the comprehensive comparative transcriptome, we propose that artificial selection favored higher expression of SP1 in the domestic silkworm, which would influence the genes or pathways vital for egg development and eggshell formation. Artificial selection also consistently favored activated ribosome activities and improved amide and peptide biosynthesis in the ova, like what they may act in the silk gland to increase silk-cocoon yield. We highlighted a novel case in which artificial selection could directly act on a nitrogen resource protein associated with a human-desired domestication trait.
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Affiliation(s)
- Ya-Nan Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li-Zhi Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Cen-Cen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yong Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Man Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yong-Jian Lin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Poly-technical University, Xi’an, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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25
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Bertolini F, Schiavo G, Tinarelli S, Santoro L, Utzeri VJ, Dall'Olio S, Nanni Costa L, Gallo M, Fontanesi L. Exploiting phenotype diversity in a local animal genetic resource: Identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous Casertana pig breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Xiang H, Liu X, Li M, Zhu Y, Wang L, Cui Y, Liu L, Fang G, Qian H, Xu A, Wang W, Zhan S. The evolutionary road from wild moth to domestic silkworm. Nat Ecol Evol 2018; 2:1268-1279. [PMID: 29967484 DOI: 10.1038/s41559-018-0593-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Abstract
The Silk Road, which derives its name from the trade of silk produced by the domestic silkworm Bombyx mori, was an important episode in the development and interaction of human civilizations. However, the detailed history behind silkworm domestication remains ambiguous, and little is known about the underlying genetics with respect to important aspects of its domestication. Here, we reconstruct the domestication processes and identify selective sweeps by sequencing 137 representative silkworm strains. The results present an evolutionary scenario in which silkworms may have been initially domesticated in China as trimoulting lines, then subjected to independent spreads along the Silk Road that gave rise to the development of most local strains, and further improved for modern silk production in Japan and China, having descended from diverse ancestral sources. We find that genes with key roles in nitrogen and amino acid metabolism may have contributed to the promotion of silk production, and that circadian-related genes are generally selected for their adaptation. We additionally identify associations between several candidate genes and important breeding traits, thereby advancing the applicable value of our resources.
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Affiliation(s)
- Hui Xiang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaojing Liu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Muwang Li
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ya'nan Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lizhi Wang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yong Cui
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyuan Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Heying Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Anying Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.
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27
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Yang Y, Adeola AC, Xie HB, Zhang YP. Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs. Zool Res 2018; 39:424-430. [PMID: 29955027 PMCID: PMC6085766 DOI: 10.24272/j.issn.2095-8137.2018.068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Bama Xiang pig (BMX) is a famous early-maturing Chinese indigenous breed with a two-end black coat. To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650204, China; E-mails:; .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650204, China; E-mails:;
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650204, China; E-mails:;
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650204, China; E-mails:; .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
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28
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Changes in pituitary gene expression may underlie multiple domesticated traits in chickens. Heredity (Edinb) 2018; 122:195-204. [PMID: 29789643 DOI: 10.1038/s41437-018-0092-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/05/2018] [Accepted: 04/26/2018] [Indexed: 12/29/2022] Open
Abstract
Domesticated animals share a unique set of morphological and behavioral traits, jointly referred to as the domesticated phenotype. Striking similarities amongst a range of unrelated domesticated species suggest that similar regulatory mechanisms may underlie the domesticated phenotype. These include color pattern, growth, reproduction, development and stress response. Although previous studies have focused on the brain to find mechanisms underlying domestication, the potential role of the pituitary gland as a target of domestication is highly overlooked. Here, we study gene expression in the pituitary gland of the domesticated White Leghorn chicken and its wild ancestor, the Red Junglefowl. By overlapping differentially expressed genes with a previously published list of functionally important genes in the pituitary gland, we narrowed down to 34 genes. Amongst them, expression levels of genes with inhibitory function on pigmentation (ASIP), main stimulators of metabolism and sexual maturity (TSHB and DIO2), and a potential inhibitor of broodiness (PRLR), were higher in the domesticated breed. Additionally, expression of 2 key inhibitors of the stress response (NR3C1, CRHR2) was higher in the domesticated breed. We suggest that changes in the transcription of important modulatory genes in the pituitary gland can account not only for domestication of the stress response in domestic chickens, but also for changes in pigmentation, development, and reproduction. Given the pivotal role of the pituitary gland in the regulation of multiple shared domesticated traits, we suggest that similar changes in pituitary transcriptome may contribute to the domesticated phenotype in other species as well.
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29
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Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Ginns EI, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton GD, Warren WC, Wasim M, Lyons LA. Applications and efficiencies of the first cat 63K DNA array. Sci Rep 2018; 8:7024. [PMID: 29728693 PMCID: PMC5935720 DOI: 10.1038/s41598-018-25438-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/16/2018] [Indexed: 12/02/2022] Open
Abstract
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
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Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Safat, Kuwait.
| | - Mona Abdi
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Leslie H Bach
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,University of San Francisco, San Francisco, CA, USA
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Nicholas H Dodman
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Edward I Ginns
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer C Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bianca Haase
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Jens Haggstrom
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michael J Hamilton
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Biochemistry, University of California - Riverside, Riverside, CA, USA
| | | | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Foothill College, Los Altos Hills, CA, USA
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, and The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Richard Malik
- Centre for Veterinary Education, University of Sydney, New South Wales, Australia
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael J Montague
- Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Carlyn B Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Clare Rusbridge
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Rashid Saif
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - G Diane Shelton
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Muhammad Wasim
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA.
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30
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Fam BS, Paré P, Felkl AB, Vargas-Pinilla P, Paixão-Côrtes VR, Viscardi LH, Bortolini MC. Oxytocin and arginine vasopressin systems in the domestication process. Genet Mol Biol 2018; 41:235-242. [PMID: 29668014 PMCID: PMC5913714 DOI: 10.1590/1678-4685-gmb-2017-0069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/01/2017] [Indexed: 11/22/2022] Open
Abstract
Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication process. Furthermore, AVPR1a, which plays a role in social behavior, is under relaxed selective constraint in domesticated species. These results provide new insights into the nature of the domestication process and its impact on the OXT-AVP system.
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Affiliation(s)
- Bibiana S.O. Fam
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pamela Paré
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Aline B. Felkl
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | | | | | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
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31
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Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
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Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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32
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Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol 2017; 49:81. [PMID: 29115919 PMCID: PMC5674817 DOI: 10.1186/s12711-017-0354-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
Background With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Results Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. Conclusions Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0354-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain.
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain.,Fundación Centro Supercomputación de Castilla y León, Campus de Vegazana, León, 24071, Spain
| | - Pamela Wiener
- Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Praveen Krishna Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - Juan-Jose Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
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33
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Kwon T, Yoon J, Heo J, Lee W, Kim H. Tracing the breeding farm of domesticated pig using feature selection (Sus scrofa). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1540-1549. [PMID: 29073733 PMCID: PMC5666188 DOI: 10.5713/ajas.17.0561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/28/2017] [Accepted: 10/09/2017] [Indexed: 11/27/2022]
Abstract
Objective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP) markers strictly selected through least absolute shrinkage and selection operator (LASSO) feature selection. Methods We performed farm tracing of domesticated pig (Sus scrofa) from SNP markers and selected the most relevant features for accurate prediction. Considering multi-breed composition of our data, we performed feature selection using LASSO penalization on 4,002 SNPs that are shared between breeds, which also includes 179 SNPs with small between-breed difference. The 100 highest-scored features were extracted from iterative simulations and then evaluated using machine-leaning based classifiers. Results We selected 1,341 SNPs from over 45,000 SNPs through iterative LASSO feature selection, to minimize between-breed differences. We subsequently selected 100 highest-scored SNPs from iterative scoring, and observed high statistical measures in classification of breeding farms by cross-validation only using these SNPs. Conclusion The study represents a successful application of LASSO feature selection on multi-breed pig SNP data to trace the farm information, which provides a valuable method and possibility for further researches on genetic traceability.
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Affiliation(s)
- Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Joon Yoon
- Interdisciplinary Program in Bioinformatics Department of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Jaeyoung Heo
- International Agricultural Development and Cooperation Center, Chonbuk National University, Jeonju 54896, Korea
| | - Wonseok Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,Institute for Biomedical Sciences, Shinshu University, Nagano 390-0802, Japan
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34
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Böhmer C, Böhmer E. Shape Variation in the Craniomandibular System and Prevalence of Dental Problems in Domestic Rabbits: A Case Study in Evolutionary Veterinary Science. Vet Sci 2017; 4:vetsci4010005. [PMID: 29056664 PMCID: PMC5606619 DOI: 10.3390/vetsci4010005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 12/20/2022] Open
Abstract
In contrast to wild lagomorphs, pet rabbits exhibit a noticeably high frequency of dental problems. Although dietary habits are considered as a major factor contributing to acquired malocclusions, the exact causes and interrelationships are still under debate. In this regard, an important aspect that has not been considered thoroughly to date is the effect of diet-induced phenotypic plasticity in skull morphology. Therefore, we conducted a geometric morphometric analysis on skull radiological images of wild and pet rabbits in order to quantify intraspecific variation in craniomandibular morphology. The statistical analyses reveal a significant morphological differentiation of the craniomandibular system between both groups. Furthermore, the analysis of covariance shows that the force-generating modules (cranium and mandible) vary independently from the force-receiving module (hypselodont teeth) in pet rabbits, which is in contrast to their wild relatives. Our findings suggest that the phenotypic changes in domestic rabbits impact mastication performance and, consequently, oral health. An adequate close-to-nature nutrition throughout the whole life and especially beginning early parallel to weaning (phase of increased phenotypic plasticity) is necessary to ensure a normal strain on the teeth by promoting physiological lateral gliding movements and avoiding direct axial loads.
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Affiliation(s)
- Christine Böhmer
- UMR 7179 CNRS, Muséum National d'Histoire Naturelle, CP 55, 57 rue Cuvier, 75231 Paris Cedex 05, France.
| | - Estella Böhmer
- Chirurgische und Gynäkologische Kleintierklinik ,Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstr 13, München 80539, Germany.
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35
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A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken. Sci Rep 2016; 6:36433. [PMID: 27808177 PMCID: PMC5093740 DOI: 10.1038/srep36433] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/17/2016] [Indexed: 11/26/2022] Open
Abstract
Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5′ terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds.
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36
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Gao G, Zhao X, Li Q, He C, Zhao W, Liu S, Ding J, Ye W, Wang J, Chen Y, Wang H, Li J, Luo Y, Su J, Huang Y, Liu Z, Dai R, Shi Y, Meng H, Wang Q. Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose. Sci Rep 2016; 6:32961. [PMID: 27608918 PMCID: PMC5016989 DOI: 10.1038/srep32961] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 08/18/2016] [Indexed: 01/01/2023] Open
Abstract
The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Qin Li
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Chuan He
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China.,Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Wenjing Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Shuyun Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Jinmei Ding
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Weixing Ye
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Jun Wang
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Ye Chen
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Haiwei Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Jing Li
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Yi Luo
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Jian Su
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Yong Huang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Zuohua Liu
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Ronghua Dai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Yixiang Shi
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Qigui Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
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37
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Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. A Meta-Assembly of Selection Signatures in Cattle. PLoS One 2016; 11:e0153013. [PMID: 27045296 PMCID: PMC4821596 DOI: 10.1371/journal.pone.0153013] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/31/2022] Open
Abstract
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
- * E-mail:
| | - Mehar S. Khatkar
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Peter C. Thomson
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Herman W. Raadsma
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
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38
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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Zhang Y, Lu Y, Yindee M, Li K, Kuo H, Ju Y, Ye S, Faruque MO, Li Q, Wang Y, Cuong VC, Pham LD, Bouahom B, Yang B, Liang X, Cai Z, Vankan D, Manatchaiworakul W, Kowlim N, Duangchantrasiri S, Wajjwalku W, Colenbrander B, Zhang Y, Beerli P, Lenstra JA, Barker JSF. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol Ecol 2016; 25:1530-50. [DOI: 10.1111/mec.13518] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yongfang Lu
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Marnoch Yindee
- Department of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 Thailand
| | - Kuan‐Yi Li
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Hsiao‐Yun Kuo
- Livestock Research Institute Council of Agriculture Tainan 71246 Taiwan
| | - Yu‐Ten Ju
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Shaohui Ye
- College of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
| | - Qiang Li
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Vu Chi Cuong
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Bounthong Bouahom
- National Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.R
| | - Bingzhuang Yang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Xianwei Liang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Zhihua Cai
- College of Animal Science Anhui Science and Technology University Fengyang 233100 China
| | - Dianne Vankan
- The School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 Australia
| | - Wallaya Manatchaiworakul
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Nonglid Kowlim
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Somphot Duangchantrasiri
- Khao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 Thailand
| | - Worawidh Wajjwalku
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Ben Colenbrander
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - Yuan Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USA
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
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Sorbolini S, Marras G, Gaspa G, Dimauro C, Cellesi M, Valentini A, Macciotta NP. Detection of selection signatures in Piemontese and Marchigiana cattle, two breeds with similar production aptitudes but different selection histories. Genet Sel Evol 2015; 47:52. [PMID: 26100250 PMCID: PMC4476081 DOI: 10.1186/s12711-015-0128-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/20/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Domestication and selection are processes that alter the pattern of within- and between-population genetic variability. They can be investigated at the genomic level by tracing the so-called selection signatures. Recently, sequence polymorphisms at the genome-wide level have been investigated in a wide range of animals. A common approach to detect selection signatures is to compare breeds that have been selected for different breeding goals (i.e. dairy and beef cattle). However, genetic variations in different breeds with similar production aptitudes and similar phenotypes can be related to differences in their selection history. METHODS In this study, we investigated selection signatures between two Italian beef cattle breeds, Piemontese and Marchigiana, using genotyping data that was obtained with the Illumina BovineSNP50 BeadChip. The comparison was based on the fixation index (Fst), combined with a locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach. In addition, analyses of Fst were carried out to confirm candidate genes. In particular, data were processed using the varLD method, which compares the regional variation of linkage disequilibrium between populations. RESULTS Genome scans confirmed the presence of selective sweeps in the genomic regions that harbour candidate genes that are known to affect productive traits in cattle such as DGAT1, ABCG2, CAPN3, MSTN and FTO. In addition, several new putative candidate genes (for example ALAS1, ABCB8, ACADS and SOD1) were detected. CONCLUSIONS This study provided evidence on the different selection histories of two cattle breeds and the usefulness of genomic scans to detect selective sweeps even in cattle breeds that are bred for similar production aptitudes.
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Affiliation(s)
- Silvia Sorbolini
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
| | - Gabriele Marras
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
| | - Giustino Gaspa
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
| | - Corrado Dimauro
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
| | - Massimo Cellesi
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
| | - Alessio Valentini
- Dipartimento per l'Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy.
| | - Nicolò Pp Macciotta
- Dipartimento di Agraria, Sezione di Scienze Zootecniche Università degli Studi di Sassari, 07100, Sassari, Italy.
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Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, Feng S, Huang G, Guan R, Shen W, Bunch R, McCulloch R, Li Q, Li B, Zhang G, Xu X, Kijas JW, Salekdeh GH, Wang W, Jiang Y. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 2015; 16:431. [PMID: 26044654 PMCID: PMC4455334 DOI: 10.1186/s12864-015-1606-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/01/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.
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Affiliation(s)
- Yang Dong
- Kunming University of Science and Technology, Kunming, 650093, China.
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Xiaolei Zhang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Min Xie
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Babak Arefnezhad
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
| | - Zongji Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
| | | | | | | | - Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Wenjing Shen
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Rowan Bunch
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | | | - Qiye Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - James W Kijas
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | - Ghasem Hosseini Salekdeh
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Wen Wang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Yu Jiang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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43
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Moon S, Kim TH, Lee KT, Kwak W, Lee T, Lee SW, Kim MJ, Cho K, Kim N, Chung WH, Sung S, Park T, Cho S, Groenen MA, Nielsen R, Kim Y, Kim H. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics 2015; 16:130. [PMID: 25765548 PMCID: PMC4349229 DOI: 10.1186/s12864-015-1330-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/06/2015] [Indexed: 11/10/2022] Open
Abstract
Background Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunjin Moon
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. .,Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea. .,Current address: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Woori Kwak
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Taeheon Lee
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Si-Woo Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Myung-Jick Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Kyuho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea.
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.
| | - Won-Hyong Chung
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.
| | - Samsun Sung
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea.
| | - Seoae Cho
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
| | - Martien Am Groenen
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, 94820, USA.
| | - Yuseob Kim
- Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea.
| | - Heebal Kim
- Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. .,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
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Hocking PM. Unexpected consequences of genetic selection in broilers and turkeys: problems and solutions. Br Poult Sci 2014; 55:1-12. [PMID: 24397366 DOI: 10.1080/00071668.2014.877692] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
1. Genetic theory leads to the expectation that unexpected consequences of genetic selection for production traits will inevitably occur and that these changes are likely to be undesirable. 2. Both artificial selection for production efficiency and "natural" selection for adaptation to the production environment result in selection sweeps that increase the frequencies of rare recessive alleles that have a negative effect on fitness. 3. Fitness is broadly defined as any trait that affects the ability to survive, reproduce and contribute to the next generation, such as musculoskeletal disease in growing broiler chickens and multiple ovulation in adult broiler parents. 4. Welfare concerns about the negative effects of genetic selection on bird welfare are sometimes exaggerated but are nevertheless real. Breeders have paid increasing attention to these traits over several decades and have demonstrated improvement in pedigree flocks. There is an urgent need to monitor changes in commercial flocks to ensure that genetic change is accompanied by improvements in that target population. 5. New technologies for trait measurement, whole genome selection and targeted genetic modification hold out the promise of efficient and rapid improvement of welfare traits in future breeding of broiler chickens and turkeys. The potential of targeted genetic modification for enhancing welfare traits is considerable, but the goal of achieving public acceptability for the progeny of transgenic poultry will be politically challenging.
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Affiliation(s)
- P M Hocking
- a The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Easter Bush , Midlothian , EH25 9RG , UK
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Xu L, Bickhart DM, Cole JB, Schroeder SG, Song J, Tassell CPV, Sonstegard TS, Liu GE. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Mol Biol Evol 2014; 32:711-25. [PMID: 25431480 DOI: 10.1093/molbev/msu333] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.
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Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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Lyimo CM, Weigend A, Msoffe PL, Eding H, Simianer H, Weigend S. Global diversity and genetic contributions of chicken populations from African, Asian and European regions. Anim Genet 2014; 45:836-48. [DOI: 10.1111/age.12230] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2014] [Indexed: 01/15/2023]
Affiliation(s)
- C. M. Lyimo
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
- Animal Breeding and Genetics Group; Department of Animal Sciences; Georg-August-Universität Göttingen; 37075 Göttingen Germany
- Sokoine University of Agriculture; PO Box 3000 Morogoro Tanzania
| | - A. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
| | - P. L. Msoffe
- Sokoine University of Agriculture; PO Box 3000 Morogoro Tanzania
- School of Biological Sciences; University of Dodoma; PO Box 259 Dodoma Tanzania
| | - H. Eding
- Animal Evaluations Unit; CRV; PO Box 454, 6800 AL Arnhem The Netherlands
| | - H. Simianer
- Animal Breeding and Genetics Group; Department of Animal Sciences; Georg-August-Universität Göttingen; 37075 Göttingen Germany
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
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Abstract
Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals.
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48
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de Simoni Gouveia JJ, da Silva MVGB, Paiva SR, de Oliveira SMP. Identification of selection signatures in livestock species. Genet Mol Biol 2014; 37:330-42. [PMID: 25071397 PMCID: PMC4094609 DOI: 10.1590/s1415-47572014000300004] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/27/2014] [Indexed: 11/22/2022] Open
Abstract
The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.
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Affiliation(s)
- João José de Simoni Gouveia
- Colegiado Acadêmico de Zootecnia , Universidade Federal do Vale do São Francisco , Petrolina, PE , Brazil . ; Programa de Doutorado Integrado em Zootecnia , Universidade Federal do Ceará , Fortaleza, CE , Brazil
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49
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Genetic diversity of GH1 and LEP genes in Argentine llama (Lama glama) populations. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata. Gene 2014; 542:8-15. [DOI: 10.1016/j.gene.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 12/20/2013] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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