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Chai J, Long X, Wu P, Wang J, Wu X, Tu Z, Wei M, Guo Z, Zhang T, Chen L. Lactobacillus sp. participated in the adaptation of Rongchang piglets to cold stress. VET MED-CZECH 2023; 68:392-402. [PMID: 38028206 PMCID: PMC10666660 DOI: 10.17221/54/2023-vetmed] [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: 05/14/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
Rongchang piglets were easily induced to cold stress and diarrhoea in the winter when raised in an open hog house. However, they also gradually recovered under mid-cold stress. Other studies have suggested gut microbiome might be involved in the host energy metabolism to relieve stress. To study how to adapt Rongchang piglets to cold stress by gut microbiome, thirty Rongchang piglets were randomly divided into a mild cold stress group and a control group for 30 consecutive days. The findings revealed that the piglets had low growth performance and a high diarrhoea rate and mortality rate during the first half of the cold treatment, but subsequently stabilised. The level of cortisol (COR) also displayed a similar trend. In the mild cold stress group, the relative abundance of Muribaculaceae significantly increased on day 15, and the predominant bacterial on day 30 was Lactobacillus sp. Our results indicated that the Rongchang piglet's production performance and health were impaired at the start of the mild cold stress. However, as time passed, the body could progressively adapt to the low temperature, and Lactobacillus sp. participated in this process. This study provides new insight into how to alleviate health damage caused by cold stress.
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Affiliation(s)
- Jie Chai
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Xi Long
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Pingxian Wu
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Xiaoqian Wu
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Zhi Tu
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Minghong Wei
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Zongyi Guo
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Tinghuan Zhang
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
| | - Li Chen
- Chongqing Academy of Animal Science, Chong Qing, Rongchang, P.R. China
- National Center of Technology Innovation for Pigs, Chong Qing, Rongchang, P.R. China
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Grohmann CJ, Shull CM, Crum TE, Schwab C, Safranski TJ, Decker JE. Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping. Genet Sel Evol 2023; 55:62. [PMID: 37710159 PMCID: PMC10500877 DOI: 10.1186/s12711-023-00836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 08/25/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294-46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives. RESULTS The GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations. CONCLUSIONS This work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production.
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Tao X, Kong FJ, Liang Y, Yang XM, Yang YK, Zhong ZJ, Wang Y, Hu ZH, Chen XH, Gong JJ, Pang JH, Zhu KP, Wang Y, Liao K, Lv XB, He ZP, Gu YR. Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds. Physiol Genomics 2023; 55:147-153. [PMID: 36847439 DOI: 10.1152/physiolgenomics.00157.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the Fst method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.
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Affiliation(s)
- Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Fan-Jing Kong
- Luzhou Modern Agriculture Development Promotion Center, Luzhou, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xue-Mei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yue-Kui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhi-Jun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yan Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zi-Hui Hu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xiao-Hui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jian-Jun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | | | - Kang-Ping Zhu
- Sichuan Dekon Livestock Foodstuff Group, Zigong, China
| | - Yong Wang
- Luzhou Agricultural and Rural Bureau, Luzhou, China
| | - Kun Liao
- Tongjiang County Animal Husbandry Station, Bazhong, China
| | - Xue-Bin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhi-Ping He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yi-Ren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
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Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection. Animals (Basel) 2022; 12:ani12111423. [PMID: 35681887 PMCID: PMC9179914 DOI: 10.3390/ani12111423] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Fatness-related traits are economically very important in sheep production and are associated with serious diseases in humans. Using a denser set of SNP markers and a variety of statistical approaches, our results were able to refine the regions associated with fat deposition and to suggest new insights into molecular aspects of fat tail selection. These results may provide a strong foundation for studying the regulation of fat deposition in sheep and do offer hope that the causal mutations and the mode of inheritance of this trait will soon be discovered by further investigation. Abstract The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.
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Zheng Z, Li Y, Li M, Li G, Du X, Hongyin H, Yin M, Lu Z, Zhang X, Shrestha N, Liu J, Yang Y. Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species. FRONTIERS IN PLANT SCIENCE 2021; 12:581704. [PMID: 33643339 PMCID: PMC7902934 DOI: 10.3389/fpls.2021.581704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.
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Affiliation(s)
- Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guiting Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hu Hongyin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
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Genetic Signatures of Selection for Cashmere Traits in Chinese Goats. Animals (Basel) 2020; 10:ani10101905. [PMID: 33080940 PMCID: PMC7603090 DOI: 10.3390/ani10101905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cashmere goats are a unique husbandry resource in China. These goats are well known for producing the highest cashmere yield and best fiber quality in the world. Although cashmere is highly valued and also known as “fiber gem” and “soft gold”, few studies have examined the genetic basis of cashmere traits in cashmere goats. Here, we identified selection signals by comparing Fst and XP-EHH (the cross population extend haplotype homozygosity test) of a non-cashmere breed (Huanghuai goat) with those of two cashmere breeds (Inner Mongolia and Liaoning cashmere goats). Two genes (WNT10A and CSN3) were potentially associated with cashmere traits. This information may be valuable for studying the genetic uniqueness of cashmere goats and elucidating the mechanisms underlying cashmere traits in cashmere goats. Abstract Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.
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Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality. G3-GENES GENOMES GENETICS 2020; 10:3765-3773. [PMID: 32859686 PMCID: PMC7534417 DOI: 10.1534/g3.120.401628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc's excellent phenotypic traits.
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Bovo S, Ribani A, Muñoz M, Alves E, Araujo JP, Bozzi R, Čandek-Potokar M, Charneca R, Di Palma F, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Margeta V, Martins JM, Mercat MJ, Moscatelli G, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genet Sel Evol 2020; 52:33. [PMID: 32591011 PMCID: PMC7318759 DOI: 10.1186/s12711-020-00553-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Estefania Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Riccardo Bozzi
- DAGRI - Animal Science Section, Università di Firenze, Via delle Cascine 5, 50144, Florence, Italy
| | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Polo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - Graham Etherington
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - Ana I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Fabián García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Juan García-Casco
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - Vladimir Margeta
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - José Manuel Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Polo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Marie J Mercat
- IFIP Institut du porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Juliette Riquet
- GenPhySE, INRAE, Université de Toulouse, Chemin de Borde-Rouge 24, Auzeville Tolosane, 31326, Castanet Tolosan, France
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Graziano Usai
- AGRIS SARDEGNA, Loc. Bonassai, 07100, Sassari, Italy
| | - Valerio J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
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Almeida OAC, Moreira GCM, Rezende FM, Boschiero C, de Oliveira Peixoto J, Ibelli AMG, Ledur MC, de Novais FJ, Coutinho LL. Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 2019; 20:449. [PMID: 31159736 PMCID: PMC6547531 DOI: 10.1186/s12864-019-5811-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.
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Affiliation(s)
| | | | | | | | | | | | | | - Francisco José de Novais
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
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10
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Wang L, Mu Y, Xu L, Li K, Han J, Wu T, Liu L, Gao Q, Xia Y, Hou G, Yang S, He X, Liu GE, Feng S. Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs. Animals (Basel) 2019; 9:E314. [PMID: 31159442 PMCID: PMC6617223 DOI: 10.3390/ani9060314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 11/29/2022] Open
Abstract
The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred WZSP, with its unique genetic properties, can be utilized as a novel genetic resource for pig genome studies. Inbreeding depression and run of homozygosity (ROH) analyses revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSPs, respectively. By investigating ROH number, length, and distribution across generations, we further briefly studied the impacts of recombination and demography on ROH in these WZSPs. Finally, we explored the SNPs with higher heterozygosity across generations and their potential functional implications in the inbred WZSP. We detected 56 SNPs showing constant heterozygosity with He = 1 across six generations in inbred pigs, while only one was found in the non-inbred population. Among these SNPs, we observed nine SNPs located in swine RefSeq genes, which were found to be involved in signaling and immune processes. Together, our findings indicate that the inbred-specific pattern of homozygosity and heterozygosity in inbred pigs can offer valuable insights for elucidating the mechanisms of inbreeding in farm animals.
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Affiliation(s)
- Ligang Wang
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Yulian Mu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Linyang Xu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Kui Li
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Jianlin Han
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Tianwen Wu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Lan Liu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Qian Gao
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Ying Xia
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Guanyu Hou
- Institute of Tropical Crop Variety Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| | - Shulin Yang
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Xiaohong He
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Services, Beltsville, MD 20705, USA.
| | - Shutang Feng
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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11
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Diao S, Huang S, Chen Z, Teng J, Ma Y, Yuan X, Chen Z, Zhang H, Li J, Zhang Z. Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs. Genes (Basel) 2019; 10:genes10050346. [PMID: 31067806 PMCID: PMC6563113 DOI: 10.3390/genes10050346] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/28/2019] [Accepted: 05/02/2019] [Indexed: 01/11/2023] Open
Abstract
South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (FST) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.
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Affiliation(s)
- Shuqi Diao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Shuwen Huang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Zitao Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jinyan Teng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Zanmou Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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12
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Ma H, Zhang S, Zhang K, Zhan H, Peng X, Xie S, Li X, Zhao S, Ma Y. Identifying Selection Signatures for Backfat Thickness in Yorkshire Pigs Highlights New Regions Affecting Fat Metabolism. Genes (Basel) 2019; 10:genes10040254. [PMID: 30925743 PMCID: PMC6523431 DOI: 10.3390/genes10040254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying the genetic basis of improvement in pigs contributes to our understanding of the role of artificial selection in shaping the genome. Here we employed the Cross Population Extended Haplotype Homozogysity (XPEHH) and the Wright's fixation index (FST) methods to detect trait-specific selection signatures by making phenotypic gradient differential population pairs, and then attempted to map functional genes of six backfat thickness traits in Yorkshire pigs. The results indicate that a total of 283 and 466 single nucleotide polymorphisms (SNPs) were identified as trait-specific selection signatures using FST and XPEHH, respectively. Functional annotation suggested that the genes overlapping with the trait-specific selection signatures such as OSBPL8, ASAH2, SMCO2, GBE1, and ABL1 are responsible for the phenotypes including fat metabolism, lean body mass and fat deposition, and transport in mouse. Overall, the study developed the methods of gene mapping on the basis of identification of selection signatures. The candidate genes putatively associated with backfat thickness traits can provide important references and fundamental information for future pig-breeding programs.
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Affiliation(s)
- Haoran Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Saixian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Kaili Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huiwen Zhan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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13
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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14
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Edea Z, Dadi H, Dessie T, Uzzaman MR, Rothschild MF, Kim ES, Sonstegard TS, Kim KS. Genome-wide scan reveals divergent selection among taurine and zebu cattle populations from different regions. Anim Genet 2018; 49:550-563. [PMID: 30246258 DOI: 10.1111/age.12724] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 01/02/2023]
Abstract
In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (FST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (FST ≥ 0.53), representing the top 1% smoothed FST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.
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Affiliation(s)
- Z Edea
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
| | - H Dadi
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia
| | - T Dessie
- International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - M R Uzzaman
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea.,Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, S. Korea
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - E-S Kim
- Recombinetics, Inc., Saint Paul, MN, 55104, USA
| | | | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
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15
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Onzima RB, Upadhyay MR, Doekes HP, Brito LF, Bosse M, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds. Front Genet 2018; 9:318. [PMID: 30154830 PMCID: PMC6102322 DOI: 10.3389/fgene.2018.00318] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
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Affiliation(s)
- Robert B. Onzima
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Maulik R. Upadhyay
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harmen P. Doekes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Luiz. F. Brito
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, ON, Canada
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Egbert Kanis
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Martien A. M. Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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16
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Avila F, Mickelson JR, Schaefer RJ, McCue ME. Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations. Front Genet 2018; 9:249. [PMID: 30105047 PMCID: PMC6060370 DOI: 10.3389/fgene.2018.00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/22/2018] [Indexed: 11/13/2022] Open
Abstract
Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di ) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.
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Affiliation(s)
- Felipe Avila
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
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17
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A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing. Animal 2018; 13:683-693. [PMID: 29987993 DOI: 10.1017/s1751731118001714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.
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Chen M, Wang J, Wang Y, Wu Y, Fu J, Liu JF. Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle. BMC Genet 2018; 19:31. [PMID: 29776331 PMCID: PMC5960162 DOI: 10.1186/s12863-018-0622-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Background Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. Result In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Conclusions Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies. Electronic supplementary material The online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minhui Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jinluan Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Yuan Z, Liu E, Liu Z, Kijas JW, Zhu C, Hu S, Ma X, Zhang L, Du L, Wang H, Wei C. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Anim Genet 2016; 48:55-66. [PMID: 27807880 DOI: 10.1111/age.12477] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2016] [Indexed: 01/19/2023]
Abstract
Fat-tailed sheep have commercial value because consumers prefer high-protein and low-fat food and producers care about feed conversion rate. However, fat-tailed sheep still have some scientific significance, as the fat tail is commonly regarded as a characteristic of environmental adaptability. Finding the candidate genes associated with fat tail formation is essential for breeding and conservation. To identify these candidate genes, we applied FST and hapFLK approaches in fat- and thin-tailed sheep with available 50K SNP genotype data. These two methods found 6.24 Mb of overlapped regions and 43 genes that may associated with fat tail development. Gene annotation showed that HOXA11, BMP2, PPP1CC, SP3, SP9, WDR92, PROKR1 and ETAA1 may play important roles in fat tail formation. These findings provide insight into tail fat development and a guide for molecular breeding and conservation.
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Affiliation(s)
- Z Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - E Liu
- School of Life Sciences, Capital Normal University, Beijing, China
| | - Z Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - J W Kijas
- CSIRO Agriculture Flagship, Brisbane, Australia
| | - C Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - S Hu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - H Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - C Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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