1
|
Nisa FU, Naqvi RZ, Arshad F, Ilyas I, Asif M, Amin I, Mrode R, Mansoor S, Mukhtar Z. Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan. Biochem Genet 2024; 62:4137-4156. [PMID: 38664326 DOI: 10.1007/s10528-024-10809-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/08/2024] [Indexed: 09/28/2024]
Abstract
Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.
Collapse
Affiliation(s)
- Fakhar Un Nisa
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Fazeela Arshad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Iram Ilyas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, UK
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
- International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan.
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan.
| |
Collapse
|
2
|
Bao J, Xiong J, Huang J, Yang P, Shang M, Zhang L. Genetic Diversity, Selection Signatures, and Genome-Wide Association Study Identify Candidate Genes Related to Litter Size in Hu Sheep. Int J Mol Sci 2024; 25:9397. [PMID: 39273345 PMCID: PMC11395453 DOI: 10.3390/ijms25179397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Hu sheep is a renowned prolific local sheep breed in China, widely distributed across the country due to its excellent reproductive performance. Deciphering the molecular mechanisms underlying the high fecundity of Hu sheep is crucial for improving the litter size of ewes. In this study, we genotyped 830 female Hu sheep using the Illumina OvineSNP50 BeadChip and performed genetic diversity analysis, selection signature detection, and a genome-wide association study (GWAS) for litter size. Our results revealed that the Hu sheep population exhibits relatively high genetic diversity. A total of 4927 runs of homozygosity (ROH) segments were detected, with the majority (74.73%) being short in length. Different genomic inbreeding coefficients (FROH, FHOM, FGRM, and FUNI) ranged from -0.0060 to 0.0126, showing low levels of inbreeding in this population. Additionally, we identified 91 candidate genomic regions through three complementary selection signature methods, including ROH, composite likelihood ratio (CLR), and integrated haplotype score (iHS), and annotated 189 protein-coding genes. Moreover, we observed two significant SNPs related to the litter size of Hu sheep using GWAS analysis based on a repeatability model. Integrating the selection signatures and the GWAS results, we identified 15 candidate genes associated with litter size, among which BMPR1B and UNC5C were particularly noteworthy. These findings provide valuable insights for improving the reproductive performance and breeding of high-fecundity lines of Hu sheep.
Collapse
Affiliation(s)
- Jingjing Bao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jinke Xiong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Jupeng Huang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Peifu Yang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Mingyu Shang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Li Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| |
Collapse
|
3
|
Ben-Jemaa S, Boussaha M, Mandonnet N, Bardou P, Naves M. Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing. PLoS One 2024; 19:e0309411. [PMID: 39186744 PMCID: PMC11346954 DOI: 10.1371/journal.pone.0309411] [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: 07/05/2023] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.
Collapse
Affiliation(s)
- Slim Ben-Jemaa
- INRAE, ASSET, 97170, Petit-Bourg, France
- Institut National de la Recherche Agronomique de Tunisie, Laboratoire des Productions Animales et Fourragères, Université de Carthage, 2049, Ariana, Tunisia
| | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, Ecole Nationale Vétérinaire de Toulouse (ENVT), 31320, Castanet-Tolosan, France
- Sigenae, INRAE, 31320, Castanet-Tolosan, France
| | | |
Collapse
|
4
|
Sarviaho K, Uimari P, Martikainen K. Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population. J Dairy Sci 2024; 107:4822-4832. [PMID: 38490540 DOI: 10.3168/jds.2024-24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits (e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G) overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.
Collapse
Affiliation(s)
- Katri Sarviaho
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland.
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Katja Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
5
|
Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [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: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
Collapse
Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
| |
Collapse
|
6
|
Ameri NF, Moradian H, Koshkoiyeh AE, Montazeri M, Madabi ER, Fozi MA. Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran. Genome 2024; 67:31-42. [PMID: 37962065 DOI: 10.1139/gen-2022-0106] [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: 11/15/2023]
Abstract
Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, FST, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.
Collapse
Affiliation(s)
- Nader Forough Ameri
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hasan Moradian
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Mahdiyeh Montazeri
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Elaheh Rostamzadeh Madabi
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
7
|
Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
Collapse
Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| |
Collapse
|
8
|
Wang S, Raza SHA, Zhang K, Mei C, Alamoudi MO, Aloufi BH, Alshammari AM, Zan L. Selection signatures of Qinchuan cattle based on whole-genome sequences. Anim Biotechnol 2023; 34:1483-1491. [PMID: 35152846 DOI: 10.1080/10495398.2022.2033252] [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: 11/01/2022]
Abstract
Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on Fst, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that KMT2E, LTBP1 and NIPBL were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. ARIH2, DACT1 and DNM2, et al. are related to meat quality. Meanwhile, TBXA2R can be used as a gene associated with reproductive function, and USH2A affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.
Collapse
Affiliation(s)
- Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Muna O Alamoudi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | - Bandar H Aloufi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
| |
Collapse
|
9
|
Ben-Jemaa S, Adam G, Boussaha M, Bardou P, Klopp C, Mandonnet N, Naves M. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle. Sci Rep 2023; 13:12155. [PMID: 37500674 PMCID: PMC10374910 DOI: 10.1038/s41598-023-38774-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.
Collapse
Affiliation(s)
- Slim Ben-Jemaa
- INRAE, ASSET, 97170, Petit-Bourg, France.
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia.
| | | | - Mekki Boussaha
- AgroParisTech, GABI, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Philippe Bardou
- GenPhySE, Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA, Université de Toulouse, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
- Sigenae, INRAE, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Christophe Klopp
- Genotoul Bioinfo, BioInfoMics, MIAT UR875, Sigenae, INRAE, Castanet-Tolosan, France
| | | | | |
Collapse
|
10
|
Rojas-Espinoza R, Macedo R, Suaña A, Delgado A, Manrique YP, Rodríguez H, Quispe YM, Perez-Guerra UH, Pérez-Durand MG, García-Herreros M. Phenotypic Characterization of Creole Cattle in the Andean Highlands Using Bio-Morphometric Measures and Zoometric Indices. Animals (Basel) 2023; 13:1843. [PMID: 37417307 DOI: 10.3390/ani13111843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 07/08/2023] Open
Abstract
Several Creole cattle biotypes can be found in the Andean highlands, and most of them are considered as being in risk of extinction. The main aim of the present study was to perform a phenotypic characterization of the Creole cattle in the Andean highlands using bio-morphometric measures and zoometric indices. Individuals from three different biotypes (Black 'Negro' (n = 57), Colour-Sided 'Callejón' (n = 20), and Brindle 'Atigrado' (n = 18)) from an experimental research center located in the Peruvian highlands were enrolled in the study. In total, seventeen morphometric parameters were evaluated and ten zoometric indices were calculated in each biotype. To test the relationship between biometric traits, correlation analyses were carried out between morphometric parameters. Differences were observed regarding different morphometric variables such as head length (HL) and rump length (RL) among cattle biotypes (p ≤ 0.05). The coefficient of variation (CV; %) regarding different morphometric parameters ranged between 11.32 for neck length (NL) and 3.63 for height at withers (HaW), which indicated low-moderate variability among morphometric variables. Differences were observed in the longitudinal pelvic index (LPI) when different zoometric indices were compared among biotypes (p ≤ 0.05). The CV regarding different zoometric indices, which ranged between 10.78 for the cephalic index (CEI) and 5.05 for LPI, indicated low variability among indices. No differences were observed in any other morphometric parameter or zoometric index among cattle biotypes or genders (p > 0.05). Finally, multiple correlations were observed between morphometric variables (p ≤ 0.05). In conclusion, it was determined that Peruvian Andean Creole cattle can be considered as a dairy-related biotype with a slight tendency for beef production (dual-purpose). The great homogeneity regarding zoometric characteristics among biotypes and genders may indicate that the Andean Creole cattle have been maintained quite isolated, avoiding the genetic influence of other foreign breeds. Finally, the phenotypic characterization including bio-morphometric measurements and zoometric indices obtained from the different Creole bovine biotypes is crucial in order to begin different conservation programs to preserve cattle breeds in the Peruvian Andean highlands.
Collapse
Affiliation(s)
- Rolando Rojas-Espinoza
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Rassiel Macedo
- Facultad de Ciencias Agrarias, Universidad Nacional San Antonio Abad del Cusco, Cusco 08000, Peru
| | - Alex Suaña
- Independent Researcher, Puno 21001, Peru
| | - Alfredo Delgado
- Facultad de Medicina Veterinária, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Yan P Manrique
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Halley Rodríguez
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | | | - Uri H Perez-Guerra
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Manuel G Pérez-Durand
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Manuel García-Herreros
- National Institute for Agricultural and Veterinary Research (INIAV), 2005-048 Santarém, Portugal
| |
Collapse
|
11
|
Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean ( Phaseolus coccineus L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
Collapse
Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKS7N 5A2Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Environmental GenomicsMax Planck Institute for Evolutionary Biology24306PlönGermany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome CenterUniversity of California, DavisDavisCalifornia95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed AmbientaliUniversità Politecnica delle MarcheAncona60131Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
| |
Collapse
|
12
|
Kooverjee BB, Soma P, Van Der Nest MA, Scholtz MM, Neser FWC. Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation. Front Genet 2022; 13:909012. [PMID: 35783284 PMCID: PMC9247466 DOI: 10.3389/fgene.2022.909012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa.
Collapse
Affiliation(s)
- Bhaveni B. Kooverjee
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
- *Correspondence: Bhaveni B. Kooverjee, ; Pranisha Soma,
| | - Pranisha Soma
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- *Correspondence: Bhaveni B. Kooverjee, ; Pranisha Soma,
| | | | - Michiel M. Scholtz
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Frederick W. C. Neser
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| |
Collapse
|
13
|
Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed. Genes (Basel) 2022; 13:genes13050866. [PMID: 35627251 PMCID: PMC9140571 DOI: 10.3390/genes13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
There is a growing concern about the loss of animal genetic resources. The aim of this study was to analyze the genetic diversity and potential peculiarity of the endangered Kosovar sheep breed Balusha. For this purpose, a dataset consisting of medium-density SNP chip genotypes (39,879 SNPs) from 45 Balusha sheep was generated and compared with SNP chip genotypes from 29 individuals of a second Kosovar breed, Bardhoka. Publicly available SNP genotypes from 39 individuals of the relatively closely located sheep breeds Istrian Pramenka and Ruda were additionally included in the analyses. Analysis of heterozygosity, allelic richness and effective population size was used to assess the genetic diversity. Inbreeding was evaluated using two different methods (FIS, FROH). The standardized FST (di) and cross-population extended haplotype homozygosity (XPEHH) methods were used to detect signatures of selection. We observed the lowest heterozygosity (HO = 0.351) and effective population size (Ne5 = 25, Ne50 = 228) for the Balusha breed. The mean allelic richness levels (1.780–1.876) across all analyzed breeds were similar and also comparable with those in worldwide breeds. FROH estimates (0.023–0.077) were highest for the Balusha population, although evidence of decreased inbreeding was observed in FIS results for the Balusha breed. Two Gene Ontology (GO) TERMs were strongly enriched for Balusha, and involved genes belonging to the melanogenesis and T cell receptor signaling pathways, respectively. This could result from selection for the special coat color pattern of Balusha (black head) and resistance to certain infectious diseases. The analyzed diversity parameters highlight the urgency to preserve the local Kosovar Balusha sheep as it is clearly distinguished from other sheep of Southeastern Europe, has the lowest diversity level and may harbor valuable genetic variants, e.g., for resistance to infectious diseases.
Collapse
|
14
|
Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
Collapse
Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| |
Collapse
|
15
|
Seo D, Lee DH, Jin S, Won JI, Lim D, Park M, Kim TH, Lee HK, Kim S, Choi I, Lee JH, Gondro C, Lee SH. Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. Sci Rep 2022; 12:6438. [PMID: 35440706 PMCID: PMC9018707 DOI: 10.1038/s41598-022-09425-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/01/2022] [Indexed: 11/09/2022] Open
Abstract
Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < –6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.
Collapse
Affiliation(s)
- Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Jung Il Won
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Mina Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, RDA, Seonghwan, South Korea
| | - Tae Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, South Korea
| | - Sidong Kim
- Poultry Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Inchul Choi
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Cedric Gondro
- Beacon Center for the Study of Evolution in Action and Department of Animal Science, Michigan State University, East Lansing, USA
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea.
| |
Collapse
|
16
|
Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
Collapse
Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
| |
Collapse
|
17
|
Yougbaré B, Ouédraogo D, Tapsoba ASR, Soudré A, Zoma BL, Orozco-terWengel P, Moumouni S, Ouédraogo-Koné S, Wurzinger M, Tamboura HH, Traoré A, Mwai OA, Sölkner J, Khayatzadeh N, Mészáros G, Burger PA. Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso. Front Genet 2021; 12:670390. [PMID: 34646296 PMCID: PMC8504455 DOI: 10.3389/fgene.2021.670390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.
Collapse
Affiliation(s)
- Bernadette Yougbaré
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Dominique Ouédraogo
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Arnaud S R Tapsoba
- Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Albert Soudré
- Unité de Formation et de Recherche en Sciences et Technologies, Université Norbert Zongo, Koudougou, Burkina Faso
| | - Bienvenue L Zoma
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | | | - Sanou Moumouni
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | | | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Hamidou H Tamboura
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Amadou Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,SUISAG, Sempach, Switzerland
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, Vienna, Austria
| |
Collapse
|
18
|
Gourdine JL, Fourcot A, Lefloch C, Naves M, Alexandre G. Assessment of ecosystem services provided by livestock agroecosystems in the tropics: a case study of tropical island environment of Guadeloupe. Trop Anim Health Prod 2021; 53:435. [PMID: 34392430 PMCID: PMC8364902 DOI: 10.1007/s11250-021-02880-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/04/2021] [Indexed: 11/26/2022]
Abstract
The present study aims to assess (1) the ecosystem services (ES) provided by LFS and (2) the differential ES between local (Creole) and exotic breeds from pig, cattle and goat. The ES are defined as the benefits that humans derive from LFS. They were summarized in 12 ES indicators that cover services related to provisioning, ecological and socio-cultural aspects and territorial vitality. A total of 106 LFS units that covers the five agroecological zones of Guadeloupe were analysed. Functional typologies of LFS per species were created from surveys. The effect of breed on the ES indicators was tested. Results showed that the 40 pig LFS units were separated into 3 clusters that were differentiated in ES according to provisioning ES (cluster 1), cultural use and sale to the neighborhood (cluster 2) and pork self-consumption (cluster 3). The typology of the 57 farms with cattle distinguished 4 clusters with differences in ES provided in self-consumption (cluster1), ecological ES (cluster 2), socio-cultural ES for racing or draught oxen (cluster 3) and ES associated with territory vitality (cluster 4). The 66 goat LFS units were classified into 3 clusters different in ES concerning self-consumption (cluster 1), cultural aspects (cluster 2) and provisioning ES (cluster 3). Our study highlights that ES indicators are not breed dependent (P > 0.10) but rather livestock farming system dependent. The ES rely more on the rearing management than on the breed type, and up to now, there are no specifications in Guadeloupe to differentiate management between breeds.
Collapse
Affiliation(s)
- J-L Gourdine
- Unité de Recherches Zootechniques, INRAE, URZ, 97170, Petit-Bourg, France.
| | - A Fourcot
- Université de Lorraine, INRAE, USC 340, UR AFPA, 54518, Vandœuvre-lès-Nancy, France
| | - C Lefloch
- Unité de Recherches Zootechniques, INRAE, URZ, 97170, Petit-Bourg, France
| | - M Naves
- Unité de Recherches Zootechniques, INRAE, URZ, 97170, Petit-Bourg, France
| | - G Alexandre
- Unité de Recherches Zootechniques, INRAE, URZ, 97170, Petit-Bourg, France
| |
Collapse
|
19
|
Goyache F, Pérez-Pardal L, Fernández I, Traoré A, Menéndez-Arias NA, Álvarez I. Ancient autozygous segments subject to positive selection suggest adaptive immune responses in West African cattle. Gene 2021; 803:145899. [PMID: 34400278 DOI: 10.1016/j.gene.2021.145899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]
Abstract
Small-sized and trypanotolerant West African taurine (Bos taurus) cattle are a unique case of human-mediated process of adaptation to a challenging environment. Extensive gene flow with Sahelian zebu (B. indicus), bigger and with some resistance to tick attack, occurred for centuries and allowed the apparition of stable crossbred populations (sanga) having intermediate characteristics. Up to 237 individuals belonging to 10 different taurine, zebu and sanga cattle populations sampled in Benin, Burkina Faso and Niger were typed using the BovineHD BeadChip of Illumina to identify signatures of selection, assessed using three different Extended-Haplotype-Homozygosity-based statistics, overlapping with ancient, originated 1024 or 2048 generations ago, Homozygosity-By-Descent segments in the cattle genome. Candidate genomic regions were defined ensuring their importance within cattle type and using zebu as reference. Functional annotation analysis identified four statistically significant Annotation Clusters in taurine cattle (from ACt1 to ACt4), one (ACs1) in sanga, and another (ACz1) in zebu cattle, fitting well with expectations. ACt1 included genes primarily associated with innate immunity; ACt2 involved bitter taste receptor genes of importance to adaptation to changing environments; ACt3 included 68 genes coding ATP-binding proteins, some of them located on trypanotolerance-related QTL regions, that can partially underlie immune response and the additive mechanism of trypanotolerance; ACt4 was associated with growth and small size (NPPC gene); ACs1 included genes involved in immune response; and ACz1 is related with ectoparasite resistance. Our results provide a new set of genomic areas and candidate genes giving new insights on the genomic impact of adaptation in West African cattle.
Collapse
Affiliation(s)
- Félix Goyache
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain.
| | | | - Iván Fernández
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou 04 BP 8645, Burkina Faso
| | | | - Isabel Álvarez
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
| |
Collapse
|
20
|
Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
Collapse
Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| |
Collapse
|
21
|
Pandey J, Scheuring DC, Koym JW, Coombs J, Novy RG, Thompson AL, Holm DG, Douches DS, Miller JC, Vales MI. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Sci Rep 2021; 11:8344. [PMID: 33863959 PMCID: PMC8052460 DOI: 10.1038/s41598-021-87284-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components.
The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.
Collapse
Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Joseph Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard G Novy
- USDA-Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID, 83210, USA
| | - Asunta L Thompson
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - David G Holm
- San Luis Valley Research Center, Department of Horticulture and Landscape Architecture, Colorado State University, Center, CO, 81125, USA
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - J Creighton Miller
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA.
| |
Collapse
|
22
|
Baecklund TM, Morrison J, Donaldson ME, Hueffer K, Kyle CJ. The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes). PLoS One 2021; 16:e0249176. [PMID: 33831031 PMCID: PMC8031376 DOI: 10.1371/journal.pone.0249176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022] Open
Abstract
Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).
Collapse
Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- * E-mail:
| | - Jaycee Morrison
- Forensic Science Undergraduate Program, Trent University, Peterborough, Ontario, Canada
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, Ontario, Canada
| |
Collapse
|
23
|
Gautason E, Schönherz AA, Sahana G, Guldbrandtsen B. Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle. Anim Genet 2021; 52:251-262. [PMID: 33829515 DOI: 10.1111/age.13058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.
Collapse
Affiliation(s)
- E Gautason
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - A A Schönherz
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Science, Aarhus University, Tjele, 8830, Denmark
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - B Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| |
Collapse
|
24
|
Duan G, Bao J, Chen X, Xie J, Liu Y, Chen H, Zheng H, Tang W, Wang Z. Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex. Microorganisms 2021; 9:562. [PMID: 33803140 PMCID: PMC8000120 DOI: 10.3390/microorganisms9030562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.
Collapse
Affiliation(s)
- Guohua Duan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Xiaomin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahui Xie
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuchan Liu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Huiquan Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Huakun Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| |
Collapse
|
25
|
Gebrehiwot NZ, Strucken EM, Aliloo H, Marshall K, Gibson JP. The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data. BMC Genomics 2020; 21:869. [PMID: 33287702 PMCID: PMC7720612 DOI: 10.1186/s12864-020-07270-x] [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: 06/02/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07270-x.
Collapse
Affiliation(s)
- N Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - E M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - H Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - K Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - J P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| |
Collapse
|
26
|
Ivell R, Alhujaili W, Kohsaka T, Anand-Ivell R. Physiology and evolution of the INSL3/RXFP2 hormone/receptor system in higher vertebrates. Gen Comp Endocrinol 2020; 299:113583. [PMID: 32800774 DOI: 10.1016/j.ygcen.2020.113583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022]
Abstract
Although the insulin-like peptide hormone INSL3 and its cognate receptor RXFP2 (relaxin-family peptide receptor 2) have existed throughout chordate evolution, their physiological diversification appears to be linked closely with mammalian emergence and radiation. In contrast, they have been lost in birds and reptiles. Both hormone and receptor are expressed from autosomal genes which have maintained their synteny across vertebrate evolution. Whereas the INSL3 gene comprises only two exons closely linked to the JAK3 gene, RXFP2 is normally encoded by 18 exons. Both genes, however, are subject to alternative splicing to yield a variety of possibly inactive or antagonistic molecules. In mammals, the INSL3-RXFP2 dyad has maintained a probably primitive association with gametogenesis, seen also in fish, whereby INSL3 promotes the survival, growth and differentiation of male germ cells in the testis and follicle development in the ovary. In addition, however, the INSL3/RXFP2 system has adopted a typical 'neohormone' profile, essential for the promotion of internal fertilisation and viviparity; fetal INSL3 is essential for the first phase of testicular descent into a scrotum, and also appears to be associated with male phenotype, in particular horn and skeletal growth. Circulating INSL3 is produced exclusively by the mature testicular Leydig cells in male mammals and acts as a potent biomarker for testis development during fetal and pubertal development as well as in ageing. As such it can be used also to monitor seasonally breeding animals as well as to investigate environmental or lifestyle conditions affecting development. Nevertheless, most information about INSL3 and RXFP2 comes from a very limited selection of species; it will be especially useful to gain further information from a more diverse range of animals, especially those whose evolution has led them to express unusual reproductive phenotypes.
Collapse
Affiliation(s)
- Richard Ivell
- School of Bioscience, University of Nottingham, Sutton Bonington, LE2 5RD, UK; School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, LE2 5RD, UK.
| | - Waleed Alhujaili
- School of Bioscience, University of Nottingham, Sutton Bonington, LE2 5RD, UK
| | - Tetsuya Kohsaka
- Dept. of Applied Life Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Japan
| | | |
Collapse
|
27
|
Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
Collapse
Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| |
Collapse
|
28
|
Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U, Lasagna E. The genetics of phenotypic plasticity in livestock in the era of climate change: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1809540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Giacomo Rovelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Eymen Demir
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Fabio Abeni
- Centro di ricerca Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Lodi, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | - Martino Cassandro
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| | - Umberto Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Viterbo, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| |
Collapse
|
29
|
Wu F, Sun H, Lu S, Gou X, Yan D, Xu Z, Zhang Z, Qadri QR, Zhang Z, Wang Z, Chen Q, Li M, Wang X, Dong X, Wang Q, Pan Y. Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing. Front Genet 2020; 11:733. [PMID: 32849777 PMCID: PMC7406676 DOI: 10.3389/fgene.2020.00733] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F ROH) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed.
Collapse
Affiliation(s)
- Fen Wu
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxiong Lu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dawei Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyang Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qamar Raza Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhen Wang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Mingli Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiaoyi Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
30
|
Aliloo H, Mrode R, Okeyo AM, Gibson JP. Ancestral Haplotype Mapping for GWAS and Detection of Signatures of Selection in Admixed Dairy Cattle of Kenya. Front Genet 2020; 11:544. [PMID: 32582285 PMCID: PMC7296079 DOI: 10.3389/fgene.2020.00544] [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: 10/24/2019] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the genetic structure of adaptation and productivity in challenging environments is necessary for designing breeding programs that suit such conditions. Crossbred dairy cattle in East Africa resulting from over 60 years of crossing exotic dairy breeds with indigenous cattle plus inter se matings form a highly variable admixed population. This population has been subject to natural selection in response to environmental stresses, such as harsh climate, low-quality feeds, poor management, and strong disease challenge. Here, we combine two complementary sets of analyses, genome-wide association (GWA) and signatures of selection (SoS), to identify genomic regions that contribute to variation in milk yield and/or contribute to adaptation in admixed dairy cattle of Kenya. Our GWA separates SNP effects due to ancestral origin of alleles from effects due to within-population linkage disequilibrium. The results indicate that many genomic regions contributed to the high milk production potential of modern dairy breeds with no region having an exceptional effect. For SoS, we used two haplotype-based tests to compare haplotype length variation within admixed and between admixed and East African Shorthorn Zebu cattle populations. The integrated haplotype score (iHS) analysis identified 16 candidate regions for positive selection in the admixed cattle while the between population Rsb test detected 24 divergently selected regions in the admixed cattle compared to East African Shorthorn Zebu. We compare the results from GWA and SoS in an attempt to validate the most significant SoS results. Only four candidate regions for SoS intersect with GWA regions using a low stringency test. The identified SoS candidate regions harbored genes in several enriched annotation clusters and overlapped with previously found QTLs and associations for different traits in cattle. If validated, the GWA and SoS results indicate potential for SNP-based genomic selection for genetic improvement of smallholder crossbred cattle.
Collapse
Affiliation(s)
- Hassan Aliloo
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya.,Animal and Veterinary Science, Scotland's Rural College, Edinburgh, United Kingdom
| | - A M Okeyo
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
| | - John P Gibson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| |
Collapse
|
31
|
Abied A, Bagadi A, Bordbar F, Pu Y, Augustino SM, Xue X, Xing F, Gebreselassie G, Han JL, Mwacharo JM, Ma Y, Zhao Q. Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments. Genes (Basel) 2020; 11:genes11050494. [PMID: 32365888 PMCID: PMC7290715 DOI: 10.3390/genes11050494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (FST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by FST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.
Collapse
Affiliation(s)
- Adam Abied
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Alnoor Bagadi
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Farhad Bordbar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Yabin Pu
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Serafino M.A. Augustino
- College of Animal Science and Technology, China Agricultural University (CAU), Beijing 100193, China;
| | - Xianglan Xue
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Feng Xing
- College of Animal Science, Talimu University (TU), Xinjiang, Alar 843300, China;
| | - Gebremedhin Gebreselassie
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Joram M. Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa 1108-2010, Ethiopia;
| | - Yuehui Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Qianjun Zhao
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Correspondence:
| |
Collapse
|
32
|
Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese production system. Animal 2020; 14:921-932. [PMID: 31928542 DOI: 10.1017/s1751731119003318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that characterise Reggiana and define the diversity of this local cattle breed. A total of 168 Reggiana sires (all bulls born over 35 years for which semen was available) and other 3321 sires from 3 cosmopolitan breeds (Brown, Holstein and Simmental) were genotyped with the Illumina BovineSNP50 panel. ADMIXTURE analysis suggested that Reggiana breed might have been influenced, at least in part, by the other three breeds included in this study. Selection signatures in the Reggiana genome were identified using three statistical approaches based on allele frequency differences among populations or on properties of haplotypes segregating in the populations (fixation index (FST); integrated haplotype score; cross-population extended haplotype homozygosity). We identified several regions under peculiar selection in the Reggiana breed, particularly on bovine chromosome (BTA) 6 in the KIT gene region, that is known to be involved in coat colour pattern distribution, and within the region of the LAP3, NCAPG and LCORL genes, that are associated with stature, conformation and carcass traits. Another already known region that includes the PLAG1 gene (BTA14), associated with conformation traits, showed a selection signature in the Reggiana cattle. On BTA18, a signal of selection included the MC1R gene that causes the red coat colour in cattle. Other selection sweeps were in regions, with high density of quantitative trait loci for milk production traits (on BTA20) and in several other large regions that might have contributed to shape and define the Reggiana genome (on BTA17 and BTA29). All these results, overall, indicate that the Reggiana genome might still contain several signs of its multipurpose and non-specialised utilisation, as already described for other local cattle populations, in addition to footprints derived by its ancestral origin and by its adaptation to the specialised Parmigiano-Reggiano cheese production system.
Collapse
|
33
|
Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genomics 2019; 42:203-215. [DOI: 10.1007/s13258-019-00888-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
|
34
|
Flori L, Moazami-Goudarzi K, Alary V, Araba A, Boujenane I, Boushaba N, Casabianca F, Casu S, Ciampolini R, Coeur D'Acier A, Coquelle C, Delgado JV, El-Beltagi A, Hadjipavlou G, Jousselin E, Landi V, Lauvie A, Lecomte P, Ligda C, Marinthe C, Martinez A, Mastrangelo S, Menni D, Moulin CH, Osman MA, Pineau O, Portolano B, Rodellar C, Saïdi-Mehtar N, Sechi T, Sempéré G, Thévenon S, Tsiokos D, Laloë D, Gautier M. A genomic map of climate adaptation in Mediterranean cattle breeds. Mol Ecol 2019; 28:1009-1029. [PMID: 30593690 DOI: 10.1111/mec.15004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022]
Abstract
Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.
Collapse
Affiliation(s)
- Laurence Flori
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Véronique Alary
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, ICARDA, Rabat, Morocco
| | - Abdelillah Araba
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Ismaïl Boujenane
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Nadjet Boushaba
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | | | - Sara Casu
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | | | | | | | | | | | | | | | - Vincenzo Landi
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Anne Lauvie
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Philippe Lecomte
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, Montpellier, France
| | - Christina Ligda
- HAO-Demeter, Veterinary Research Institute, Thessaloniki, Greece
| | | | - Amparo Martinez
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Dalal Menni
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Charles-Henri Moulin
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | | | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Clementina Rodellar
- LAGENBIO, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Nadhira Saïdi-Mehtar
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | - Tiziana Sechi
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | - Guilhem Sempéré
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | - Sophie Thévenon
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | | | - Denis Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, University of Montpellier, Montferrier-sur-Lez, France.,Institut de Biologie Computationnelle (IBC), Montpellier, France
| |
Collapse
|
35
|
Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019; 10:E976. [PMID: 31783652 PMCID: PMC6947233 DOI: 10.3390/genes10120976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 01/12/2023] Open
Abstract
The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.
Collapse
Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sasha Tetu
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Åsa Viklund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| |
Collapse
|
36
|
Zhang S, Cai Y, Guo J, Li K, Peng R, Liu F, Roberts JA, Miao Y, Zhang X. Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints. Evol Bioinform Online 2019; 15:1176934319889948. [PMID: 31798299 PMCID: PMC6868568 DOI: 10.1177/1176934319889948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.
Collapse
Affiliation(s)
- Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Yaling Cai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Renhai Peng
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, China
| | - Jeremy A Roberts
- School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Devon, UK
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Xuebin Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| |
Collapse
|
37
|
Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps. PLoS Comput Biol 2019; 15:e1007426. [PMID: 31710623 PMCID: PMC6872172 DOI: 10.1371/journal.pcbi.1007426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/21/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Selective sweeps, the genetic footprint of positive selection, have been extensively studied in the past decades, with dozens of methods developed to identify swept regions. However, these methods suffer from both false positive and false negative reports, and the candidates identified with different methods are often inconsistent with each other. We propose that a biological cause of this problem can be population subdivision, and a technical cause can be incomplete, or inaccurate, modeling of the dynamic process associated with sweeps. Here we used simulations to show how these effects interact and potentially cause bias. In particular, we show that sweeps maybe misclassified as either hard or soft, when the true time stage of a sweep and that implied, or pre-supposed, by the model do not match. We call this "temporal misclassification". Similarly, "spatial misclassification (softening)" can occur when hard sweeps, which are imported by migration into a new subpopulation, are falsely identified as soft. This can easily happen in case of local adaptation, i.e. when the sweeping allele is not under positive selection in the new subpopulation, and the underlying model assumes panmixis instead of substructure. The claim that most sweeps in the evolutionary history of humans were soft, may have to be reconsidered in the light of these findings.
Collapse
|
38
|
Distinct genetic variation and heterogeneity of the Iranian population. PLoS Genet 2019; 15:e1008385. [PMID: 31550250 PMCID: PMC6759149 DOI: 10.1371/journal.pgen.1008385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Iran, despite its size, geographic location and past cultural influence, has largely been a blind spot for human population genetic studies. With only sparse genetic information on the Iranian population available, we pursued its genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups. We show that Iranians, while close to neighboring populations, present distinct genetic variation consistent with long-standing genetic continuity, harbor high heterogeneity and different levels of consanguinity, fall apart into a cluster of similar groups and several admixed ones and have experienced numerous language adoption events in the past. Our findings render Iran an important source for human genetic variation in Western and Central Asia, will guide adequate study sampling and assist the interpretation of putative disease-implicated genetic variation. Given Iran's internal genetic heterogeneity, future studies will have to consider ethnic affiliations and possible admixture.
Collapse
|
39
|
Fang ZH, Pausch H. Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle. BMC Genomics 2019; 20:695. [PMID: 31481029 PMCID: PMC6724290 DOI: 10.1186/s12864-019-6066-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/27/2019] [Indexed: 01/02/2023] Open
Abstract
Background Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci. Results To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10− 8) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL. Conclusions Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants. Electronic supplementary material The online version of this article (10.1186/s12864-019-6066-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zih-Hua Fang
- Animal Genomics, Institute of Agricultural Science, ETH Zürich, 8092, Zürich, Switzerland.
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Science, ETH Zürich, 8092, Zürich, Switzerland
| |
Collapse
|
40
|
Ginja C, Gama LT, Cortés O, Burriel IM, Vega-Pla JL, Penedo C, Sponenberg P, Cañón J, Sanz A, do Egito AA, Alvarez LA, Giovambattista G, Agha S, Rogberg-Muñoz A, Lara MAC, Delgado JV, Martinez A. The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers. Sci Rep 2019; 9:11486. [PMID: 31391486 PMCID: PMC6685949 DOI: 10.1038/s41598-019-47636-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.
Collapse
Affiliation(s)
- Catarina Ginja
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Luis Telo Gama
- CIISA.Faculdade de Medicina Veterinaria, Universidade de Lisboa, Lisbon, Portugal
| | - Oscar Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
| | - Inmaculada Martin Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Jose Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Servicio de Cría Caballar de las Fuerzas Armadas, Córdoba, Spain
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California, Davis, California, USA
| | - Phil Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine. Virginia Tech, Virginia, USA
| | - Javier Cañón
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Arianne Sanz
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | | | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | | | | | | | - Juan Vicente Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Amparo Martinez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Animal Beeding Consulting S.L. Universidad de Córdoba, Córdoba, Spain
| |
Collapse
|
41
|
Genome scan for selection in South American chickens reveals a region under selection associated with aggressiveness. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
42
|
Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics 2019; 20:494. [PMID: 31200634 PMCID: PMC6570941 DOI: 10.1186/s12864-019-5822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Background Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. Results We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. Conclusions Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.
Collapse
|
43
|
Wang Z, Ma H, Xu L, Zhu B, Liu Y, Bordbar F, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. Animals (Basel) 2019; 9:ani9060296. [PMID: 31151238 PMCID: PMC6617538 DOI: 10.3390/ani9060296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5'-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population.
Collapse
Affiliation(s)
- Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haoran Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
44
|
Cheruiyot EK, Bett RC, Amimo JO, Zhang Y, Mrode R, Mujibi FDN. Signatures of Selection in Admixed Dairy Cattle in Tanzania. Front Genet 2018; 9:607. [PMID: 30619449 PMCID: PMC6305962 DOI: 10.3389/fgene.2018.00607] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.
Collapse
Affiliation(s)
- Evans Kiptoo Cheruiyot
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.,USOMI Limited, Nairobi, Kenya
| | - Rawlynce Cheruiyot Bett
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Joshua Oluoch Amimo
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Raphael Mrode
- International Livestock Research Institute, Nairobi, Kenya.,Scotland's Rural College, Edinburgh, United Kingdom
| | - Fidalis D N Mujibi
- USOMI Limited, Nairobi, Kenya.,Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| |
Collapse
|
45
|
Bahbahani H, Afana A, Wragg D. Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia. PLoS One 2018; 13:e0202479. [PMID: 30114214 PMCID: PMC6095569 DOI: 10.1371/journal.pone.0202479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022] Open
Abstract
Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively. Nine and 23 regions show candidate signatures of positive selection following extended haplotype homozygosity (EHH)-based analyses (iHS and Rsb), respectively. The results support natural selection before admixture for one iHS, one Rsb and three zebu ancestry-deficient regions. Genes and/or QTL associated with bovine immunity, fertility, heat tolerance, trypanotolerance and lactation are present within candidate selected regions. The identification of candidate regions under selection in Sheko cattle warrants further investigation of a larger sample size using full genome sequence data to better characterise the underlying haplotypes. The results can then support informative genomic breeding programmes to sustainably enhance livestock productivity in East African trypanosomosis infested areas.
Collapse
Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
- * E-mail: ,
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, United Kingdom
| |
Collapse
|
46
|
Maiorano AM, Lourenco DL, Tsuruta S, Ospina AMT, Stafuzza NB, Masuda Y, Filho AEV, Cyrillo JNDSG, Curi RA, Silva JAIIDV. Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information. PLoS One 2018; 13:e0200694. [PMID: 30071036 PMCID: PMC6071998 DOI: 10.1371/journal.pone.0200694] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.
Collapse
Affiliation(s)
- Amanda Marchi Maiorano
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
- * E-mail:
| | - Daniela Lino Lourenco
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Shogo Tsuruta
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Alejandra Maria Toro Ospina
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Yutaka Masuda
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Rogério Abdallah Curi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, Sao Paulo, Brazil
| | | |
Collapse
|
47
|
Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| |
Collapse
|
48
|
Miller JM, Festa-Bianchet M, Coltman DW. Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium ® HD SNP BeadChip. PeerJ 2018; 6:e4364. [PMID: 29473002 PMCID: PMC5817937 DOI: 10.7717/peerj.4364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
Collapse
Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Current affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
49
|
Abstract
Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.
Collapse
|
50
|
Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLoS One 2018; 13:e0190446. [PMID: 29300786 PMCID: PMC5754058 DOI: 10.1371/journal.pone.0190446] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023] Open
Abstract
Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.
Collapse
Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
- * E-mail: ,
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum Khartoum North, Sudan
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Hasa, Kingdom of Saudi Arabia
| | - Fahad Al Enezi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
| | - Joram M. Mwacharo
- Small Ruminant Genomics Group, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| |
Collapse
|