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Sun X, Niu Q, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Xu L, Ren H. Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes (Basel) 2023; 14:1183. [PMID: 37372363 DOI: 10.3390/genes14061183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.
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Affiliation(s)
- Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Qunhao Niu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Jie Li
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Cancan Chen
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hangxing Ren
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
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2
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Sun X, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Li N, Xia Y, Ren H. Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China. Anim Biosci 2023; 36:191-199. [PMID: 35760404 PMCID: PMC9834730 DOI: 10.5713/ab.21.0577] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats. METHODS The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip. RESULTS A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color. CONCLUSION The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.
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Affiliation(s)
- Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Jie Li
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Cancan Chen
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China
| | - Nianfu Li
- Youyang County Livestock Industry Development Center, Chongqing, 409800,
China
| | - Yuanyou Xia
- Youyang County Livestock Industry Development Center, Chongqing, 409800,
China
| | - Hangxing Ren
- Chongqing Academy of Animal Sciences, Chongqing, 402460,
China,Chongqing Engineering Research Center for Goats, Chongqing, 402460,
China,Corresponding Author: Hangxing Ren, Tel: +86-023-46777341, E-mail:
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3
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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5
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Narayan E, Sawyer G, Fox D, Smith R, Tilbrook A. Interplay Between Stress and Reproduction: Novel Epigenetic Markers in Response to Shearing Patterns in Australian Merino Sheep (Ovis aries). Front Vet Sci 2022; 9:830450. [PMID: 35464367 PMCID: PMC9021797 DOI: 10.3389/fvets.2022.830450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/15/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, we determined the effect(s) of early shearing on Australian Merino ewes (Ovis aries) and their lambs. To test this research question, we used a suite of field and laboratory methods including GPS collars, wool cortisol, and epigenetic change between ewes and lambs identified using Illumina NovaSeq RRBS. Once shorn ewes (n = 24) were kept on their full fleece throughout the entire gestation period, whereas twice (early) shorn ewes (n = 24) had their wool shorn pre-joining. Top-knot wool sample was taken from ewes during pre-joining, day 50 (mid-gestation), and day 90 (late gestation) for laboratory analysis. Ewes were pregnancy scanned at mid-gestation to determine whether they were early or late parturition (this confirmation is provided by the pregnancy scanner based on fetus size). Top-knot wool sample was also taken from the lambs at weaning for hormone and wool quality testing. Ear tissue was taken from ewes at day 50 (mid-gestation) and from lambs at lamb marking for DNA analysis. Results showed that twice or early shorn ewes grazed 10% higher and maintained stronger body condition than once shorn ewes. Wool cortisol levels were also significantly lower in the early shorn ewes between mid- and late gestation. Lambs bred from twice shorn ewes had on average better visual wool quality parameters in terms of micron, spin finesses, and curvature. For the DNA methylation results, when comparing a group of once sheared with twice sheared ewes, we have discovered one locus (Chr20:50404014) that was significantly differentially methylated [False Discovery Rate (FDR) = 0.005]. This locus is upstream of a protein-coding gene (ENSOARG00000002778.1), which shows similarities to the forkhead box C1 (FOXC1) mRNA using BLAST searches. To further our understanding of the potential interaction between pregnancy status and shearing frequency of the ewes, we performed further differential methylation analysis using a combination of shearing treatment and pregnancy scanning status. The comparisons (1) late pregnancy vs. early pregnancy for ewes with one shearing treatment and (2) late pregnancy vs. early pregnancy for sheep with two shearing treatments were carried out to identify associations between loci and pregnancy duration for sheep with either one or two shearing events. We discovered that 36 gene loci were significantly modulated either between different shearing treatments or late vs. early pregnancy status of ewes. This result suggests that maternal pregnancy and nutritional status during gestation influence DNA methylation. We further investigated DNA methylation in lambs and identified 16 annotated gene loci that showed epigenetic modulation as a result of being born from an early or late stage pregnancy. From the genomics data, we pointed out that ewes go through epigenetic modifications during gestation, and there is a degree of intra-individual variation in the reproductive performance of ewes, which could be due to combination of intrinsic (genetic and physiological) and extrinsic (management and climatic) factors. Collectively, this research provides novel dataset combining physiological, molecular epigenetics, and digital tracking indices that advances our understanding of how Merino ewes respond to shearing frequency, and this information could guide further research on Merino sheep breeding and welfare.
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Affiliation(s)
- Edward Narayan
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, QLD, Australia
- *Correspondence: Edward Narayan
| | - Gregory Sawyer
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Dylan Fox
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
| | - Ryan Smith
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Alan Tilbrook
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, QLD, Australia
- School of Veterinary Science, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
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6
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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.
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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
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7
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Guo T, Zhao H, Yuan C, Huang S, Zhou S, Lu Z, Niu C, Liu J, Zhu S, Yue Y, Yang Y, Wang X, Chen Y, Yang B. Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China. Front Genet 2021; 12:604235. [PMID: 33708236 PMCID: PMC7940688 DOI: 10.3389/fgene.2021.604235] [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: 09/09/2020] [Accepted: 02/01/2021] [Indexed: 11/23/2022] Open
Abstract
Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (FST), polymorphism levels θπ, and Tajima’s D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of FST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.
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Affiliation(s)
- Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Zengkui Lu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chun'e Niu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yaojing Yue
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuxin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
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8
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari "Aldo Moro," Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari "Aldo Moro," Bari, Italy
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9
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Salavati M, Bush SJ, Palma-Vera S, McCulloch MEB, Hume DA, Clark EL. Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep. Front Genet 2019; 10:863. [PMID: 31608110 PMCID: PMC6761296 DOI: 10.3389/fgene.2019.00863] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Pervasive allelic variation at both gene and single nucleotide level (SNV) between individuals is commonly associated with complex traits in humans and animals. Allele-specific expression (ASE) analysis, using RNA-Seq, can provide a detailed annotation of allelic imbalance and infer the existence of cis-acting transcriptional regulation. However, variant detection in RNA-Seq data is compromised by biased mapping of reads to the reference DNA sequence. In this manuscript, we describe an unbiased standardized computational pipeline for allele-specific expression analysis using RNA-Seq data, which we have adapted and developed using tools available under open license. The analysis pipeline we present is designed to minimize reference bias while providing accurate profiling of allele-specific expression across tissues and cell types. Using this methodology, we were able to profile pervasive allelic imbalance across tissues and cell types, at both the gene and SNV level, in Texel×Scottish Blackface sheep, using the sheep gene expression atlas data set. ASE profiles were pervasive in each sheep and across all tissue types investigated. However, ASE profiles shared across tissues were limited, and instead, they tended to be highly tissue-specific. These tissue-specific ASE profiles may underlie the expression of economically important traits and could be utilized as weighted SNVs, for example, to improve the accuracy of genomic selection in breeding programs for sheep. An additional benefit of the pipeline is that it does not require parental genotypes and can therefore be applied to other RNA-Seq data sets for livestock, including those available on the Functional Annotation of Animal Genomes (FAANG) data portal. This study is the first global characterization of moderate to extreme ASE in tissues and cell types from sheep. We have applied a robust methodology for ASE profiling to provide both a novel analysis of the multi-dimensional sheep gene expression atlas data set and a foundation for identifying the regulatory and expressed elements of the genome that are driving complex traits in livestock.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sergio Palma-Vera
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Reproductive Biology, Dummerstorf, Germany
| | - Mary E. B. McCulloch
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Emily L. Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
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10
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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11
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Combined haplotype blocks regression and multi-locus mixed model analysis reveals novel candidate genes associated with milk traits in dairy sheep. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Marete A, Lund MS, Boichard D, Ramayo-Caldas Y. A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds. PLoS One 2018; 13:e0199931. [PMID: 29965995 PMCID: PMC6028091 DOI: 10.1371/journal.pone.0199931] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/15/2018] [Indexed: 01/22/2023] Open
Abstract
Using GWAS to identify candidate genes associated with cattle morphology traits at a functional level is challenging. The main difficulty of identifying candidate genes and gene interactions associated with such complex traits is the long-range linkage disequilibrium (LD) phenomenon reported widely in dairy cattle. Systems biology approaches, such as combining the Association Weight Matrix (AWM) with a Partial Correlation in an Information Theory (PCIT) algorithm, can assist in overcoming this LD. Used in a multi-breed and multi-phenotype context, the AWM-PCIT could aid in identifying udder traits candidate genes and gene networks with regulatory and functional significance. This study aims to use the AWM-PCIT algorithm as a post-GWAS analysis tool with the goal of identifying candidate genes underlying udder morphology. We used data from 78,440 dairy cows from three breeds and with own phenotypes for five udder morphology traits, five production traits, somatic cell score and clinical mastitis. Cows were genotyped with medium (50k) or low-density (7 to 10k) chips and imputed to 50k. We performed a within breed and trait GWAS. The GWAS showed 9,830 significant SNP across the genome (p < 0.05). Five thousand and ten SNP did not map a gene, and 4,820 SNP were within 10-kb of a gene. After accounting for 1SNP:1gene, 3,651 SNP were within 10-kb of a gene (set1), and 2,673 significant SNP were further than 10-kb of a gene (set2). The two SNP sets formed 6,324 SNP matrix, which was fitted in an AWM-PCIT considering udder depth/ development as the key trait resulting in 1,013 genes associated with udder morphology, mastitis and production phenotypes. The AWM-PCIT detected ten potential candidate genes for udder related traits: ESR1, FGF2, FGFR2, GLI2, IQGAP3, PGR, PRLR, RREB1, BTRC, and TGFBR2.
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Affiliation(s)
- Andrew Marete
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Didier Boichard
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Yuliaxis Ramayo-Caldas
- Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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13
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Koseniuk A, Ropka-Molik K, Rubiś D, Smołucha G. Genetic background of coat colour in sheep. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-173-2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The coat colour of animals is an extremely important trait that affects their
behaviour and is decisive for survival in the natural environment. In farm
animal breeding, as a result of the selection of a certain coat colour type,
animals are characterized by a much greater variety of coat types. This makes
them an appropriate model in research in this field. A very important aspect
of the coat colour types of farm animals is distinguishing between breeds and
varieties based on this trait. Furthermore, for the sheep breeds which are
kept for skins and wool, coat/skin colour is an important economic trait.
Until now the study of coat colour inheritance in sheep proved the dominance
of white colour over pigmented/black coat or skin and of black over brown.
Due to the current knowledge of the molecular basis of ovine coat colour
inheritance, there is no molecular test to distinguish coat colour types in
sheep although some are available for other species, such as cattle, dogs,
and horses. Understanding the genetic background of variation in one of the
most important phenotypic traits in livestock would help to identify new
genes which have a great effect on the coat colour type. Considering that
coat colour variation is a crucial trait for discriminating between breeds
(including sheep), it is important to broaden our knowledge of the genetic
background of pigmentation. The results may be used in the future to
determine the genetic pattern of a breed. Until now, identified candidate
genes that have a significant impact on colour type in mammals mainly code
for factors located in melanocytes. The proposed candidate genes code for the
melanocortin 1 receptor (MC1R), agouti signaling
protein (ASIP), tyrosinase-related protein 1 (TYRP1),
microphthalmia-associated transcription factor MITF, and v-kit
Hardy–Zuckerman 4 feline sarcoma viral oncogene homologue (KIT).
However, there is still no conclusive evidence of established polymorphisms
for specific coat colour types in sheep.
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14
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Fejzo MS, Sazonova OV, Sathirapongsasuti JF, Hallgrímsdóttir IB, Vacic V, MacGibbon KW, Schoenberg FP, Mancuso N, Slamon DJ, Mullin PM. Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum. Nat Commun 2018; 9:1178. [PMID: 29563502 PMCID: PMC5862842 DOI: 10.1038/s41467-018-03258-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/30/2018] [Indexed: 01/01/2023] Open
Abstract
Hyperemesis gravidarum (HG), severe nausea and vomiting of pregnancy, occurs in 0.3-2% of pregnancies and is associated with maternal and fetal morbidity. The cause of HG remains unknown, but familial aggregation and results of twin studies suggest that understanding the genetic contribution is essential for comprehending the disease etiology. Here, we conduct a genome-wide association study (GWAS) for binary (HG) and ordinal (severity of nausea and vomiting) phenotypes of pregnancy complications. Two loci, chr19p13.11 and chr4q12, are genome-wide significant (p < 5 × 10-8) in both association scans and are replicated in an independent cohort. The genes implicated at these two loci are GDF15 and IGFBP7 respectively, both known to be involved in placentation, appetite, and cachexia. While proving the casual roles of GDF15 and IGFBP7 in nausea and vomiting of pregnancy requires further study, this GWAS provides insights into the genetic risk factors contributing to the disease.
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Affiliation(s)
- Marlena S Fejzo
- Division of Hematology-Oncology, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Maternal-Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | | | | | | | | | | | - Frederic P Schoenberg
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Dennis J Slamon
- Division of Hematology-Oncology, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Patrick M Mullin
- Department of Maternal-Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
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15
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Rochus CM, Tortereau F, Plisson-Petit F, Restoux G, Moreno-Romieux C, Tosser-Klopp G, Servin B. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep. BMC Genomics 2018; 19:71. [PMID: 29357834 PMCID: PMC5778797 DOI: 10.1186/s12864-018-4447-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/11/2018] [Indexed: 01/11/2023] Open
Abstract
Background One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Results Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Conclusions Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina Marie Rochus
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France. .,UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France. .,Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Flavie Tortereau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | | | - Gwendal Restoux
- UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France.,Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
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16
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Leroy G, Boettcher P, Hoffmann I, Mottet A, Teillard F, Baumung R. An exploratory analysis on how geographic, socioeconomic, and environmental drivers affect the diversity of livestock breeds worldwide. J Anim Sci 2017; 94:5055-5063. [PMID: 28046135 DOI: 10.2527/jas.2016-0813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This study investigates the relationships between various environmental and geographic, demographic, and socioeconomic factors with the diversity of livestock breeds reported within countries across the world. Statistical analyses were performed considering the numbers of breeds reported by 158 countries for 4 livestock mammalian species (cattle, sheep, goats, and pigs). Organization for Economic Cooperation and Development (OECD) countries reported more breeds than non-OECD countries in general. Strong and positive correlations were found between agricultural area, human population size, species population size, and number of breeds per country. When considering regression models, the species population size was found as the most important explanatory factor for the number of breeds reported by countries in the 4 species. Diversity of production systems in the country had a significant association with the number of breeds reported for sheep, goats, and pigs. The number of ruminant breeds was positively associated with the size of agricultural area and the diversity of land cover in the country. While demographic and cultural importance of a given species is a major factor associated with the number of livestock breeds within countries, this diversity is also connected to the variability in environmental and production conditions.
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17
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Seroussi E, Rosov A, Shirak A, Lam A, Gootwine E. Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed. Genet Sel Evol 2017; 49:19. [PMID: 28187715 PMCID: PMC5301402 DOI: 10.1186/s12711-017-0296-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene. RESULTS Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes. CONCLUSIONS Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alexander Rosov
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Andrey Shirak
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alon Lam
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Elisha Gootwine
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
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18
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Wei C, Wang H, Liu G, Wu M, Cao J, Liu Z, Liu R, Zhao F, Zhang L, Lu J, Liu C, Du L. Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics 2015; 16:194. [PMID: 25888314 PMCID: PMC4404018 DOI: 10.1186/s12864-015-1384-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 02/24/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Traditionally, Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. Herein, we aimed to evaluate the population structure and genome selection among 140 individuals from ten representative Chinese indigenous sheep breeds: Ujimqin, Hu, Tong, Large-Tailed Han and Lop breed (Mongolian group); Duolang and Kazakh (Kazakh group); and Diqing, Plateau-type Tibetan, and Valley-type Tibetan breed (Tibetan group). RESULTS We analyzed the population using principal component analysis (PCA), STRUCTURE and a Neighbor-Joining (NJ)-tree. In PCA plot, the Tibetan and Mongolian groups were clustered as expected; however, Duolang and Kazakh (Kazakh group) were segregated. STRUCTURE analyses suggested two subpopulations: one from North China (Kazakh and Mongolian groups) and the other from the Southwest (Tibetan group). In the NJ-tree, the Tibetan group formed an independent branch and the Kazakh and Mongolian groups were mixed. We then used the d i statistic approach to reveal selection in Chinese indigenous sheep breeds. Among the 599 genome sequence windows analyzed, sixteen (2.7%) exhibited signatures of selection in four or more breeds. We detected three strong selection windows involving three functional genes: RXFP2, PPP1CC and PDGFD. PDGFD, one of the four subfamilies of PDGF, which promotes proliferation and inhibits differentiation of preadipocytes, was significantly selected in fat type breeds by the Rsb (across pairs of populations) approach. Two consecutive selection regions in Duolang sheep were obviously different to other breeds. One region was in OAR2 including three genes (NPR2, SPAG8 and HINT2) the influence growth traits. The other region was in OAR 6 including four genes (PKD2, SPP1, MEPE, and IBSP) associated with a milk production quantitative trait locus. We also identified known candidate genes such as BMPR1B, MSRB3, and three genes (KIT, MC1R, and FRY) that influence lambing percentage, ear size and coat phenotypes, respectively. CONCLUSIONS Based on the results presented here, we propose that Chinese native sheep can be divided into two genetic groups: the thin type (Tibetan group), and the fat type (Mongolian and Kazakh group). We also identified important genes that drive valuable phenotypes in Chinese indigenous sheep, especially PDGFD, which may influence fat deposition in fat type sheep.
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Affiliation(s)
- Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Gang Liu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China.
| | - Mingming Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Jiaxve Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Zhen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
| | - Jian Lu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China.
| | - Chousheng Liu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China.
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China.
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Fariello MI, Servin B, Tosser-Klopp G, Rupp R, Moreno C, Cristobal MS, Boitard S. Selection signatures in worldwide sheep populations. PLoS One 2014; 9:e103813. [PMID: 25126940 PMCID: PMC4134316 DOI: 10.1371/journal.pone.0103813] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 07/05/2014] [Indexed: 12/31/2022] Open
Abstract
The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.
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Affiliation(s)
- Maria-Ines Fariello
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
- Instituto de matemática y Estadística Prof. Ing. Rafael Laguardia, Facultad de Ingeniera, Universidad de la República, Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur, Montevideo, Uruguay
| | - Bertrand Servin
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Gwenola Tosser-Klopp
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Rachel Rupp
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Carole Moreno
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | | | - Magali San Cristobal
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Simon Boitard
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique & AgroParisTech, Jouy-en-Josas, France
- Origine, Structure et Evolution de la Biodiversité, Museum National d'Histoire Naturelle & Ecole Pratique des Hautes Etudes & CNRS, Paris, France
- * E-mail:
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20
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Fan R, Xie J, Bai J, Wang H, Tian X, Bai R, Jia X, Yang L, Song Y, Herrid M, Gao W, He X, Yao J, Smith GW, Dong C. Skin transcriptome profiles associated with coat color in sheep. BMC Genomics 2013; 14:389. [PMID: 23758853 PMCID: PMC3689618 DOI: 10.1186/1471-2164-14-389] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/04/2013] [Indexed: 01/06/2023] Open
Abstract
Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
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21
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Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, Ding B, Dodson MV, El-Halawany NK, Lewis GS, Jiang Z. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep. PLoS One 2013; 8:e65942. [PMID: 23762451 PMCID: PMC3677876 DOI: 10.1371/journal.pone.0065942] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/30/2013] [Indexed: 11/18/2022] Open
Abstract
Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of FST, significant genetic differentiation appeared between Suffolk and Rambouillet (FST = 0.1621), while Rambouillet and Targhee had the closest relationship (FST = 0.0681). A scan of the genome revealed 45 and 41 differentially selected regions (DSRs) between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.
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Affiliation(s)
- Lifan Zhang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michelle R. Mousel
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Xiaolin Wu
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Bo Ding
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael V. Dodson
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Nermin K. El-Halawany
- Cell Biology Department, Division of Genetic Engineering and Biotechnology, National Research Center, Dokki, Gueza, Egypt
| | - Gregory S. Lewis
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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22
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Raadsma HW, Jonas E, Fleet MR, Fullard K, Gongora J, Cavanagh CR, Tammen I, Thomson PC. QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects. Anim Genet 2013; 44:547-59. [PMID: 23451726 DOI: 10.1111/age.12033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2013] [Indexed: 11/30/2022]
Abstract
The pursuits of white features and white fleeces free of pigmented fibre have been important selection objectives for many sheep breeds. The cause and inheritance of non-white colour patterns in sheep has been studied since the early 19th century. Discovery of genetic causes, especially those which predispose pigmentation in white sheep, may lead to more accurate selection tools for improved apparel wool. This article describes an extended QTL study for 13 skin and fibre pigmentation traits in sheep. A total of 19 highly significant, 10 significant and seven suggestive QTL were identified in a QTL mapping experiment using an Awassi × Merino × Merino backcross sheep population. All QTL on chromosome 2 exceeded a LOD score of greater than 4 (range 4.4-30.1), giving very strong support for a major gene for pigmentation on this chromosome. Evidence of epistatic interactions was found for QTL for four traits on chromosomes 2 and 19. The ovine TYRP1 gene on OAR 2 was sequenced as a strong positional candidate gene. A highly significant association (P < 0.01) of grandparental haplotypes across nine segregating SNP/microsatellite markers including one non-synonymous SNP with pigmentation traits could be shown. Up to 47% of the observed variation in pigmentation was accounted for by models using TYRP1 haplotypes and 83% for models with interactions between two QTL probabilities, offering scope for marker-assisted selection for these traits.
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Affiliation(s)
- H W Raadsma
- ReproGen-Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, NSW 2570, Australia.
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23
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Snelling WM, Cushman RA, Keele JW, Maltecca C, Thomas MG, Fortes MRS, Reverter A. BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3. J Anim Sci 2013; 91:537-52. [DOI: 10.2527/jas.2012-5784] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- W. M. Snelling
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - R. A. Cushman
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - J. W. Keele
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - C. Maltecca
- Department of Animal Science, North Carolina State University, Raleigh 27606
| | - M. G. Thomas
- Department of Animal Science, Colorado State University, Fort Collins 80523
| | - M. R. S. Fortes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Gatton Campus, QLD 4343, Australia
| | - A. Reverter
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, Brisbane, QLD 4067, Australia
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24
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Wang M, Wang Q, Pan Y. From QTL to QTN: candidate gene set approach and a case study in porcine IGF1-FoxO pathway. PLoS One 2013; 8:e53452. [PMID: 23341942 PMCID: PMC3544924 DOI: 10.1371/journal.pone.0053452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 11/30/2012] [Indexed: 01/15/2023] Open
Abstract
Unraveling the genetic background of economic traits is a major goal in modern animal genetics and breeding. Both candidate gene analysis and QTL mapping have previously been used for identifying genes and chromosome regions related to studied traits. However, most of these studies may be limited in their ability to fully consider how multiple genetic factors may influence a particular phenotype of interest. If possible, taking advantage of the combined effect of multiple genetic factors is expected to be more powerful than analyzing single sites, as the joint action of multiple loci within a gene or across multiple genes acting in the same gene set will likely have a greater influence on phenotypic variation. Thus, we proposed a pipeline of gene set analysis that utilized information from multiple loci to improve statistical power. We assessed the performance of this approach by both simulated and a real IGF1-FoxO pathway data set. The results showed that our new method can identify the association between genetic variation and phenotypic variation with higher statistical power and unravel the mechanisms of complex traits in a point of gene set. Additionally, the proposed pipeline is flexible to be extended to model complex genetic structures that include the interactions between different gene sets and between gene sets and environments.
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Affiliation(s)
- Minghui Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Shanghai Key Lab of Animal Biotechnology, Shanghai, People’s Republic of China
| | - Qishan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Shanghai Key Lab of Animal Biotechnology, Shanghai, People’s Republic of China
| | - Yuchun Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Shanghai Key Lab of Animal Biotechnology, Shanghai, People’s Republic of China
- * E-mail:
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25
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Reverter A, Fortes MRS. Breeding and Genetics Symposium: building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies. J Anim Sci 2012; 91:530-6. [PMID: 23097399 DOI: 10.2527/jas.2012-5780] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The advent of economically viable high-throughput genetic and genomic techniques has equipped animal geneticists with an unprecedented ability to generate massive amounts of molecular data. As a result, large lists of genes differentially expressed in many experimental conditions of interests have been reported and, likewise, the association of an ever growing number of DNA variants with phenotypes of importance is now a routine endeavor. Although these studies have greatly improved our understanding of the genetic basis of complex phenotypes, they have also revealed the difficulty in explaining more than a fraction of the genetic variance. Inspired by this data-rich and knowledge-poor dichotomy, systems biology aims at the formal integration of seemingly disparate datasets allowing for a holistic view where key properties of the systems emerge as an intuitive feature and enable the generation of testable hypotheses. Herein, we present 2 examples of integrating molecular data anchored in the power of gene network inference. The first example is concerned with the onset of puberty in Bos indicus-influenced cows bred in Australia. Using the results from genomewide association studies across a range of phenotypes, we developed what we termed an association weight matrix to generate a gene network underlying phenotypes of puberty in cattle. The network was mined for the minimal set of transcription factor genes whose predicted target spanned the majority of the topology of the entire network. The second example deals with piebald, a pigmentation phenotype in Merino sheep. Two networks were developed: a regulatory network and an epistatic network. The former is inferred based on promoter sequence analysis of differentially expressed genes. The epistatic network is built from 2-locus models among all pairwise associated polymorphisms. At the intersection between these 2 networks, we revealed a set of genes and gene-gene interactions of validated and de novo predicted relevance to the piebald phenotype. We argue that these new approaches are holistic and therefore more appropriate than traditional approaches for investigating genetic mechanisms underlying complex phenotypes of importance in livestock species.
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Affiliation(s)
- A Reverter
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, Brisbane, QLD 4067, Australia.
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26
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García-Gámez E, Gutiérrez-Gil B, Sahana G, Sánchez JP, Bayón Y, Arranz JJ. GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene. PLoS One 2012; 7:e47782. [PMID: 23094085 PMCID: PMC3475704 DOI: 10.1371/journal.pone.0047782] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/17/2012] [Indexed: 12/14/2022] Open
Abstract
In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half-sib families with available records for milk yield (MY), milk protein and fat yields (PY and FY) and milk protein and fat contents (PP and FP). The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3). These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP. Further associations were detected at the chromosome-wise significance level on 14 other chromosomal regions. The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association. Sequencing this gene in the 16 Churra rams of the studied resource population identified additional polymorphisms. One out of the 31 polymorphisms identified was located within the coding gene sequence (LALBA_g.242T>C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status of the sires, were utilized to assess the role of this mutation as a putative QTN for the genetic effects detected on OAR3. Our results strongly support the polymorphism LALBA_g.242T>C as the most likely causal mutation of the studied OAR3 QTL affecting PP and FP, although we cannot rule out the possibility that this SNP is in perfect linkage disequilibrium with the true causal polymorphism.
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Affiliation(s)
| | | | - Goutam Sahana
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Yolanda Bayón
- Departmento Producción Animal, Universidad de León, León, Spain
| | - Juan-José Arranz
- Departmento Producción Animal, Universidad de León, León, Spain
- * E-mail:
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27
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Fortes MRS, Snelling WM, Reverter A, Nagaraj SH, Lehnert SA, Hawken RJ, DeAtley KL, Peters SO, Silver GA, Rincon G, Medrano JF, Islas-Trejo A, Thomas MG. Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors. J Anim Sci 2012; 90:2894-906. [PMID: 22739780 DOI: 10.2527/jas.2011-4601] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.
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Affiliation(s)
- M R S Fortes
- School of Veterinary Science, The University of Queensland, Gatton Campus, QLD 4343, Australia
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