1
|
Zuo P, Zhang C, Gao Y, Zhao L, Guo J, Yang Y, Yu Q, Li Y, Wang Z, Yang H. Genome-wide unraveling SNP pairwise epistatic effects associated with sheep body weight. Anim Biotechnol 2023; 34:3416-3427. [PMID: 36495095 DOI: 10.1080/10495398.2022.2152349] [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: 12/14/2022]
Abstract
Epistatic effects are an important part of the genetic effect of complex traits in livestock. In this study, we used 218 synthetic ewes from the Xinjiang Academy of Agricultural Reclamation in China to identify interacting paired with genome-wide single nucleotide polymorphisms (SNPs) associated with birth weight, weaning weight, and one-yearling weight. We detected 2 and 66 SNP-SNP interactions of sheep birth weight and weaning weight, respectively. No significant epistatic interaction of one-year-old body weight was detected. The genetic interaction of sheep body weight is dynamic and time-dependent. Most significant interactions of weaning body weight contributed 1% or higher. In the weaning weight trait, 66 significant SNP pairs consisted of 98 single SNPs covering 23 chromosomes, 5 of which were nonsynonymous SNPs (nsSNPs), resulting in single amino acid substitution. We found that genes that interact with transcription factors (TFs) are target genes for the corresponding TFs. Four epitron networks affecting weaning weight, including subnetworks of HIVEP3 and BACH2 transcription factors, constructed using significant SNP pairs, were also analyzed and annotated. These results suggest that transcription factors may play an important role in explaining epistatic effects. It provides a new idea to study the genetic mechanism of weight developing.
Collapse
Affiliation(s)
- Peng Zuo
- College of Science, Northeast Agricultural University, Harbin
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Chaoxin Zhang
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yupeng Gao
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Engineering, Northeast Agricultural University, Harbin, China
| | - Lijunyi Zhao
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Information and Electrical Engineering, Northeast Agricultural University, Harbin, China
| | - Jiaxu Guo
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Yunna Li
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhipeng Wang
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| |
Collapse
|
2
|
Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
Collapse
Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Paris JM, Letko A, Häfliger IM, Ammann P, Flury C, Drögemüller C. Identification of two TYRP1 loss-of-function alleles in Valais Red sheep. Anim Genet 2019; 50:778-782. [PMID: 31571241 DOI: 10.1111/age.12863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/30/2022]
Abstract
The Valais Red sheep breed is a local breed of the Swiss canton Valais. Although the breed is characterised by its brown colour, black animals occasionally occur and the objective of this study was to identify the causative genetic variants responsible for the obvious difference. A GWAS using high-density SNP data to compare 51 brown and 38 black sheep showed a strong signal on chromosome 2 at the TYRP1 locus. Haplotype analyses revealed three different brown-associated alleles. The WGS of three sheep revealed four protein-changing variants within the TYRP1 gene. Three of these variants were associated with the recessively inherited brown coat colour. This includes the known missense variant TYRP1:c.869G>T designated as bS oay and two novel loss-of-function variants. We propose to designate the frame-shift variant TYRP1:c.86_87delGA as bVS 1 and the nonsense variant TYRP1:c.1066C>T as bVS 2 . Interestingly, the bVS 1 allele occurs only in local breeds of Switzerland whereas the bVS 2 allele seems to be more widespread across Europe.
Collapse
Affiliation(s)
- J M Paris
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - I M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - P Ammann
- ProSpecieRara, 4052, Basel, Switzerland
| | - C Flury
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, 3052, Zollikofen, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| |
Collapse
|
5
|
Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One 2017; 12:e0176780. [PMID: 28463982 PMCID: PMC5413029 DOI: 10.1371/journal.pone.0176780] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.
Collapse
Affiliation(s)
- Deirdre C. Purfield
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
- * E-mail:
| | - Sinead McParland
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Eamon Wall
- Sheep Ireland, Bandon, Co. Cork, Ireland
| | - Donagh P. Berry
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Gong H, Zhou H, Forrest RHJ, Li S, Wang J, Dyer JM, Luo Y, Hickford JGH. Wool Keratin-Associated Protein Genes in Sheep-A Review. Genes (Basel) 2016; 7:E24. [PMID: 27240405 PMCID: PMC4929423 DOI: 10.3390/genes7060024] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/03/2016] [Accepted: 05/25/2016] [Indexed: 12/18/2022] Open
Abstract
The importance of sheep's wool in making textiles has inspired extensive research into its structure and the underlying genetics since the 1960s. Wool keratin-associated proteins (KAPs) are a key structural component of the wool fibre. The characterisation of the genes encoding these proteins has progressed rapidly with advances in the nucleotide and protein sequencing. This review describes our knowledge of ovine KAPs, their categorisation into families, polymorphism in the proteins and genes, the clustering and chromosomal location of the genes, some characteristics of gene expression and some potential effects of the KAPs on wool traits. The extent and nature of genetic variation in wool KAP genes and its association with fibre characteristics, provides an opportunity for the development of gene-markers for selective breeding of sheep to produce better wool with properties highly matched to specific end-uses.
Collapse
Affiliation(s)
- Hua Gong
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Huitong Zhou
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Rachel H J Forrest
- Faculty of Health and Sport Sciences, Eastern Institute of Technology, Private Bag 1201, Napier 4142, New Zealand.
| | - Shaobin Li
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiqing Wang
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jolon M Dyer
- Food & Bio-Based Products, Lincoln Research Centre, AgResearch Limited, Lincoln 7608, New Zealand.
| | - Yuzhu Luo
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jon G H Hickford
- International Wool Research Institute, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-marker Laboratory, Faculty of Agricultural and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| |
Collapse
|
8
|
Cirera S, Markakis MN, Kristiansen T, Vissenberg K, Fredholm M, Christensen K, Anistoroaei R. A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in American mink. Mamm Genome 2016; 27:135-43. [DOI: 10.1007/s00335-016-9620-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/31/2016] [Indexed: 02/03/2023]
|
9
|
Phua SH, Cullen NG, Dodds KG, Scobie DR, Bray AR. An ovine quantitative trait locus affecting fibre opacity in wool. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|