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Kang DY, Kim HC. Functional relation of agouti signaling proteins (ASIPs) to pigmentation and color change in the starry flounder, Platichthys stellatus. Comp Biochem Physiol A Mol Integr Physiol 2024; 291:111524. [PMID: 37981006 DOI: 10.1016/j.cbpa.2023.111524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/30/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023]
Abstract
We investigated the involvement of agouti-signaling proteins (ASIPs) in morphological pigmentation and physiological color change in flatfishes. We isolated ASIP1 and 2 mRNAs from the skin of starry flounder (Platichthys stellatus), and compared their amino acid (aa) structures to those of other animals. Then, we examined the mRNA expression levels of two ASIPs (Sf-ASIPs) in the pigmented ocular body and in the unpigmented blind body, as well as in the ordinary skin and in albino skin, in flatfishes. To investigate the role of Sf-ASIPs in physiological color change (color camouflage), we compared the expression of the two genes in two background colors (dark-green and white). Sf-ASIP1 cDNA had a 375-bp open reading frame (ORF) that encoded a protein consisting of 125 aa residues, and Sf-ASIP2 cDNA had a 402-bp ORF that encoded a protein consisting of 132 aa residues. RT-PCR revealed that the strongest Sf-ASIP1 and Sf-ASIP2 expression levels were observed in the eye and blind-skin, respectively. In Sf-ASIP1, the gene expression did not differ between the ocular-side skin and blind-side skin, nor between ordinary skin and abnormal skin of the fish. However, in Sf-ASIP2, the expression level was significantly higher in blind-side skin, compared to ocular-side skin, suggesting that the ASIP2 gene is related to the countershading body pigment pattern of the fish. In addition, the Sf-ASIP2 gene expression level was lower in the pigmented spot regions than in the unpigmented spot regions of the malpigmented pseudo-albino skins on the ocular side, implying that ASIP2 is responsible for the ocular-side pseudo-albino. Additionally, ASIP2 gene expression in the blind-side skin of ordinary fish was enhanced by a white tank, implying that a bright background color could inhibit hypermelanosis in the blind-side skin of cultured flounder by increasing the activity of the Sf-ASIP2 gene. However, we did not find any relationship of ASIPs with camouflage color changes. In conclusion, the ASIP2 gene is related to the morphological pigmentation (countershading and malpigmentation) of the skin in starry flounder, but not with physiological color changes (color camouflage) in the ocular-side skin.
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Affiliation(s)
- Duk-Young Kang
- National Institute of Fisheries Science, West Sea Fisheries Research Institute, 707 Eulwang-dong, Jung-gu, Incheon, Republic of Korea.
| | - Hyo-Chan Kim
- KMS & MC, Molecular research, Haneulbyeolbit-ro, YoungJong-1 dong, Joong-gu, Incheon, Republic of Korea
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Giuliotti L, Benvenuti MN, Preziuso G, Ventura E, Fresi P, Cecchi F. Demography and Genealogical Analysis of Massese Sheep, a Native Breed of Tuscany. Animals (Basel) 2024; 14:582. [PMID: 38396550 PMCID: PMC10886389 DOI: 10.3390/ani14040582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population-WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007-2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average FPED of 13.56%, and 2713 in the RP, with an average FPED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates.
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Affiliation(s)
- Lorella Giuliotti
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Maria Novella Benvenuti
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Giovanna Preziuso
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Emilia Ventura
- Veterinarian Free lance, Via dell’alberaccio 15, 56017 San Giuliano Terme, Italy;
| | - Pancrazio Fresi
- Asso.Na.Pa (Associazione Nazionale della Pastorizia), Via XXIV Maggio 44, 00187 Roma, Italy;
| | - Francesca Cecchi
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
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Zeng L, Li A, Qu K, Zhang J, Huang B, Lei C. TRPM4 gene variation associated with climatic conditions in Chinese cattle. Anim Biotechnol 2023; 34:3256-3260. [PMID: 35994677 DOI: 10.1080/10495398.2022.2112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A > G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (TRPM4) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A > G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the TRPM4 gene in Chinese cattle might be a candidate locus associated with heat tolerance.
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Affiliation(s)
- LuLan Zeng
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - AiXin Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Su P, Wu H, Huang Y, Lu X, Yin J, Zhang Q, Lan X. The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene. Animals (Basel) 2023; 13:3218. [PMID: 37893942 PMCID: PMC10603658 DOI: 10.3390/ani13203218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.
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Affiliation(s)
- Peng Su
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hui Wu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yangming Huang
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaofang Lu
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Jing Yin
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Qingfeng Zhang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Cao C, Kang Y, Zhou Q, Nanaei HA, Bo D, Liu P, Bai Y, Li R, Jiang Y, Lan X, Pan C. Whole-genome resequencing reveals the genomic diversity and signatures of selection in Romanov sheep. J Anim Sci 2023; 101:skad291. [PMID: 37680132 PMCID: PMC10516466 DOI: 10.1093/jas/skad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023] Open
Abstract
Romanov sheep are adapted to the extremely cold and harsh environment and display a distinctive grey color. Herein, we analyzed the population structure, genetic diversity, and selection signatures of Romanov sheep based on whole-genome sequencing data of 17 Romanov sheep, 114 individuals from other 10 European breeds. The results of PCA, ADMIXTURE, and NJ-tree showed that the Romanov sheep was closely related to other northern European breeds. A relative high level of genetic diversity, low inbreeding coefficient, and large effective population size was observed in Romanov sheep when compared with other European breeds. We then screened the genomic selection signatures of Romanov sheep using FST, XP-XLP, and XP-EHH methods. The most significant region under selection (CHR14:14.2 to 14.3 Mb) harbored a haplotype that contained MC1R gene. Furthermore, this haplotype was also found in other grey-body breeds including Gotland sheep, Grey Tronder Sheep, and German grey heath sheep, suggesting that it was associated with the unique coat color of these breeds. We also found one region (CHR10:40.8Mb- 41.0Mb) harboring PCDH9 gene which was potentially associated with cold environmental adaptation. In summary, this study identified candidate genes that were associated with the unique grey color and environmental adaptation in Romanov sheep, which provided a basis for understanding the genetic background and utilization of this breed.
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Affiliation(s)
- Chunna Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Didi Bo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiyao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Ferreira J, McManus CM, Freitas Silveira RM, Tavares da Silva WS, Guilhermino MM, Asensio LAB, Bozzi R, Façanha DAE. Reference patterns for thermoregulation in Italian Massese ewes. J Therm Biol 2023; 113:103483. [PMID: 37055110 DOI: 10.1016/j.jtherbio.2023.103483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The Massese is an autochthonous Italian sheep breed, used for meat and mainly milk production and thermoregulatory variations can directly affect the performance of these animals. We evaluated the thermoregulatory patterns of Massese ewes and identified the changes due to environmental variations. Data was collected from 159 healthy ewes from herds of four farms/institutions. For thermal environmental characterization, air temperature (AT), relative humidity (RH) and wind speed were measured, and Black Globe Temperature, Humidity Index (BGHI) and Radiant Heat Load (RHL) were calculated. The thermoregulatory responses evaluated were: respiratory (RR), heart rate (HR), rectal temperature (RT) and coat surface temperature (ST). All variables were subjected to analysis of variance with repeated measures over time. A factor analysis was conducted to determine the relationship between environmental and thermoregulatory variables. Multiple regression analyses were also examined using General Linear Models, and Variance Inflation Factors were calculated. Logistic and Broken line non-linear regressions for RR, HR and RT were analyzed. The RR and HR values were outside reference values and associated with normal values of RT. In the factor analysis, most environmental variables were seen to affect the thermoregulation pattern of the ewes, except for RH. In the logistic regression analysis, RT was not affected by any of the variables studied, maybe because BGHI and RHL were not sufficiently high enough. Nevertheless, BGHI and RHL affected RR and HR. The study shows a divergence for Massese ewes from reference thermoregulatory values for sheep.
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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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Hu L, Zhang L, Li Q, Liu H, Xu T, Zhao N, Han X, Xu S, Zhao X, Zhang C. Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing. Front Genet 2022; 13:971464. [PMID: 36160022 PMCID: PMC9490000 DOI: 10.3389/fgene.2022.971464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.
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Affiliation(s)
- Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Na Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Shixiao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Cunfang Zhang,
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Taghizadeh S, Gholizadeh M, Rahimi-Mianji G, Moradi MH, Costilla R, Moore S, Di Gerlando R. Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds. Sci Rep 2022; 12:8834. [PMID: 35614300 PMCID: PMC9132911 DOI: 10.1038/s41598-022-12778-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.
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Affiliation(s)
- Shadan Taghizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Roy Costilla
- Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Stephen Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Rosalia Di Gerlando
- Dipartimento Di Scienze Agrarie, Alimentari E Forestali, Università Degli Studi Di Palermo, Palermo, Italy
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Ji RL, Tao YX. Melanocortin-1 receptor mutations and pigmentation: Insights from large animals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:179-213. [PMID: 35595349 DOI: 10.1016/bs.pmbts.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The melanocortin-1 receptor (MC1R) is a G protein-coupled receptor expressed in cutaneous and hair follicle melanocytes, and plays a central role in coat color determination in vertebrates. Numerous MC1R variants have been identified in diverse species. Some of these variants have been associated with specific hair and skin color phenotypes in humans as well as coat color in animals. Gain-of-function mutations of the MC1R gene cause dominant or partially dominant black/dark coat color, and loss-of-function mutations of the MC1R gene cause recessive or partially recessive red/yellow/pale coat color phenotypes. These have been well documented in a large number of mammals, including human, dog, cattle, horse, sheep, pig, and fox. Higher similarities between large mammals and humans makes them better models to understand pathogenesis of human diseases caused by MC1R mutations. High identities in MC1Rs and similar variants identified in both humans and large mammals also provide an opportunity for receptor structure and function study. In this review, we aim to summarize the naturally occurring mutations of MC1R in humans and large animals.
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Affiliation(s)
- Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.
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Bertolini F, Moscatelli G, Schiavo G, Bovo S, Ribani A, Ballan M, Bonacini M, Prandi M, Dall'Olio S, Fontanesi L. Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours. J Anim Breed Genet 2021; 139:307-319. [PMID: 34841617 PMCID: PMC9300179 DOI: 10.1111/jbg.12659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/01/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed-specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well-known Protected Designation of Origin Parmigiano-Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome-wide information in comparative FST analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% FST values, a total of 64 markers were detected in the single-marker analysis. The top FST value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window-based analyses, which included 0.5-Mb or 1-Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle.
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Affiliation(s)
- Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giulia Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anisa Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Stefania Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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12
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Wang Z, Guo Y, Liu S, Meng Q. Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population. Front Genet 2021; 12:753748. [PMID: 34721540 PMCID: PMC8552909 DOI: 10.3389/fgene.2021.753748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Qingli Meng
- Beijing Breeding Swine Center, Beijing, China
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13
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Michailidou S, Gelasakis A, Banos G, Arsenos G, Argiriou A. Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds. Front Genet 2021; 12:700489. [PMID: 34349787 PMCID: PMC8326974 DOI: 10.3389/fgene.2021.700489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
In dairy sheep industry, milk production dictates the value of a ewe. Milk production is directly related to the morphology and physiology of the mammary gland; both being designated targets of breeding strategies. Although within a flock breeding parameters are mutual, large differences in milk production among individual ewes are usually observed. In this work, we tested two of the most productive dairy sheep breeds reared intensively in Greece, one local the Chios breed and one foreign the Lacaune breed. We used transcriptome sequencing to reveal molecular mechanisms that render the mammary gland highly productive or not. While highly expressed genes (caseins and major whey protein genes) were common among breeds, differences were observed in differentially expressed genes. ENSOARG00000008077, as a member of ribosomal protein 14 family, together with LPCAT2, CCR3, GPSM2, ZNF131, and ASIP were among the genes significantly differentiating mammary gland's productivity in high yielding ewes. Gene ontology terms were mainly linked to the inherent transcriptional activity of the mammary gland (GO:0005524, GO:0030552, GO:0016740, GO:0004842), lipid transfer activity (GO:0005319) and innate immunity (GO:0002376, GO:0075528, GO:0002520). In addition, clusters of genes affecting zinc and iron trafficking into mitochondria were highlighted for high yielding ewes (GO:0071294, GO:0010043). Our analyses provide insights into the molecular pathways involved in lactation between ewes of different performances. Results revealed management issues that should be addressed by breeders in order to move toward increased milk yields through selection of the desired phenotypes. Our results will also contribute toward the selection of the most resilient and productive ewes, thus, will strengthen the existing breeding systems against a spectrum of environmental threats.
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Affiliation(s)
- Sofia Michailidou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Georgios Banos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland’s Rural College, Easter Bush, Edinburgh, United Kingdom
| | - George Arsenos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, Lemnos, Greece
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14
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Salehian-Dehkordi H, Xu YX, Xu SS, Li X, Luo LY, Liu YJ, Wang DF, Cao YH, Shen M, Gao L, Chen ZH, Glessner JT, Lenstra JA, Esmailizadeh A, Li MH, Lv FH. Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep. Front Genet 2021; 12:670582. [PMID: 34093663 PMCID: PMC8175073 DOI: 10.3389/fgene.2021.670582] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022] Open
Abstract
Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ya-Xi Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Jing Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Ali Esmailizadeh
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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15
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Shi X, Wu J, Lang X, Wang C, Bai Y, Riley DG, Liu L, Ma X. Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 2021; 9:e11122. [PMID: 33986980 PMCID: PMC8086576 DOI: 10.7717/peerj.11122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
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Affiliation(s)
- Xiaolei Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Xia Lang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Cailian Wang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China.,Key Laboratory for Sheep, Goat, and Cattle Germplasm and Straw Feed in Gansu Province, Lanzhou, Gansu Province, China
| | - Yan Bai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - David Greg Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Lishan Liu
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xiaoming Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
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16
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Pallotti S, Chandramohan B, Pediconi D, Nocelli C, La Terza A, Renieri C. Interaction between the melanocortin 1 receptor (MC1R) and agouti signalling protein genes (ASIP), and their association with black and brown coat colour phenotypes in peruvian alpaca. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1850216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Stefano Pallotti
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | | | - Dario Pediconi
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | - Cristina Nocelli
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | - Antonietta La Terza
- Scuola di Bioscienze e Medicina Veterinaria, University of Camerino, Camerino, Italy
| | - Carlo Renieri
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
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17
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Gebreselassie G, Liang B, Berihulay H, Islam R, Abied A, Jiang L, Zhao Z, Ma Y. Genomic mapping identifies two genetic variants in the MC1R gene for coat colour variation in Chinese Tan sheep. PLoS One 2020; 15:e0235426. [PMID: 32817695 PMCID: PMC7444486 DOI: 10.1371/journal.pone.0235426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Coat colour is one of the most important economic traits of sheep and is mainly used for breed identification and characterization. This trait is determined by the biochemical function, availability and distribution of phaeomelanin and eumelanin pigments. In our study, we conducted a genome-wide association study to identify candidate genes and genetic variants associated with coat colour in 75 Chinese Tan sheep using the ovine 600K SNP BeadChip. Accordingly, we identified two significant SNPs (rs409651063 at 14.232 Mb and rs408511664 at 14.228 Mb) associated with coat colour in the MC1R gene on chromosome 14 with −log10(P) = 2.47E-14 and 1.00E-13, respectively. The consequence of rs409651063 was a missense variant (g.14231948 G>A) that caused an amino acid change (Asp105Asn); however, the second SNP (rs408511664) was a synonymous substitution and is an upstream variant (g.14228343G>A). Moreover, our PCR analysis revealed that the genotype of white sheep was exclusively homozygous (GG), whereas the genotypes of black-head sheep were mainly heterozygous (GA). Interestingly, allele-specific expression analysis (using the missense variant for the skin cDNA samples from black-head sheep) revealed that only the G allele was expressed in the skin covered with white hair, while both the G and A alleles were expressed in the skin covered with black hair. This finding indicated that the missense mutation that we identified is probably responsible for white coat colour in Tan sheep. Furthermore, qPCR analysis of MC1R mRNA level in the skin samples was significantly higher in black-head than white sheep and very significantly higher in GA than GG individuals. Taken together, these results help to elucidate the genetic mechanism underlying coat colour variation in Chinese indigenous sheep.
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Affiliation(s)
- Gebremedhin Gebreselassie
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Agricultural Biotechnology, Biotechnology Center, Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Benmeng Liang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Haile Berihulay
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Rabul Islam
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Adam Abied
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lin Jiang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhengwei Zhao
- Institute of animal science, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia, Yinchuan, China
- * E-mail: (YM); (ZZ)
| | - Yuehui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- * E-mail: (YM); (ZZ)
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18
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Wang Z, Guo J, Guo Y, Yang Y, Teng T, Yu Q, Wang T, Zhou M, Zhu Q, Wang W, Zhang Q, Yang H. Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays. Front Genet 2020; 11:558. [PMID: 32582291 PMCID: PMC7297042 DOI: 10.3389/fgene.2020.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/07/2020] [Indexed: 01/30/2023] Open
Abstract
Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Teng Teng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Meng Zhou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Qiusi Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Wenwen Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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19
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Yang N, Zhao B, Hu S, Bao Z, Liu M, Chen Y, Wu X. Characterization of POU2F1 Gene and Its Potential Impact on the Expression of Genes Involved in Fur Color Formation in Rex Rabbit. Genes (Basel) 2020; 11:genes11050575. [PMID: 32443864 PMCID: PMC7288328 DOI: 10.3390/genes11050575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022] Open
Abstract
The naturally colorful fur of the Rex rabbit is becoming increasingly popular in the modern textile market. Our previous study found that POU class 2 homeobox 1 gene (POU2F1) potentially affects the expression of genes involved in fur color formation in the Rex rabbit, but the function and regulation of POU2F1 has not been reported. In this study, the expression patterns of POU2F1 in Rex rabbits of various colors, as well as in different organs, were analyzed by RT-qPCR. Interference and overexpression of POU2F1 were used to identify the potential effects of POU2F1 on other genes related to fur color formation. The results show that the levels of POU2F1 expression were significantly higher in the dorsal skin of the brown and protein yellow Rex rabbits, compared with that of the black one. POU2F1 mRNAs were widespread in the tissues examined in this study and showed the highest level in the lungs. By transfecting rabbit melanocytes with an POU2F1-overexpression plasmid, we found that the POU2F1 protein was located at the nucleus, and the protein showed the classic characteristics of a transcription factor. In addition, abnormal expression of POU2F1 significantly affected the expression of pigmentation-related genes, including SLC7A11, MITF, SLC24A5, MC1R, and ASIP, revealing the regulatory roles of POU2F1 on pigmentation. The results provide the basis for further exploration of the role of POU2F1 in fur color formation of the Rex rabbit.
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Affiliation(s)
- Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (N.Y.); (B.Z.); (S.H.); (Z.B.); (M.L.); (Y.C.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-514-8799-7194
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Baazaoui I, McEwan J, Anderson R, Brauning R, McCulloch A, Van Stijn T, Bedhiaf-Romdhani S. GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds. Animals (Basel) 2019; 10:ani10010005. [PMID: 31861491 PMCID: PMC7022847 DOI: 10.3390/ani10010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker FST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.
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Affiliation(s)
- Imen Baazaoui
- Faculty of Science of Bizerte, University of Carthage, Carthage 1054, Tunisia
| | - John McEwan
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Rayna Anderson
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Alan McCulloch
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Tracey Van Stijn
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Sonia Bedhiaf-Romdhani
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, Ariana 1004, Tunisia
- Correspondence: ; Tel.: +216-25-113-344
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Xiong Q, Tao H, Zhang N, Zhang L, Wang G, Li X, Suo X, Zhang F, Liu Y, Chen M. Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats. Genomics 2019; 112:1853-1860. [PMID: 31678151 DOI: 10.1016/j.ygeno.2019.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 11/19/2022]
Abstract
To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.
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Affiliation(s)
- Qi Xiong
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Hu Tao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Nian Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Liqing Zhang
- Hubei Livestock and Poultry Breeding Centre, Wuhan 430070, China
| | - Guiqiang Wang
- Hubei Livestock and Poultry Breeding Centre, Wuhan 430070, China
| | - Xiaofeng Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Xiaojun Suo
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Feng Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Yang Liu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
| | - Mingxin Chen
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China.
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22
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Almathen F, Elbir H, Bahbahani H, Mwacharo J, Hanotte O. Polymorphisms in MC1R and ASIP Genes are Associated with Coat Color Variation in the Arabian Camel. J Hered 2019; 109:700-706. [PMID: 29893870 PMCID: PMC6108395 DOI: 10.1093/jhered/esy024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Pigmentation in mammals is primarily determined by the distribution of eumelanin and pheomelanin, the ratio of which is mostly controlled by the activity of melanocortin 1 receptor (MC1R) and agouti signaling protein (ASIP) genes. Using 91 animals from 10 Arabian camel populations, that included the 4 predominant coat color phenotypes observed in the dromedary (light brown, dark brown, black, and white), we investigated the effects of the MC1R and ASIP sequence variants and identified candidate polymorphisms associated with coat color variation. In particular, we identified a single nucleotide polymorphism (SNP), found in the coding region of MC1R (901C/T), linked to the white coat color, whereas a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP are associated with both black and dark-brown coat colors. Our results also indicate support that the light-brown coat color is likely the ancestral coat color for the dromedary. These sequence variations at the MC1R and ASIP genes represent the first documented evidence of candidate polymorphisms associated with Mendelian traits in the dromedary.
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Affiliation(s)
- Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Saudi Arabia.,The Camel Research Center, King Faisal University, Saudi Arabia
| | - Haitham Elbir
- The Camel Research Center, King Faisal University, Saudi Arabia
| | - Hussain Bahbahani
- The Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Joram Mwacharo
- The International Centre for Agricultural Research in the Dry Areas (ICARDA) c/o ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- The School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.,LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
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23
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Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Anim Genet 2019; 50:712-717. [PMID: 31475378 DOI: 10.1111/age.12837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 01/03/2023]
Abstract
By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.
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Affiliation(s)
- C M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden.,UFR Génétique, Élevage et Reproduction, Sciences de la Vie et Santé, AgroParisTech, Université Paris Saclay, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France.,Génétique Physiologie Systèmes d'Elevage, Animal Genetics Division, INRA, 24 chemin de Borde-Rouge-Auzeville Tolosane, F-31326 Castanet-Tolosan, France
| | - K Westberg Sunesson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - E Jonas
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
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24
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Adaptation Mechanisms of Small Ruminants to Environmental Heat Stress. Animals (Basel) 2019; 9:ani9030075. [PMID: 30823364 PMCID: PMC6466405 DOI: 10.3390/ani9030075] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Heat stress is an intriguing factor that negatively influences livestock production and reproduction performance. Sheep and goat are among the livestock that can adapt to environmental heat stress via a combination of physiological, morphological, behavioral, and genetic bases. Sheep and goat are able to minimize adverse effect of high thermal stress by invoking behavioral responses such as feeding, water intake, shade seeking, and increased frequency of drinking. Their morphological mechanisms are comprised of body shape and size, light hair color, lightly pigmented skin, and less subcutaneous fat, and the physiological means are that of increased respiration rate (RR), increased sweating rate (SW), reduced metabolic rate, and change in endocrine function. Adaptation in terms of genetics is the heritable trait of animal characteristics which favor the survival of populations. For instance, genes like heat shock proteins 70 (HSP70) and ENOX2 are commonly expressed proteins which protect animals against heat stress. Abstract Small ruminants are the critical source of livelihood for rural people to the development of sustainable and environmentally sound production systems. They provided a source of meat, milk, skin, and fiber. The several contributions of small ruminants to the economy of millions of rural people are however being challenged by extreme heat stress difficulties. Heat stress is one of the most detrimental factors contributing to reduced growth, production, reproduction performance, milk quantity and quality, as well as natural immunity, making animals more vulnerable to diseases and even death. However, small ruminants have successfully adapted to this extreme environment and possess some unique adaptive traits due to behavioral, morphological, physiological, and largely genetic bases. This review paper, therefore, aims to provide an integrative explanation of small ruminant adaptation to heat stress and address some responsible candidate genes in adapting to thermal-stressed environments.
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25
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Marín JC, Rivera R, Varas V, Cortés J, Agapito A, Chero A, Chávez A, Johnson WE, Orozco-terWengel P. Genetic Variation in Coat Colour Genes MC1R and ASIP Provides Insights Into Domestication and Management of South American Camelids. Front Genet 2018; 9:487. [PMID: 30483307 PMCID: PMC6242857 DOI: 10.3389/fgene.2018.00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023] Open
Abstract
The domestication of wild vicuña and guanaco by early pre-Inca cultures is an iconic example of wildlife management and domestication in the Americas. Although domestic llamas and alpacas were clearly selected for key, yet distinct, phenotypic traits, the relative patterns and direction of selection and domestication have not been confirmed using genetic approaches. However, the detailed archaeological records from the region suggest that domestication was a process carried out under significant control and planning, which would have facilitated coordinated and thus extremely effective selective pressure to achieve and maintain desired phenotypic traits. Here we link patterns of sequence variation in two well-characterised genes coding for colour variation in vertebrates and interpret the results in the context of domestication in guanacos and vicuñas. We hypothesise that colour variation in wild populations of guanacos and vicunas were strongly selected against. In contrast, variation in coat colour variation in alpaca was strongly selected for and became rapidly fixed in alpacas. In contrast, coat colour variants in llamas were of less economic value, and thus were under less selective pressure. We report for the first time the full sequence of MC1R and 3 exons of ASIP in 171 wild specimens from throughout their distribution and which represented a range of commonly observed colour patterns. We found a significant difference in the number of non-synonymous substitutions, but not synonymous substitutions among wild and domestics species. The genetic variation in MC1R and ASIP did not differentiate alpaca from llama due to the high degree of reciprocal introgression, but the combination of 11 substitutions are sufficient to distinguish domestic from wild animals. Although there is gene flow among domestic and wild species, most of the non-synonymous variation in MC1R and ASIP was not observed in wild species, presumably because these substitutions and the associated colour phenotypes are not effectively transmitted back into wild populations. Therefore, this set of substitutions unequivocally differentiates wild from domestic animals, which will have important practical application in forensic cases involving the poaching of wild vicuñas and guanacos. These markers will also assist in identifying and studying archaeological remains pre- and post-domestication.
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Affiliation(s)
- Juan C. Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Romina Rivera
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Ciencias Básicas, Universidad Santo Tomas, Iquique, Chile
| | - Valeria Varas
- Doctorado en Ciencias, Mención Ecología y Evolución, Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Cortés
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Zoología, Universidad de Concepción, Concepción, Chile
| | - Ana Agapito
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Ana Chero
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alexandra Chávez
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Warren E. Johnson
- Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, United States
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Divergent Evolutional Mode and Purifying Selection of the KIT Gene in European and Asian Domestic Pig Breeds. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8932945. [PMID: 30211229 PMCID: PMC6120332 DOI: 10.1155/2018/8932945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022]
Abstract
The recent geographic expansion of wild boars and the even more recent development of numerous domestic pigs have spurred exploration on pig domestic origins. The porcine KIT gene has been showed to affect pleiotropic effects, blood parameters, and coat colour phenotypes, especially the white colour phenotype formation in European commercial breeds. Here, we described the use of SNPs to identify different selection patterns on the porcine KIT gene and the phylogenetic relationships of the inferred haplotypes. The phylogenetic tree revealed four clades in European and Asian wild and domestic pigs: two major clades with European and Asian origins and one minor clade with Iberian origins as well as the other minor clade in Asia, consistent with the major introgression of domestic Asian pigs in Europe around 18th -19th century. The domestication history of pigs, which occurred in the domestication centers (Europe and Asia), has also been demonstrated by mtDNA analysis. Furthermore, both Asian and European domestic pigs evolved under purifying selection. This study indicated that domestic pigs in Europe and Asia have different lineage origins but the porcine KIT gene was undergoing a purifying selection during their evolutional histories.
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27
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RNAi-mediated SLC7A11 knockdown inhibits melanogenesis-related genes expression in rabbit skin fibroblasts. J Genet 2018. [DOI: 10.1007/s12041-018-0945-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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28
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Janiak MC. No Evidence of Copy Number Variation in Acidic Mammalian Chitinase Genes (CHIA) in New World and Old World Monkeys. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0037-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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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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30
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Stamatis C, Giannoulis T, Galliopoulou E, Billinis C, Mamuris Z. Genetic analysis of melanocortin 1 receptor gene in endangered Greek sheep breeds. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Song X, Xu C, Liu Z, Yue Z, Liu L, Yang T, Cong B, Yang F. Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour. Sci Rep 2017; 7:12461. [PMID: 28963476 PMCID: PMC5622100 DOI: 10.1038/s41598-017-12754-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022] Open
Abstract
Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.
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Affiliation(s)
- Xingchao Song
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Chao Xu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zongyue Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zhigang Yue
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Linling Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tongao Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Bo Cong
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Fuhe Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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32
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Adeola AC, Oluwole OO, Oladele BM, Olorungbounmi TO, Boladuro B, Olaogun SC, Nneji LM, Sanke OJ, Dawuda PM, Omitogun OG, Frantz L, Murphy RW, Xie HB, Peng MS, Zhang YP. Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs. Genet Sel Evol 2017. [PMID: 28651519 PMCID: PMC5485568 DOI: 10.1186/s12711-017-0326-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. Results Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. Conclusions Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Bukola M Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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Ma Q, Liu X, Pan J, Ma L, Ma Y, He X, Zhao Q, Pu Y, Li Y, Jiang L. Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array. Sci Rep 2017; 7:912. [PMID: 28424525 PMCID: PMC5430420 DOI: 10.1038/s41598-017-00847-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 12/21/2022] Open
Abstract
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.
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Affiliation(s)
- Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China
| | - Xuexue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jianfei Pan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaohong He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yingkang Li
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China.
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China. .,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination. Proc Natl Acad Sci U S A 2016; 113:13815-13820. [PMID: 27849592 DOI: 10.1073/pnas.1616948113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.
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Polymorphisms in MC1R and ASIP genes and their association with coat color phenotypes in llamas (Lama glama). Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Wang X, Niu Y, Zhou J, Yu H, Kou Q, Lei A, Zhao X, Yan H, Cai B, Shen Q, Zhou S, Zhu H, Zhou G, Niu W, Hua J, Jiang Y, Huang X, Ma B, Chen Y. Multiplex gene editing via CRISPR/Cas9 exhibits desirable muscle hypertrophy without detectable off-target effects in sheep. Sci Rep 2016; 6:32271. [PMID: 27562433 PMCID: PMC4999810 DOI: 10.1038/srep32271] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/04/2016] [Indexed: 01/20/2023] Open
Abstract
The CRISPR/Cas9 system provides a flexible approach for genome engineering of genetic loci. Here, we successfully achieved precise gene targeting in sheep by co-injecting one-cell-stage embryos with Cas9 mRNA and RNA guides targeting three genes (MSTN, ASIP, and BCO2). We carefully examined the sgRNAs:Cas9-mediated targeting effects in injected embryos, somatic tissues, as well as gonads via cloning and sequencing. The targeting efficiencies in these three genes were within the range of 27–33% in generated lambs, and that of simultaneously targeting the three genes was 5.6%, which demonstrated that micro-injection of zygotes is an efficient approach for generating gene-modified sheep. Interestingly, we observed that disruption of the MSTN gene resulted in the desired muscle hypertrophy that is characterized by enlarged myofibers, thereby providing the first detailed evidence supporting that gene modifications had occurred at both the genetic and morphological levels. In addition, prescreening for the off-target effect of sgRNAs was performed on fibroblasts before microinjection, to ensure that no detectable off-target mutations from founder animals existed. Our findings suggested that the CRISPR/Cas9 method can be exploited as a powerful tool for livestock improvement by simultaneously targeting multiple genes that are responsible for economically significant traits.
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Affiliation(s)
- Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiankui Zhou
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Honghao Yu
- College of Life Science, Yulin University, Yulin 719000, China
| | - Qifang Kou
- Ningxia Tianyuan Sheep Farm, Hongsibu, 751999, China
| | - Anmin Lei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,College of Life Science, Yulin University, Yulin 719000, China
| | - Bei Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiaoyan Shen
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shiwei Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Haijing Zhu
- College of Life Science, Yulin University, Yulin 719000, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenzhi Niu
- Ningxia Tianyuan Sheep Farm, Hongsibu, 751999, China
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Muniz MMM, Caetano AR, McManus C, Cavalcanti LCG, Façanha DAE, Leite JHGM, Facó O, Paiva SR. Application of genomic data to assist a community-based breeding program: A preliminary study of coat color genetics in Morada Nova sheep. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Hepp D, Gonçalves GL, Moreira GRP, de Freitas TRO. Epistatic Interaction of the Melanocortin 1 Receptor and Agouti Signaling Protein Genes Modulates Wool Color in the Brazilian Creole Sheep. J Hered 2016; 107:544-52. [PMID: 27288530 DOI: 10.1093/jhered/esw037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/29/2016] [Indexed: 02/01/2023] Open
Abstract
Different pigmentation genes have been associated with color diversity in domestic animal species. The melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are candidate genes responsible for variation in wool color among breeds of sheep. Although the influence of these genes has been described in some breeds, in many others the effect of interactions among genes underlying wool color has not been investigated. The Brazilian Creole sheep is a local breed with a wide variety of wool color, ranging from black to white with several intermediate hues. We analyzed in this study the influence of the genes MC1R, ASIP, TYRP1, and KIT on the control of wool color in this breed. A total of 410 samples were analyzed, including 148 white and 262 colored individuals. The MC1R and ASIP polymorphisms were significantly associated with the segregation of either white or colored wool. The dominant MC1R allele (E(D) p.M73K and p.D121N) was present only in colored animals. All white individuals were homozygous for the MC1R recessive allele (E(+)) and carriers of the duplicated copy of ASIP A gene expression assay showed that only the carrier of the duplicated copy of ASIP produces increased levels in skin, not detectable in the single homozygous copy. These results demonstrate that the epistatic interaction of the genotypes in the MC1R and ASIP gene is responsible for the striking color variation in the Creole breed.
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Affiliation(s)
- Diego Hepp
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp).
| | - Gislene Lopes Gonçalves
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Gilson Rudinei Pires Moreira
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Thales Renato Ochotorena de Freitas
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
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Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015; 14:358-68. [PMID: 26003631 DOI: 10.1093/bfgp/elv019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
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Abitbol M, Legrand R, Tiret L. A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light points coat phenotype in donkeys. Genet Sel Evol 2015; 47:28. [PMID: 25887951 PMCID: PMC4389795 DOI: 10.1186/s12711-015-0112-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/18/2015] [Indexed: 11/23/2022] Open
Abstract
Background Seven donkey breeds are recognized by the French studbook and are characterized by a black, bay or grey coat colour including light cream-to-white points (LP). Occasionally, Normand bay donkeys give birth to dark foals that lack LP and display the no light points (NLP) pattern. This pattern is more frequent and officially recognized in American miniature donkeys. The LP (or pangare) phenotype resembles that of the light bellied agouti pattern in mouse, while the NLP pattern resembles that of the mammalian recessive black phenotype; both phenotypes are associated with the agouti signaling protein gene (ASIP). Findings We used a panel of 127 donkeys to identify a recessive missense c.349 T > C variant in ASIP that was shown to be in complete association with the NLP phenotype. This variant results in a cysteine to arginine substitution at position 117 in the ASIP protein. This cysteine is highly-conserved among vertebrate ASIP proteins and was previously shown by mutagenesis experiments to lie within a functional site. Altogether, our results strongly support that the identified mutation is causative of the NLP phenotype. Conclusions Thus, we propose to name the c.[349 T > C] allele in donkeys, the anlp allele, which enlarges the panel of coat colour alleles in donkeys and ASIP recessive loss-of-function alleles in animals. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0112-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie Abitbol
- Inra, Unité de Génétique Fonctionnelle et Médicale, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, 94700, France. .,Inserm, U955 IMRB, Equipe 10, Université Paris-Est, Créteil, 94000, France.
| | - Romain Legrand
- Inra, Unité de Génétique Fonctionnelle et Médicale, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, 94700, France. .,Inserm, U955 IMRB, Equipe 10, Université Paris-Est, Créteil, 94000, France.
| | - Laurent Tiret
- Inra, Unité de Génétique Fonctionnelle et Médicale, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, 94700, France. .,Inserm, U955 IMRB, Equipe 10, Université Paris-Est, Créteil, 94000, France.
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41
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Li MH, Tiirikka T, Kantanen J. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries). Heredity (Edinb) 2013; 112:122-31. [PMID: 24022497 DOI: 10.1038/hdy.2013.83] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 12/21/2022] Open
Abstract
In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.
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Affiliation(s)
- M-H Li
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - T Tiirikka
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | - J Kantanen
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Department of Biology, University of Eastern Finland, Kuopio, Finland
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Mutations in MC1R gene determine black coat color phenotype in Chinese sheep. ScientificWorldJournal 2013; 2013:675382. [PMID: 24082855 PMCID: PMC3776380 DOI: 10.1155/2013/675382] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 07/26/2013] [Indexed: 11/24/2022] Open
Abstract
The melanocortin receptor 1 (MC1R) plays a central role in regulation of animal coat color formation. In this study, we sequenced the complete coding region
and parts of the 5′- and 3′-untranslated regions of the MC1R gene in Chinese sheep with completely
white (Large-tailed Han sheep), black (Minxian Black-fur sheep), and brown coat colors (Kazakh Fat-Rumped sheep). The results showed five single nucleotide
polymorphisms (SNPs): two non-synonymous mutations previously associated with coat color (c.218 T>A, p.73 Met>Lys. c.361 G>A, p.121 Asp>Asn)
and three synonymous mutations (c.429 C>T, p.143 Tyr>Tyr; c.600 T>G, p.200 Leu>Leu. c.735 C>T, p.245 Ile>Ile). Meanwhile, all mutations
were detected in Minxian Black-fur sheep. However, the two nonsynonymous mutation sites were not in all studied breeds (Large-tailed Han, Small-tailed Han, Gansu Alpine Merino,
and China Merino breeds), all of which are in white coat. A single haplotype AATGT (haplotype3) was uniquely associated with black coat color in Minxian Black-fur breed (P = 9.72E − 72, chi-square test). The first and second A alleles in this haplotype 3 represent location at 218 and 361 positions, respectively. Our results suggest that the mutations
of MC1R gene are associated with black coat color phenotype in Chinese sheep.
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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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Hepp D, Gonçalves GL, Moreira GRP, Freitas TRO, Martins CTDC, Weimer TA, Passos DT. Identification of the e allele at the Extension locus (MC1R) in Brazilian Creole sheep and its role in wool color variation. GENETICS AND MOLECULAR RESEARCH 2012; 11:2997-3006. [PMID: 22653672 DOI: 10.4238/2012.may.22.5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The melanocortin 1 receptor (MC1R) gene has been described as responsible for the black color in some breeds of sheep, but little is known about its function in many colored breeds, particularly those with a wide range of pigmentation phenotypes. The Brazilian Creole is a local breed of sheep from southern Brazil that has a wide variety of wool colors. We examined the MC1R gene (Extension locus) to search for the e allele and determine its role in controlling wool color variation in this breed. One hundred and twenty-five animals, covering the most common Creole sheep phenotypes (black, brown, dark gray, light gray, and white), were sequenced to detect the mutations p.M73K and p.D121N. Besides these two mutations, three other synonymous sites (429, 600, and 725) were found. The dominant allele (E(D): p.73K, and p.121N) was found only in colored animals, whereas the recessive allele (E⁺: p.73M, and p.121D) was homozygous only in white individuals. We concluded that MC1R is involved in the control of wool color in Brazilian Creole sheep, particularly the dark phenotypes, although a second gene may be involved in the expression of the white phenotype in this breed.
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Affiliation(s)
- D Hepp
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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Analysis of polymorphisms in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes and association with coat colours in two Pramenka sheep types. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2012.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Clop A, Vidal O, Amills M. Copy number variation in the genomes of domestic animals. Anim Genet 2012; 43:503-17. [PMID: 22497594 DOI: 10.1111/j.1365-2052.2012.02317.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2011] [Indexed: 12/28/2022]
Abstract
Copy number variation (CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characterization of the genomic architecture of CNV in domestic species. First, low-resolution CNV maps were produced for cattle, goat, sheep, pig, dog, chicken, duck and turkey, showing that these structural polymorphisms comprise a significant part of these genomes. Furthermore, CNVs have been associated with several pigmentation (white coat in horse, pig and sheep) and morphological (late feathering and pea comb in chicken) traits, as well as with susceptibility to a wide array of diseases and developmental disorders, for example osteopetrosis, anhidrotic ectodermal dysplasia, copper toxicosis, intersexuality, cone degeneration, periodic fever and dermoid sinus, among others. In the future, development of high-resolution tools for CNV detection and typing combined with the implementation of databases integrating CNV, QTL and gene expression data will be essential to identify and measure the impact of this source of structural variation on the many phenotypes that are relevant to animal breeders and veterinary practitioners.
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Affiliation(s)
- A Clop
- Department of Medical and Molecular Genetics, King's College London, Great Maze Pond, SE1 9RT, London, UK
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Peñagaricano F, Zorrilla P, Naya H, Robello C, Urioste JI. Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep. J Appl Genet 2011; 53:99-106. [PMID: 21952730 DOI: 10.1007/s13353-011-0066-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 08/25/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
The white coat colour of sheep is an important economic trait. For unknown reasons, some animals are born with, and others develop with time, black skin spots that can also produce pigmented fibres. The presence of pigmented fibres in the white wool significantly decreases the fibre quality. The aim of this work was to study gene expression in black spots (with and without pigmented fibres) and white skin by microarray techniques, in order to identify the possible genes involved in the development of this trait. Five unrelated Corriedale sheep were used and, for each animal, the three possible comparisons (three different hybridisations) between the three samples of interest were performed. Differential gene expression patterns were analysed using different t-test approaches. Most of the major genes with well-known roles in skin pigmentation, e.g. ASIP, MC1R and C-KIT, showed no significant difference in the gene expression between white skin and black spots. On the other hand, many of the differentially expressed genes (raw P-value < 0.005) detected in this study, e.g. C-FOS, KLF4 and UFC1, fulfil biological functions that are plausible to be involved in the formation of black spots. The gene expression of C-FOS and KLF4, transcription factors involved in the cellular response to external factors such as ultraviolet light, was validated by quantitative polymerase chain reaction (PCR). This exploratory study provides a list of candidate genes that could be associated with the development of black skin spots that should be studied in more detail. Characterisation of these genes will enable us to discern the molecular mechanisms involved in the development of this feature and, hence, increase our understanding of melanocyte biology and skin pigmentation. In sheep, understanding this phenomenon is a first step towards developing molecular tools to assist in the selection against the presence of pigmented fibres in white wool.
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Affiliation(s)
- Francisco Peñagaricano
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la Republica, Montevideo, Uruguay.
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A first comparative map of copy number variations in the sheep genome. Genomics 2010; 97:158-65. [PMID: 21111040 DOI: 10.1016/j.ygeno.2010.11.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 11/12/2010] [Accepted: 11/16/2010] [Indexed: 12/16/2022]
Abstract
We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (P<0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance.
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