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Xu J, Fu Y, Hu Y, Yin L, Tang Z, Yin D, Zhu M, Yu M, Li X, Zhou Y, Zhao S, Liu X. Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. J Anim Sci Biotechnol 2020; 11:115. [PMID: 33292532 PMCID: PMC7713148 DOI: 10.1186/s40104-020-00520-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/15/2023] Open
Abstract
Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. Supplementary Information Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.
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Affiliation(s)
- Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
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Flesher JL, Paterson-Coleman EK, Vasudeva P, Ruiz-Vega R, Marshall M, Pearlman E, MacGregor GR, Neumann J, Ganesan AK. Delineating the role of MITF isoforms in pigmentation and tissue homeostasis. Pigment Cell Melanoma Res 2019; 33:279-292. [PMID: 31562697 DOI: 10.1111/pcmr.12828] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 01/01/2023]
Abstract
MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, encodes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. It is not completely understood how these isoforms influence pigmentation in different tissues and how the expression of these independent isoforms of MITF is regulated. Here, we show that melanocytes express two isoforms of MITF, MITF-A and MITF-M. The expression of MITF-A is partially regulated by a newly identified retinoid enhancer element located upstream of the MITF-A promoter. Mitf-A knockout mice have only subtle changes in melanin accumulation in the hair and reduced Tyr expression in the eye. In contrast, Mitf-M-null mice have enlarged kidneys, lack neural crest-derived melanocytes in the skin, choroid, and iris stroma, yet maintain pigmentation within the retinal pigment epithelium and iris pigment epithelium of the eye. Taken together, these studies identify a critical role for MITF-M in melanocytes, a minor role for MITF-A in regulating pigmentation in the hair and Tyr expression in the eye, and a novel role for MITF-M in size control of the kidney.
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Affiliation(s)
- Jessica L Flesher
- Department of Biological Chemistry, University of California, Irvine, CA, USA.,Center for Cancer Systems Biology, University of California, Irvine, CA, USA
| | | | - Priya Vasudeva
- Department of Dermatology, University of California, Irvine, CA, USA
| | - Rolando Ruiz-Vega
- Center for Cancer Systems Biology, University of California, Irvine, CA, USA.,Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.,Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Michaela Marshall
- Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Eric Pearlman
- Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.,Irvine Transgenic Mouse Facility, University Laboratory Animal Resources, Office of Research, Universitiy of California, Irvine, CA, USA
| | - Jonathan Neumann
- Irvine Transgenic Mouse Facility, University Laboratory Animal Resources, Office of Research, Universitiy of California, Irvine, CA, USA
| | - Anand K Ganesan
- Department of Biological Chemistry, University of California, Irvine, CA, USA.,Center for Cancer Systems Biology, University of California, Irvine, CA, USA.,Department of Dermatology, University of California, Irvine, CA, USA
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Abstract
In this review, Goding and Arnheiter present the current understanding of MITF's role and regulation in development and disease and highlight key areas where our knowledge of MITF regulation and function is limited. All transcription factors are equal, but some are more equal than others. In the 25 yr since the gene encoding the microphthalmia-associated transcription factor (MITF) was first isolated, MITF has emerged as a key coordinator of many aspects of melanocyte and melanoma biology. Like all transcription factors, MITF binds to specific DNA sequences and up-regulates or down-regulates its target genes. What marks MITF as being remarkable among its peers is the sheer range of biological processes that it appears to coordinate. These include cell survival, differentiation, proliferation, invasion, senescence, metabolism, and DNA damage repair. In this article we present our current understanding of MITF's role and regulation in development and disease, as well as those of the MITF-related factors TFEB and TFE3, and highlight key areas where our knowledge of MITF regulation and function is limited.
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Affiliation(s)
- Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Heinz Arnheiter
- National Institute of Neurological Disorders and Stroke, National Institutes of Heath, Bethesda, Maryland 20824, USA
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Nooron N, Ohba K, Takeda K, Shibahara S, Chiabchalard A. Dysregulated Expression of MITF in Subsets of Hepatocellular Carcinoma and Cholangiocarcinoma. TOHOKU J EXP MED 2017; 242:291-302. [DOI: 10.1620/tjem.242.291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nattakarn Nooron
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University
| | - Koji Ohba
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine
| | - Kazuhisa Takeda
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine
| | - Shigeki Shibahara
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine
- Faculty of Sports Science, Sendai University
| | - Anchalee Chiabchalard
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University
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Ohba K, Takeda K, Furuse T, Suzuki T, Wakana S, Suzuki T, Yamamoto H, Shibahara S. Microphthalmia-associated transcription factor ensures the elongation of axons and dendrites in the mouse frontal cortex. Genes Cells 2016; 21:1365-1379. [PMID: 27859996 DOI: 10.1111/gtc.12450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Long interspersed element-1 (LINE-1) is a mammalian transposable element, and its genomic insertion could cause neurological disorders in humans. Incidentally, LINE-1 is present in intron 3 of the microphthalmia-associated transcription factor (Mitf) gene of the black-eyed white mouse (Mitfmi-bw allele). Mice homozygous for the Mitfmi-bw allele show the white coat color with black eye and deafness. Here, we explored the functional consequences of the LINE-1 insertion in the Mitf gene using homozygous Mitfmi-bw mice on the C3H background (C3H-bw mice) or on the C57BL/6 background (bw mice). The open-field test showed that C3H-bw mice moved more irregularly in an unfamiliar environment during the 20-min period, compared to wild-type mice, suggesting the altered emotionality. Moreover, C3H-bw mice showed the lower serum creatinine levels, which may reflect the creatine deficiency. In fact, morphologically abnormal neurons and astrocytes were detected in the frontal cortex of bw mice. The immunohistochemical analysis of bw mouse tissues showed the lower intensity for expression of guanidinoacetate methyltransferase, a key enzyme in creatine synthesis, in neurons of the frontal cortex and in glomeruli and renal tubules. Thus, Mitf may ensure the elongation of axons and dendrites by maintaining creatine synthesis in the frontal cortex.
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Affiliation(s)
- Koji Ohba
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Kazuhisa Takeda
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Tamio Furuse
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BRC, Tsukuba, Ibaraki, 305-0074, Japan
| | - Tomohiro Suzuki
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BRC, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BRC, Tsukuba, Ibaraki, 305-0074, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Hiroaki Yamamoto
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Shigeki Shibahara
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi, 980-8575, Japan.,Faculty of Sports Science, Sendai University, Shibata-Gun, Miyagi, 989-1693, Japan
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Takeda K, Hozumi H, Ohba K, Yamamoto H, Shibahara S. Regional Fluctuation in the Functional Consequence of LINE-1 Insertion in the Mitf Gene: The Black Spotting Phenotype Arisen from the Mitfmi-bw Mouse Lacking Melanocytes. PLoS One 2016; 11:e0150228. [PMID: 26930598 PMCID: PMC4773177 DOI: 10.1371/journal.pone.0150228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/10/2016] [Indexed: 11/19/2022] Open
Abstract
Microphthalmia-associated transcription factor (Mitf) is a key regulator for differentiation of melanoblasts, precursors to melanocytes. The mouse homozygous for the black-eyed white (Mitfmi-bw) allele is characterized by the white-coat color and deafness with black eyes due to the lack of melanocytes. The Mitfmi-bw allele carries LINE-1, a retrotransposable element, which results in the Mitf deficiency. Here, we have established the black spotting mouse that was spontaneously arisen from the homozygous Mitfmi-bw mouse lacking melanocytes. The black spotting mouse shows multiple black patches on the white coat, with age-related graying. Importantly, each black patch also contains hair follicles lacking melanocytes, whereas the white-coat area completely lacks melanocytes. RT-PCR analyses of the pigmented patches confirmed that the LINE-1 insertion is retained in the Mitf gene of the black spotting mouse, thereby excluding the possibility of the somatic reversion of the Mitfmi-bw allele. The immunohistochemical analysis revealed that the staining intensity for beta-catenin was noticeably lower in hair follicles lacking melanocytes of the homozygous Mitfmi-bw mouse and the black spotting mouse, compared to the control mouse. In contrast, the staining intensity for beta-catenin and cyclin D1 was higher in keratinocytes of the black spotting mouse, compared to keratinocytes of the control mouse and the Mitfmi-bw mouse. Moreover, the keratinocyte layer appears thicker in the Mitfmi-bw mouse, with the overexpression of Ki-67, a marker for cell proliferation. We also show that the presumptive black spots are formed by embryonic day 15.5. Thus, the black spotting mouse provides the unique model to explore the molecular basis for the survival and death of developing melanoblasts and melanocyte stem cells in the epidermis. These results indicate that follicular melanocytes are responsible for maintaining the epidermal homeostasis; namely, the present study has provided evidence for the link between melanocyte development and the epidermal microenvironment.
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Affiliation(s)
- Kazuhisa Takeda
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi 980–8575, Japan
| | - Hiroki Hozumi
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi 980–8575, Japan
| | - Koji Ohba
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi 980–8575, Japan
| | - Hiroaki Yamamoto
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526–0829, Japan
| | - Shigeki Shibahara
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Miyagi 980–8575, Japan
- * E-mail:
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Ohba K, Takeda K, Yamamoto H, Shibahara S. Microphthalmia-associated transcription factor is expressed in projection neurons of the mouse olfactory bulb. Genes Cells 2015; 20:1088-102. [DOI: 10.1111/gtc.12312] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Koji Ohba
- Department of Molecular Biology and Applied Physiology; Tohoku University School of Medicine; 2-1 Seiryo-machi Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Kazuhisa Takeda
- Department of Molecular Biology and Applied Physiology; Tohoku University School of Medicine; 2-1 Seiryo-machi Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Hiroaki Yamamoto
- Faculty of Bioscience; Nagahama Institute of Bio-Science and Technology; 1266 Tamura-cho Nagahama Shiga 526-0829 Japan
| | - Shigeki Shibahara
- Department of Molecular Biology and Applied Physiology; Tohoku University School of Medicine; 2-1 Seiryo-machi Aoba-ku Sendai Miyagi 980-8575 Japan
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l-tyrosine induces melanocyte differentiation in novel pink-eyed dilution castaneus mouse mutant showing age-related pigmentation. J Dermatol Sci 2015; 80:203-11. [PMID: 26475433 DOI: 10.1016/j.jdermsci.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 10/01/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND The mouse pink-eyed dilution (oculocutaneous albinism II; p/Oca2(p)) locus is known to control tyrosinase activity, melanin content, and melanosome development in melanocytes. Pink-eyed dilution castaneus (p(cas)/Oca2(p-cas)) is a novel mutant allele on mouse chromosome 7 that arose spontaneously in Indonesian wild mice, Mus musculus castaneus. Mice homozygous for Oca2(p-cas) usually exhibit pink eyes and beige-colored coat on nonagouti C57BL/6 (B6) background. Recently, a novel spontaneous mutation occurred in the progeny between this mutant and B6 mice. The eyes of this novel mutant progressively become black from pink and the coat becomes dark gray from beige with aging. OBJECTIVE The aim of this study is to clarify whatever differences exist in melanocyte proliferation and differentiation between the ordinary (pink-eyed) and novel (black-eyed) mutant using serum-free primary culture system. METHODS The characteristics of melanocyte proliferation and differentiation were investigated by serum-free primary culture system using melanocyte-proliferation medium (MDMD). RESULTS The proliferation of melanoblasts in MDMD did not differ between the two mice. However, when the epidermal cell suspensions were cultured with MDMD supplemented with l-tyrosine (Tyr), the differentiation of black-eyed melanocytes was greatly induced in a concentration-dependent manner compared with pink-eyed melanocytes. Immunocytochemistry demonstrated that the expression of tyrosinase and tyrosinase-related protein-1 (Tyrp1) was greatly induced or stimulated both in pink-eyed and black-eyed melanocytes, whereas the expression of microphthalmia-associated transcription factor (Mitf) was stimulated only in black-eyed melanocytes. CONCLUSION These results suggest that the age-related coat darkening in black-eyed mutant may be caused by the increased ability of melanocyte differentiation dependent on l-Tyr through the upregulation of tyrosinase, Tyrp1, and Mitf. This mutant mouse may be useful for animal model to clarify the mechanisms of age-related pigmentation in human skin, such as melasma and solar lentigines.
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Microphthalmia-associated transcription factor as the molecular target of cadmium toxicity in human melanocytes. Biochem Biophys Res Commun 2014; 454:594-9. [DOI: 10.1016/j.bbrc.2014.10.141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 10/28/2014] [Indexed: 12/26/2022]
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Wang C, Wang H, Zhang Y, Tang Z, Li K, Liu B. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs. Mol Ecol Resour 2014; 15:414-24. [PMID: 25132237 DOI: 10.1111/1755-0998.12311] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/12/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022]
Abstract
Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two-end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white-spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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