滩羊毛色的全基因组关联分析

doi:10.3969/j.issn.1004-1524.2020.01.04

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (1): 28-34.DOI: 10.3969/j.issn.1004-1524.2020.01.04

滩羊毛色的全基因组关联分析

王晓薇, 马青

宁夏农林科学院动物科学研究所,宁夏银川 750002

收稿日期:2019-06-11 出版日期:2020-01-25 发布日期:2020-03-11
作者简介:王晓薇(1988—),女,宁夏银川人,硕士,研究实习员,研究方向为动物遗传育种。E-mail: wxw0812@126.com
基金资助:
宁夏回族自治区农业科技自主创新专项科技创新引导项目(NKYQ-18-01); 宁夏回族自治区科技基础条件建设计创新平台专项资金(DKS-18-05)

Genome-wide association studies for coat color in Tan sheep

WANG Xiaowei, MA Qing

Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, China

Received:2019-06-11 Online:2020-01-25 Published:2020-03-11

摘要/Abstract

摘要： 滩羊不仅肉质鲜美,其所产的二毛裘皮在国内外也享有盛誉,毛色是滩羊重要的经济性状。为检测影响滩羊毛色的基因组区域,利用美国Affymetrix绵羊600K基因分型芯片对宁夏盐池地区具有代表性毛色的96只滩羊个体(全白、白毛黑头、白毛褐或黄头)进行基因分型,并采用Logistic回归方法进行全基因组关联分析。通过Bonferroni校正,检测到5个与毛色显著关联的SNPs。这些SNPs分别位于或邻近2个已知基因(MC1R和TCF25)。其中MC1R基因参与调控黑色素的合成,研究表明其与绵羊毛色相关。而TCF25基因与MC1R基因距离很近,可能由于存在一定程度的连锁不平衡而被鉴定到。本研究进一步解析了滩羊毛色性状的遗传机理,为滩羊毛色性状的标记辅助选育提供科学依据。

关键词: 滩羊, 毛色, 全基因组关联分析

Abstract: Tan sheep, not only famous for its delicious meat, but also enjoys high reputation at home and abroad for its one-month lamb's fur. Therefore, the coat color is an important economic trait of Tan sheep. To detect the genomic regions which affecting the coat color of Tan sheep, the genome-wide association studies (GWAS) were performed based on Logistic regression method using genotypes from the America Affymetrix 600K genotyping chips for this trait. Genotyping was performed on 96 representative tan sheep of Yanchi, Ningxia, which had pure white bodies, white bodies with black heads and white bodies with brown or yellow heads. By Bonferroni correction, we have found five SNPs significantly associated with coat color, which were located within or close to 2 known genes (MC1R and TCF25). The MC1R is involved in the regulation of melanin synthesis that has been shown to be related to the color of sheep by numerous studies. The TCF25 is located nearby MC1R, so the identification of TCF25 maybe a result of linkage disequilibrium between these two genes. Our studies explained the genetic mechanism of coat color of Tan sheep, and provided scientific basis for assisted breeding by mark the color traits of Tan sheep.

Key words: Tan sheep, coat color, genome-wide association study

中图分类号:

S818.9

王晓薇, 马青. 滩羊毛色的全基因组关联分析[J]. 浙江农业学报, 2020, 32(1): 28-34.

WANG Xiaowei, MA Qing. Genome-wide association studies for coat color in Tan sheep[J]. , 2020, 32(1): 28-34.

参考文献

[1] 王晓薇, 马青, 马丽娜, 等. 滩羊裘皮毛色调控基因的研究进展[J]. 生物资源, 2019, 41(2): 143-148.
WANG X W, MA Q, MA L N, et al.Research progress of regulator genes of Tan sheep fur color[J]. Biotic Resources, 2019, 41(2): 143-148.(in Chinese with English abstract)
[2] 孟浩浩, 许瑞霞, 代蓉, 等. 绵羊黑色素合成相关基因的研究进展[J]. 生物技术通报, 2014(8): 34-39.
MENG H H, XU R X, DAI R, et al.Research progress of genes related to melanin synthesis in sheep[J]. Biotechnology Bulletin, 2014(8): 34-39.(in Chinese with English abstract)
[3] RISCH N, MERIKANGAS K.The future of genetic studies of complex human diseases[J]. Science, 1996, 273(5281): 1516-1517.
[4] 张统雨, 朱才业, 杜立新, 等. 羊重要性状全基因组关联分析研究进展[J]. 遗传, 2017, 39(6): 491-500.
ZHANG T Y, ZHU C Y, DU L X, et al.Advances in genome-wide association studies for important traits in sheep and goats[J]. Hereditas, 2017, 39(6): 491-500.(in Chinese with English abstract)
[5] LI M H, 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)[J]. Heredity, 2014, 112(2): 122-131.
[6] PURCELL S, NEALE B, TODD-BROWN K, et al.PLINK: A tool set for whole-genome association and population-based linkage analyses[J]. The American Journal of Human Genetics, 2007, 81(3): 559-575.
[7] PRICE A L, PATTERSON N J, PLENGE R M, et al.Principal components analysis corrects for stratification in genome-wide association studies[J]. Nature Genetics, 2006, 38(8): 904-909.
[8] 印崇, 高峰, 李傲楠, 等. 猪毛色基因黑色素受体1的基因型分析[J]. 中国畜牧兽医, 2014, 41(11): 44-49.
YIN C, GAO F, LI A N, et al.The genotype analysis of coat color gene MC1R in swine[J]. China Animal Husbandry & Veterinary Medicine, 2014, 41(11): 44-49.(in Chinese with English abstract)
[9] 赵珊珊. 马MC1R基因多态位点与毛色相关性研究[D]. 南宁: 广西大学, 2018.
ZHAO S S.Polymorphism loci of MC1R gene and coat color in horses[D]. Nanning: Guangxi University, 2018.(in Chinese with English abstract)
[10] 付冬丽. 10个中国地方绵羊品种MC1R和ASIP基因多态性及其与毛色关联性分析[D]. 兰州: 甘肃农业大学, 2013.
FU D L.Polymorphisms of MC1R and ASIP genes and their association with coat colours in ten Chinese indigenous sheep breeds[D]. Lanzhou: Gansu Agricultural University, 2013.(in Chinese with English abstract)
[11] 聂庆华, 刘清神, 方梅霞, 等. 犬MC1R基因的分子进化分析[J]. 遗传, 2008, 30(4): 469-474.
NIE Q H, LIU Q S, FANG M X, et al.Analysis on molecular evolution of MC1R gene in dog[J]. Hereditas, 2008, 30(4): 469-474.(in Chinese with English abstract)
[12] ROBBINS L.Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MSH receptor function[J]. Cell, 1993, 72(6): 827-834.
[13] 王乐, 张斌, 郑文新, 等. 动物毛色与黑色素皮质素受体1(MC1R)基因[J]. 草食家畜, 2009(2): 10-12.
WANG L, ZHANG B, ZHENG W X, et al.The hair color of animal and melanocortin receptor 1(MC1R)[J]. Grass-Feeding Livestock, 2009(2): 10-12.(in Chinese with English abstract)
[14] PARSONS Y M, FLEET M R, COOPER D W.The Agouti gene: a positional candidate for recessive self-colour pigmentation in Australian Merino sheep[J]. Australian Journal of Agricultural Research, 1999, 50(6): 1099.
[15] DENG W D, XI D M, GOU X, et al.Pigmentation in black-boned sheep (Ovis aries): association with polymorphism of the tyrosinase gene[J]. Molecular Biology Reports, 2008, 35(3): 379-385.
[16] FONTANESI L, DALL’OLIO S, BERETTI F, et al. Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes[J]. Animal, 2011, 5(1): 8-17.
[17] 何军敏, 孙军, 余雄, 等. MC1R与Slc7a11基因多态性与哈萨克羊毛色相关的研究[J]. 中国畜牧杂志, 2017, 53(10): 39-42.
HE J M, SUN J, YU X, et al.Study on the relationship between polymorphism of MC1R and SLC7A11 gene and Kazakh wool color[J]. Chinese Journal of Animal Science, 2017, 53(10): 39-42.(in Chinese)
[18] 景炅婕, 贾秀生, 梁琛, 等. MC1R基因在不同毛色太行山羊皮肤组织中的表达[J]. 中国畜牧杂志, 2017, 53(3): 33-39.
JING J J, JIA X S, LIANG C, et al.The expression of MC1R gene in the skin tissues of Tai-hang goat with different coat colors[J]. Chinese Journal of Animal Science, 2017, 53(3): 33-39.(in Chinese with English abstract)
[19] STEEN H, LINDHOLM D.Nuclear localized protein-1 (Nulp1) increases cell death of human osteosarcoma cells and binds the X-linked inhibitor of apoptosis protein[J]. Biochemical and Biophysical Research Communications, 2008, 366(2): 432-437.
[20] ISHIDA K, SATO J J, KINOSHITA G, et al.Evolutionary history of the sable (Martes zibellina Brachyura) on Hokkaido inferred from mitochondrial cytb and nuclear Mc1r and Tcf25 gene sequences[J]. Acta Theriologica, 2013, 58(1): 13-24.
[21] LI Y J, KIJAS J, HENSHALL J M, et al.Using random forests (RF) to prescreen candidate genes: a new prospective for GWAS[C]//10th World Congress on Genetics Applied to Livestock Production, British Columbia, Vancouver, 2014.
[22] KIM S, CHEONG H S, SHIN H D, et al.Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip[J]. Asian-Australasian Journal of Animal Sciences, 2018, 31(11): 1691-1699.
[23] HYSI P G, VALDES A M, LIU F, et al.Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability[J]. Nature Genetics, 2018, 50(5): 652-656.
[24] MORGAN M D, PAIRO-CASTINEIRA E, RAWLIK K, et al.Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability[J]. Nature Communications, 2018, 9: 5271.

滩羊毛色的全基因组关联分析

Genome-wide association studies for coat color in Tan sheep

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