|
|
|
| Screening of Candidate Genes and Their nsSNPs for Coat Color in Arctic White Fox (Vulpes lagopus) and Arctic Blue Fox Based on Whole- genome Resequencing Technology |
| GUO Jian-Xu1*, WANG Dong-Xian1, XIE Yu-Chun1, QIAO Xian1, PENG Yong-Dong2, GONG Yuan-Fang1, LIU Zheng-Zhu1* |
1 College of Animal Science and Technology/Key Laboratory of Special Animal Germplasm Resources Exploitation and Innovation in Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;
2. College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252059, China |
|
|
|
|
Abstract The diversity of coat color in Arctic foxes (Vulpes lagopus) provides an important model for studying the genetic regulation of coat color, and understanding its regulatory mechanisms is crucial for the breeding of fur-bearing animals. In this study, whole-genome resequencing was performed on Arctic white foxes and Arctic blue foxes. Nonsynonymous single nucleotide polymorphism (nsSNP) sites located in exon regions were selected as candidate loci, and the corresponding candidate genes were analyzed. Candidate genes involved in coat color regulation were identified through functional enrichment analysis. The epidermalgrowth factor (EGF) and adenomatous polyposis coli (APC) genes containing homozygous nsSNP mutationswere further validated using genomic DNA extracted from skin tissues of 42 Arctic foxes (21 white and 21 blue foxes). The results revealed that 8 860 718 SNPs and 21 150 nsSNPs were identified through resequencing, with 5 787 genes annotated. The nsSNP results of candidate genes were consistent with those obtained from whole-genome resequencing. Association analysis demonstrated that the c. 3571C>A variant inthe EGF gene and the c. 6812G>A variant in the APC gene were significantly (P<0.05) and extremelysignificantly (P<0.01) associated with coat color traits in Arctic white and blue foxes. These results indicated that specific variant sites in the APC and EGF genes identified through whole-genome resequencing and functional enrichment analysis might influence the formation of coat color in Arctic foxes. This study providescritical data for understanding the genetic mechanisms underlying coat color formation in Arctic white and blue foxes. Furthermore, it provides a theoretical freference for molecular breeding and the conservation of coat color diversity in fur animals.
|
|
Received: 21 August 2024
|
|
|
|
Corresponding Authors:
*liuzhengzhu@163.com
|
|
|
|
[1] 陈启昀.2011. 基于第二代测序技术中国大肠癌病例 APC 基因单核苷酸多态性分析[D]. 硕士学位论文, 浙江大学 , 导师 : 林标扬 , 郑树 , pp. 8-10.
(Chen Q Y.2011. Analysis of single nucleotide polymorphisms of APC gene in Chinese colorectal cancer cases based on second generation sequencing[D]. Thesis for M. S, Zhejiang University, Supervisors: Lin B Y, Zheng S, pp. 8-10.)
[2] 郭跃跃, 宋兴超, 王海军, 等. 2018. 褪黑素对毛皮动物生产性能及皮肤毛囊相关基因表达影响研究进展[J]. 动物医学进展,(039): 97-101.
(Guo Y Y, Song X C, Wang H J, et al. 2018. Progress on the effects of melatonin on the production performance and expression of skin folli-cle-related genes in fur-bearing animals[J]. Advances in Animal Medicine,(039): 97-101.)
[3] 李寒妹.2020. 狐狸毛色差异表达基因筛选及功能研究[D]. 硕士学位论文, 河北科技师范学院, 导师: 巩元芳, pp.1.
(Li H M. 2020. Screening of differentially expressed genes for fox coat colour and functional study[D]. The-sis for M. S., Hebei Normal University of Science and Technology, Supervisor: Gong Y F, pp. 1.
[4] 刘石平.2016. 北极熊比较基因组学和群体遗传学的研究[D]. 博士学位论文, 华南理工大学, 导师: 王俊, pp. 55-56.
(Liu, S P.2016. Comparative genomics and popula-tion genetics of polar bears[D]. Thesis for Ph. D., South China University of Technology, Supervisor: Wang J. pp. 55-56.)
[5] 李寒妹, 葛丛丛, 王国森, 等. 2019. MITF 在白色北极狐不同组织器官中的差异表达[J]. 黑龙江畜牧兽医 ,(11): 151-153+157.
[6] 陆佳毓, 王明, 肖鑫辉, 等. 2023. 基于木薯全基因组重测序的 InDel 标记开发及应用[J]. 分子植物育种, 1-22.
(Lu J Y, Wang M, Xiao X H, et al.2023. Development and application of InDel markers based on whole genome re-sequencing of cassava[J]. Molecular Plant Breeding: 1-22.)
[7] 宋明坤.2022. 基于全基因组重测序鉴定影响家兔生长性状的候选基因及验证[D]. 硕士学位论文, 河南农业大学, 导师: 李明, 王克君, pp. 17.
(Song M K. 2022. Identifi-cation and validation of candidate genes affecting growth traits in rabbits based on whole genome rese-quencing[D]. Thesis for M. S., Henan Agricultural Uni-versity, Supervisor: Li M, Wang K J, pp. 17)
[8] 宋兴超.2017. 水貂被毛色素沉积机理及基于高通量 RNA-seq 皮肤转录组注释研究[D]. 博士学位论文, 中国农业科学院 , 导师 : 杨福合 , pp. 7-14.
(Song X C.2017. Mechanism of mink coat pigmentation and annotation study based on high-throughput RNA-seq skin transcrip-tome[D]. Thesis for Ph. D., Chinese Academy of Agri-cultural Sciences, Supervisor: Yang F H, pp. 7-14.)
[9] 王静.2023. CCND1 基因 SNP 位点引起的可变剪接方式差异调控乳腺癌化疗敏感性的研究[D]. 博士学位论文, 兰州大学 , 导师 : 谢小冬 , 狄翠霞 , pp. 8-10.
(Wang J.2023. Differential regulation of breast cancer chemosen-sitivity by variable splicing induced by the SNP locus of the CCND1 gene[D]. Thesis for Ph. D., Lanzhou Univer-sity, Supervisor: Xie X D, Di C X, pp. 8-10.)
[10] 王瑞宁.2020. 北极狐 Wnt3a 基因在黑色素形成过程中的作用及机制研究[D]. 硕士学位论文, 河北科技师范学院, 导师 : 李祥龙 , pp. 4-6.
(Wang, R N.2020. Role and mechanism of Wnt3a gene in melanin formation in the Arctic fox[D]. Thesis for M.S., Hebei Normal Universi-ty of Science and Technology, Supervisor: Li X L, pp.4-6.)
[11] 张成岗, 贺福初. 2003. 生物信息学在新基因全长 cDNA 序列分析及功能预测中的应用[J]. 生物化学与生物物理进展, 30(1): 159-162.
(Zhang C G, He F C.2003. Appli-cation of bioinformatics in full-length cDNA sequence analysis and function prediction of new genes[J]. Ad-vances in Biochemistry and Biophysics, 30(1): 159-162.)
[12] 张丹丽, 田雪, 范瑞文, 等. 2014. APC 在羊驼皮肤组织中的表达和定位分析[J]. 畜牧兽医学报 ,(45): 327-332.
(Zhang D L, Tian X, Fan R W, et al. 2014. Expression and localisation of APC in alpaca skin tissues[J]. Jour-nal of Animal Husbandry and Veterinary Science,(45): 327-332.)
[13] 章誉兴,吴宏,于黎. 2021. 哺乳动物毛色调控机制及其适应性进化研究进展[J]. 遗传, 43(2): 118-133.
(Zhang Y X, Wu H, Li Y.2021. Progress on coat color regulation mechanism and its association with the adaptive evolu-tion in mammals[J]. Hereditas(Beijing), 43(2): 118-133.
[14] Chang C C, Chow C C, Tellier L C, et al.2015. Second-gener-ation PLINK: Rising to the challenge of larger and rich-er datasets[J]. GigaScience, 4: 7.
[15] Darnell D K, Kaur S, Stanislaw S, et al.2007. MicroRNA ex-pression during chick embryo development[J]. Develop-mental Dynamics, 236: 333.
[16] Firdous A S, Celus C S, Sakshi V, et al.2023. Read-depth based approach on whole genome resequencing data re-veals important insights into the copy number variation(CNV)map of major global buffalo breeds[J]. BMC Ge-nomics, 24: 616.
[17] Genovese G, Rockweiler N B, Gorman B R, et al.2024.BCFtools/liftover: An accurate and comprehensive tool to convert genetic variants across genome assemblies[J]. Bioinformatics, 40: 1367-4811.
[18] Han J L, Kraft P, Nan H M, et al.2008. A genome-wide asso-ciation study identifies novel alleles associated with hair color and skin pigmentation[J]. PLOS Genetics, 4: e1000074.
[19] Hong Z L, Liu H, Xie Y, et al.2025. RNA sequencing-based transcriptome analysis of seasonal coat color change in arctic fox(Vulpes lagopus)[J]. Russian Journal of Genet-ics, 61(1): 77-87.
[20] Hayes B J, Pryce J E, Chamberlain A J, et al.2010. Genetic ar-chitecture of complex traits and accuracy of genomic prediction: Coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits[J]. PLOS Ge-netics, 6: e1001139.
[21] Horton M W, Hancock A M, Huang Y S, et al.2011. Genome-wide patterns of genetic variation in worldwide Arabi-dopsis thaliana accessions from the RegMap panel[J]. Nature Genetics, 44: 212-216.
[22] Iqbal N, Liu X, Yang T, et al.2019. Genomic variants identi-fied from whole-genome resequencing of indicine cattle breeds from Pakistan[J]. PLOS ONE, 14: e0215065.
[23] James M R, Hayward N K, Dumenil T, et al.2004. Epidermal growth factor gene(EGF)polymorphism and risk of me-lanocytic neoplasia[J]. The Journal of Investigative Der-matology, 123: 760-762.
[24] Järvinen H J, Peltomäki P.2004. The complex genotype-phe-notype relationship in familial adenomatous polyposis[J]. European Journal of Gastroenterology & Hepatolo-gy, 16: 5-8.
[25] Johnson J L, Kozysa A, Kharlamova A V, et al.2015. Plati-num coat color in red fox(Vulpes vulpes)is caused by a mutation in an autosomal copy of KIT[J]. Animal Genet-ics, 46: 190-199.
[26] Kersey P J, Allen J E, Christensen M B, et al.2013. Ensembl Genomes 2013: Scaling up access to genome-wide data[J]. Nucleic Acids Research, 42: D546-D552.
[27] Kijas J, Lenstra J A, Hayes B J, et al.2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection[J]. PLOS Biology, 10: e1001258.
[28] Kukekova A V, Johnson J L, Kharlamova A V, et al.2016. Georgian white coat color of red fox(Vulpes vulpes)maps to fox chromosome 2 in the region containing KIT gene[J]. Animal Genetics, 47: 514-515.
[29] Li H, Handsaker R E, Wysoker A, et al.2009. The sequence alignment/map format and SAMtools[J]. Bioinformat-ics, 25: 2078-2079.
[30] Mardis E R.2008. Next-generation DNA sequencing methods[J]. Annual Review of Genomics and Human Genetics,9: 387-402.
[31] Normanno N, Bianco C, De L A, et al.2001. The role of EGF-related peptides in tumor growth[J]. Frontiers in Biosci-ence, 6: D685-707.
[32] Shahbazi M, Pravica V, Nasreen N, et al.2002. Association between functional polymorphism in EGF gene and ma-lignant melanoma[J]. The Lancet, 359: 397-401.
[33] Shendure J A, Porreca G, Reppas N B, et al.2004. Accurate multiplex polony sequencing of an evolved bacterial ge-nome[J]. Science, 309: 1728-1732.
[34] Våge D I, Fuglei E, Snipstad K, et al.2005. Two cysteine sub-stitutions in the MC1R generate the blue variant of the arctic fox(Alopex lagopus)and prevent expression of the white winter coat[J]. Peptides, 26: 1814-1817.
[35] Våge D I, Lu D, Klungland H, et al.1997. A non-epistatic in-teraction of agouti and extension in the fox, Vulpes vulpes[J]. Nature Genetics, 15: 311-315.
[36] van Noort M, Meeldijk J, van der Zee R, et al.2002. Wnt sig-naling controls the phosphorylation status of β -catenin[J]. The Journal of Biological Chemistry, 277: 17901-17905.
[37] Wang G S, Cooper T A.2007. Splicing in disease: Disruption of the splicing code and the decoding machinery[J]. Na-ture Reviews Genetics, 8: 749-761.
[38] Wang K, Li M Y, Hakonarson H.2010. ANNOVAR: Function-al annotation of genetic variants from high-throughput sequencing data[J]. Nucleic Acids Research, 38: e164.
[39] Wu P X, Wang K, Yang Q, et al.2019. Whole-genome re-se-quencing association study for direct genetic effects and social genetic effects of six growth traits in Large White pigs[J]. Scientific Reports, 9: 1-12.
[40] Xie H L, Li W, Guo Y Q, et al.2023. Long-read-based single sperm genome sequencing for chromosome-wide haplo-type phasing of both SNPs and SVs[J]. Nucleic Acids Research, 51: 8020-8034.
[41] Yamaguchi J Y, Hearing V J.2009. Physiological factors that regulate skin pigmentation[J]. BioFactors, 35: 193-199.
[42] Yan S Q, Hou J N, Bai C Y, et al.2014. A base substitution in the donor site of intron 12 of KIT gene is responsible for the dominant white coat colour of blue fox(Alopex lagopus)[J]. Animal Genetics, 45: 293-296.
[43] Yarden Y, Sliwkowski M X.2001. Untangling the ErbB sig-nalling network[J]. Nature Reviews Molecular Cell Biol-ogy, 2: 127-137.
[44] Yu G C, Wang L G, Han Y Y, et al.2012. clusterProfiler: An R package for comparing biological themes among gene clusters[J]. OMICS: A Journal of Integrative Biology,16: 284-287. |
|
|
|
