鸡FGF6基因生物学特性及其多态性与经济性状的关联分析

doi:10.11843/j.issn.0366-6964.2024.04.018

Abstract

Abstract: The purpose of this study was to explore the biological characteristics of chicken fibroblast growth factor 6 (FGF6) gene, excavate the single nucleotide polymorphism (SNP) site located in FGF6 gene and analyze its correlation with chicken economic traits, and provide reference for the subsequent research on the effect of FGF6 gene on growth traits in chickens. Bioinformatics analysis was performed for FGF6 protein sequences. Based on the GBS data and phenotypic data of 768 individuals from Gushi-Anka chicken F₂ resource population, the SNP in the FGF6 gene including the promoter 2 kb region were screened, linkage disequilibrium and association analysis were conducted to explore the correlation of SNP and haplotype of FGF6 gene with economic traits of chickens. The results showed that the amino acid sequence of chicken FGF6 was 91.26% homologous to turkey; phylogenetic analysis showed that chicken was the most closely related to turkey, followed by green sea turtle, and had the greatest genetic distance from zebrafish. Conservative analysis showed that FGF6 was highly conservative among different species. Chicken FGF6 was a hydrophilic protein with one transmembrane region, and mainly localized in the cytoplasm. Its secondary and tertiary structures were consistent. Chicken FGF6 protein was modified by 22 phosphorylation sites and 1 N-glycosylation site, and potentially interacted with 5 proteins of its receptor family, FGFR1-4 and EGF. Six SNPs sites were screened in the promoter region of chicken FGF6, all of which were located in intron 1. Polymorphism analysis showed that the 6 SNPs sites had high polymorphic, and 5 of them were in Hardy-Weinberg equilibrium and strongly interlinked (D′=1, r²=1). The results of association analysis showed that rs73399071 was significantly correlated with 17 growth traits including body weight (BW), shank length (SL), shank girth (SG), and body slanting length (BSL), etc. at different stages of F₂ resource population (P < 0.05), and 10 carcass traits such as evisceration weight (EW), semi-evisceration weight (SEW), carcass weight (CW), and breast muscle weight (BMW), etc. (P < 0.05). The rs73399071 was not significantly correlated with meat quality traits (P>0.05), and significantly correlated with high-density lipoprotein (HDL) and choline esterase (ChE) (P < 0.05). The phenotype average values of most traits in CC genotype individuals were higher than those of GG genotype individuals. Haplotype combination analysis showed that body weights of individuals carrying with CCTTCCTTCC combinations at different stages were higher than those of other haplotype combinations. The results of this study provide a theoretical reference for further exploring the function of FGF6 gene in chickens. Five SNP sites in FGF6 gene were found to be significantly associated with body weight, body size, carcass traits and blood biochemical indexes of Gushi-Anka chicken F₂ resource population, providing candidate molecular markers for chicken breeding and a new idea for marker assisted selection in chicken.

Key words: chicken, FGF6 gene, bioinformatics analysis, linkage disequilibrium analysis, haplotype, economic traits, association analysis

CLC Number:

S831.2

CAO Yuzhu, XING Yuxin, MA Chenglin, GUAN Hongbo, JIA Qihui, KANG Xiangtao, TIAN Yadong, LI Zhuanjian, LIU Xiaojun, LI Hong. Biological Characterization of Chicken FGF6 Gene and Association of Its Polymorphisms with Economic Traits[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1536-1550.

References

[1] ARMAND A S, LAZIZ I, CHANOINE C. FGF6 in myogenesis[J]. Biochim Biophys Acta, 2006, 1763(8):773-778.
[2] ZHENG J, JIANG C, LI X K, et al. The progression of fibroblast growth factor 6[J]. China Biotechnology, 2017, 37(4):110-114. (in Chinese)
郑婕, 姜潮, 李校堃, 等. 成纤维细胞生长因子6(FGF6)的研究进展[J]. 中国生物工程杂志, 2017, 37(4):110-114.
[3] LI L L. Research progress on the relationship between fibroblast growth factor and choroidal neovascularization[J]. Eye Science, 2020, 35(2):99-105. (in Chinese)
李乐乐. 成纤维细胞生长因子与脉络膜新生血管关系的研究进展[J]. 眼科学报, 2020, 35(2):99-105.
[4] ZHI Y L, CAI C K, XU T X, et al. Silencing of FGF6 hampers aerobic glycolysis and angiogenesis in bladder cancer by regulating PI3K/Akt and MAPK signaling pathways[J]. J Biochem Mol Toxicol, 2023, 37(8):e23399.
[5] HAN D, ZHAO H, PARADA C, et al. A TGFβ-Smad4-Fgf6 signaling cascade controls myogenic differentiation and myoblast fusion during tongue development[J]. Development, 2012, 139(9):1640-1650.
[6] CAI Q C, WU G B, ZHU M, et al. FGF6 enhances muscle regeneration after nerve injury by relying on ERK1/2 mechanism[J]. Life Sci, 2020, 248:117465.
[7] XU B, LIU C Z, ZHANG H, et al. Skeletal muscle-targeted delivery of Fgf6 protects mice from diet-induced obesity and insulin resistance[J]. JCI Insight, 2021, 6(19):e149969.
[8] SHAMSI F, XUE R D, HUANG T L, et al. FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis[J]. Nat Commun, 2020, 11(1):1421.
[9] LIU C Z, MENG M Y, XU B, et al. Fibroblast growth factor 6 promotes adipocyte progenitor cell proliferation for adipose tissue homeostasis[J]. Diabetes, 2023, 72(4):467-482.
[10] HU Z C, CHEN P, WANG L L, et al. FGF6 promotes cardiac repair after myocardial infarction by inhibiting the Hippo pathway[J]. Cell Prolif, 2022, 55(5):e13221.
[11] CREIGHTON C J, ZHANG F, ZHANG Y Q, et al. Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer[J]. Epigenetics, 2023, 18(1):2180585.
[12] KUMAR M, CHAPMAN S C. Cloning and expression analysis of Fgf5, 6 and 7 during early chick development[J]. Gene Expr Patterns, 2012, 12(7/8):245-253.
[13] CAO Y Z, JIA Q H, XING Y X, et al. Bioinformatics characteristics and expression regulation of chicken fibroblast growth factor family[J]. Journal of Henan Agricultural University, 2023, 57(3):422-435. (in Chinese)
曹玉珠, 贾其辉, 邢雨欣, 等. 鸡成纤维细胞生长因子家族生物信息学特性及表达调控[J]. 河南农业大学学报, 2023, 57(3):422-435.
[14] FU J X, GUO H W, LI C, et al. Polymorphism of exon 7 of DGAT2 gene and its association with growth traits in chicken(Gallus gallus)[J]. Journal of Agricultural Biotechnology, 2016, 24(5):689-696. (in Chinese)
付金秀, 郭红威, 李超, 等. 鸡DGAT2基因第7外显子多态性与生产性能的关联[J]. 农业生物技术学报, 2016, 24(5):689-696.
[15] ZHANG Y H, WANG Y Z, LI Y Y, et al. Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F₂ chicken population[J]. Heredity (Edinb), 2021, 126(2):293-307.
[16] SU L. Study of polymorphisms and gene expression profile of chicken PNPLA3 gene[D]. Zhengzhou:Henan Agricultural University, 2012. (in Chinese)
苏玲. 鸡PNPLA3基因多态性及组织表达规律的研究[D]. 郑州:河南农业大学, 2012.
[17] SONG H J, LI W T, LI Y F, et al. Genome-wide association study of 17 serum biochemical indicators in a chicken F₂ resource population[J]. BMC Genomics, 2023, 24(1):98.
[18] MEI C J. Studies on the corralation between serum biochemical indexes and some fat traits and got isozymes in chickens[D]. Zhengzhou:Henan Agricultural University, 2007. (in Chinese)
梅承君. 鸡血清生化指标与部分脂肪性状相关性及谷草转氨酶同工酶的研究[D]. 郑州:河南农业大学, 2007.
[19] LIANG Q J, WANG P C, BAI Y R. Summarization on the progress in protein phosphorylation[J]. Science & Technology Review, 2012, 30(31):73-79. (in Chinese)
梁前进, 王鹏程, 白燕荣. 蛋白质磷酸化修饰研究进展[J]. 科技导报, 2012, 30(31):73-79.
[20] TAN T, KE B Y, LIANG Q J. Research progress on protein phosphorylation modification and its role in regulating cell cycle progression[J]. Journal of Beijing Normal University:Natural Science, 1-8.http://kns.cnki.net/kcms/detail/11.1991.n.20230720.1204.002.html. (in Chinese)
谭锬, 柯柏怡, 梁前进. 蛋白质磷酸化修饰及其在细胞周期调控中的作用研究进展[J/OL]. 北京师范大学学报:自然科学版, 1-8.http://kns.cnki.net/kcms/detail/11.1991.n.20230720.1204.002.html.
[21] WANG W Q, ZHANG Y W, LI J H, et al. Research progress on the effect of protein phosphorylation on postmortem meat quality[J]. Food Science, 2023, 44(9):221-230. (in Chinese)
王文琪, 张雅玮, 李加慧, 等. 蛋白质磷酸化对宰后肉品质影响研究进展[J]. 食品科学, 2023, 44(9):221-230.
[22] JIA Y F, WANG Y M, LI G Y. Recent progress of protein glycosylation characterization utilizing native conformer-resolved mass spectrometry[J/OL]. Journal of China Pharmaceutical University, 1-13.http://kns.cnki.net/kcms/detail/32.1157.r.20230921.1134.004.html. (in Chinese)
贾翼菲, 王雅梅, 李功玉. 蛋白质糖基化修饰的非变性构象分辨质谱研究进展[J/OL]. 中国药科大学学报, 1-13.http://kns.cnki.net/kcms/detail/32.1157.r.20230921.1134.004.html.
[23] LI J, DU X, HOSSEINI M S H, et al. The research progress in protein glycosylation modification[J]. Bulletin of Science and Technology, 2009, 25(6):773-778, 783. (in Chinese)
李军, 杜鑫, HOSSEINI M S H, 等. 蛋白质糖基化修饰研究进展[J]. 科技通报, 2009, 25(6):773-778, 783.
[24] WANG J H, TONG Y, ZHU Y, et al. The research progress in protein glycosylation[J]. Pharmaceutical Biotechnology, 2011, 18(1):77-80. (in Chinese)
王家红, 童玥, 朱玥, 等. 蛋白质糖基化的研究进展[J]. 药物生物技术, 2011, 18(1):77-80.
[25] LI W. Advances in the study of acidic fibroblast factors[J]. Science & Technology Information, 2010(22):493, 496. (in Chinese)
李伟. 酸性成纤维细胞因子的研究进展[J]. 科技信息, 2010(22):493, 496.
[26] ZHANG L Q, FU P, YI S F, et al. Role of fibroblast growth factor (FGF) in skeletal muscle development[J]. Animals Breeding and Feed, 2016(1):6-10. (in Chinese)
张力青, 付平, 易四凤, 等. 成纤维细胞生长因子(FGF)在骨骼肌发育中的作用[J]. 养殖与饲料, 2016(1):6-10.
[27] ARMAND A S, LAUNAY T, PARISET C, et al. Injection of FGF6 accelerates regeneration of the soleus muscle in adult mice[J]. Biochim Biophys Acta, 2003, 1642(1/2):97-105.
[28] HAN J K, MARTIN G R. Embryonic expression of Fgf-6 is restricted to the skeletal muscle lineage[J]. Dev Biol, 1993, 158(2):549-554.
[29] YIN T, KÖNIG S. Genome-wide associations and detection of potential candidate genes for direct genetic and maternal genetic effects influencing dairy cattle body weight at different ages[J]. Genet Sel Evol, 2019, 51(1):4.
[30] GHOREISHIFAR S M, ERIKSSON S, JOHANSSON A M, et al. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds[J]. Genet Sel Evol, 2020, 52(1):52.
[31] WEI Y L, GUO D S, BAI Y B, et al. Transcriptome analysis of mRNA and lncRNA related to muscle growth and development in Gannan yak and jeryak[J]. Int J Mol Sci, 2023, 24(23):16991.
[32] LI Q, WANG H H, LU Z K, et al. Association of the PDGF-D gene genetic variation with sheep tail traits[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(4):688-700. (in Chinese)
李青, 王慧华, 卢曾奎, 等. 绵羊PDGF-D基因多态性与尾型的关联[J]. 畜牧兽医学报, 2019, 50(4):688-700.
[33] WU S L, WANG Y T, DANG W Y, et al. Genetic diversity analysis of donkey populations in western Liaoning based on SSR molecular markers[J]. The Chinese Livestock and Poultry Breeding, 2023, 19(5):27-32. (in Chinese)
武师良, 王昱彤, 党婉怡, 等. 基于SSR分子标记的辽西地区驴群体遗传多样性分析[J]. 中国畜禽种业, 2023, 19(5):27-32.
[34] WANG P G, ZHANG J Q, JIA H C, et al. Development of KASP markers for soybean PRR family genes[J]. Soybean Science, 2023, 42(4):385-395. (in Chinese)
王培国, 张君权, 贾鸿昌, 等. 大豆PRR家族基因KASP标记的开发[J]. 大豆科学, 2023, 42(4):385-395.
[35] ZHANG Z C, LIU C, HAO W J, et al. Novel single nucleotide polymorphisms and haplotype of MYF5 gene are associated with body measurements and ultrasound traits in grassland short-tailed sheep[J]. Genes (Basel), 2022, 13(3):483.
[36] PENG X W, CHENG J L, LI H, et al. Whole-genome sequencing reveals adaptations of hairy-footed jerboas (Dipus, Dipodidae) to diverse desert environments[J]. BMC Biol, 2023, 21(1):182.
[37] PENG Y X, LIU J, ZHAO S Y, et al. Detection of SNPs in porcine RXRB gene and their association analysis with growth, fattening and reproduction traits[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(3):596-609. (in Chinese)
彭雅鑫, 刘军, 赵诗瑜, 等. 猪RXRB基因SNPs检测及其与生长育肥和繁殖性状的关联分析[J]. 畜牧兽医学报, 2021, 52(3):596-609.
[38] JO B S, CHOI S S. Introns:the functional benefits of introns in genomes[J]. Genomics Inform, 2015, 13(4):112-118.
[39] ELIZA L Y Y, YIE S Y, SAY Y H, et al. Deep intronic 9q21.11 polymorphism contributes to atopic dermatitis risk through methylation regulated expression of tight junction protein 2[J]. J Investig Allergol Clin Immunol, 2023.doi:10.18176/jiaci.0978.
[40] OROZCO G, HINKS A, EYRE S, et al. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23[J]. Hum Mol Genet, 2009, 18(14):2693-2699.
[41] ZHAO P F, HE Z H, XI Q M, et al. Variations in HIF-1α contributed to high altitude hypoxia adaptation via affected oxygen metabolism in tibetan sheep[J]. Animals (Basel), 2021, 12(1):58.
[42] DA Y. Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers[J]. BMC Genet, 2015, 16:144.
[43] YUAN Y M, JIANG H O, KUANG J Y, et al. Genetic variations in ADIPOQ gene are associated with chronic obstructive pulmonary disease[J]. PLoS One, 2012, 7(11):e50848.
[44] HU Y L. Study on the methods of genome multi-loci association analysis for complex trait[D]. Shanghai:Shanghai Jiao Tong University, 2009. (in Chinese)
胡艳玲. 复杂性状与基因组多位点的关联分析方法研究[D]. 上海:上海交通大学, 2009.

Biological Characterization of Chicken FGF6 Gene and Association of Its Polymorphisms with Economic Traits

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LEI Yanru, HU Xiaoyu, XU Chunhong, ZHANG Chenxi, DU Wenping, WANG Yangguang, LI Donghua, SUN Guirong, LI Wenting, KANG Xiangtao. Comparative Analysis of Growth, Carcass and Meat Quality Traits of Five Hybrid Combinations of Houdan Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1521-1535.
[2]	YANG Yang, YU Qian, LIU Yucheng, YANG Hua, ZHAO Zhuo, WANG Limin, ZHOU Ping, YANG Qingyong, DAI Rong. Identification and Tissue Expression Analysis of the Sheep MYL Gene Family [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1551-1564.
[3]	TIAN Rui, XU Sixiang, XIE Feng, LIU Guangjin, WANG Gang, LI Qingxia, DAI Lei, XIE Guoxin, ZHANG Qiongwen, LU Yajing, WANG Guangwen, WANG Jinxiu, ZHANG Wei. Bioinformatics Analysis of the Genome of Clostridium perfringens Isolated from Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1707-1715.
[4]	LUO Xiaoqin, GUO Zhiting, WANG He, ZHANG Jingyan, ZHANG Kang, WANG Lei, MA Yonghua, LI Jianxi. The Therapeutic Effect of Changshan Oral Liquid on Chicken Coccidiosis [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1747-1755.
[5]	SU Chuanchen, JIAO Jingya, WANG Yongshuai, LUO Pengna, CHANG Xinghai, HUANG Yanqun. Effect of Introducing 25% Rhode Island Red Chicken Blood on Related Indexes of Henan Fighting Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 1007-1018.
[6]	ZHENG Lin, WEI Bingdong, HUA Feng, CHEN Long, DING Yuan. Therapeutic Effect of Lytic Phage on Salmonella enteritidis Infection in Broilers [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 1314-1327.
[7]	ZHONG Xin, ZHANG Hui, ZHANG Chong, LIU Xiaohong. Research Progress on Genetic Breeding of Reproductive Performance in Sows [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(2): 438-450.
[8]	REN Yuwei, CHEN Xing, LIN Yanning, HUANG Xiaoxian, HONG Lingling, WANG Feng, SUN Ruiping, ZHANG Yan, LIU Hailong, ZHENG Xinli, CHAO Zhe. Investigating the Influencing Factors of Egg Laying Performance in Wenchang Chickens Based on Whole Genome Resequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(2): 502-514.
[9]	ZHU Xueli, ZHANG Longchao, WANG Lixian, PU Lei, LIU Xin. Association Analysis of AQP9 and RPS10 Gene Polymorphisms with Backfat Thickness in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 87-98.
[10]	TANG Xinxin, ZHENG Jumei, LUO Na, YING Fan, ZHU Dan, LI Sen, LIU Dawei, AN Bingxing, WEN Jie, ZHAO Guiping, LI Hegang. Genetic Mechanism of Broiler Leg Disease Based on Genome-Wide Association Analysis [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 99-109.
[11]	CHEN Yuetong, LIU Xiaohan, WANG Zhiyang, ZHAO Yuxin, ZHOU Tiezhong, HU Zengjin, ZHU Yue, WANG Shaohui, TIAN Mingxing, DING Siyu, QI Jingjing, YU Shengqing. Isolation, Identification, Pathogenicity and Drug Susceptibility of Mycoplasma gallisepticum from Dead Chicken Embryos in Large-scale Chicken Farms in Guangdong Province [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 290-299.
[12]	ZHENG Gang, LIAN Ling. Research Progress of Key Regulatory Gene DMRT1 in Chicken Sex Determination and Differentiation [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3152-3163.
[13]	BAI Lu, WANG Mengjie, MA Xiaochun, HE Zhengxiao, TAN Xiaodong, LIU Jie, ZHAO Guiping, WEN Jie, LIU Ranran. A Method for Quickly Mining the Characteristic SNP Markers Set of Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3252-3261.
[14]	CHEN Chun, KANG Zhaofeng, WEI Yue, LI Guanhong, WU Yanping, XIE Jinfang. Correlation of Wnt3a Gene Polymorphism with Skin Follicle Traits in Chongren Partridge Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2810-2823.
[15]	LIU Hang, WANG Huanhuan, GE Ying, ZHANG Lei, ZHANG Weiwu, WEI Yinghui, LI Qinghai, FAN Jinghui, ZHANG Xuedong. Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2320-2329.