山羊<i>FN</i>1基因InDel位点鉴定及其与生长性状的关联性分析

吴贤锋; 刘远; 王迎港; 张富; 李文杨

doi:10.19303/j.issn.1008-0384.2023.01.001

山羊FN1基因InDel位点鉴定及其与生长性状的关联性分析

doi: 10.19303/j.issn.1008-0384.2023.01.001

福建省农业科学院畜牧兽医研究所，福建　福州　350013

基金项目: 福建省科技计划公益类专项（2020R10260012、2020R10260014）

详细信息

作者简介:
吴贤锋（1990−），男，硕士，助理研究员，研究方向：动物遗传育种（E-mail：wuxianfeng3080@163.com）

通讯作者:
李文杨（1972−），男，硕士，副研究员，研究方向：动物遗传育种（E-mail：Wy369@sina.com）

中图分类号: S 828.2
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出版历程
- 收稿日期: 2022-05-18
- 修回日期: 2022-12-04
- 网络出版日期: 2023-03-06
- 刊出日期: 2023-01-28

Relationship between InDel Polymorphism of FN1 Gene and Growth Traits of Goats

Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian　350013, China

摘要

摘要: 目的转录组候选基因纤维连接蛋白1（Fibronectin 1，FN1）对于骨分化、骨形成和骨细胞迁移起关键作用。对FN1基因预测突变位点进行DNA池检测，并与山羊生长性状进行关联分析，以期为山羊的遗传育种和性状改良提供分子标记。方法利用DNA池检测和PCR-RFLP技术，分析福清山羊、努比亚黑山羊和简阳大耳羊中FN1基因的7个预测突变位点的遗传多态性，并与其生长性状进行关联分析。结果通过DNA池检测和PCR-RFLP发现，7个预测位点中只有Del66652位点存在多态性，且在3个山羊群体中都只存在II和ID基因型，都不处于哈迪温伯格平衡（P＞0.05），多态性信息含量小于0.25。关联分析发现，努比亚黑山羊ID基因型个体的管围显著优于II基因型（P＜0.05），ID基因型的胸围指数极显著优于II基因型（P＜0.01）。简阳大耳羊ID基因型个体的胸围指数和管围指数显著优于II基因型（P＜0.05）。结论 Del66652位点与努比亚山羊和简阳大耳羊的生长性状显著相关，且ID基因型为优势基因型。Del66652位点可作为影响山羊生长性状的分子标记位点，为提高山羊生长性状的品种改良提供研究基础。
- 山羊 /
- FN1基因 /
- 插入缺失(InDel) /
- 生长性状 /
- 关联分析
Abstract: Objective Detection of fibronectin 1 (FN1) gene in DNA pool and association of the gene InDel polymorphism with bone differentiation, formation, and cell migration of goats were studied to locate the molecular marker and to confirm target for breeding and trait improvement. Method Genetic polymorphisms of the FN1 gene in Fuqing, Nubian, and Jianyang Daer goats were detected in the DNA pool with PCR-RFLP. Relationship between the genotypes and meat production traits of the goats were analyzed. Result Among the 7 predicted sites in all 3 goat species, only Del66652 locus exhibited a polymorphism belonging to the II and ID genotypes with a frequency not in HWE (P＞0.05) and less than 0.25 on the polymorphism information content. The cannon circumference of the ID genotype was significantly greater than that of the II genotype (P＜0.05), while the chest circumference index of the ID genotype significantly greater than that of the II genotype (P＜0.01) in the Nubian goats. In the Jianyang Daer goats, the chest circumference and the cannon circumference indices of the ID genotype were significantly greater than those of the II genotype (P＜0.05). Conclusion Del66652 locus significantly correlated with the growth traits of Nubian and Jianyang Daer goats with the ID being the dominant genotype. The locus closely associated with the growth traits of the goats and was considered a candidate molecular marker to be use in breeding programs.
- Goat /
- FN1 gene /
- Insertion/Deletion (InDel) /
- growth trait /
- association analysis

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图 1 FN1基因7个位点测序峰图（a—g）和Del66652位点琼脂糖凝胶电泳图（h）

Figure 1. Sequencing chromes of 7 loci (a—g) and electrophoresis of Del66652 locus (h) of FN1 gene

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表 1 引物信息

Table 1. Information on primer

引物 Primer	引物序列（5′-3′） Sequence of primer（5′-3′）	退火温度 Temperature/℃	产物大小 Product size/bp	检测位点 Identified site
P1	TGCAAACTCAACTGTTTTCAAGGG	62	268	Del3837
P1	CGTTTAAATGAAGGTGGGCTGT	62	268	Del3837
P2	GGCTGAGGTGGTAACAATGGA	61	651	11697A＞T
P2	GCACTGGAGGGCTTTTCCTT	61	651	11697A＞T
P3	CACGTGGAACTTTCTTCTTACCC	59.5	204	Del29318
P3	GGCTGACTTTGATCCTGTGGAA	59.5	204	Del29318
P4	AGTCACTGATATTCCACTACTTCCT	61	268	Del50927
P4	GCAAAAAGCCTAGATTTTGTACATT	61	268	Del50927
P5	AGATTGGAGAGAAGTGGGATC	60	299	65122G＞A
P5	CGGAGAAGTGCTAAAGTGCC	60	299	65122G＞A
P6	ACCAGATCTTAGACAACATGAAGA	62	257	Del62401
P6	GAGGGCGCCTTTTGCTTTTAAT	62	257	Del62401
P7	TGCCAGTACTTCTCAACCATTTCT	60	291	Del66652
P7	TGGGTACCTGCAACTGGCTA	60	291	Del66652

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表 2 山羊FN1基因InDel位点基因型频率和等位基因频率

Table 2. Genotypic and allelic frequencies of InDel polymorphism of FN1 gene in goat

位点 Locus	品种(数量) Breeds (Amount)	基因型频率 Genotypic frequencies/%		基因频率 Allelic frequencies/%		纯合性 Ho	杂合性 He	有效等位基因数 Ne	多态信息含量 PIC	哈代-温伯格平衡 HWE P value
位点 Locus	品种(数量) Breeds (Amount)	ID	II	D	I	纯合性 Ho	杂合性 He	有效等位基因数 Ne	多态信息含量 PIC	哈代-温伯格平衡 HWE P value
Del66652	FQ (n=118)	0.076(9)	0.924(109)	0.038	0.927	0.927	0.073	1.079	0.071	P＜0.05
	NB (n=141)	0.028 (4)	0.972(137)	0.014	0.986	0.972	0.028	1.029	0.028	P＜0.05
	JY (n=120)	0.050 (6)	0.950 (114)	0.025	0.975	0.951	0.049	1.051	0.048	P＜0.05

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表 3 FN1基因InDel位点与山羊生长性状关联分析

Table 3. Association between the InDel loci of the FN1 gene and growth traits in goat

品种 Breeds	生长性状 Growth traits	基因型 Genotype
品种 Breeds	生长性状 Growth traits	II	ID
福清山羊 FQ	体重 Body weight/kg	30.68 ±0.65	29.68 ±1.92
	体高 Body height/cm	55.10 ±0.38	55.22 ±0.62
	体长 Body length/cm	55.10 ±0.44	53.68 ±0.93
	胸围 Chest circumference/cm	73.57 ±0.61	73.64 ±1.78
	胸宽 Chest width/cm	16.50 ±0.18	16.60 ±0.55
	胸深 Chest depth/cm	30.16 ±0.34	30.39 ±1.00
	管围 Cannon circumference/cm	7.45 ±0.06	7.47 ±0.20
	尻宽 Huckle bone width /cm	14.92 ±0.14	15.59 ±0.55
	体躯指数 Trunk index	133.85 ±0.98	137.37 ±3.41
	体长指数 Body length index	100.29 ±0.86	97.24 ±1.61
	胸围指数 Chest circumference index	133.76 ±1.04	133.48 ±3.49
	管围指数 Cannon circumference index	13.55 ±0.11	13.53 ±0.34
	髋骨指数 Huckle bone width index	110.94 ±1.08	106.79 ±2.68
努比亚山羊 NB	体重 Body weight/kg	48.96±0.94	57.40±8.34
	体高 Body height/cm	71.25±0.48	74.00±4.20
	体长 Body length/cm	64.55±0.47	69.80±1.23
	胸围 Chest circumference/cm	85.91±0.72	94.33±4.71
	胸宽 Chest width/cm	21.03±0.35	22.55±2.51
	胸深 Chest depth/cm	34.01±0.40	37.58±3.89
	管围 Cannon circumference/cm	9.85±0.29b	10.09±0.62a
	尻宽 Huckle bone width /cm	17.60±0.19	20.03±1.27
	体躯指数 Trunk index	133.34±0.91	135.05±5.42
	体长指数 Body length index	90.81±0.59	95.05±4.56
	胸围指数 Chest circumference index	120.61±0.66B	127.63±0.89A
	管围指数 Cannon circumference index	14.20±0.90	13.38±0.54
	髋骨指数 Huckle bone width index	119.77±1.63	112.33±8.28
简阳大耳羊 JY	体重 Body weight/kg	34.13±0.73	34.38±3.89
	体高 Body height/cm	62.47±0.49	60.67±2.27
	体长 Body length/cm	57.56±0.50	56.40±2.15
	胸围 Chest circumference/cm	74.80±0.57	77.37±2.58
	胸宽 Chest width/cm	17.40±0.16	17.17±0.71
	胸深 Chest depth/cm	29.65±0.30	29.83±1.07
	管围 Cannon circumference/cm	7.72±0.08	7.82±0.27
	尻宽 Huckle bone width /cm	14.06±0.18	13.62±0.85
	体躯指数 Trunk index	130.30±0.71	132.45±2.99
	体长指数 Body length index	92.21±0.51	93.02±1.48
	胸围指数 Chest circumference index	120.05±0.80b	127.67±1.52a
	管围指数 Cannon circumference index	12.35±0.11b	13.49±.31a
	髋骨指数 Huckle bone width index	125.26±1.45	127.12±4.23
不同大、小写字母表示不同基因型之间差异极显著（P＜0.01）或差异显著（P＜0.05）。 Different uppercase or lowercase letters indicate extremely significant difference (P＜0.01) or significant difference (P＜0.05).

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参考文献(20)

[1]	刘远, 李文杨, 吴贤锋, 等. 福清山羊与努比亚黑山羊背最长肌比较转录组分析 [J]. 中国农业科学, 2019, 52(14):2525−2537. doi: 10.3864/j.issn.0578-1752.2019.14.011 LIU Y, LI W Y, WU X F, et al. Transcriptome analysis of differentially gene expression associated with longissimus Doris tissue in Fuqing goat and Nubian black goat [J]. Scientia Agricultura Sinica, 2019, 52(14): 2525−2537.(in Chinese) doi: 10.3864/j.issn.0578-1752.2019.14.011
[2]	GOOSSENS K, VAN SOOM A, VAN ZEVEREN A, et al. Quantification of fibronectin 1 (FN₁) splice variants, including two novel ones, and analysis of integrins as candidate FN₁ receptors in bovine preimplantation embryos [J]. BMC Developmental Biology, 2009, 9: 1. doi: 10.1186/1471-213X-9-1
[3]	MARCONI G D, FONTICOLI L, DELLA ROCCA Y, et al. Human periodontal ligament stem cells response to titanium implant surface: Extracellular matrix deposition [J]. Biology, 2021, 10(9): 931. doi: 10.3390/biology10090931
[4]	ALVES R D A M, EIJKEN M, SWAGEMAKERS S, et al. Proteomic analysis of human osteoblastic cells: Relevant proteins and functional categories for differentiation [J]. Journal of Proteome Research, 2010, 9(9): 4688−4700. doi: 10.1021/pr100400d
[5]	ZHANG H L, CHEN X, XUE P, et al. FN1 promotes chondrocyte differentiation and collagen production via TGF-β/PI3K/Akt pathway in mice with femoral fracture [J]. Gene, 2021, 769: 145253. doi: 10.1016/j.gene.2020.145253
[6]	STUCZYŃSKA A, PIÓRKOWSKA K, TYRA M, et al. The effect of QTL-rich region polymorphisms identified by targeted DNA-seq on pig production traits [J]. Molecular Biology Reports, 2018, 45(3): 361−371. doi: 10.1007/s11033-018-4170-3
[7]	ZHANG W, KROSCHER K A, MURRAY R L, et al. Dietary calcium and phosphorus amounts affect development and tissue-specific stem cell characteristics in neonatal pigs [J]. The Journal of Nutrition, 2020, 150(5): 1086−1092. doi: 10.1093/jn/nxaa011
[8]	SOARES R A N, VARGAS G, MUNIZ M M M, et al. Differential gene expression in dairy cows under negative energy balance and ketosis: A systematic review and meta-analysis [J]. Journal of Dairy Science, 2021, 104(1): 602−615. doi: 10.3168/jds.2020-18883
[9]	GILBERT R P, BAILEY D R, SHANNON N H. Linear body measurements of cattle before and after 20 years of selection for postweaning gain when fed two different diets [J]. Journal of Animal Science, 1993, 71(7): 1712−1720. doi: 10.2527/1993.7171712x
[10]	吴贤锋, 王金宝, 刘远, 等. 基于转录组测序的ITGAD基因InDel位点鉴定及其与山羊生长性状的关联性分析 [J]. 农业生物技术学报, 2022, 30(9):1763−1770. doi: 10.3969/j.issn.1674-7968.2022.09.010 WU X F, WANG J B, LIU Y, et al. Identification of InDel locus of ITGAD gene based on transcriptome sequencing and its association with goat(Capra hircus) growth traits [J]. Journal of Agricultural Biotechnology, 2022, 30(9): 1763−1770.(in Chinese) doi: 10.3969/j.issn.1674-7968.2022.09.010
[11]	LI W Y, LIU Y, GAO C F, et al. A novel duplicated insertion/deletion (InDel) of theCPT1a gene and its effects on growth traits in goat [J]. Animal Biotechnology, 2021, 32(3): 343−351. doi: 10.1080/10495398.2019.1698433
[12]	KLINKENBERG E, ONWONA-AGYEMAN K A, MCCALL P J, et al. Cohort trial reveals community impact of insecticide-treated nets on malariometric indices in urban Ghana [J]. Transactions of the Royal Society of Tropical Medicine and Hygiene, 2010, 104(7): 496−503. doi: 10.1016/j.trstmh.2010.03.004
[13]	YAN H L, JIANG E H, ZHU H J, et al. The novel 22 bp insertion mutation in a promoter region of the PITX2 gene is associated with litter size and growth traits in goats [J]. Archives Animal Breeding, 2018, 61(3): 329−336. doi: 10.5194/aab-61-329-2018
[14]	NYMAN L R, COX K B, HOPPEL C L, et al. Homozygous carnitine palmitoyltransferase 1a (liver isoform) deficiency is lethal in the mouse [J]. Molecular Genetics and Metabolism, 2005, 86(1/2): 179−187.
[15]	SEEVAGAN M, JEICHITRA V, RAJENDRAN R, et al. Detection of lethal SNP (A781G) in growth hormone (GH) gene of Indian sheep [J]. Small Ruminant Research, 2015, 126: 13−15. doi: 10.1016/j.smallrumres.2015.03.003
[16]	WU X F, JIA W C, ZHANG J J, et al. Determination of the novel genetic variants of goat STAT5A gene and their effects on body measurement traits in two Chinese native breeds [J]. Small Ruminant Research, 2014, 121(2/3): 232−243.
[17]	BERULAVA T, HORSTHEMKE B. The obesity-associated SNPs in intron 1 of the FTO gene affect primary transcript levels [J]. European Journal of Human Genetics, 2010, 18(9): 1054−1056. doi: 10.1038/ejhg.2010.71
[18]	REN F, YU S, CHEN R, et al. Identification of a novel 12-bp insertion/deletion (indel) of iPS-related Oct4 gene and its association with reproductive traits in male piglets [J]. Animal Reproduction Science, 2017, 178: 55−60. doi: 10.1016/j.anireprosci.2017.01.009
[19]	WANG Z, ZHANG X, JIANG E, et al. InDels within caprine IGF₂BP₁ intron 2 and the 3'-untranslated regions are associated with goat growth traits [J]. Animal Genetics, 2020, 51(1): 117−121. doi: 10.1111/age.12871
[20]	VAN LAERE A S, NGUYEN M, BRAUNSCHWEIG M, et al. A regulatory mutation in IGF₂ causes a major QTL effect on muscle growth in the pig [J]. Nature, 2003, 425(6960): 832−836. doi: 10.1038/nature02064