全基因组选择信号鉴定高原型藏羊毛用性状候选基因及关联分析

doi:10.11843/j.issn.0366-6964.2024.12.017

摘要/Abstract

摘要：

旨在通过全基因组受选择区域信号检测结合单核苷酸多态性与性状关联分析鉴定出高原型藏羊羊毛性状新的分子标记和候选基因。本研究采集3~4周岁健康母羊耳组织与羊毛作为试验素材，其中高原型藏羊母羊119只，欧拉型藏羊母羊89只，总计208只。利用群体遗传分化指数(Fst)和碱基多样性比值(Pi Ratio)进行全基因组选择性清除分析，通过功能注释筛选候选基因，并进行GO和KEGG富集分析，对108只高原型藏羊进行候选基因外显子Sanger测序单核苷酸多态性与表型数据关联分析，鉴定出与羊毛性状相关的功能位点。分析结果表明：共有1 084个受选择区域，注释到1 037个候选基因；通过对功能基因的注释并结合文献分析，发现GHR、FGFR3、MC1R、MITF、FGF5、WNT2B和WNT5A等7个基因与羊毛性状有潜在关联，其中FGF5(exon6:c.954C/T: p.227P/P)同义突变位点和首次发现的FGFR3(exon6:c.1092C/T: p.364A/A)同义突变位点与羊毛纤维性能关联，并且2个位点均未偏离哈温平衡，这2个基因可能是高原型藏羊羊毛性状重要的候选基因。本研究发现有助于了解高原型藏羊羊毛性状的生产遗传基础，为该品种绵羊的分子育种技术提供参考，也为保护与利用地方优异种质遗传资源提供科学依据。

关键词: 高原型藏羊, 全基因组选择信号, 毛用性状, 关联分析

Abstract:

The objective of this study was to identify novel molecular markers and candidate genes associated with wool traits in plateau Tibetan sheep through a combination of genome-wide selected region signal detection, single nucleotide polymorphism analysis, and trait association analysis. In this study, ear tissue and wool samples were collected from 208 healthy ewes aged 3-4 years old, including 119 plateau-type ewes and 89 Euler-type ewes. Population genetic differentiation index (Fst) and base diversity ratio (Pi Ratio) were employed for genome-wide selective clearance analysis. Candidate genes were identified through functional annotation, followed by GO and KEGG enrichment analyses. Furthermore, correlation analysis between single nucleotide polymorphisms and phenotypic data was conducted using exon Sanger sequencing on a subset of 108 Tibetan plateau sheep to identify functional loci related to wool traits. The results revealed that a total of 1 084 selected regions with annotations for 1 037 candidate genes. Through functional gene annotation and literature analysis, 7 potential candidate genes related to wool traits were identified: GHR, FGFR3, MC1R, MITF, FGF5, WNT2B, and WNT5A. Notably, FGF5 (exon6:c.954C/T: p227P/P) synonymous mutation site and FGFR3 (exon6: c1092C/T: p364A/A) synonym mutation sites were found to be associated with wool fiber performance without deviation from Hardy-Weinberg equilibrium.These two genes may serve as important candidate genes for the improvement of wool traits in plateau Tibetan sheep.This study provides valuable insights into the genetic basis underlying the production of wool traits in plateau Tibetan sheep.It also offers guidance for molecular breeding techniques specific to this breed while providing a scientific foundation for the conservation and utilization of local germplasm resources.

Key words: Tibetan sheep, genome-wide selection signal, wool traits, association analysis

中图分类号:

S826.2

祁军英, 裴全帮, 张文魁, 徐腾, 左明星, 韩步鹰, 李雪, 刘德会, 王松, 周佰成, 赵凯, 田得红. 全基因组选择信号鉴定高原型藏羊毛用性状候选基因及关联分析[J]. 畜牧兽医学报, 2024, 55(12): 5511-5526.

QI Junying, PEI Quanbang, ZHANG Wenkui, XU Teng, ZUO Mingxing, HAN Buying, LI Xue, LIU Dehui, WANG Song, ZHOU Baicheng, ZHAO Kai, TIAN Dehong. Genome-wide Selective Signal Identification and Association Analysis of Candidate Genes for Tibetan Sheep Wool Traits[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5511-5526.

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SNP	正向引物 Forward primer	反向引物 Reverse primer	片段长度/bp Length	Tm/℃
FGF5	TTCCTCTAGGCCAAATTTAC	TAGTCCTCACCGTTGAACTT	641	60
FGFR3	TGCTGAAGACTCAACGAGGC	TCCAGCCCCATATTCATCAG	948	68

染色体 Chromosome	基因 Gene	编号 ID	描述 Description
6	FGF5	ENSOARG00020008615	fibroblast growth factor 5
6	FGFR3	ENSOARG00020023492	fibroblast growth factor receptor 3
19	MITF	ENSOARG00020020821	melanocyte inducing transcription factor
14	MC1R	ENSOARG00020003524	melanocortin 1 receptor
16	GHR	ENSOARG00020006196	growth hormone receptor
1	WNT2B	ENSOARG00020013948	Wnt family member 2B
19	WNT5A	ENSOARG00020020359	Wnt family member 5A

数量 (N) Number	基因 Gene	染色体 Chromosome	外显子 Exon	长度/bp Length	基因纯合度 (Ho) Gene homogeneity	基因杂合度 (He) Gene heterozygosity	有效等位基因数 (Ne) Effective number of alleles	多态信息含量 (PIC) Polymorphism information content	P
108	FGF5	6	3	1 742	0.510	0.493	1.970	0.371	0.722
108	FGFR3	6	10	2 589	0.480	0.467	1.878	0.358	0.797

数量 Number	基因 Gene	基因型频率 Genotype frequency			等位基因频率 Allele frequency		X²	P
数量 Number	基因 Gene	TT	CT	CC	T	C	X²	P
108	FGF5	0.31	0.50	0.19	0.56	0.44	16.22	0.000 3
108	FGFR3	0.39	0.48	0.13	0.63	0.37	21.56	0.000 02

性状 Trait	Mean±SE			P
性状 Trait	TT (n=34)	CT (n=54)	CC (n=20)	P
羊绒长度/mm Cashmere length	106.74±14.28	107.76±17.84	115.35±19.48	0.169
羊毛长度/mm Wool length	241.26±47.78^A	253.39±53.92^A	308.7±33.29^B	0.000 009
羊绒细度/μm Cashmere fineness	24.98±2.30^A	25.98±2.47^AB	27.20±3.53^B	0.013
羊毛细度/μm Wool fineness	46.17±4.84^A	46.66±6.03^A	53.19±5.87^B	0.000 028
有髓毛含量/% Medullary content	22.49±14.30^A	28.19±17.24^AB	36.08±22.27^B	0.025
无髓毛含量/% Non-medullary content	60.77±15.09^A	51.28±12.99^BCa	43.74±15.09^BCb	0.000 113
两型毛含量/% Two types of hair content	9.32±9.03^a	16.59±14.46^bc	17.91±19.49^bc	0.035
干死毛含量/% Dry dead hair content	7.15±9.40	4.39±8.54	2.28±4.45	0.098
断裂强力/N Breaking force	36.46±13.03	35.00±13.25	39.89±9.86	0.339
断裂强度/(N·ktex^-1) Breaking strength	56.96±21.34	55.38±22.07	62.82±18.20	0.408
断裂伸长率/% Elongation at break	14.32±4.40	14.27±4.37	15.93±3.99	0.312
洗净率/% Cleaning rate	86.36±7.96	86.19±7.66	84.06±8.38	0.530