敖汉细毛羊羊毛经济性状的全基因组关联分析

doi:10.11843/j.issn.0366-6964.2024.10.010

摘要/Abstract

摘要：

旨在利用全基因组关联分析探寻敖汉细毛羊羊毛性状新的分子标记和候选基因。本研究采集1~2周岁的健康敖汉细毛羊耳组织与羊毛作为试验素材，其中，母羊248只，公羊81只，总计329只。羊毛进行性状测定(包括纤维直径、自然长度、伸直长度、伸直率)，并对表型数据进行描述性统计和相关性分析。利用绵羊40K液相SNP芯片对全部个体进行基因分型。使用Plink 1.07软件对芯片数据进行质控，使用GCTA软件和PopLDdecay软件对质控数据进行群体结构分析。利用GMEMA混合线性模型对4种羊毛性状进行了全基因组关联分析(genome-wide association study，GWAS)，利用在线软件对候选基因进行GO和KEGG富集分析。质控后得到329只个体的30 079个SNPs位点用于后续分析。通过GWAS分析筛选出4个在全基因组上显著相关的SNPs位点可能影响羊毛经济性状，分别位于1号、6号及8号染色体上。筛选出9个在染色体水平上显著相关的SNPs位点可能对羊毛性状具有潜在意义，分别位于3、5、8、11、18、21、22、25号染色体，寻找到39个可能影响羊毛性状的候选基因。本研究结果为后续探究敖汉细毛羊羊毛性状的遗传机制及分子育种标记开发提供重要参考。

关键词: 敖汉细毛羊, 羊毛性状, 全基因组关联分析, 候选基因

Abstract:

The study aimed to identify new molecular markers and candidate genes for wool traits in Aohan fine wool sheep using genome-wide association study. The ear tissue and wool of 1-2 years old healthy Aohan fine wool sheep were collected as experimental materials, 248 ewes and 81 rams, totaling 329. The wool traits were detected (including fiber diameter, natural length, elongation length, and elongation ratio), and the phenotypic data were subjected to descriptive statistics and correlation analysis. All individuals were genotyped using the 40K liquid phase SNP chip for sheep. The chip data were quality controlled using PLINK 1.07 software, and the quality-controlled data were analyzed for population structure using GCTA software and PopLDdecay software. The GMEMA mixed linear model was used to perform a genome-wide association study (GWAS) on 4 wool traits, and online software was used to conduct GO and KEGG enrichment analyses on candidate genes. After quality control, 329 individuals with 30 079 SNP loci were used for subsequent analysis. Through GWAS analysis, 4 SNP loci were identified as significantly associated with wool economic traits across the genome, located on chromosomes 1, 6, and 8. Additionally, 9 SNP loci were identified as significantly associated with wool traits at the chromosome level, located on chromosomes 3, 5, 8, 11, 18, 21, 22, and 25, and 39 candidate genes were identified as potentially affecting wool traits. The results of this study provide important references for further exploring the genetic mechanisms and molecular breeding markers of wool traits in Baohan fine wool sheep.

Key words: Aohan fine wool sheep, wool traits, genome-wide association study, candidate gene

中图分类号:

S826.2

林晓坤, 都萌萌, 周李生, 黄振刚, 王頔, 周东辉, 曹欣欣, 贺建宁, 赵金山, 李和刚. 敖汉细毛羊羊毛经济性状的全基因组关联分析[J]. 畜牧兽医学报, 2024, 55(10): 4346-4359.

Xiaokun LIN, Mengmeng DU, Lisheng ZHOU, Zhengang HUANG, Di WANG, Donghui ZHOU, Xinxin CAO, Jianning HE, Jinshan ZHAO, Hegang LI. Genome-Wide Association Study of Wool Economic Traits in Aohan Fine Wool Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4346-4359.

图/表 11

表 1

图 1

图 2

图 3

图 4

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表 2

表 3

4种羊毛性状相关候选基因信息"

性状 Trait	候选基因 Candidate gene	染色体 Chromosome	基因位置 Gene location	基因功能 Gene function
纤维直径	TTC14	1	207206481-207216314	四肽重复结构域14
Fiber diameter	PEX5L	1	207822971-208123012	过氧化物酶体生物发生因子5like
	SORCS3	22	24906767-25561739	sortilin相关VPS10结构域，含受体3
	RAB38	21	7038110-7103501	RAB38，RAS癌基因家族成员
	LAMP3	1	204736807-204768779	溶酶体相关膜蛋白3
	MCF2L2	1	204444714-204732827	MCF.2细胞系衍生的转化序列样2
	CCSER2	25	38308913-38471583	卷曲螺旋富含丝氨酸的蛋白2
	MCCC1	1	204782521-204835946	甲基巴豆酰辅酶A羧化酶亚基1
	CTSC	21	6903530-6946938	组织蛋白酶C
	LOC121817525	21	6905340-6909181	未注释
	B3GNT5	1	204616280-204633302	UDP-GlcNAc：βGal-β-1, 3-N-乙酰氨基葡萄糖转移酶5
	LOC101103203	1	204557231-204633105	LINE-1逆转录转座元件ORF2蛋白
	LOC101114083	25	38590609-38591984	大核糖体亚基蛋白uL4样
	LOC121816833	1	204742573-204782381	未注释
	TRNAG-CCC	25	39009860-39009930	转移RNA甘氨酸(反密码子CCC)
	TRNAE-UUC	21	6973404-6973477	转移RNA谷氨酸(反密码子UUC)
自然长度	RPTOR	11	51177578-51498963	MTOR复合物1的调节相关蛋白
Natural length	ENDOV	11	51502682-51606025	核酸内切酶V
	DNAH6	3	56369583-56658741	动力蛋白轴突重链6
	SUCLG1	3	51243758-55249958	编码异二聚酶琥珀酸辅酶A连接酶的α亚单位
伸直长度	ATG5	8	30899311-31078799	自噬相关5
Elongation length	PRDM1	8	31122682-31145193	PR/SET域1
	CRYBG1	8	30674397-30900029	含有1个晶体蛋白β-γ结构域
	LOC114116251	8	30756462-30756568	U6剪接体RNA
	LOC105611045	8	31060111-31060993	小核糖体亚基蛋白eS1样
	LOC114116256	8	30877462-30877568	U6剪接体RNA
伸直率	MSX1	6	104950903-104955183	MSH同源盒1
Elongation rate	TRNAY-GUA	6	105056806-105056878	转移RNA酪氨酸(反密码子GUA)
	ERAP2	5	93929009-93975030	内质网氨肽酶2
	LNPEP	5	93989905-94095313	亮氨酰和半胱氨酸氨基肽酶
	NUBPL	18	39830178-40060069	NUBP铁硫簇组装因子，线粒体
	LOC132658121	18	40026308-40029156	5-羟色胺受体1D样
	NPAS3	18	41081921..42048771	神经元PAS结构域蛋白3
	STX18	6	105262592-105380010	突触融合蛋白18
	ZBTB49	6	105467844-105494203	锌指和BTB结构域含有49
	NSG1	6	105379653-105413849	神经元囊泡运输相关1
	TRNAC-ACA	6	105278250-105278322	转移RNA半胱氨酸(反密码子ACA)
	TRNAS-GGA	18	41753552-41753623	转移RNA丝氨酸(反密码子GGA)
	LOC132659842	5	94094403-94098907	未注释

表 3

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图 8

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性状 Trait	平均值 Mean	标准差 Standard deviation	最大值 Maximum	最小值 Minimum	标准误 Standard error	变异系数 Coefficient of variation
纤维直径/μm Fiber diameter	19.633	2.248	28.124	12.935	0.124	0.115
自然长度/cm Natural length	7.643	0.562	11.758	5.913	0.031	0.074
伸直长度/cm Elongation length	10.150	0.550	4.800	7.950	0.030	0.054
伸直率/% Elongation rate	0.331	0.061	0.612	0.167	0.003	0.183

性状Trait	染色体Chromosome	位置Location	P值P-value
纤维直径Fiber diameter	1^*	204762729^*	2.71×10^-5*
	21	6974831	6.25×10^-5
	25	39039643	7.88×10^-5
	22	25513088	8.52×10^-5
自然长度Natural length	11	51282011	5.29×10^-5
	3	55043579	5.38×10^-5
伸直长度Elongation length	8^*	30842589^*	7.05×10^-7*
	8^*	30837398^*	1.40×10^-5*
	8	30838595	4.26×10^-5
	8	30839612	4.26×10^-5
伸直率Elongation rate	6^*	103863192^*	3.68×10^-5*
	18	41285606	6.97×10^-5
	5	102267048	7.98×10^-5

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