湖羊群体结构分析与经济性状相关选择信号检测

doi:10.11843/j.issn.0366-6964.2025.05.017

摘要/Abstract

摘要：

旨在对湖羊SNP芯片基因分型结果进行选择信号检测，探索湖羊的种群结构，挖掘与湖羊重要经济性状相关的候选基因，为进一步创新利用湖羊品种提供理论基础。本研究对高繁殖湖羊群体中396只个体(320只母羊、76只公羊)使用绵羊50K SNP芯片进行基因分型。经质控后对所选湖羊群体进行主成分分析与亲缘关系评估。通过整合单倍体型得分(iHS)、中性检验统计量(Tajima’s D)、复合似然比检验(CLR)和连续性纯合片段(ROH)四种选择信号方法综合筛选候选区域并进行基因注释，通过GO-KEGG富集分析、NCBI数据库、检索文献及GWAS ATLAS数据库确定候选基因的功能。主成分分析结果显示，大部分湖羊个体集中分布，亲缘关系结果表明湖羊个体间亲缘关系较远，湖羊群体平均近交指数F_ROH=0.010 3，表明湖羊种群近交水平较低，同时ROH分析结果显示绝大多数ROH片段为 < 10 Mb的短ROH片段，说明湖羊在较远世代发生过近交。设置群体内iHS、Tajima ’s D、CLR以及ROH结果的top5%为受选择区域，共找到45.86 Mb的候选区域，约占绵羊参考基因组的1.75%。经基因注释后iHS检测到1 424个基因，Tajima ’s D检测到760个基因，CLR检测到964个基因，ROH检测到647个基因，取两种及以上方法得到的基因交集部分挖掘到337个候选基因。GO-KEGG富集结果显示，GO分析富集(P < 0.05)到角质化、中间长丝组织和骨骼系统发育等条目，KEGG分析富集(P < 0.05)到ECM受体相互作用、致心律失常性右心室心肌病与GnRH分泌等通路。功能注释发现65个与重要经济性状相关的候选基因，其中大部分候选基因与生长和繁殖性状相关。本试验对湖羊高繁单群体进行分析，筛选出与湖羊生长性状相关的基因包括：初生重(CAPN3、ERLEC1、LAP3)、骨骼发育(ACAN、COL5A2、HAPLN1、HAPLN3)、肌肉发育(FLVCR1、MUSTN1、PDLIM5)、饲料转化率与采食量(PLIN1、CCSER1、LAP3)和体尺(CSMD3、GPC6、LCORL)等，与湖羊繁殖性状相关的基因包括产羔数(BMPR1B、GPRIN3、HCRTR1、MEPE、MAST4)等，以及与其他经济性状相关的基因，对提升湖羊品种选育效率，优化绵羊品种选育方法提供了一定的理论依据和技术支撑。

关键词: 选择信号, 湖羊, 经济性状, 候选基因

Abstract:

The purpose of this study was to detect the selection signal of SNPs microarray genotyping results of Hu sheep, explore the population structure of Hu sheep, and mine candidate genes related to important economic traits of Hu sheep, so as to provide a theoretical basis for further innovation and utilization of Hu sheep breeds. The total of 396 individuals (320 ewes and 76 rams) from the high breeding Hu sheep population were genotyped using sheep 50K SNP chip. After quality control, the selected Hu sheep populations were analyzed by principal component analysis and genetic relationship evaluation. The candidate regions were comprehensively screened and annotated by integrating haplotype score (IHS), neutral test statistic (Tajima 's D), composite likelihood ratio test (CLR) and continuous homozygous fragment (ROH). The functions of candidate genes were determined by GO-KEGG enrichment analysis, NCBI database, literature retrieval and GWAS ATLAS database. The results of principal component analysis showed that most Hu sheep individuals were concentrated in distribution, and the results of genetic relationship showed that the relationship between Hu sheep individuals was far, and the average inbreeding index of Hu sheep population was F_ROH=0.010 3, indicating that the inbreeding level of Hu sheep population was low. At the same time, the results of ROH analysis showed that the vast majority of ROH fragments were short ROH fragments < 10 Mb, indicating that Hu sheep had been inbred in the distant generation. Set the top 5% of IHS, Tajima 's D, CLR and ROH results in the population as the selected region, and a total of 45.86 MB candidate regions were found, accounting for about 1.75% of the sheep reference genome. After gene annotation, 1 424 genes were detected by iHS, 760 genes were detected by Tajima 's D, 964 genes were detected by CLR, 647 genes were detected by ROH, and 337 candidate genes were mined from the gene intersection obtained by two or more methods. GO-KEGG enrichment results showed that GO analysis enriched (P < 0.05) to items such as keratinization, intermediate filament tissue and skeletal system development, and KEGG analysis enriched (P < 0.05) to pathways such as ECM receptor interaction, arrhythmogenic right ventricular cardiomyopathy and GnRH secretion. Functional annotation found 65 candidate genes related to important economic traits, most of which were related to growth and reproduction traits. This experiment analyzed the high breeding single population of Hu sheep, and screened out the genes related to the growth traits of Hu sheep, including birth weight (CAPN3、ERLEC1、LAP3), bone development (ACAN、COL5A2、HAPLN1、HAPLN3), muscle development (FLVCR1、MUSTN1、PDLIM5), feed conversion rate and feed intake (PLIN1、CCSER1、LAP3) and body size (CSMD3、GPC6、LCORL). The genes related to the reproductive traits of Hu sheep included litter size (BMPR1B、GPRIN3、HCRTR1、MEPE、MAST4).And the genes related to other economic traits provide a certain theoretical basis and technical support for improving the breeding efficiency of Hu sheep breeds and optimizing the breeding methods of sheep breeds.

Key words: selection signal, Hu sheep, economic traits, candidate gene

中图分类号:

S826.2

孙国欣, 李蕴华, 赛音, 郭文华, 赵艳红, 张满新, 刘佳森. 湖羊群体结构分析与经济性状相关选择信号检测[J]. 畜牧兽医学报, 2025, 56(5): 2168-2181.

SUN Guoxin, LI Yunhua, SAI Yin, GUO Wenhua, ZHAO Yanhong, ZHANG Manxin, LIU Jiasen. Population Structure Analysis and Economic Traits Related Selection Signal Detection of Hu Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(5): 2168-2181.

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基因 Gene	染色体 Chromosome	检测方法 Test method	相关性状 Related trait	参考文献 Reference
ACAN	18	ROH、Tajima’s D	骨骼发育	^[30]
CSMD3	9	iHS、ROH、Tajima’s D	体尺	^[35]^[36]
CCSER1	6	iHS、ROH	采食量	^[42]
CAPN3	7	iHS、CLR	初生重	^[52]
COL5A2	2	iHS、ROH	骨骼发育与皮肤发育	^[31]
ERLEC1	3	iHS、CLR、ROH	初生重	^[37]
FLVCR1	12	iHS、ROH	肌肉发育	^[45]
FAM184B	6	iHS、ROH	14月龄体重	^[38]^[39]
GALNTL6	2	iHS、CLR、ROH	平均日增重	^[15]
GPC6	10	iHS、Tajima’s D	体尺	^[53]
HAPLN1	5	iHS、CLR	骨骼发育	无
HAPLN3	18	ROH、Tajima’s D	骨骼发育	无
IBSP	6	iHS、ROH、Tajima’s D	眼肌面积	^[15]
LAP3	6	iHS、ROH	初生重、采食量	^[42]^[43]
LCORL	6	iHS、ROH	体尺	^[8]
MED28	6	iHS、ROH	宰前活重	^[43]
MUSTN1	19	ROH、Tajima’s D	肌肉发育	^[54]
PLIN1	18	iHS、ROH	饲料转化率	^[44]
PDE9A	1	iHS、CLR	肠胃发育	^[55]
PDLIM5	6	iHS、ROH	肌肉发育	^[46]
STRN3	18	iHS、CLR	肥尾发育	^[56]
SUCLG2	19	CLR、Tajima’s D	能量代谢	^[57]
SLC13A1	4	iHS、Tajima’s D	软骨发育	^[58]

基因 Gene	染色体 Chromosome	检测方法 Test method	相关性状 Related trait	参考文献 Reference
SPP1	6	iHS、ROH、Tajima’s D	卵细胞发育与受精	^[38]
CACNA1D	19	CLR、ROH	受胎率	^[33]
KCNN3	1	iHS、ROH	早产	^[34]
ABHD2	18	iHS、ROH、Tajima’s D	精液品质	^[40]
PPM1K	6	iHS、ROH	引发多囊卵巢综合征	^[47]
ADGRB3	9	iHS、ROH	胚胎发育	^[48]
BMPR1B	6	iHS、ROH	产羔数的主效基因	^[29]
CDCA7	2	iHS、CLR	高排卵	^[49]
COL4A3	2	iHS、ROH	繁殖相关生物过程	^[50]
GPRIN3	6	CLR、ROH	产羔数	^[59]
FSIP2	2	CLR、ROH	精子活力	^[62]
HSD3B1	1	iHS、Tajima’s D	卵泡发育	^[64]
HCRTR1	2	iHS、ROH	产羔数	^[60]
MEPE	6	iHS、ROH、Tajima’s D	产羔数	^[41]
MAST4	16	iHS、CLR	产羔数	^[61]
ROBO2	1	iHS、Tajima’s D	卵泡发育、母羊生产次数	^[64]^[66]
SLIT2	6	iHS、CLR	卵泡发育	^[65]
NDRG1	9	iHS、CLR	精子发生	^[63]

结构域 Domain	相关性状 Related trait	基因 Gene
骨骼Skeleton	身高、胸高、腰臀围、骨密度	ACAN、ERLEC1、FLVCR1、FAM184B、GPC6、HAPLN1、HAPLN3、 IBSP、LAP3、LCORL、MED28、MUSTN1、PLIN1、PDE9A、PDLIM5、 ABHD2、CACNA1D、HCRTR1、KCNN3、MEPE、MAST4、ROBO2、 SLIT2、SPP1、NDRG1、COL4A4、ABCG2、DPY19L1、HTR1B、DNAJC18、 SND1、GPATCH3、STAB1、BRAF、
新陈代谢 Metabolism	初生重、体重、	ACAN、ERLEC1、GALNTL6、GPC6、HAPLN3、IBSP、LAP3、LCORL、 MUSTN1、PDLIM5、CACNA1D、HCRTR1、KCNN3、MAST4、ROBO2、 SLIT2、COL4A4、ABCG2、DPY19L1、HTR1B、DNAJC18、SND1、STAB1、 PRG4、TNIK、FABP3、KLF12、LINGO2
生殖Reproduction	初情期	ABHD2、CACNA1D、MAST4、COL4A4、STAB1、KLF12
免疫学 Immunology	血细胞体积、血细胞比容、血红蛋白浓度	WDHD1 FBLN1、GPATCH3、DOCK10、MSR1、TNIK、KLF12

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