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

Abstract

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

CLC Number:

S826.2

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.

Figures/Tables 10

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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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Population Structure Analysis and Economic Traits Related Selection Signal Detection of Hu Sheep

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