基于全基因组重测序分析雷州山羊群体遗传多样性和群体结构

doi:10.11843/j.issn.0366-6964.2025.10.016

Abstract

Abstract:

The objective of this study was to investigate the genetic diversity and population structure of Leizhou goats to provide the theoretical basis for conservation and sustainable utilization of their germplasm resources. In this study, whole-genome resequencing was performed on blood samples from 20 Leizhou goats, with an average sequencing depth of ~10×. The genome-wide data from 43 additional goats was downloaded, including Yunshang black goats, Jintang black goats, Jining grey goats, Tibetan goats, and Longlin goats, from the NCBI database. Using these whole-genome data, then linkage disequilibrium (LD) analysis was performed using PopLDdecay software. We calculated genetic distances using Plink software and constructed and visualized a genetic relationship matrix using GCTA software. In addition, we employed Plink for principal component analysis (PCA), Phylip to construct a neighbor-joining (NJ) phylogenetic tree, and ADMIXTURE for population structure analysis, collectively assessing the genetic diversity and population structure of goat populations. Finally, runs of homozygosity (ROH) were analyzed and fixation index (F_ST) values between populations were calculated. Subsequently, the identified genomic regions were annotated for candidate genes and subjected to functional enrichment analysis. We identified a total of 18 810 921 SNPs, with the majority (65.71%) located in intergenic regions. For Leizhou goats, we found the overall average values of H_O, H_E, MAF, Pi, PIC, Ne and F_IS were 0.298, 0.295, 0.211, 0.001 8, 0.808, 65.488 and 0.086, respectively. The higher H_O compared to H_E indicated normal levels of population genetic diversity. For LD analysis, we found the fastest LD decay in Leizhou goats, suggesting higher genetic diversity and weaker selection pressure on their genome. We calculated identity-by-state (IBS) distance matrices and genetic relationship matrices (G matrices), which demonstrated close genetic relatedness among Leizhou goats but significant genetic differentiation from other goat populations. Analysis of ROH revealed that the Leizhou goat population exhibited a reduced inbreeding level. Using PCA, we observed discrete clustering of Leizhou goats, clearly distinguishing them from other populations. We constructed a neighbor-joining (NJ) phylogenetic tree, which further supported the independent evolutionary branch of Leizhou goats. For population structure analysis, we determined that the optimal clustering occurred at K=3, revealing a unique genetic architecture in Leizhou goats. Genome-wide F_ST analysis identified significant selection signals in the ADGRL3, CXCR1, and HTR1F gene regions after screening the top 1% of highly differentiated loci, suggesting these genes may be associated with adaptation. In this study, we comprehensively analyzed the genetic diversity, kinship relationships, and population structure of Leizhou goats. The study results provide a scientific basis for understanding the genetic background of Leizhou goats and lay a theoretical foundation for developing effective conservation strategies and sustainable utilization plans.

Key words: Leizhou goat, whole genome resequencing, genetic diversity, population structure

CLC Number:

S827.2

FENG Da, WEI Chen, HU Siyi, DU Chunmei, MA Jian, WU Jiang, ZHOU Guangxian, GAN Shangquan. Genetic Diversity and Population Structure Analysis of Leizhou Goat Based on Whole Genome Resequencing Analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4947-4962.

Figures/Tables 12

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References 54

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群体 Population	最小等位基因频率 MAF	观测杂合度 H_O	期望杂合度 H_E	有效群体含量 Ne	多态信息含量 PIC	核苷酸多态性 Pi	近交系数 F_IS
雷州山羊 LZ	0.211	0.298	0.295	65.488	0.808	1.798×10^-3	0.086
云上黑山羊 YS	0.207	0.305	0.290	21.312	0.938	2.179×10^-3	0.053
金堂黑山羊 JT	0.198	0.280	0.281	23.478	0.845	1.730×10^-3	0.092
济宁青山羊 JN	0.188	0.276	0.269	24.300	0.947	2.354×10^-3	0.299
西藏山羊 TB	0.188	0.250	0.270	25.879	0.947	2.080×10^-3	0.083
隆林山羊 LL	0.227	0.313	0.315	16.124	0.750	2.043×10^-3	0.075

GO条目 GO term	P值 Pvalue	基因 Gene
olfactory receptor activity	1.9×10^-4	LOC102185414, LOC102183215, LOC102183415, LOC102182462, LOC102184860, LOC102183344等
G protein-coupled receptor activity	2.8×10^-4	ADGRL3, LOC102185414, LOC102183215, LOC102183415, LOC102182462, LOC102184860等
G protein-coupled receptor signaling pathway	7.1×10^-4	CXCR1, LOC102185414, LOC102183215, LOC102183415, LOC102182462, LOC102184860等
plasma membrane	0.001 1	ADGRL3, SHC2, GRIA4, CRIPTO, NPC1, DNAJC5等
odorant binding	0.002 0	LOC102185414, LOC102183215, LOC102175834, LOC102169980, LOC102182462, LOC102184860
sensory perception of smell	0.002 2	LOC102185414, LOC102183215, LOC102175834, LOC102169980, LOC102182462, LOC102184860
lysozyme activity	0.003 9	LOC102185900, LOC102172331, LOC108633237
defense response to Gram-negative bacterium	0.004 3	LOC102171106, LOC102185900, LOC102172331, LOC108633237
killing of cells of another organism	0.009 9	LOC102185900, LOC102172331, LOC108633237

GO条目 GO term	P值 P value	基因 Gene
G protein-coupled receptor signaling pathway	1.1×10^-6	LOC102187858, LOC102182402, LOC102183415, LOC108634193, LOC102186762, LOC102187045等
olfactory receptor activity	1.9×10^-6	LOC102187858, LOC102182402, LOC102183415, LOC108634193, LOC102186762, LOC102187045等
membrane	1.2×10^-5	CEBPZOS, UPK3BL2, NUDT4, SEC11C, TMEM254, BST2, NAT8, DNAJC5, OSBPL1A等
G protein-coupled receptor activity	1.5×10^-5	LOC102187858, LOC102182402, LOC102183415, LOC108634193, LOC102186762, LOC102187045等
structural constituent of eye lens	0.005 9	CRYGC, LOC102191000, LOC102188265
lens development in camera-type eye	0.011	CRYGC, LOC102191000, LOC102188265
cyanamide hydratase activity	0.019	LOC106502860, LOC108637506
plasma membrane	0.028	HTR1F, SHC2, PIEZO2, GRIA4, SYTL2, DNAJC5, OSBPL1A
Glycerophosphodiester phosphodiesterase activity	0.031	LOC102183767, LOC102183296
lipid transport	0.047	OSBPL1A, LOC102172041, LOC102172606

染色体 Chromosome	基因 Gene	编号 ID	描述 Description
2	ADGRL3	ENSCHIG00000012101	Adhesion G Protein-Coupled Receptor L3
6	CXCR1	ENSCHIG00000020632	C-X-C motif chemokine receptor 1
1	HTR1F	ENSCHIG00000003029	5-hydroxytryptamine receptor 1F

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Genetic Diversity and Population Structure Analysis of Leizhou Goat Based on Whole Genome Resequencing Analysis

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