基于全基因组重测序对武雪山羊的遗传进化分析

doi:10.11843/j.issn.0366-6964.2025.08.020

Abstract

Abstract:

This study aimed to provide an in-depth understanding of its population structure, which can explore the genetic variation and differentiation within populations and genetic differences between populations as well as geographic distribution characteristics, and provide an important basis for germplasm resource utilization and development of this breed. Ear tissues of 18 Wuxue goats (WXG), 9 Xiangdong Black goats (XDB), 9 Hechuan White goats (HCW), 9 Dazu Black goats (DZB), 11 Maguan Poll goat (MGG), and 10 Yunling goats (YLG) were collected and used for whole genome resequencing, with an average sequencing depth of about 10×. In this study, principal component analysis, phylogenetic analysis, population genetic structure analysis, heterozygosity analysis, population differentiation analysis, and linkage disequilibrium analysis were performed on 6 populations based on genome-wide data using GCTA, Plink, Admixture, Vcftools, and PopLDdecay software, respectively. The results of principal component analysis showed that Wuxue goats and Xiangdong Black goats were clustered into the same category, indicating that these two goat breeds have similar genetic backgrounds. In the phylogenetic analysis, Wuxue goats and other breeds of goat populations could be clustered into a single cluster, and were genetically closer to Xiangdong Black goats in the evolutionary tree. The results of the analysis of the genetic structure of the population showed that when the CV value was the smallest (K=3), Wuxue goats and Xiangdong Black goats had the same genetic components, indicating that the degree of genetic differentiation index between the two populations was small and the genetic backgrounds were similar. The results of heterozygosity analysis showed that Wuxue goats had lower nucleotide polymorphism (π), the lowest observed heterozygosity (Ho) and lower than the expected heterozygosity (He); ROH (runs of homozygosity) analyses showed that the number and length of ROHs in Wuxue goats were also significantly higher than those in other breeds, and the genomic inbreeding coefficient (F_ROH) was significantly higher than that of the other 5 populations, which suggests that there was a significant accumulation of purity fragments and a decrease in genetic diversity at the genomic level in Wuxue goats. The results of linkage disequilibrium analyses showed that Wuxue goats exhibited the highest degree of linkage disequilibrium, which further illustrated the low genetic diversity of the population. In conclusion, this study systematically analysed the genetic characteristics and population structure of the Wuxue goat, and found that the genetic background of Wuxue goats is similar to that of Xiangdong Black goats, and that the genetic diversity of their populations is low and there is a certain tendency of inbreeding, which suggests that we should pay attention to the expansion of the population size and the control of the inbreeding coefficient in the subsequent work of breeding conservation. These findings not only provide a scientific basis for the in-depth understanding of the genetic background, but also provide an important theoretical reference for the conservation and rational development and utilization of genetic resources of this breed.

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

CLC Number:

S827.2

REN Qianzi, ZHANG Baizhong, WANG Zhenqing, WANG Xianglin, GONG Ying, HU Renke, PU Yabin, SU Peng, LI Yefang, MA Yuehui, LI Haobang, JIANG Lin. Genetic Evolutionary Analysis of Wuxue Goat Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(8): 3787-3801.

Figures/Tables 14

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群体Group	英文名称English name	数量Number	样品来源Source
武雪山羊WXG	Wuxue goat	18	湖南省湘西土家族苗族自治州
湘东黑山羊XDB	Xiangdong Black goat	9	湖南省浏阳市
合川白山羊HCW	Hechuan White goat	9	重庆市合川县
大足黑山羊DZB	Dazu Black goat	9	重庆市大足县
云岭山羊YLG	Yunling goat	10	云南省楚雄彝族自治州
马关无角山羊MGG	Maguan Poll goat	11	云南省文山壮族苗族自治州马关县

类型Type (alphabetical order)	数量Count	占比/% Percent
DOWNSTREAM	2 135 800	5.031
EXON	270 736	0.638
INTERGENIC	9 102 451	21.440
INTRON	14 166 150	33.367
SPLICE_SITE_ACCEPTOR	239	0.001
SPLICE_SITE_DONOR	252	0.001
SPLICE_SITE_REGION	22 952	0.054
TRANSCRIPT	14 442 290	34.018
UPSTREAM	2 107 844	4.965
UTR_3_PRIME	164 145	0.387
UTR_5_PRIME	42 447	0.100
3_prime_UTR_variant	164 145	0.386
5_prime_UTR_premature_start_codon_gain_variant	6 098	0.014
5_prime_UTR_variant	36 349	0.086
downstream_gene_variant	2 135 800	5.028
initiator_codon_variant	9	0.000
intergenic_region	9 102 451	21.428
intragenic_variant	168 001	0.395
intron_variant	14 185 337	33.394
missense_variant	69 583	0.164
non_coding_transcript_exon_variant	53 867	0.127
non_coding_transcript_variant	14 274 289	33.603
splice_acceptor_variant	239	0.001
splice_donor_variant	263	0.001
splice_region_variant	24 149	0.057
start_lost	78	0.000
start_retained_variant	30	0.000
stop_gained	648	0.002
stop_lost	92	0.000
stop_retained_variant	127	0.000
synonymous_variant	149 823	0.353
upstream_gene_variant	2 107 844	4.962

品种 Breed	核苷酸多态性 π(mean)	观测杂合度 Observed heterozygosity(Ho)	期望杂合度 Expected heterozygosity(He)
大足黑山羊DZB	0.001 671 572	0.253 802	0.272 038
合川白山羊HCW	0.001 481 751	0.242 553	0.242 862
马关无角山羊MGG	0.001 706 207	0.296 721	0.275 427
武雪山羊WXG	0.001 585 495	0.235 027	0.261 443
湘东黑山羊XDB	0.001 637 571	0.265 953	0.264 043
云岭山羊YLG	0.001 523 224	0.238 900	0.250 394

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Genetic Evolutionary Analysis of Wuxue Goat Based on Whole Genome Resequencing

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