基于80K SNP芯片的梅花星猪群体遗传结构解析及全基因组连续纯合片段特征研究

doi:10.11843/j.issn.0366-6964.2025.08.017

Abstract

Abstract:

This study aimed to analyze the population structure and genetic diversity of the Meihuaxing pig to promote the effective conservation and utilization of its genetic resources. SNP typing was performed on 307 Meihuaxing pigs by using the 'Porcine 80K Functional Variants Genotyping Array', and the population genetic structure and runs of homozygosity (ROH) analyses were performed based on the SNP chip data. Principal component analysis (PCA) and population ancestry component analysis showed that there was obvious genetic stratification in the Meihuaxing pig resource population, and kinship based G matrix and clustering analysis further revealed that the studied population could be divided into 4 lineages. Some of these individuals were closely related, and the degree of inbreeding in family line 2 was relatively high, which requires reasonable selection measures to prevent inbreeding decline. A total of 18 442 ROHs were detected by ROH analysis, with an average length of 4.65 Mb. In addition, a total of 13 ROH islands were identified, and 164 genes were annotated. Further comparison of the ROH island regions of different family lines and functional annotation with literature and tissue expression profiles identified a number of genes associated with reproduction (RAB23, PRKD1, G2E3, etc.), growth (RUNX1T1, TMEM8B, NPR2, etc.), meat quality (DECR1, NFKBIA), carcass (PPP1R9A, PEG10), adaptability (DST, SLC26A7, IRF9), immunity (SIT1), feed efficiency (SLC2A2, PHKB, GPT2), disease (AKAP6) and other trait-related candidate genes.This study systematically analyzes the genetic structure of the Meihuaxing pig population and its ROH distribution at the genome-wide level, which lays the foundation for the in-depth analysis of the population characteristics of this excellent local pig breed, the genetic basis for the development of important traits, and the scientific conservation and utilization of the core population.

Key words: Meihuaxing pig, population genetic structure, runs of homozygosity, genetic diversity, SNP chips

CLC Number:

S828.2

LIU Sha, YANG Caichun, ZHANG Xiaoyu, CHEN Qiong, LIU Xiong, CHEN Hongbo, ZHOU Huanhuan, SHI Liangyu. Population Genetic Structure and Genome-wide Runs of Homozygosity Analysis in Meihuaxing Pigs Based on 80K SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(8): 3749-3760.

Figures/Tables 11

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ROH分类 ROH classification	数量 Number	数量百分比/% Percent	均值±标准差/Mb Mean±SD	总长度/Mb Total length	长度百分比/% Length percentage
0~5 Mb	13 908	75.41	2.42±1.04	33 628.31	39.22
5~10 Mb	2 797	15.17	6.92±1.38	19 349.33	22.56
>10 Mb	1 737	9.42	18.87±10.02	32 782.82	38.22

ROH长度 ROH length	样本数 Sample size	均值 Mean	标准差 Standard deviation	最小值 Minimum	最大值 Maximum
总长度Total	307	0.123	0.041	0.043	0.274
0~5 Mb	307	0.048	0.012	0.023	0.099
5~10 Mb	306	0.028	0.012	0.004	0.068
>10 Mb	303	0.048	0.035	0.004	0.184

染色体 Chromosome	起始位点/bp Start site	终止位点/bp End site	长度/bp Length	SNPs数目 Number of SNPs	基因数目 Number of genes
1	236 150 856	236 554 494	403 638	15	20
2	29 416 962	32 427 185	3 010 223	68	7
4	44 943 952	49 689 676	4 745 724	105	16
4	50 087 861	53 278 776	3 190 915	87	16
7	27 892 821	29 166 944	1 274 123	77	8
7	68 593 944	75 591 285	6 997 341	140	51
9	32 385 323	32 922 009	536 686	13	6
9	72 730 719	75 643 707	2 912 988	57	25
11	10 283 011	11 674 505	1 391 494	67	3
13	84 810 974	88 123 512	3 312 538	58	9
14	84 657 706	85 208 724	551 018	23	1
15	107 456 185	107 639 796	183 611	6	0
17	44 058 583	44 806 701	748 118	11	2

重要经济性状 Economically important trait	基因Gene
繁殖Reproduction	RAB23⁴、PRKD1⁵、G2E3⁵、ASTN1⁴、NFATC4⁵、PLSCR4⁵、KIF18A¹、DYNC1I1⁵、BAG2⁴、YAP1⁵、WWTR1⁵、SLC26A7⁵、FXR1³、MORC2¹、TDRD5⁴、SGCE⁵
生长Growth	RUNX1T1¹、TMEM8B¹、NPR2⁵、SPAG8⁵、NOVA1⁵
免疫Immune	SIT1¹
胴体Carcass	PPP1R9A⁵、PEG10⁵
环境适应性 Environmental adaptation	DST⁴、SLC26A7⁵、IRF9⁵
肉质Meat quality	DECR1⁵、NFKBIA⁵
饲料效率Feed efficiency	SLC2A2³、PHKB⁴、GPT2⁴
疾病Diseases	AKAP6²

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Population Genetic Structure and Genome-wide Runs of Homozygosity Analysis in Meihuaxing Pigs Based on 80K SNP Chip

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