基于50K SNP芯片评估广东省四类地方猪保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2024.12.013

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (12): 5464-5477.doi: 10.11843/j.issn.0366-6964.2024.12.013

基于50K SNP芯片评估广东省四类地方猪保种群体的遗传结构

程昕琰¹(), 王诗媛¹, 吉叶标¹, 黄思秀¹, 杨杰¹, 孟繁明²^,³, 张茂⁴, 蔡更元¹, 刘琅青¹^,*()

1. 华南农业大学动物科学学院, 国家生猪种业工程技术研究中心, 广州 510642
2. 广东省农业科学院动物科学研究所, 猪禽种业全国重点实验室, 广东省畜禽育种与营养研究重点实验室, 广州 510640
3. 清远龙发种猪有限公司, 广东省生猪育种工程技术研究中心, 英德 513057
4. 韶关学院生物与农业学院, 韶关 512000

收稿日期:2024-06-11 出版日期:2024-12-23 发布日期:2024-12-27
通讯作者: 刘琅青 E-mail:cheng.xinyan@foxmail.com;langqing.liu@scau.edu.cn
作者简介:程昕琰(1999-), 女, 新疆乌鲁木齐人, 硕士生, 主要从事猪遗传育种与繁殖研究, E-mail: cheng.xinyan@foxmail.com
基金资助:
广东省乡村振兴战略专项资金种业振兴项目(2022-XJS-00-002);广东省普通高校重点领域专项(2021ZDZX4040);清远市创新创业研究团队项目(2018002)

Evaluation of the Genetic Structure of Conservation Populations of Four Major Local Pig Breeds in Guangdong Province Based on a 50K SNP Chip

CHENG Xinyan¹(), WANG Shiyuan¹, JI Yebiao¹, HUANG Sixiu¹, YANG Jie¹, MENG Fanming²^,³, ZHANG Mao⁴, CAI Gengyuan¹, LIU Langqing¹^,*()

1. National Engineering Research Center for Swine Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
2. Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
3. Guangdong Engineering Technology Research Center of Pig Breeding, Qingyuan Longfa Pig Breeding Co., Ltd., Yingde 513057, China
4. College of Biology and Agriculture, Shaoguan University, Shaoguan 512000, China

Received:2024-06-11 Online:2024-12-23 Published:2024-12-27
Contact: LIU Langqing E-mail:cheng.xinyan@foxmail.com;langqing.liu@scau.edu.cn

摘要/Abstract

摘要：

旨在揭示广东省4类重点保护地方猪种的保种情况，评估其保种群体的遗传结构信息，辅助保护和利用地方猪种质资源。本研究采用2023年采集自6个保种场的广东省4类地方猪共488头(新丰板岭大花白猪92头、新丰板岭蓝塘猪34头、紫金东瑞蓝塘猪68头、乐家庄小耳花猪77头、壹号食品小耳花猪109头、北礤粤东黑猪108头)。使用50K SNP芯片对比了包括欧洲野猪、瘦肉型猪、其他华南地方猪以及其他中国地方猪在内的41个地方猪品种，共2 144头。质控后保留20 590个SNPs位点。对广东4类地方猪种保种群体进行遗传多样性、血缘纯度、亲缘关系以及家系结构分析。结果显示：新丰板岭大花白猪的近交系数(F值)为0.409，观测杂合度(Ho)为0.181，期望杂合度(He)为0.172，连续纯和片段(ROH)长度为475.81 Mb，连锁不平衡(LD)长度为467.88 kb，平均F_ROH值为0.212，保种场内分为5个家系；新丰板岭蓝塘猪的F值为0.316，Ho为0.210，He为0.189，ROH长度为441.76 Mb，LD长度为475.78 kb，F_ROH值为0.201，分为4个家系；紫金东瑞蓝塘猪的F值为0.239，Ho为0.233，He为0.218，ROH长度为224.13 Mb，LD长度为463.53 kb，F_ROH值为0.100，分为5个家系；乐家庄小耳花猪的F值为0.319，Ho为0.208，He为0.221，ROH长度为262.62 Mb，LD长度为460.88 kb，F_ROH值为0.117，分为7个家系；壹号小耳花猪的F值为0.435，Ho为0.173，He为0.171，ROH长度为113.41 Mb，LD长度为418.59 kb，F_ROH值为0.051，分为6个家系；北礤粤东黑猪的F值为-0.028，Ho为0.314，He为0.300，ROH长度为247.47 Mb，LD长度为467.88 kb，F_ROH值为0.110，分为5个家系。对各保种群体血缘组成进行分析，除粤东黑猪群体血缘仍大量受瘦肉型猪血缘影响，平均中国猪血缘比例为69.37%，其他4个群体均受瘦肉型群体血缘影响较小，血缘较纯，平均中国猪血缘比例大于90%，保种情况较好。综上，广东省各地方猪保种场后期应加强对地方猪的扩繁和选育工作，在保持血缘纯度稳定的情况下，降低近交程度。

关键词: 华南地方猪, SNP芯片, 保种, 遗传多样性, 群体遗传结构

Abstract:

This study aimed to reveal the conservation status of the 4 major local pig breeds in Guangdong Province, evaluate the genetic structure for their conservation populations, and provide guidance for protection and utilization of local pig genetic resources. In 2023, a total of 488 pigs from 6 conservation farms representing the 4 major local pig breeds in Guangdong Province were sampled (92 Xinfeng Large black-white pigs, 34 Xinfeng Lantang pigs, 68 Zijin Lantang pigs, 77 Lejiazhuang Small-ear Spotted pigs, 109 Yihao Small-ear Spotted pigs, and 108 Beica Yuedong Black pigs). Samples were genotyped using a 50K SNP chip and compared with 41 pig breeds, including European wild boars, Western Commercial pigs, South China local pigs, and other Chinese local pigs, in total 2 144 individuals. After quality control, 20 590 SNP loci were retained. Genetic diversity, inbreeding status, ancestry composition and family structure analyses were conducted. The results showed that the inbreeding coefficient (F) of Xinfeng Large black-white pigs was 0.409, observed heterozygosity (Ho) was 0.181, expected heterozygosity (He) was 0.172, the total length of runs of homozygosity (ROH) was 475.81 Mb, linkage disequilibrium (LD) length was 467.88 kb, the average F_ROH was 0.212, and the population was divided into 5 families. The inbreeding coefficient (F) of Xinfeng Lantang pigs was 0.316, Ho was 0.210, He was 0.189, ROH length was 441.76 Mb, LD length was 475.78 kb, F_ROH was 0.201, and the population was divided into 4 families. The inbreeding coefficient (F) of Zijin Lantang pigs was 0.239, Ho was 0.233, He was 0.218, ROH length was 224.13 Mb, LD length was 463.53 kb, F_ROH was 0.100, and the population was divided into 5 families. The inbreeding coefficient (F) of Lejiazhuang Small-ear Spotted pigs was 0.319, Ho was 0.208, He was 0.221, ROH length was 262.62 Mb, LD length was 460.88 kb, F_ROH was 0.117, and the population was divided into 7 families. The inbreeding coefficient (F) of Yihao Small-ear Spotted pigs was 0.435, Ho was 0.173, He was 0.171, ROH length was 113.41 Mb, LD length was 418.59 kb, F_ROH was 0.051, and the population was divided into 6 families. The inbreeding coefficient (F) of Beica Yuedong Black pigs was -0.028, Ho was 0.314, He was 0.300, ROH length was 247.47 Mb, LD length was 467.88 kb, F_ROH was 0.110, and the population was divided into 5 families. Ancestry composition analysis of each conservation population showed that, except for the Yuedong Black pig population, which was still significantly genetically influenced by Western commercial pig ancestry with an average Chinese pig ancestry proportion of 69.37%, the other 4 populations had less Western commercial pig ancestry, with an average Chinese pig ancestry proportion greater than 90%. In summary, conservation farms for local pig breeds in Guangdong Province should focus more on increasing the population size and improving breeding scheme within captivity, aiming to reduce the degree of inbreeding while maintaining stable genetic integrity.

Key words: South China local pigs, SNP chip, conservation population, genetic diversity, population genetic structure

中图分类号:

S828.2

程昕琰, 王诗媛, 吉叶标, 黄思秀, 杨杰, 孟繁明, 张茂, 蔡更元, 刘琅青. 基于50K SNP芯片评估广东省四类地方猪保种群体的遗传结构[J]. 畜牧兽医学报, 2024, 55(12): 5464-5477.

CHENG Xinyan, WANG Shiyuan, JI Yebiao, HUANG Sixiu, YANG Jie, MENG Fanming, ZHANG Mao, CAI Gengyuan, LIU Langqing. Evaluation of the Genetic Structure of Conservation Populations of Four Major Local Pig Breeds in Guangdong Province Based on a 50K SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5464-5477.

图/表 9

表 1

表 2

各类生态型中代表性品种的遗传多样性"

生态型 Ecotype	省份 Province	品种 Breed	数量 Number	F	Ho	He	ROH/Mb	r_0.3²/kb	F_ROH
华南型South China	广东	大花白猪	86	0.255	0.228	0.222	259.22	465.587	0.116
华南型South China	广东	大花白猪-2023年新丰	92	0.409	0.181	0.172	475.81	467.88	0.212
华南型South China	广东	蓝塘猪	117	0.398	0.184	0.201	270.48	441.28	0.120
华南型South China	广东	蓝塘猪-2023年新丰	34	0.316	0.210	0.189	441.76	475.78	0.201
华南型South China	广东	蓝塘猪-2023年紫金	68	0.239	0.233	0.218	224.13	463.53	0.100
华南型South China	广东	小耳花猪	29	0.032	0.296	0.244	275.63	479.96	0.126
华南型South China	广东	小耳花猪-2021年乐家庄	225	0.295	0.216	0.207	299.18	471.14	0.133
华南型South China	广东	小耳花猪-2023年乐家庄	77	0.319	0.208	0.221	262.62	460.88	0.117
华南型South China	广东	小耳花猪-2023年壹号	109	0.435	0.173	0.171	113.41	418.59	0.051
华南型South China	广西	陆川猪	112	0.471	0.162	0.160	164.71	441.82	0.073
华南型South China	广东	粤东黑猪-2015年北礤	20	-0.111	0.335	0.308	81.84	469.85	0.038
华南型South China	广东	粤东黑猪-2020年北礤	18	-0.134	0.341	0.327	140.64	463.93	0.066
华南型South China	广东	粤东黑猪-2023年北礤	108	-0.028	0.314	0.300	247.47	467.88	0.110
华南型South China	广东	粤东黑猪-2019年泰农	20	-0.263	0.379	0.344	72.92	458.24	0.034
华南型South China	广东	粤东黑猪-2020年泰农	20	-0.111	0.335	0.308	81.84	469.85	0.038
华南型South China	福建	莆田黑猪	20	0.324	0.207	0.197	236.11	470.16	0.109
华南型South China	海南	屯昌黑猪	35	0.188	0.249	0.222	87.59	463.18	0.042
华中型Central China	湖北	通城猪	16	0.320	0.208	0.199	92.01	458.64	0.041
华中型Central China	湖南	沙子岭猪	11	0.340	0.202	0.176	135.62	477.25	0.065
华东型East China	安徽	皖南黑猪	18	0.372	0.192	0.184	401.83	468.85	0.187
华东型East China	江苏	二花脸猪	32	0.404	0.182	0.182	171.56	450.36	0.078
华北型North China	内蒙古	河套大耳猪	16	0.088	0.279	0.251	84.53	471.03	0.040
华北型North China	山西	梅山猪	20	0.523	0.146	0.172	642.14	464.76	0.298
西南型Southwest China	云南	滇南小耳猪	15	0.432	0.174	0.197	509.55	471.94	0.240
西南型Southwest China	四川	荣昌猪	18	0.384	0.188	0.182	83.71	432.29	0.039
欧洲型European	—	杜洛克	35	0.090	0.278	0.294	349.58	421.99	0.159
欧洲型European	—	欧洲野猪	20	0.301	0.214	0.233	331.72	412.33	0.154
欧洲型European	—	皮特兰	20	-0.118	0.342	0.333	315.03	448.97	0.146

表 2

图 1

图 2

图 3

图 4

图 5

表 3

图 6

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质量控制标准 Quality control standard	SNPs标记数目 Number of SNPs
标记总数 Total number	71 172
保留常染色体位点数目 Retained autosomal number	68 637
保留标记基因缺失率＜0.1 geno＜0.1	20 598
保留最小等位基因频率＞0.01 MAF＞0.01	20 590

品种 Breed	最大值/% Maxmun	最小值/% Minmun	平均值/% Average	标准差/% Deviation
大花白猪Large Black-White pig	100.00	57.90	94.33	7.18
大花白猪-2023年新丰Large Black-White pig-2023 Xinfeng	100.00	91.94	99.12	1.19
蓝塘猪Lantang pig	100.00	77.53	98.64	3.14
蓝塘猪-2023年新丰Lantang pig-2023 Xinfeng	97.88	82.01	92.18	3.30
蓝塘猪-2023年紫金Lantang pig-2023 Zijin	100.00	80.22	90.70	4.84
小耳花猪Small-Ear Spotted pig	99.65	68.75	80.35	6.62
小耳花猪-2021年乐家庄Small-Ear Spotted pig-2021 Lejiazhuang	100.00	73.87	97.77	4.22
小耳花猪-2023年乐家庄Small-Ear Spotted pig-2023 Lejiazhuang	100.00	71.50	96.36	6.83
小耳花猪-2023年壹号Small-Ear Spotted pig-2023 Yihao	100.00	97.62	99.81	0.42
粤东黑猪-2015年北礤Yuedong Black pig-2015 Beica	88.72	47.34	68.92	10.72
粤东黑猪-2020年北礤Yuedong Black pig-2020 Beica	94.67	43.88	65.34	11.66
粤东黑猪-2023年北礤Yuedong Black pig-2023 Beica	91.70	46.12	69.37	8.95

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基于50K SNP芯片评估广东省四类地方猪保种群体的遗传结构

Evaluation of the Genetic Structure of Conservation Populations of Four Major Local Pig Breeds in Guangdong Province Based on a 50K SNP Chip

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