利用高密度SNP芯片评估中国地方肉牛品种基因组亲缘关系

doi:10.11843/j.issn.0366-6964.2023.10.016

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (10): 4174-4185.doi: 10.11843/j.issn.0366-6964.2023.10.016

利用高密度SNP芯片评估中国地方肉牛品种基因组亲缘关系

马浩然¹, 张路培¹, 金生云², 宝金山³, 李红艳⁴, 高会江¹, 徐凌洋¹, 王泽昭^1*, 李俊雅^1*

1. 中国农业科学院北京畜牧兽医研究所牛遗传育种创新团队, 北京 100193;
2. 乌拉盖管理区农牧技术推广中心, 乌拉盖 026321;
3. 乌拉盖管理区供销合作社, 乌拉盖 026321;
4. 内蒙古通辽市畜牧业发展中心, 通辽 028000

收稿日期:2023-03-16 出版日期:2023-10-23 发布日期:2023-10-26
通讯作者: 李俊雅,主要从事数量遗传学研究,E-mail:lijunya@caas.cn;王泽昭,主要从事数量遗传学研究,E-mail:wangzezhao@caas.cn
作者简介:马浩然(1997-),男,内蒙古赤峰人,硕士,主要从事数量遗传学研究,E-mail:17671710421@163.com
基金资助:
国家自然科学基金青年科学基金项目（32102505）；中国农业科学院北京畜牧兽医研究所中央级公益性科研院所基本科研业务费专项资金项目（2022-YWF-ZYSQ-02）；内蒙古自治区"科技兴蒙"行动重点专项（KJXM2020002-01）；财政部和农业农村部：国家现代农业产业技术体系资助（CARS-37）

Assessment of the Genomic Relationships for Chinese Indigenous Beef Cattle Using High-density SNP Chip

MA Haoran¹, ZHANG Lupei¹, JIN Shengyun², BAO Jinshan³, LI Hongyan⁴, GAO Huijiang¹, XU Lingyang¹, WANG Zezhao^1*, LI Junya^1*

1. Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
2. Agricultural and Animal Husbandry Technology Extension Center of Ulagai Precinct, Ulagai 026321, China;
3. Ulagai Management District Supply and Marketing Cooperative, Ulagai 026321, China;
4. Tongliao Animal Agriculture Development Service Center, Tongliao 028000, China

Received:2023-03-16 Online:2023-10-23 Published:2023-10-26

摘要/Abstract

摘要： 旨在在系统对比分析亲缘关系不同计算方法基础上探索适合我国肉牛地方品种的亲缘关系评估方法。本研究主要以柴达木牛等10个肉牛地方品种为研究对象，使用重抽样方法获得地方品种的模拟数据，以此为基础使用PCA聚类结果为参照，分别利用预测误差方差、广义决定系数、预测误差相关系数及SNP与QTL的连锁一致性程度系统对比了不同评估方法对地方品种亲缘关系的分类结果，并探索了遗传力因素对不同亲缘关系评估方法的影响。通过PCA分析可知10个肉牛地方品种可分为3大类，分别为北方牛品种（柴达木牛、西藏牛、蒙古牛以及延黄牛）、南方牛品种（文山牛、南丹牛以及雷琼牛）和西南牛品种（平武牛、凉山牛以及昭通牛），该分类结果与上述品种地理分布较为一致。与PCA结果对比发现，基于LD一致性的亲缘关系评估方法的评估结果与PCA聚类结果一致，且该方法能够使用皮尔逊相关系数量化品种间亲缘关系，具有较好的准确性。PEVD法、CD法与r法3种方法与上述方法相比评估群体间亲缘关系时容易受到性状估计育种值的误差方差影响，从而造成种间亲缘关系评估结果出现误差。评估结果影响因素分析发现，PEVD法、CD法和r法与PCA和LD一致性评估法相比，易受到评估性状遗传力的影响，评估结果稳定较差。而PCA和LD一致性评估法由于仅依赖基因组数据，不受到遗传力影响，能够更稳定的量化评估品种间亲缘关系，具有更好的可靠性。因此，基于LD一致性评估方法结果可准确量化评估肉牛品种间亲缘关系且评估结果稳定性较高。

关键词: 多品种基因组选择, 亲缘关系, 肉牛地方品种, 高密度SNP芯片, 连锁不平衡

Abstract: This study aimed to explore a suitable method for assessing the genetic relationships of indigenous beef breeds in China, based on a systematic comparative analysis of different computational methods for determining kinship. This study focused on 10 local beef cattle breeds, such as Chaidamu cattle, and utilized the resampling method to generate simulated data for these local breeds. Based on this, the study utilized PCA clustering results as a reference and systematically compared different evaluation methods, including predictive error variance, generalized coefficient of determination, predictive error correlation coefficient, and the degree of linkage consistency between SNPs and QTLs, to classify the genetic relationships of these local breeds. Additionally, the study explored the influence of genetic factors on different methods of assessing kinship. The PCA analysis showed that the 10 indigenous beef cattle breeds could be classified into 3 major categories, northern cattle breeds (Chaidamu cattle, Xizang cattle, Mongolian cattle and Yanhuang cattle), southern cattle breeds (Wenshan cattle, Nandan cattle and Leiqiong cattle) and southwestern cattle breeds (Pingwu cattle, Liangshan cattle and Zhaotong cattle). The classification results were consistent with the geographical distribution of the above breeds. Compared with the PCA results, the correlation of persistence of LD phase affinity assessment method was consistent with the PCA clustering results, and the method was able to quantify the relationship using Pearson correlation coefficient relationships with better accuracy. The 3 methods, PEVD, CD and r, were susceptible to the influence of the error variance of the estimated breeding values of the traits when assessing the relationship compared to the above methods, resulting in errors in the assessment results of the relationship. The analysis of factors affecting the assessment results revealed that the PEVD, CD and r methods were susceptible to the influence of the heritability of the assessed traits compared to the PCA and LD phase consistent assessment methods, and the assessment results were less stable. On the other hand, the PCA and LD phase consistent assessment methods are more stable and quantitative in assessing relatedness among breeds because they rely only on genomic data and are not affected by heritability and have better reliability. Therefore, the results based on LD phase consistent assessment method can accurately and quantitatively assess the relationship between breeds and the assessment results are more stable.

Key words: multi-breed genomic selection, relationship, indigenous beef cattle breed, high-density SNP chip, linkage disequilibrium

中图分类号:

S823.2

马浩然, 张路培, 金生云, 宝金山, 李红艳, 高会江, 徐凌洋, 王泽昭, 李俊雅. 利用高密度SNP芯片评估中国地方肉牛品种基因组亲缘关系[J]. 畜牧兽医学报, 2023, 54(10): 4174-4185.

MA Haoran, ZHANG Lupei, JIN Shengyun, BAO Jinshan, LI Hongyan, GAO Huijiang, XU Lingyang, WANG Zezhao, LI Junya. Assessment of the Genomic Relationships for Chinese Indigenous Beef Cattle Using High-density SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4174-4185.

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利用高密度SNP芯片评估中国地方肉牛品种基因组亲缘关系

Assessment of the Genomic Relationships for Chinese Indigenous Beef Cattle Using High-density SNP Chip

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