基于芯片数据估计不同方法对槐猪近交系数的影响

doi:10.11843/j.issn.0366-6964.2023.03.009

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (3): 947-955.doi: 10.11843/j.issn.0366-6964.2023.03.009

基于芯片数据估计不同方法对槐猪近交系数的影响

韩云珍¹, 阳文攀^2,3,4, 洪渊¹, 龙毅^2,3, 刘相杰^2,4, 范小萍^2,4, 李文静^2,4, 邓政^2,4, 刘鸣慧^2,4, 郑素梅¹, 阮国荣¹, 丁能水^2,3,5*

1. 福建农业职业技术学院, 福州 350119;
2. 福建傲芯种业科技有限公司, 漳州 363000;
3. 上杭傲农槐猪产业发展有限公司, 龙岩 364200;
4. 福建傲农生物科技集团股份有限公司, 漳州 363000;
5. 江西农业大学猪遗传改良与养殖技术国家重点实验室, 南昌 330045

收稿日期:2022-09-09 出版日期:2023-03-23 发布日期:2023-03-21
通讯作者: 阮国荣,主要从事动物遗传育种与繁殖研究,E-mail:rgr001@126.com;丁能水,主要从事种猪遗传及育种新技术、生猪养殖新技术方向的研究与开发工作,E-mail:dingyd2005@hotmail.com
作者简介:韩云珍(1977-)，女，福建建瓯人,硕士，副教授，主要从事动物遗传育种与繁殖研究，E-mail:14502248@qq.com；阳文攀(1994-)，男，湖北孝感人，硕士，主要从事动物遗传育种与繁殖研究，E-mail:945226087@qq.com。
基金资助:
福建省现代农业(生猪)产业技术体系建设项目(闽财教指 [2021] 61号)；福州市科技计划项目(2020-PT-147)

Estimating the Inbreeding Coefficient of Huai Pigs by Different Methods Based on Chip Data

HAN Yunzhen¹, YANG Wenpan^2,3,4, HONG Yuan¹, LONG Yi^2,3, LIU Xiangjie^2,4, FAN Xiaoping^2,4, LI Wenjing^2,4, DENG Zheng^2,4, LIU Minghui^2,4, ZHENG Sumei¹, RUAN Guorong¹, DING Nengshui^2,3,5*

1. Fujian Vocational College of Agriculture, Fuzhou 350119, China;
2. Fujian Aoxin Seed Industry Technology Co. Ltd., Zhangzhou 363000, China;
3. Shanghang Aonong Huai Pig Industry Development Co. LTD., Longyan 364200, China;
4. Fujian Aonong BiologicaI Science and Technology Group Co. Ltd., Zhangzhou 363000, China;
5. National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China

Received:2022-09-09 Online:2023-03-23 Published:2023-03-21

摘要/Abstract

摘要： 旨在选取适用的方法评估槐猪群体的近交情况。本试验采用“中芯一号”育种芯片分别计算Fhom1、Fhom2、Fvan1、Fvan2和Fyang来进行247头槐猪(300日龄)个体近交系数的估计，探究SNP数目对近交估计值的影响以及不同估计方法之间的相关性。结果发现，随着SNP数目增加，近交系数Fhom1、Fhom2、Fvan1和Fyang的极差逐渐减少，当SNP数目达到10 000时近交系数趋于稳定，与质控后的31 545个SNPs计算的近交系数接近。Fhom1、Fhom2、Fvan1、Fvan2和Fyang的值分别为-0.216 5~0.344 0、-0.354 8~0.321 7、-0.322 8~0.892 1、-0.243 6~0.790 9、-0.189 4~0.543 3。Froh1和Froh2的值分别为0.008 7~0.406 9和0.002 2~0.402 4。通过比较不同基因组近交系数Person相关与Spearman秩相关可知，Fhom1与Fhom2、Froh1、Froh5间有较强的正相关；Fvan2与Fvan1、Fyang间有较强的正相关；Froh1与Froh5间有较强的正相关；而Fhom2与Fvan1、Fvan2呈负相关。由于Froh的取值范围在0~1之间，与系谱近交系数相同，符合近交系数评估习惯；同时，Froh同Fhom、Fvan、Fyang等基因组近交系数评估方式有着一定的正相关，适用度高。SNP密度影响近交系数的评估，其数目与密度充足时，采用Froh进行基因组近交系数评估较为适宜，这可为评估地方猪的近交水平、防止近交衰退、优化选种选配方案提供有利的技术手段。

关键词: 槐猪, 基因芯片, 近交系数, 相关性

Abstract: The study aimed to select applicable methods to assess the inbreeding degree of Huai pigs. In this study, Fhom1, Fhom2, Fvan1, Fvan2 and Fyang were calculated with “No.1 Zhongxin” porcine breeding chip data to estimate the inbreeding coefficient of 247 Huai pigs (300-days-old), and to explore the influence of SNP number on the inbreeding estimation and the correlation between different estimation methods. The results showed that the extreme variance of inbreeding coefficient Fhom1, Fhom2, Fvan1 and Fyang gradually decreased as the number of SNPs increased. When the number of SNPs reached 10 000, the inbreeding coefficients tended to be stable, which was close to the inbreeding coefficient calculated from 31 545 SNPs after quality control. The values of Fhom1, Fhom2, Fvan1, Fvan2 and Fyang were -0.216 5-0.344 0, -0.354 8-0.321 7, -0.322 8-0.892 1, -0.243 6-0.790 9, and -0.189 4-0.543 3, respectively. The values of Froh1 and Froh2 were 0.008 7-0.406 9 and 0.002 2-0.402 4, respectively. Person correlation and Spearman rank correlation of genomic inbreeding coefficients showed strong positive correlations between Fhom1 and Fhom2, Froh1, Froh5; The strong positive correlations were found between Fvan2 and Fvan1, Fyang; The strong positive correlation was observed between Froh1 and Froh5; Whereas Fhom2 was negatively correlated with Fvan1 and Fvan2. Since Froh took values from 0 to 1 that were identical to the inbreeding coefficient of a pedigree, it conformed to the evaluation habit of inbreeding coefficient; Moreover, Froh was positively correlated with the way in which genomic inbreeding coefficients were assessed, such as Fhom, Fvan and Fyang, with high applicability. The density of SNPs influenced the assessment of inbreeding coefficient, it was more appropriate to use Froh for genomic inbreeding coefficient estimation when the number and density were sufficient. The results may provide an advantageous technical means for assessing the inbreeding level of local pigs, preventing inbreeding depression and optimizing seed selection.

Key words: Huai pig, gene chip, inbreeding coefficient, correlation

中图分类号:

S828.2

韩云珍, 阳文攀, 洪渊, 龙毅, 刘相杰, 范小萍, 李文静, 邓政, 刘鸣慧, 郑素梅, 阮国荣, 丁能水. 基于芯片数据估计不同方法对槐猪近交系数的影响[J]. 畜牧兽医学报, 2023, 54(3): 947-955.

HAN Yunzhen, YANG Wenpan, HONG Yuan, LONG Yi, LIU Xiangjie, FAN Xiaoping, LI Wenjing, DENG Zheng, LIU Minghui, ZHENG Sumei, RUAN Guorong, DING Nengshui. Estimating the Inbreeding Coefficient of Huai Pigs by Different Methods Based on Chip Data[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 947-955.

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基于芯片数据估计不同方法对槐猪近交系数的影响

Estimating the Inbreeding Coefficient of Huai Pigs by Different Methods Based on Chip Data

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