3款猪50K SNP芯片基因型填充至序列数据的效果评估

S828.2; [目的]利用猪50K SNP(Single nucleotide polymorphisms)芯片开展基因组育种已经得到了广泛的应用与认可.基因型填充可在不增加基因型检测成本的前提下大幅提高基因型数据量,有利于开展复杂性状的遗传解析与遗传评估.本研究旨在评估3款猪SNP芯片基因型填充至序列数据的填充效果.[方法]选用3款芯片共同检测的48头杜洛克猪群体作为填充的目标群体,260头猪的全基因组测序数据作为参考群体,使用Beagle5.1软件进行基因型填充,对比3款不同猪SNP芯片纽勤50K、中芯一号50K和液相50K基因型填充至序列数据的填充效果.[结果]3款芯片原始的SNP数分...

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Published in华南农业大学学报 Vol. 43; no. 4; pp. 10 - 15
Main Authors 曾浩南, 钟展明, 徐志婷, 滕金言, 袁晓龙, 李加琪, 张哲
Format Journal Article
LanguageChinese
Published 华南农业大学动物科学学院/广东省农业动物基因组学与分子育种重点实验室/国家生猪种业工程技术研究中心,广东广州510642 01.07.2022
Subjects
猪
序列数据
SNP芯片
基因型一致性
基因型填充
Online AccessGet full text
ISSN1001-411X
DOI10.7671/j.issn.1001-411X.202110032

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Abstract S828.2; [目的]利用猪50K SNP(Single nucleotide polymorphisms)芯片开展基因组育种已经得到了广泛的应用与认可.基因型填充可在不增加基因型检测成本的前提下大幅提高基因型数据量,有利于开展复杂性状的遗传解析与遗传评估.本研究旨在评估3款猪SNP芯片基因型填充至序列数据的填充效果.[方法]选用3款芯片共同检测的48头杜洛克猪群体作为填充的目标群体,260头猪的全基因组测序数据作为参考群体,使用Beagle5.1软件进行基因型填充,对比3款不同猪SNP芯片纽勤50K、中芯一号50K和液相50K基因型填充至序列数据的填充效果.[结果]3款芯片原始的SNP数分别为50697、57466和50885个.填充至序列后,未质控时位点填充准确性(基因型一致性)分别为0.886、0.886和0.898,质控过滤DR2(Dosage R-squared)＜0.95的位点后,填充准确性(基因型一致性)分别提升至0.974、0.976和0.969,位点数分别为3393066、3139095和3320627个.[结论]不同芯片基因型填充至序列数据具有可行性,通过基因型填充可获得高质量的高密度基因型数据,可为后续的育种应用研究打下基础.
AbstractList S828.2; [目的]利用猪50K SNP(Single nucleotide polymorphisms)芯片开展基因组育种已经得到了广泛的应用与认可.基因型填充可在不增加基因型检测成本的前提下大幅提高基因型数据量,有利于开展复杂性状的遗传解析与遗传评估.本研究旨在评估3款猪SNP芯片基因型填充至序列数据的填充效果.[方法]选用3款芯片共同检测的48头杜洛克猪群体作为填充的目标群体,260头猪的全基因组测序数据作为参考群体,使用Beagle5.1软件进行基因型填充,对比3款不同猪SNP芯片纽勤50K、中芯一号50K和液相50K基因型填充至序列数据的填充效果.[结果]3款芯片原始的SNP数分别为50697、57466和50885个.填充至序列后,未质控时位点填充准确性(基因型一致性)分别为0.886、0.886和0.898,质控过滤DR2(Dosage R-squared)＜0.95的位点后,填充准确性(基因型一致性)分别提升至0.974、0.976和0.969,位点数分别为3393066、3139095和3320627个.[结论]不同芯片基因型填充至序列数据具有可行性,通过基因型填充可获得高质量的高密度基因型数据,可为后续的育种应用研究打下基础.
Author 钟展明
徐志婷
滕金言
李加琪
张哲
袁晓龙
曾浩南
AuthorAffiliation 华南农业大学动物科学学院/广东省农业动物基因组学与分子育种重点实验室/国家生猪种业工程技术研究中心,广东广州510642
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Author_FL TENG Jinyan
YUAN Xiaolong
XU Zhiting
LI Jiaqi
ZHANG Zhe
ZHONG Zhanming
ZENG Haonan
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DocumentTitle_FL Evaluation on genotype imputation performance of three porcine 50K SNP chips from chip data to sequencing data
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Keywords 猪
序列数据
SNP芯片
基因型一致性
基因型填充
Language Chinese
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Publisher 华南农业大学动物科学学院/广东省农业动物基因组学与分子育种重点实验室/国家生猪种业工程技术研究中心,广东广州510642
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Snippet S828.2; [目的]利用猪50K SNP(Single nucleotide polymorphisms)芯片开展基因组育种已经得到了广泛的应用与认可.基因型填充可在不增加基因型检测成本的前提下大幅提高基因...
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Title 3款猪50K SNP芯片基因型填充至序列数据的效果评估
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