Bias and accuracy body weight trait evaluations of an F2 chicken using single-step genomic best linear unbiased prediction (ssGBLUP)

IF 1.2 4区 农林科学 Q3 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Hamed asadolahi, saeid ansari mahyari, Rasoul Vaez Torshizi, hossein emrani, Alireza ehsani
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引用次数: 0

Abstract

The objectives of this study were (i) to compare the accuracy and bias of estimates of breeding values for body weight (BW) at 2–7 weeks of age using pedigree-based best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP) methods, and (ii) to determine the best level of minor allele frequencies (MAFs) for pre-selection of SNPs for genomic prediction (GP). Records of 488 F2 broiler chickens obtained from crossbreeding of fast-growing Arian chickens and slow-growing Iranian native chickens at 2–7 weeks of age were used. Samples were genotyped using Illumina Chicken 60K BeadChip. To investigate the effect of MAFs on the accuracy of prediction, 48 379 quality-controlled SNPs were grouped into five subgroups with MAF bins 0.05–0.1, 0.1–0.2, 0.2–0.3, 0.3–0.4, and 0.4–0.5. Our results confirmed the superiority of ssGBLUP compared to traditional BLUP methodology. The average accuracy of GP improved by 59.03%, 220.34%, 0.46%, 5.61%, 0.45%, and 2.73% using ssGBLUP compared to BLUP for BW at 2–7 weeks of age, respectively. Depending on the age group, using a subset of SNPs with a specific MAF bin compared to all SNPs resulted in a remarkable improvement of GP accuracy for the observed traits.
利用单步基因组最佳线性无偏预测(ssGBLUP)评价F2鸡体重性状的偏倚和准确性
本研究的目的是:(1)比较使用基于家系的最佳线性无偏预测(BLUP)和单步基因组BLUP (ssGBLUP)方法估计2-7周龄体重(BW)育种值的准确性和偏倚性,以及(2)确定用于基因组预测(GP)的snp预选的次要等位基因频率(MAFs)的最佳水平。采用2-7周龄快速生长的阿里乌尔鸡与缓慢生长的伊朗土鸡杂交获得的488只F2肉鸡记录。使用Illumina Chicken 60K珠芯片对样品进行基因分型。为了研究MAF对预测准确性的影响,将48379个质量控制snp分为5个亚组,MAF为0.05-0.1、0.1-0.2、0.2-0.3、0.3-0.4和0.4-0.5。我们的结果证实了ssGBLUP与传统BLUP方法相比的优越性。与2-7周龄BW的BLUP相比,ssGBLUP的GP平均准确率分别提高了59.03%、220.34%、0.46%、5.61%、0.45%和2.73%。根据年龄组的不同,与所有snp相比,使用具有特定MAF bin的snp子集可显著提高所观察性状的GP准确性。
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来源期刊
Canadian Journal of Animal Science
Canadian Journal of Animal Science 农林科学-奶制品与动物科学
CiteScore
2.30
自引率
0.00%
发文量
51
审稿时长
6 months
期刊介绍: Published since 1957, this quarterly journal contains new research on all aspects of animal agriculture and animal products, including breeding and genetics; cellular and molecular biology; growth and development; meat science; modelling animal systems; physiology and endocrinology; ruminant nutrition; non-ruminant nutrition; and welfare, behaviour, and management. It also publishes reviews, letters to the editor, abstracts of technical papers presented at the annual meeting of the Canadian Society of Animal Science, and occasionally conference proceedings.
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