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breed identification using breed‑informative SNPs and machine learning based on whole genome sequence data and SNP chip data

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畜牧与生物技术杂志:英文版 2023年第5期14卷 1941-1953页

作者： Changheng Zhao Dan Wang Jun Teng Cheng Yang Xinyi Zhang Xianming Wei Qin Zhang Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention College of Animal Science and Veterinary MedicineShandong Agricultural UniversityTai’an 271018China

Background breed identification is useful in a variety of biological contexts.breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are several methods proposed.However,what is the optimal combination of these methods remain unclear.In this study,using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project,we compared the combinations of three methods(Delta,FST,and In)for breed-informative SNP detection and five machine learning methods(KNN,SVM,RF,NB,and ANN)for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs.In addition,we evaluated the accuracy of breed identification using SNP chip data of different densities.Results We found that all combinations performed quite well with identification accuracies over 95%in all scenarios.However,there was no combination which performed the best and robust across all scenarios.We proposed to inte-grate the three breed-informative detection methods,named DFI,and integrate the three machine learning methods,KNN,SVM,and RF,named KSR.We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99%in most cases and was very robust in all scenarios.The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases.Conclusions The current study showed that the combination of DFI and KSR was the optimal strategy.Using sequence data resulted in higher accuracies than using chip data in most cases.However,the differences were gener-ally small.In view of the cost of genotyping,using chip data is also a good option for breed identification.

关键词： breed identification breed-informative SNPs Genomic breed composition Machine learning Whole genome sequence data

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