Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms
Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms
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DOI：
10.3168/jds.2009-2849
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发表时间：
2010-05-01
影响因子：
3.5
通讯作者：
Wiggans, G. R.
中科院分区：
文献类型：
--
作者：
Weigel, K. A.;Van Tassell, C. P.;Wiggans, G. R.
奶牛的高密度单核苷酸多态性（SNP）基因型的可用性创造了令人兴奋的研究机会，并彻底改变了实际的育种计划。该技术的更广泛应用将导致来自不同低、中或高密度平台的基因型必须组合的情况。在这种情况下，缺失的SNP基因型可以使用基于家族或群体的算法进行估算。我们的目的是评估泽西牛插补的准确性，使用包括2，542头具有43，385个SNP基因型的动物的参考组和604头动物的研究样本，其中基因型可用于1，2，5，10，20，40或80%的基因座。两个基于群体的算法，fastPHASE 1.2（P. Scheet和M. Stevens;华盛顿大学技术转移数字风险投资项目，西雅图，华盛顿州）和IMPUTE 2.0（B。Howie和J. Marchini; Department of Statistics，University of Oxford，UK）用于估算普通牛常染色体1、15和28上的基因型。当研究样本中有1 - 2%的基因型可用时，正确插补的基因型平均比例范围为0.659 - 0.801，当有5 - 20%的基因型可用时，插补的基因型平均比例范围为0.733 - 0.964，当有40 - 80%的基因型可用时，插补的基因型平均比例范围为0.896 - 0.995。在没有近亲的谱系或基因型的情况下，来自参考群体的插补的准确性可能是适度的（通常40，000 SNP）。从廉价的低或中密度平台准确估算高密度基因型可以大大提高奶牛全基因组选择程序的效率。
The availability of dense single nucleotide polymorphism (SNP) genotypes for dairy cattle has created exciting research opportunities and revolutionized practical breeding programs. Broader application of this technology will lead to situations in which genotypes from different low-, medium-, or high-density platforms must be combined. In this case, missing SNP genotypes can be imputed using family-or population-based algorithms. Our objective was to evaluate the accuracy of imputation in Jersey cattle, using reference panels comprising 2,542 animals with 43,385 SNP genotypes and study samples of 604 animals for which genotypes were available for 1, 2, 5, 10, 20, 40, or 80% of loci. Two population-based algorithms, fastPHASE 1.2 (P. Scheet and M. Stevens; University of Washington Tech-Transfer Digital Ventures Program, Seattle, WA) and IMPUTE 2.0 (B. Howie and J. Marchini; Department of Statistics, University of Oxford, UK), were used to impute genotypes on Bos taurus autosomes 1, 15, and 28. The mean proportion of genotypes imputed correctly ranged from 0.659 to 0.801 when 1 to 2% of genotypes were available in the study samples, from 0.733 to 0.964 when 5 to 20% of genotypes were available, and from 0.896 to 0.995 when 40 to 80% of genotypes were available. In the absence of pedigrees or genotypes of close relatives, the accuracy of imputation may be modest (generally 40,000 SNP) from a reference population. Accurate imputation of high-density genotypes from inexpensive low-or medium-density platforms could greatly enhance the efficiency of whole-genome selection programs in dairy cattle.