Shook Johnathon M, Lourenco Daniela, Singh Asheesh K
Department of Agronomy, Iowa State University, Ames, IA, United States.
Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States.
Front Plant Sci. 2021 Sep 29;12:676269. doi: 10.3389/fpls.2021.676269. eCollection 2021.
The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present "Parental Allele Tracing, Recombination Identification, and Optimal predicTion" (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.
基因分型成本的降低正在引发全球植物育种计划对基因组预测和选择更广泛的关注和采用。然而，标记与基因之间历史连锁不平衡和近期连锁不平衡的不当合并限制了基因组预测（GP）的高精度。多个祖先可能在一个基因周围共享一个共同的单倍型，但不共享该基因的相同等位基因。这使得无法在祖先单倍型组中解析与该基因潜在等位基因相关的遗传效应。我们提出了“亲本等位基因追踪、重组识别和最优预测”（即PATRIOT）方法，该方法利用标记数据快速识别携带特定等位基因的品系，提高基因组亲缘关系和多样性估计的准确性，并改进基因组预测。利用同源关系，PATRIOT相对于传统的rrBLUP方法，GP准确性提高了16.6%。这种方法将有助于提高遗传增益率，并使育种计划中的可用信息得到更有效利用。
