Vales M I, Schön C C, Capettini F, Chen X M, Corey A E, Mather D E, Mundt C C, Richardson K L, Sandoval-Islas J S, Utz H F, Hayes P M
Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA.
Theor Appl Genet. 2005 Nov;111(7):1260-70. doi: 10.1007/s00122-005-0043-y. Epub 2005 Nov 15.
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
许多数量性状基因座（QTL）检测实验中使用的有限群体规模可能导致QTL数量被低估、QTL效应被高估以及无法对QTL互作进行量化。我们利用大麦/大麦条锈菌互作系统来评估群体规模对QTL参数估计的影响。我们通过两个自交系BCD47和Baronesse杂交产生了一个大型（n = 409）双单倍体系群体。该群体在墨西哥托卢卡山谷和美国华盛顿州的田间条件下对大麦条锈病严重程度进行了评估。BCD47是抗性QTL等位基因的主要供体，但感病亲本也贡献了一些抗性等位基因。位于4H染色体长臂上靠近Mlo基因的主要QTL，解释了高达34%的表型变异。使用三种方法——重抽样、选择性基因分型和选择性表型分型——生成了不同规模的亚群体，以评估群体规模对QTL参数估计的影响。在所有情况下，检测到的QTL数量都随着群体规模的增加而增加。即使在小群体中也能检测到效应大的QTL，但效应小的QTL只有通过增加群体规模才能检测到。选择性基因分型和/或选择性表型分型方法可能是降低在大群体中进行QTL分析相关成本的有效策略。选择的方法将取决于基因分型与表型分型的相对成本。
