Biometris, Wageningen University and research Center, P.O Box 100, Wageningen, 6700AC, The Netherlands.
KWS SAAT SE, Einbeck, Germany.
BMC Genom Data. 2021 Feb 3;22(1):4. doi: 10.1186/s12863-021-00960-9.
Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversity, which can be an important factor influencing the detection of QTLs. In MPPs, the allelic effects can be more or less specific. They can depend on an ancestor, a parent or the combination of parents in a cross. In this paper, we evaluated the effect of QTL allelic diversity on the QTL detection power in MPPs.
We simulated: a) cross-specific QTLs; b) parental and ancestral QTLs; and c) bi-allelic QTLs. Inspired by a real application in sugar beet, we tested different MPP designs (diallel, chessboard, factorial, and NAM) derived from five or nine parents to explore the ability to sample genetic diversity and detect QTLs. Using a fixed total population size, the QTL detection power was larger in MPPs with fewer but larger crosses derived from a reduced number of parents. The use of a larger set of parents was useful to detect rare alleles with a large phenotypic effect. The benefit of using a larger set of parents was however conditioned on an increase of the total population size. We also determined empirical confidence intervals for QTL location to compare the resolution of different designs. For QTLs representing 6% of the phenotypic variation, using 1600 F offspring individuals, we found average 95% confidence intervals over different designs of 49 and 25 cM for cross-specific and bi-allelic QTLs, respectively.
MPPs derived from less parents with few but large crosses generally increased the QTL detection power. Using a larger set of parents to cover a wider genetic diversity can be useful to detect QTLs with a reduced minor allele frequency when the QTL effect is large and when the total population size is increased.
多亲群体（MPP）是研究植物遗传结构和检测数量性状位点（QTL）的重要资源。在 MPP 中，QTL 效应可以表现出各种水平的等位基因多样性，这可能是影响 QTL 检测的一个重要因素。在 MPP 中，等位基因效应可以或多或少地具有特异性。它们可以依赖于一个祖先、一个亲本或杂交亲本的组合。在本文中，我们评估了 QTL 等位基因多样性对 MPP 中 QTL 检测能力的影响。
我们模拟了：a）交叉特异性 QTL；b）亲本和祖先 QTL；c）双等位基因 QTL。受甜菜实际应用的启发，我们测试了来自 5 个或 9 个亲本的不同 MPP 设计（双列杂交、棋盘设计、析因设计和 NAM），以探索对遗传多样性进行采样和检测 QTL 的能力。在固定的总群体大小下，来自较少亲本但更大杂交的 MPP 具有更大的 QTL 检测能力，这些亲本数量减少了。使用更大的亲本集有助于检测具有较大表型效应的稀有等位基因。然而，使用更大的亲本集的好处取决于总群体大小的增加。我们还确定了 QTL 位置的经验置信区间，以比较不同设计的分辨率。对于代表 6%表型变异的 QTL，使用 1600 个 F 后代个体，我们发现不同设计的平均 95%置信区间分别为交叉特异性和双等位基因 QTL 的 49 和 25cM。
来自较少亲本但具有较少但较大杂交的 MPP 通常会增加 QTL 检测能力。使用更大的亲本集来覆盖更广泛的遗传多样性，可以在 QTL 效应较大且总群体大小增加时，用于检测等位基因频率较低但 QTL 效应较小的 QTL。
