Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Limagrain Vegetable Seeds, Vilmorin & Cie, 28 Route d'Ennezat, Chappes, Zip 63720, France.
BMC Genomics. 2024 Sep 2;25(1):822. doi: 10.1186/s12864-024-10699-z.
Traditional recombinant inbred lines (RILs) are generated from repeated self-fertilization or brother-sister mating from the F hybrid of two inbred parents. Compared with the F population, RILs cumulate more crossovers between loci and thus increase the number of recombinants, resulting in an increased resolution of genetic mapping. Since they are inbred to the isogenic stage, another consequence of the heterozygosity reduction is the increased genetic variance and thus the increased power of QTL detection. Self-fertilization is the primary form of developing RILs in plants. Brother-sister mating is another way to develop RILs but in small laboratory animals. To ensure that the RILs have at least 98% of homozygosity, we need about seven generations of self-fertilization or 20 generations of brother-sister mating. Prior to homozygosity, these lines are called pre-recombinant inbred lines (PRERIL). Phenotypic values of traits in PRERILs are often collected but not used in QTL mapping. To perform QTL mapping in PRERILs, we need the recombination fraction between two markers at generation t for t < 7 (selfing) or t < 20 (brother-sister mating) so that the genotypes of QTL flanked by the markers can be inferred.
In this study, we developed formulas to calculate the recombination fractions of PRERILs at generation t in self-fertilization, brother-sister mating, and random mating. In contrast to existing works in this topic, we used computer code to construct the transition matrix to form the Markov chain of genotype array between consecutive generations, the so-called recurrent equations.
We provide R functions to calculate the recombination fraction using the newly developed recurrent equations of ordered genotype array. With the recurrent equations and the R code, users can perform QTL mapping in PRERILs. Substantial time and effort can be saved compared with QTL mapping in RILs.
传统的重组近交系（RIL）是通过两个近交系亲本的 F 杂种的自交或兄妹交配重复产生的。与 F 群体相比，RIL 在基因座之间积累了更多的交叉，从而增加了重组体的数量，从而提高了遗传图谱的分辨率。由于它们被近交至同系化阶段，杂合性降低的另一个后果是遗传方差增加，从而提高了 QTL 检测的能力。自交是植物中发展 RIL 的主要形式。兄妹交配是另一种发展 RIL 的方法，但在小型实验室动物中。为了确保 RIL 至少有 98%的纯合性，我们需要大约 7 代的自交或 20 代的兄妹交配。在纯合之前，这些品系被称为预重组近交系（PRERIL）。PRERIL 中性状的表型值通常会被收集，但不会用于 QTL 作图。为了在 PRERIL 中进行 QTL 作图，我们需要在世代 t 时两个标记之间的重组分数，对于 t<7（自交）或 t<20（兄妹交配），以便可以推断标记侧翼的 QTL 的基因型。
在这项研究中，我们开发了用于计算自交、兄妹交配和随机交配中世代 t 的 PRERIL 重组分数的公式。与该主题中现有的工作不同，我们使用计算机代码构建了转移矩阵，以形成连续世代基因型数组的马尔可夫链，即所谓的递归方程。
我们提供了使用新开发的有序基因型数组递归方程计算重组分数的 R 函数。有了递归方程和 R 代码，用户可以在 PRERIL 中进行 QTL 作图。与在 RIL 中进行 QTL 作图相比，可以节省大量的时间和精力。
