Data from: Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping.

The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction, a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost-efficient method for large-scale, high-precision genotyping-by-sequencing.减数分裂过程中现有遗传变异的重排，在进化与育种领域均具有重要价值。遗传变异的重组依赖于同源染色体间交叉互换（crossovers, COs）的形成。全基因组范围内的交叉互换分布模式，可通过对F2群体（F2 populations）个体开展短读长测序（short-read sequencing）得以快速且精准地解析，该方法亦可用于数量性状位点（quantitative trait locus, QTL）定位。尽管近年来测序成本已大幅下降，但针对数百个个体的文库制备（library preparation）成本仍居高不下。为实现对大型作图群体开展低覆盖度全基因组测序（low-coverage whole-genome sequencing），从而快速、低成本地完成交叉互换检测与数量性状位点定位，我们开发了一种全新的文库制备方法，并搭配训练型个体基因组重建（Trained Individual GenomE Reconstruction）——这是一种用于重组个体基因型与交叉互换预测的概率模型。以源自两个拟南芥（Arabidopsis thaliana）生态型的数百个F2群体个体为例，我们将绝大多数交叉互换断点精确定位至2 kb范围内，并将一个主效开花时间数量性状位点缩小至9 kb的区间内。此外，一处异常低重组的延伸区域揭示了4号染色体长臂上存在1.8 Mb的倒位多态性。我们未观察到携带与不携带DNA解旋酶基因RECQ4A（DNA helicase gene RECQ4A）功能拷贝的F2个体之间，交叉互换的频率与分布存在显著差异。综上，我们提出了一种适用于大规模、高精度测序分型的低成本新方法。