Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.

许多重要的作物（例如块茎、块根和树木作物）是异花授粉的。对于这些作物，没有可用于遗传研究和育种的自交系，因为它们是自交不亲和、无性繁殖或世代时间长，这使得鉴定农艺重要基因变得困难，特别是在具有复杂同源多倍体基因组的作物中。在本研究中，我们开发了一种方法 OutcrossSeq，用于基于大型遗传群体的全基因组低覆盖率重测序绘制异交作物中农艺学上重要的基因座，并在 OutcrossSeq 中为不同类型的异交群体设计了三种计算算法。我们将 OutcrossSeq 应用于块根作物（红薯、同源多倍体）、树木作物（核桃树、高度杂合二倍体）、和杂交作物（双交种群）为异交种群生成高密度基因型图，从而能够精确识别重要农艺性状的基因组位点。基于功能线索检测到这些位点的候选致病基因。综上所述，我们的结果表明 OutcrossSeq 是一种稳健且强大的方法，可以以经济高效的方式识别杂合物种（包括多倍体）中的农艺重要基因。OutcrossSeq 软件及其使用说明书可在 www.xhhuanglab.cn/tool/OutcrossSeq.html 下载。综上所述，我们的结果表明 OutcrossSeq 是一种稳健且强大的方法，可以以经济高效的方式识别杂合物种（包括多倍体）中的农艺重要基因。OutcrossSeq 软件及其使用说明书可在 www.xhhuanglab.cn/tool/OutcrossSeq.html 下载。综上所述，我们的结果表明 OutcrossSeq 是一种稳健且强大的方法，可以以经济高效的方式识别杂合物种（包括多倍体）中的农艺重要基因。OutcrossSeq 软件及其使用说明书可在 www.xhhuanglab.cn/tool/OutcrossSeq.html 下载。