Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F₁ (double pseudo-testcross) population from ‘Viroflay’ × ‘Cornell-NO. 9′ was used for genetic mapping by resequencing genotyping. In the paternal ‘Cornell-NO. 9′ map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal ‘Viroflay’ map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the ‘Cornell-NO. 9′ map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.

菠菜（Spinacia olracea L.）是一种雌雄异株的多叶蔬菜，具有约990 Mb的高度重复性基因组，这对于从头改造基因组组装具有挑战性。在我们的研究中，分离的F ₁（双伪testcross）人口来自“ Viroflay”ד Cornell-NO”。通过对基因分型重新测序，将9'用于遗传作图。在父亲'康奈尔-没有。9'图，共绘制了212,414个SNP，总连锁距离为476.83 cM；孕妇的“ Viroflay”图包括29,282个SNP，总遗传距离为401.28 cM。父本和母本地图都具有六个链接组（LG）的预期数量。具有5678个SNP（39个bin标记）的非重组区与性别类型共分离，位于'Cornell-NO'中LG1的45.2 cM。9'映射同时表示性别确定区域（SDR）。将两个图整合到一个共有图中可指导我们将另外的1242个重叠群锚定到来自已发布参考基因组的六个假分子中，从而根据菠菜估计的基因组大小改进了233 Mb（23.4％）的装配。尤其，与我们以前的细胞遗传学研究中的性别偏向FISH信号一致，我们大会中SDR的X对应物估计约为18.4 Mb，位于最大染色体上。该区域的特点是基因密度降低，重复序列百分比更高且没有重组。我们的连锁图提供了改善菠菜基因组重组组装和鉴定菠菜性别决定基因的资源。