时间： 2022年6月24日（星期五）14:30-16:30
会议号：腾讯会议 323 459 515
主办：www.bob.com、湖北洪山实验室
承办：生命科学技术学院
报告人1：周姚 （14:30-15：30）
题目：利用图泛基因组找回“丢失的遗传力”及促进番茄基因组育种
Graph pangenome captures missing heritability and empowers tomato genomic breeding
摘要：“遗传力丢失”是利用全基因组关联分析 (GWAS) 研究复杂性状的遗传机制时遇到的一个重要科学问题。该问题的关键解决方案是检测出所有因果遗传变异并准确估计它们的贡献。通过本研究中组装的32 个参考水平基因组，并结合已发表的基因组（共838 个番茄基因组），我们准确鉴定了1900 万个各种类型的变异，构建了番茄的图泛基因组。对20323 个基因表达和代谢物性状表型进行遗传力分析发现，利用图泛基因组的变异数据平均估计的性状遗传力为0.41，而使用传统线性参考基因组为0.33。研究发现这约24% 的遗传力增加主要是由于图泛基因组包括了更多的结构变异 (SV)，解决标记与因果变异间的不完全连锁问题。此外，通过利用多位点模型解决等位基因和位点异质性，我们可以利用SV 提高重要农艺性状的全基因组关联分析检测能力。例如，我们发现了两个潜在的可能有助于提高番茄可溶性固形物含量的基因。另外，我们的研究证明了新发现的 SV 可以通过分子标记辅助选择和基因组选择促进番茄的遗传改良。我们的研究促进了对复杂性状遗传力的理解，并展示了图泛基因组在作物育种中的作用。
Missing heritability in genome-wide association studies (GWAS) defines a major problem in genetic analyses of complex biological traits. The pivotal solution to this problem is to identify all causal genetic variants and to measure their individual contributions. Here we report a graph pangenome of tomato constructed by precisely cataloguing over 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome is used for GWAS analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41, compared to 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is due largely to resolving incomplete linkage disequilibrium via inclusion of additional causal structural variants (SVs) identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, SVs improve the power to identify genetic factors underlying agronomically important traits, for example, leading to the identification of two new genes potentially contributing to soluble solid content. The newly identified SVs will facilitate genetic improvement of tomato via both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.
报告人2：杜玉娟（15:30-16:30）
题目：植物母源调控胚根发育
Spatially expressed WIP genes control Arabidopsis embryonic root development
摘要：在动物中，胚胎与母体之间的对话对胚胎早期发育（生长轴的建立、细胞命运的特化等）以及胚胎着床有着重要的调节作用。在植物中，关于母源调控胚胎发育的研究进展缓慢。拟南芥胚根发育的模式是非常规整的，胚根细胞命运的特化和胚根组织类型的分化在时序性上被严格调控。然而，调控这种规整性的遗传机制仍然难以捉摸。我们发现WIP基因家族成员对胚根发育的调控功能可依据它们空间表达的位置划分为两组：在胚胎中和在母体组织中表达的WIP。在胚胎中表达的WIP基因正调控胚根的建成，包括胚根细胞的定向分裂和命运特化。突变掉它们可导致胚根发育的停滞，进而形成无根的幼苗。在母体组织中表达的WIP基因非细胞自主性的负调控胚根细胞命运的特化。突变掉所有的WIP基因，早期胚根的发育模式紊乱，其中胚根细胞非定向分裂，但胚根细胞命运的特化正常。这表明，早期胚根细胞的定向分裂对胚根的形态发生和胚根细胞命运的获得不具有指导性的作用。此外，我们通过EMS化学诱变筛选到了一组SIMILAR TO RCD ONE (SRO)基因家族成员，它们响应母源WIP基因对胚根细胞命运特化的抑制。综上，我们的研究发现了一个由WIP基因调控的母体组织与胚胎组织之间的‘对话’，它特异性调控胚根发育的模式，拓宽了对植物母源调控胚胎发育领域的认知。
Embryo-maternal communication in animals has been regarded to be important in early zygote/embryo development and implantation. In plants, only a few genetic mutations have been identified showing a maternal control of embryo development. In Arabidopsis, proper root development requires that distinct cell types and tissue layers are specified and formed in a restricted manner in space and over time. Despite its importance, genetic controls underlying such regularity remain elusive. Here, we found that WIP genes expressed in the embryo and suspensor functionally oppose those expressed in the surrounding maternal tissues to orchestrate cell division orientation and cell fate specification in the embryonic root, thereby promoting a regular root formation. The maternal WIPs act non-cell autonomously to repress root cell fate specification through SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) family members. When losing all WIPs, root cells divide irregularly in the early embryo, however this barely alters their fate specification and the morphology of post-embryonic roots. Our results reveal a cross-communication between the embryonic and maternal WIPs in controlling root development.