Zhiyan Gao: Plant Physiology First Author

Zhiyan Gao, first author of “Expression inheritance and constraints on cis– and trans– regulatory mutations underlying lotus color divergence”

Current Position:

Graduated Ph.D., Wuhan Botanical Garden, Chinese Academy of Sciences

Education:

College of Tropical Crops, Hainan University, Bachelor

Wuhan Botanical Garden, Chinese Academy of Sciences, Doctor of Philosophy

Non-scientific Interests:

Table tennis

Brief bio:

I started my research when I joined the CAS Key Laboratory of Aquatic Botany and Watershed Ecology in 2017 at Wuhan Botanical Garden, Chinese Academy of Sciences. Under the joint guidance of Professor Jinming Chen and Associate Professor Tao Shi, I mainly focused on the effects of cis– and trans-regulatory variants on phenotypic differentiation in lotus plants (Nelumbo).

In this study, two species, Nelumbo nucifera with red flowers and Nelumbo lutea with yellow flowers in Nelumbo, and their F1 hybrids were used as experimental subjects. Based on single nucleotide polymorphisms (SNPs) from resequencing and transcriptome sequencing among parents and F1 hybrids, the global allele-specific expression analysis (ASE) was carried out to uncover the relative contributions of genome-wide cis– and trans-regulatory divergences to differentiation of flower color in interspecies. And combing with the contents of total anthocyanidins and carotenoids in high-performance liquid chromatography (HPLC), the role of cis– and trans-regulatory variants on key genes which are involved in anthocyanin and carotenoid biosynthesis pathway was also focused on. The main results are the following: (1) Trans-regulatory variants have higher correlations on the differentiation of gene expression in petal tissues between N. nucifera and N. lutea. And genes with significantly higher expression in N. lutea tended to be regulated by trans-regulatory variants. In addition, hub genes in modules from anthocyanin- and carotenoid-related weighted co-expression networks (WGCNA) were preferentially regulated by trans-only with dominant inheritance, which involved the rewiring of the anthocyanin and carotenoid gene regulatory networks between the two species. (2) Genes with different regulatory categories preferred a specific inheritance mode of gene expression in F1 hybrids. Genes under cis-only and trans-only regulation were significantly enriched for additive inheritance and dominant inheritance, respectively. In contrast, genes under antagonistic cis– and trans-effects showed significant enrichment of transgressive inheritance. (3) In pleiotropic constraints, genes with trans-only regulation exhibited a relatively broader expression breadth and a higher expression level than genes with cis-only regulation. They were more likely to be retained after whole-genome duplication in lotus and be subjected to higher selective sweep pressure. (4) There are multiple known genes under cis– and trans-regulatory variants in modules from WGCNA involved in ABP and CBP. For example, the ACT gene underwent cis–trans compensating regulation and the GSTF11 gene with cis–trans enhancing regulation exhibited much higher expression in N. nucifera to promote anthocyanin accumulation. And the expression level of the LCYE gene was significantly higher in N. lutea to promote carotenoid accumulation, suggesting cis– and trans-regulatory variants involved in the rewiring of the anthocyanin and carotenoid gene regulatory networks. And the expression differences of these three genes have important impacts on the flower color differentiation between the two lotus species. The above results in this study would provide a new perspective on the genetic mechanism of phenotypic polymorphism in Nelumbo.

姓名：高志妍

目前职位：2022级已毕业博士生

教育经历：

海南大学热带作物学院/农学学士

中国科学院武汉植物园/理学博士

兴趣爱好：

乒乓球

个人简介：

2017至2022年，我有幸加入中国科学院武汉植物园水生植物生物地理学课题组，在陈进明研究员和石涛副研究员的指导下完成了硕博连读，主要从事顺反式调控变异对莲属植物表型性状分化作用机制的研究。本研究以莲属植物中花色上发生显著表型分化的莲（红色花）和美洲黄莲（黄色花）以及两者的杂交F1代的花瓣为研究对象，利用重测序和转录组数据中的SNP标记进行等位基因特异性表达分析，结合高效液相色谱仪对花青素或类胡萝卜素含量的测定，来探究莲属植物两物种间花色分化的顺反式调控变异相关问题，着重关注顺反式调控变异对花色合成代谢通路中关键基因的作用。主要研究结果如下：（1）反式调控变异与莲属植物物种间花瓣组织中差异表达的基因具有相对较高的相关性，同时与种间差异表达基因中美洲黄莲的高表达更相关；在花色含量相关的加权共表达网络中的连通性高的基因更易受发生反式调控变异，从而参与色素基因调控网络的种间分化；（2）不同类别受顺反式调控变异的基因在杂交F1代中倾向于特定的基因表达遗传方式，具体包括受仅顺式调控变异或仅反式调控变异的基因在杂交F1代中分别倾向于加性遗传或显性遗传方式，而受顺反式补偿或完全补偿调控的基因则显著富集于超亲遗传方式；（3）在基因多效性约束的不同方面上，受仅反式调控的基因具有更高的表达广谱性和表达水平，并更容易在莲的全基因组复制事件后保留，并受到更高的清除性选择压力作用；（4）在与花色含量显著相关的加权共表达网络的高连通性基因中有大量的已知花青素、类胡萝卜素通路关键基因，如受顺反式补偿调控的ACT基因和受顺反式增强调控的GSTF11基因在莲中显著高表达，而受仅顺式调控变异的LCYE基因在美洲黄莲中显著高表达，表明了两类花色素关键酶类基因的种间顺反式调控变异影响了花色素积累的表达分化。本研究的结果为