Zhiyan Gao, first author of “Expression inheritance and constraints on cis– and trans– regulatory mutations underlying lotus color divergence”
Graduated Ph.D., Wuhan Botanical Garden, Chinese Academy of Sciences
College of Tropical Crops, Hainan University, Bachelor
Wuhan Botanical Garden, Chinese Academy of Sciences, Doctor of Philosophy
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.