Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers

Abstract

Background Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. Results Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. Conclusions This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.

Effects of Different Chemicals on Sexual Regulation in Persimmon (Diospyros kaki Thunb.) Flowers

“…RNA-Seq analysis can provide information regarding the transcriptional regulation of gene expression; this is an effective approach for data mining in species (e.g., persimmon) where genomic data are unavailable ( Utsumi et al, 2019 ; Li Y. S. et al, 2020 ; Wang L. et al, 2020 ). Integrative analysis from biological-omics data (i.e., metabolomics combined with transcriptomics) reveals differential metabolites that are related to phenotypic changes, as well as genes that cause changes in such metabolites ( Shi et al, 2017 ; Liu D. et al, 2019 ; Qiao et al, 2021 ). In the present study, we investigated the roles of ethrel and ZT in regulating the morphological, cellular, physiological, and molecular characteristics of persimmon flowers.…”

An insight into sainfoin (Onobrychis viciifolia Scop.) breeding: Challenges and achievements

“…Although a series of genetic markers have been developed for sainfoin (Kempf et al., 2016; Mora‐Ortiz et al., 2016; Shen et al., 2019) and a full chloroplast genome sequence has recently been made available (Jin et al., 2021), no reference nuclear genome sequence exists for this species as of yet. Fortunately, research in this area has been progressing steadily in recent years, with an accumulation of transcriptomic data across various tissues from a small number of genotypes (Jin et al., 2021; Kempf et al., 2016; Mora‐Ortiz et al., 2016; Qiao et al., 2021; Shen et al., 2019; Yin et al., 2020), as well as an assessment of microRNAs (miRNAs) in sainfoin grown at low and high altitudes (Yin et al., 2020). Given the escalating interest in this forage crop, it seems highly likely that advances will continue to be made in this context in coming years, which will facilitate breeding activities going forward.…”

“…As such, the use of mixed sainfoin‐alfalfa pasture or rations is considered to be a useful management strategy to mitigate the risk of bloat in grazing animals. In addition to its promise as a high‐quality legume forage, sainfoin is also as attractive for pollinator providing nectars and habitat (Kells et al., 2001; Qiao et al., 2021). Sainfoin nectar contains a medium‐to‐high sucrose concentration of 42–72 g/100 g solution (Kells et al., 2001).…”

Construction of Tissue Culture System of Onobrychis viciaefolia Scop ‘Mengnong’ Anthers

“…Onobrychis viciaefolia Scop. is an excellent perennial leguminous fodder grass (Qiao et al 2021), mainly found in temperate climates and widely cultivated in Europe and other parts of the world. In China, wild species of Onobrychis viciaefolia Scop.…”