Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Abstract

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

Over-Expression of the Cell-Cycle Gene LaCDKB1;2 Promotes Cell Proliferation and the Formation of Normal Cotyledonary Embryos during Larix kaempferi Somatic Embryogenesis

“…This might result from changes in auxin biosynthesis and signaling [ 17 , 18 ]. Meanwhile, flavonoid biosynthesis is also enhanced in LaMIR166a -overexpressing cultures [ 14 ]. The mechanisms underlying this process were further revealed by identifying the targets of LaHDZ31–34 [ 13 ], which are regulated by miR166 and the developmental stage of somatic embryos [ 24 ].…”

“…Research on somatic embryogenesis in conifers has made remarkable progress, but there are still many problems, such as the low initiation frequency and productivity of somatic embryos [ 7 , 8 , 9 ] as well as the high frequency of abnormal embryos [ 10 ]. These problems make it important to understand the mechanisms underlying somatic embryogenesis, and, as such, in recent years, these factors have been studied in L. kaempferi [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ].…”

Analysis of Quality Changes in Mulberry Fruit at Three Developmental Stages Using Targeted Metabolomics Based on LC‒MS

“…The sample extracts were analyzed using a UPLC-ESI-MS/MS system (UPLC, SHIMADZU Nexera X2, https://www.shimadzu.com.cn/; MS, Applied Biosystems 4500QTRAP, https://www.thermo sher.cn/cn/zh/home/brands/applied-biosystems.html). The chromatographic mass spectrometry acquisition conditions were set according to the method described by Fan et al(2020). The UPLC analysis conditions were as follows: chromatographic column, Agilent SB-C18 (1.8 µm, 2.1 mm * 100 mm); mobile phase: solvent A, pure water containing 0.1% formic acid, and solvent B, acetonitrile containing 0.1% formic acid.…”

Integrated transcriptomic and metabolic analyses provide insights into the maintenance of embryogenic potential and the biosynthesis of phenolic acids and flavonoids involving transcription factors in Larix kaempferi (Lamb.) Carr.

“…Carr is one of the most important fast-growing plantation species in China. It is widely distributed in alpine coniferous forests in northeastern and northern China, Inner Mongolia, and southwestern China ( Zhang et al., 2010 ; Fan et al., 2020 ; Wu et al., 2021 ) and plays a substantial role in forest timber production as well as in ecological construction ( Fan et al., 2020 ). However, L. kaempferi features a long-life span and complex genetic background, making it difficult to breed new lines with conventional methods especially by seed propagation ( Zhang et al., 2014a ; Zhang et al., 2021a ).…”

“…To date, SE technology has been regarded as an ideal system for basic research about gymnosperm growth and development and the related regulatory mechanisms ( Zhang et al., 2021a ). For example, stable gene transformation technology has been established in L. kaempferi SE system and has been utilized to have multiple genes functionally validated ( Fan et al., 2020 ; Fan et al., 2021 ; Kang et al., 2021 ). However, micropropagation through SE technology has not been widely applied to plant regeneration in L. kaempferi due to several problems such as difficult embryonal-suspensor mass (ESM) induction, frequent abnormal embryo development, and challenges in vitro synchronization ( Zhang et al., 2012b ; Zhang et al., 2021a ).…”