Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

Abstract

Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE were still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.

Dissection of a Cell Atlas of Developing Somatic Embryos in Cotton by Single-cell RNA-sequencing and Spatial Transcriptomic and Metabolomic Analyses

“…'Globular embryo cell' (cluster 2) expressed the homologue of early embryonic vascular marker gene homeobox gene 8 (ATHB-8) (Gh_D05G049400) and the homologue of marker gene baby boom (BBM) (Gh_D08G251600) that induces somatic embryogenesis 40,41 (Supplementary information, Table S5). In section 2, 'pro-embryogenic cells_3' (cluster 3) expressed the homologue of embryonic epidermal cell marker gene protodermal factor 1 (PDF1) (Gh_D04G040400) and the homologous gene of WOX9 for embryonic pattern formation 42 , and 'pro-embryogenic cells_4' (cluster 4) expressed the homologous marker gene of AP2-like ethylene-responsive transcription factor 6 (AIL6) (Gh_D10G104500) for somatic embryogenesis 43 , 'pro-embryogenic cells_5' (cluster 5) expressed the homologous marker gene of BBM associated with somatic embryogenesis 40 . The homologous marker gene of auxin response factor 5 (ARF5) (Gh_D05G188200) and ANT for embryonic vascular tissue formation were found in 'globular embryo cell_1' (cluster 1) 35,44 , 'globular embryo cell_2' (cluster 2) expressed the homologous marker gene of oral homeotic protein apetala 2 (AP2) (Gh_A11G207700) for somatic embryogenesis 45 , and 'globular embryo cell_6' (cluster 6) also expressed the homologous marker gene of WOX9 and WOX13 29,39 (Supplementary information, Table S6).…”

Dissection of a Cell Atlas of Developing Somatic Embryos in Cotton by Single-cell RNA-sequencing and Spatial Transcriptomic and Metabolomic Analyses

“…In section 2, 'pro-embryogenic cells_3' (cluster 3) expressed the homologue of embryonic epidermal cell marker gene protodermal factor 1 (PDF1) (Gh_D04G040400) and the homologous gene of WOX9 for embryonic pattern formation 42 , and 'pro-embryogenic cells_4' (cluster 4) expressed the homologous marker gene of AP2-like ethylene-responsive transcription factor 6 (AIL6) (Gh_D10G104500) for somatic embryogenesis 43 , 'pro-embryogenic cells_5' (cluster 5) expressed the homologous marker gene of BBM associated with somatic embryogenesis 40 . The homologous marker gene of auxin response factor 5 (ARF5) (Gh_D05G188200) and ANT for embryonic vascular tissue formation were found in 'globular embryo cell_1' (cluster 1) 35,44 , 'globular embryo cell_2' (cluster 2) expressed the homologous marker gene of floral homeotic protein apetala 2 (AP2) (Gh_A11G207700) for somatic embryogenesis 45 , and 'globular embryo cell_6' (cluster 6) also expressed the homologous marker gene of WOX9 and WOX13 29,39 (Supplementary Table 6).…”

Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica

“…In woody plants, Gautier et al. [32] compared embryogenic callus (EC) and non-embryogenic callus (NEC) in Douglas-fir (P. menziesii), and more recently, Chen et al [33], Wang et al [34] and Qi et al [35] compared EC and redifferentating embryos in Dimocarpus longan, Hevea brasiliensis and hybrid sweetgum (Liquidambar styraciflua × Liquidambar formosana) respectively.…”