Deep transcriptomic study reveals the role of cell wall biosynthesis and organization networks in the developing shell of peanut pod

Abstract

Background Peanut (Arachis hypogaea L.) belongs to an exceptional group of legume plants, wherein the flowers are produced aerially, but the pods develop under the ground. In such a unique environment, the pod’s outer shell plays a vital role as a barrier against mechanical damage and soilborne pathogens. Recent studies have reported the uniqueness and importance of gene expression patterns that accompany peanut pods’ biogenesis. These studies focused on biogenesis and pod development during the early stages, but the late developmental stages and disease resistance aspects still have gaps. To extend this information, we analyzed the transcriptome generated from four pod developmental stages of two genotypes, Hanoch (Virginia-type) and IGC53 (Peruvian-type), which differs significantly in their pod shell characteristics and pathogen resistance. Results The transcriptome study revealed a significant reprogramming of the number and nature of differentially expressed (DE) genes during shell development. Generally, the numbers of DE genes were higher in IGC53 than in Hanoch, and the R5-R6 transition was the most dynamic in terms of transcriptomic changes. Genes related to cell wall biosynthesis, modification and transcription factors (TFs) dominated these changes therefore, we focused on their differential, temporal and spatial expression patterns. Analysis of the cellulose synthase superfamily identified specific Cellulose synthase (CesAs) and Cellulose synthase-like (Csl) genes and their coordinated interplay with other cell wall-related genes during the peanut shell development was demonstrated. TFs were also identified as being involved in the shell development process, and their pattern of expression differed in the two peanut genotypes. The shell component analysis showed that overall crude fiber, cellulose, lignin, hemicelluloses and dry matter increased with shell development, whereas K, N, protein, and ash content decreased. Genotype IGC53 contained a higher level of crude fiber, cellulose, NDF, ADF, K, ash, and dry matter percentage, while Hanoch had higher protein and nitrogen content. Conclusions The comparative transcriptome analysis identified differentially expressed genes, enriched processes, and molecular processes like cell wall biosynthesis/modifications, carbohydrate metabolic process, signaling, transcription factors, transport, stress, and lignin biosynthesis during the peanut shell development between two contrasting genotypes. TFs and other genes like chitinases were also enriched in peanut shells known for pathogen resistance against soilborne major pathogens causing pod wart disease and pod damages. This study will shed new light on the biological processes involved with underground pod development in an important legume crop.

QTL Mapping for Pod Quality and Yield Traits in Snap Bean (Phaseolus vulgarisL.)

“…Our results contrast with other recent research, which identified shattering QTL located on chromosomes Pv03, Pv05, Pv08, and Pv09 (Rau et al, 2019;Parker et al, 2020). Legume pod dehiscence is known to be controlled by downstream NAC and MYB family transcription factors which also regulate the formation of secondary cell walls (Nakano et al, 2015;Ohtani and Demura, 2019;Takahashi et al, 2020;Watcharatpong et al, 2020;Zhang and Singh 2020;Chen et al, 2021;Gupta et al, 2021). Additional genes responsible for controlling legume shattering, such as the soybean dirigent gene PDH1 and PvPdh1 in common bean, influence the torsion of pod valves without causing anatomical alterations, as observed in studies by Suzuki et al (2009) and Parker et al (2020).…”

Biochar alleviated the toxic effects of microplastics‐contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation

“…37 In this study, 92.31% high-abundance DEGs of the ethylene signal pathway exhibited completely opposite expression trends in comparisons T1-v-T2 and T2-v-T3. Moreover, Gupta et al 41 found that there exists a strong interaction between ethylene and auxin during pod development, and this interaction is critical for peanut pod development. According to our results, we found that microplastics contamination in the geocarposphere soil caused serious interference with the expressions of auxin and ethylene signaling pathway genes in peanut pod, which affected the synergistic regulation of pod development by auxin and ethylene, whereas the application of biochar could correct these disruptions caused by microplastics contamination, and effectively restore the development of peanut pod in a microplasticscontaminated geocarposphere soil.…”

“…In this study, 92.31% high‐abundance DEGs of the ethylene signal pathway exhibited completely opposite expression trends in comparisons T1‐v‐T2 and T2‐v‐T3. Moreover, Gupta et al 41 . found that there exists a strong interaction between ethylene and auxin during pod development, and this interaction is critical for peanut pod development.…”

Transcriptome and targeted hormone metabolome reveal the molecular mechanisms of flower abscission in camellia

“…In the current work, RNA-seq analysis indicated bidirectional changes in the expression of cell wall-related genes, which may be involved in both the continuing abscission process and the growth of undescended organs ( Merelo et al., 2017 ; Wu et al., 2021 ). Pathways associated with cell wall formation, including cell wall biogenesis, galactose and mannose metabolism, aminoglycan, pectin synthesis, and other related genes, exhibited divergent patterns at various phases of CHF and CF ( Wilmowicz et al., 2021 ; Gupta et al., 2021 ). Cell wall production is accompanied by active cell division; several cell wall-related genes may play highly specialized roles in cell wall modification, and some of these gene products may be essential for the optimal function of other genes.…”