Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume

Muhammad Amjad Nawaz,Soo In Lee,Gyuhwa Chung,Faheem Shehzad Baloch,Jeong Dong Lee,Hafiz Mamoon Rehman,Muhammad Imtiaz,Seung Hwan Yang

doi:10.1038/s41598-017-11495-4

Abstract

Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.

Highlights

None of the current crops fulfills the demands of an ideal biofuel crop, shifting the attention of scientists towards other crops such as legumes i.e. soybean[4, 6]
While degradation requires a range of pectin modifying and glycoside hydrolases such as endo-1, 4-b-glucanases, endo-xylanases, glucan1, 3-b-glucosidases, polygalacturonases, b-galactosidases, pectate and pectin lyases (PLs), rhamnogalacturonan I lyases, pectin methyl esterases and pectin acetyl esterases[10, 11]
Among the key processes involved in second generation biofuel production, cell wall hydrolysis is an essential step, which demands identification and characterization of enzymes dealing with the cell wall loosening, hydrolysis, and degradation

Summary

Introduction

None of the current crops fulfills the demands of an ideal biofuel crop, shifting the attention of scientists towards other crops such as legumes i.e. soybean[4, 6]. The recent studies on over-expression of pectin modifying enzymes resulted in increased amount of released sugars[20, 21] suggesting that it is essential to understand the mechanistic aspects underlying some natural cell-wall degrading processes. This kind of investigations could be achieved by understanding co-expression networks of gene modules related to cell wall reassembly and degradation[22, 23]. The endogenous production and secretion of plant GHs is sequential and it follows spatial and temporal characteristics and is always compatible with architecture of particular cell wall This in turn recruits enzymes (expansins and pectinases) for separation and expansion and xyloglucanases and cellulases to loosen cell wall. Gene co-expression networks were studied to visualize transcriptional coordination within studied gene families

Methods

Results

Conclusion