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

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.

Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

“…It reflects the amplification of tandem repeat genes is asymmetric between the two species. Tandem duplication also contributed to XTH gene family expansion in barley, tobacco, sorghum, and soybean [ 15 , 19 , 51 , 52 ] .…”

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

“…In addition, constitutive enzymatic responses to FO infection appear to be important with changes in glutathione S-transferases, peroxidases, and phenylalanine ammonia lyase enzyme levels and activities being significant upon pathogen attack [19]. Changes also occur in the types and levels of cell-wall proteins, proteinase inhibitors, hydrolytic enzymes, and pathogenesis-related (PR) proteins and phytoalexin biosynthetic enzymes also appear to play important roles in FO defense [19][20][21]. Upregulation of genes involved in shikimate phenylpropanoid-lignin and cellulose synthesis pathways is possibly the reason of resistance in many cultivars where reduced spores are attached and resistance to FO is enhanced [18].…”

Genome-wide identification, and phylogenetic and expression profiling analyses of XTH gene families in Brassica rapa L. and Brassica oleracea L.

“…It re ects the ampli cation of tandem repeat genes is asymmetric between the two species. Tandem duplication also contributed to XTH gene expansion in barley, tobacco, sorghum, and soybean [11,15,44,45] Since the Brassica ancestor diverged from a common ancestor with A. thaliana at ~20 Mya; subsequently, the Brassica ancestor underwent WGT event at ~15.9 Mya. Then, the Brassica ancestor diverged to form the modern B. rapa and B. oleracea about 3.75 Mya [33][34][35][36].…”