Identification, Characterization, and Expression Analysis of Cell Wall Related Genes in Sorghum bicolor (L.) Moench, a Food, Fodder, and Biofuel Crop

Abstract

Biomass based alternative fuels offer a solution to the world's ever-increasing energy demand. With the ability to produce high biomass in marginal lands with low inputs, sorghum has a great potential to meet second-generation biofuel needs. Despite the sorghum crop importance in biofuel and fodder industry, there is no comprehensive information available on the cell wall related genes and gene families (biosynthetic and modification). It is important to identify the cell wall related genes to understand the cell wall biosynthetic process as well as to facilitate biomass manipulation. Genome-wide analysis using gene family specific Hidden Markov Model of conserved domains identified 520 genes distributed among 20 gene families related to biosynthesis/modification of various cell wall polymers such as cellulose, hemicellulose, pectin, and lignin. Chromosomal localization analysis of these genes revealed that about 65% of cell wall related genes were confined to four chromosomes (Chr. 1–4). Further, 56 tandem duplication events involving 169 genes were identified in these gene families which could be associated with expansion of genes within families in sorghum. Additionally, we also identified 137 Simple Sequence Repeats related to 112 genes and target sites for 10 miRNAs in some important families such as cellulose synthase, cellulose synthase-like, and laccases, etc. To gain further insight into potential functional roles, expression analysis of these gene families was performed using publically available data sets in various tissues and under abiotic stress conditions. Expression analysis showed tissue specificity as well as differential expression under abiotic stress conditions. Overall, our study provides a comprehensive information on cell wall related genes families in sorghum which offers a valuable resource to develop strategies for altering biomass composition by plant breeding and genetic engineering approaches.

Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

“…A custom gene list of CW related genes was obtained from the aggregation of genes listed in previous publications (Petti et al, 2015;McKinley et al, 2016;Rai et al, 2016) Table S3). In addition to the GO enrichment analysis, Fisher's exact test was also performed for every module to detect enrichment in these candidate CW related genes.…”

“…Although biparental (Murray et al, 2008a,b;Shiringani and Friedt, 2011) and broad-based population analyses (Brenton et al, 2016;Li et al, 2018) allowed the identification of candidate genomic regions potentially contributing to the variability of SCW components, these approaches failed to provide an exhaustive understanding of the genetic control of SCW composition variability in sorghum. At the same time, several transcriptomic analyses attempting to elucidate the molecular pathways and mechanisms underlying SCW establishment in developing internodes highlighted the differential expression patterns of extensive gene sets (Shakoor et al, 2014;McKinley et al, 2016;Rai et al, 2016;Kebrom et al, 2017). Nevertheless low levels of congruence between the genetic (Quantitative Trait Loci/Quantitative Trait Nucleotides) and genomic (transcriptomic) approaches have been observed to date.…”

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].…”

Expression of a glucomannan mannosyltransferase gene (GMMT) from Aloe vera is induced by water deficit and abscisic acid

“…There are no reports so far on ABA regulation of the CSLA gene subfamily. However, there is a recent publication on the upregulation by ABA a xyloglucan galactosyl transferase encoded by a CSLC in Sorghum bicolor (Rai et al, 2016).…”