Sorghum bmr6 mutant analysis demonstrates that a shared MYB1 transcription factor binding site in the promoter links the expression of genes in related pathways

Abstract

Sorghum is not only an important cereal crop but also a biofuel crop. The sorghum brown midrib mutant 6 (bmr6) has a reduced lignin content in the cell walls and vascular tissues, which could potentially be advantageous for cellulosic biofuel production. Meanwhile, both dry matter yield and plant height were decreased in the bmr6 mutant. To identify genes affected in the mutant, differential gene expression analysis was performed for bmr6 and the wild type. As a result, a total of 1,052 differentially expressed genes were detected between the two samples, of which 166 genes were downregulated and 886 genes were upregulated. Five hundred seventy-nine of the 1,052 differentially expressed genes could be assigned to 154 documented pathways. These pathways mainly included primary and secondary metabolism. Therefore, mutation of the bmr6 gene, which impaired the biosynthesis of lignin, ultimately affected the expression of these genes associated with the growth and development of sorghum. Except for the bmr6 gene, 11 key enzyme genes of monolignols biosynthesis were upregulated. Promoter analysis identified that these genes have common MYB sites. It revealed that a feedback mechanism existed in the pathway and a MYB1 transcription factor (Sb02g031190) could associate with the upregulation of these genes in sorghum. In this study, we investigated gene expressions at a global level in sorghum bmr6 mutant and provided valuable insights into the mechanisms of lignin biosynthesis.

Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization

“…Until now, sorghum qPCR assays were performed using a single reference gene to quantify target gene expression in response to various experimental conditions. Traditional reference genes including 18S RNA, Actin, EIF4 α, Tubulin , and Ubiquitin have been used as calibrators for quantifying sorghum gene expression in response to abiotic stresses and during plant growth and development (Yang et al, 2004 ; Jain et al, 2008 ; Cook et al, 2010 ; Shen et al, 2010 ; Wang et al, 2010 ; Dugas et al, 2011 ; Ishikawa et al, 2011 ; Koegel et al, 2013 ; Li et al, 2013 ; Gelli et al, 2014 ; Shakoor et al, 2014 ; Yang et al, 2014b ; Yin et al, 2014 ; Kebrom and Mullet, 2015 ; Li et al, 2015 ; Walder et al, 2015 ). Nevertheless, the reference genes used in these studies were randomly selected from various sources without any experimental validation.…”

Mapping quantitative trait loci for five forage quality traits in a sorghum-sudangrass hybrid

“…According to the relative positions of the markers on the reference sorghum genome (www.gramene.org), a search was performed for candidate genes involved in cellulose and lignin biosynthesis (Li et al, 2013). A gene that is similar to glycosyltransferase (Sb03g026550) in conjugating lignin monomers was found close to qADF3 and qNDF3 on chromosome 3.…”

Tissue-Specific Expression Profiling of Seedling Stage in Early-Maturity Mutant Induced by Carbon Ion Beam in Sweet Sorghum

“…Raw sequences were transformed into clean tags by filtering off adapter-only tags and low-quality tags as described (Li et al, 2013). All the clean tags were mapped to the reference sequences of Sorghum bicolor and only 1 bp of mismatch was considered.…”