Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize

Abstract

The mechanical strength of the stalk affects the lodging resistance and digestibility of the stalk in maize. The molecular mechanisms regulating the brittleness of stalks in maize remain undefined. In this study, we constructed the maize brittle stalk mutant (bk5) by crossing the W22:Mu line with the Zheng 58 line. The brittle phenotype of the mutant bk5 existed in all of the plant organs after the five-leaf stage. Compared to wild-type (WT) plants, the sclerenchyma cells of bk5 stalks had a looser cell arrangement and thinner cell wall. Determination of cell wall composition showed that obvious differences in cellulose content, lignin content, starch content, and total soluble sugar were found between bk5 and WT stalks. Furthermore, we identified 226 differentially expressed genes (DEGs), with 164 genes significantly upregulated and 62 genes significantly downregulated in RNA-seq analysis. Some pathways related to cellulose and lignin synthesis, such as endocytosis and glycosylphosphatidylinositol (GPI)-anchored biosynthesis, were identified by the Kyoto Encyclopedia of Gene and Genomes (KEGG) and gene ontology (GO) analysis. In bulked-segregant sequence analysis (BSA-seq), we detected 2,931,692 high-quality Single Nucleotide Polymorphisms (SNPs) and identified five overlapped regions (11.2 Mb) containing 17 candidate genes with missense mutations or premature termination codons using the SNP-index methods. Some genes were involved in the cellulose synthesis-related genes such as ENTH/ANTH/VHS superfamily protein gene (endocytosis-related gene) and the lignin synthesis-related genes such as the cytochrome p450 gene. Some of these candidate genes identified from BSA-seq also existed with differential expression in RNA-seq analysis. These findings increase our understanding of the molecular mechanisms regulating the brittle stalk phenotype in maize.

Integrated Metabolome and Transcriptome Analysis of Gibberellins Mediated the Circadian Rhythm of Leaf Elongation by Regulating Lignin Synthesis in Maize

“…Meanwhile, the ZmHB34 and ZmHB70 promoted the expression of ZmBM1 , which suggested that ZmHB34 and ZmHB70 were the positive regulators of the lignin synthesis. Many studies showed that GAs may regulate the expression of cell-wall-related genes through DELLA interaction with transcription factors [ 86 , 87 , 88 , 89 , 90 ]. Here, ZmD8 might interact with ZmHB34 and ZmHB70 to inhibit the expression of ZmBM1 , affecting the conversion of sinapinaldehyde to sinapyl alcohol in lignin synthesis ( Figure 8 ).…”

“…Meanwhile, the ZmHB34 and ZmHB70 promoted the expression of ZmBM1, which suggested that ZmHB34 and ZmHB70 were the positive regulators of the lignin synthesis. Many studies showed that GAs may regulate the expression of cell-wall-related genes through DELLA interaction with transcription factors [86][87][88][89][90].…”

“…Meanwhile, the ZmHB34 and ZmHB70 promoted the expre sion of ZmBM1, which suggested that ZmHB34 and ZmHB70 were the positive regulato of the lignin synthesis. Many studies showed that GAs may regulate the expression of ce wall-related genes through DELLA interaction with transcription factors [86][87][88][89][90]. He ZmD8 might interact with ZmHB34 and ZmHB70 to inhibit the expression of ZmBM1, fecting the conversion of sinapinaldehyde to sinapyl alcohol in lignin synthesis (Figure Consequently, the proposed working model was built that GAs could regulate the expre sion of the rhythmic transcription factors ZmMYBr41/87 and ZmHB34/70 to modulate t lignin biosynthetic genes ZmHCT8 and ZmBM1 for manipulating the leaf elongati growth (Figure 8).…”