Genetic and transcriptomic analyses of lignin- and lodging-related traits in Brassica napus

Abstract

Candidate genes associated with lignin and lodging traits were identified by combining phenotypic, genotypic, and gene expression data in B. napus. Brassica napus is one of the world's most important oilseed crops, but its yield can be dramatically reduced by lodging, bending, and falling of its vertical stems. Lignin has been shown to contribute to stem mechanical strength. In this study, we found that the syringyl/guaiacyl (S/G) monolignol ratio exhibits a significant negative correlation with disease and lodging resistance. A total of 92 and 50 SNP and SSR loci, respectively, were found to be significantly associated with five traits, breaking force, breaking strength, lodging coefficient, acid detergent lignin content, and the S/G monolignol ratio using GWAS. To identify novel genes involved in lignin biosynthesis, transcriptome sequencing of high- (H) and low (L)-ADL content accessions was performed. The up-regulated genes were mainly involved in glycoside catabolic processes (especially glucosinolate catabolism) and cell wall biogenesis, while down-regulated genes were involved in glucosinolate biosynthesis, indicating that crosstalk exists between glucosinolate metabolic processes and lignin biosynthesis. Integrating this differential expression with the GWAS analysis, we identified four candidate genes regulating lignin, including glycosyl hydrolase (BnaA01g00480D), CYT1 (BnaA04g22820D), and two encoding transcription factors, SHINE1 (ERF family) and DAR6 (LIM family). This study provides insight into the genetic control of lodging and lignin in B. napus.

Genome-wide association analysis uncovers candidate genes for forage quality traits in Brassica napus stems

“…CYT1 (BnaA04g22820D) was identified at a position approximately 17.0 Mb away from chromosome A04. CYT1, which is also related to the monolignol S/G ratio, as described in a previous report, increases lignin content, and its previously reported position overlaps with the physical location determined in the current study [12]. The cyt1 mutant exhibited a 5-fold decrease in cellulose contents in embryos, impairing cell wall synthesis [42].…”

“…In addition, 84 SSR markers were selected; dominant SSR alleles were scored as present (1) or absent (0) [45]. The physical locations of the SNP and SSR markers were identified as described by Wei et al (2016) [46] and Wei et al (2017a) [12].…”

“…The GWAS threshold was set to P < 3.17 × 10 − 5 (1/ total SNPs, 31,468) for SNPs and P < 0.05 for SSRs. Candidate genes were identified by searching the 500 kb flanking region of each peak marker [12].…”

“…The ADF and NDF contents of crops are negatively related to the digestibility of forage, as well as its nutritional quality and palatability [8]. However, cellulose and lignin are important for the mechanical strength and structural integrity of the stem [9,10], and correlated with lodging and disease resistance [11][12][13]. Therefore, it is important to balance the ADF and NDF contents in stems.…”

The Effects of Planting Density on Lodging Resistance, Related Enzyme Activities, and Grain Yield in Different Genotypes of Oilseed Flax

“…Transcriptomic analyses in Brassica napus L. of lodging resistance traits showed that the upregulated genes were mainly involved in glycoside catabolic processes (especially glucosinolate catabolism) and cell wall biogenesis, whereas downregulated genes were involved in glucosinolate biosynthesis, indicating that crosstalk exists between glucosinolate metabolic processes and lignin biosynthesis. (Wei et al, 2017). Analysis of common buckwheat cultivar with different lodging resistances showed lignin content in the stem at the flowering stage is the critical period in lignin synthesis (Hu et al, 2015).…”