Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis

Abstract

Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage.

The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage

“…To further confirm the Ad/Ab distribution pattern of auxin in Chinese cabbage leaf veins, we next evaluated the expression of BrIAA30 ( BraA07g024980.3C ) and BrARF19 ( BraA08g028300.3C ), homologs of which have been used as marker genes to indicate whether auxin shows an Ad/Ab distribution pattern in leaves of Arabidopsis, in the primary leaf veins ( Li et al, 2006 ; Christie et al, 2011 ; Liu et al, 2018 ). The results showed that there were no differences in the expression of BrIAA30 and BrARF19 in the abaxial and adaxial cells before leaf curling; however, significant expression differences were indeed noted at the curling stage, which was in line with the auxin distribution pattern observed in the midribs ( Figures 3K , L ).…”

“…A leaf is the combined results of both leaf margin and vein development. In Arabidopsis, primary leaf morphogenesis temporally coincides with the formation of the major veins (i.e., the midvein and lateral veins), and a suite of mutants exist in which leaf shape and vascular pattern defects are coupled ( Liu et al, 2018 ). Although the interdependency between leaf form acquisition and vascular pattern formation remains largely unexplored, the intertwined pathways of auxin distribution, transport, and signal transduction have long been implicated in controlling all stages of both leaf and vein formation.…”

MiRNA-mediated Changes in DNA Methylation Affect the Expression of Genes Involved in the Thickness of Pod Canopy Trait in Brassica Napus

“…The A and C chromosomes of B. napus come from Chinese cabbage (Brassica rapa) and Brassica oleracea, respectively [48][49][50]. Based on separate studies, the overall methylation level of the Brassica oleracea genome is signi cantly higher than that of Brassica rapa [51][52]. Together, these ndings further support the notion that Brassica napus evolved from the hybridization of B. rapa and B. oleracea and that the methylation patterns of parental species B. rapa and B. oleracea were stably inherited by their offspring, B. napus.…”

Epigenetic Changes Occurring in Plant Inbreeding

“…This suggests that epigenetic mechanisms must be involved in the phenotypic changes. The DNA methylation level of the genome of inbred lines is significantly reduced and alters the expression of many genes that influence the occurrence of traits typical of inbreeding depression [ 146 ].…”