Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa

Abstract

Background Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa , one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GMS remain to be largely unknown. Results Detailed phenotypic observation of ‘Bcajh97-01A/B’, a B. rapa genic male sterile AB line in this study revealed that the aberrant meiotic cytokinesis and premature tapetal programmed cell death occurring in the sterile line ultimately resulted in microspore degeneration and pollen wall defect. Further gene expression profile of the sterile and fertile floral buds of ‘Bcajh97-01A/B’ at five typical developmental stages during pollen development supported the result of phenotypic observation and identified stage-specific genes associated with the main events associated with pollen wall development, including tapetum development or functioning, callose metabolism, pollen exine formation and cell wall modification. Additionally, by using ChIP-sequencing, the genomic and gene-level distribution of trimethylated histone H3 lysine 4 (H3K4) and H3K27 were mapped on the fertile floral buds, and a great deal of pollen development-associated genes that were covalently modified by H3K4me 3 and H3K27me 3 were identified. Conclusions Our study provids a deeper understanding into the gene expression and regulation network during pollen development and pollen wall formation in B. rapa , and enabled the identification of a set of candidate genes for further functional annotation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5637-x) contains supplementary material, which is available to authorized users.

Functional Similarity and Difference among Bra-MIR319 Family in Plant Development

“…In Arabidopsis, except TCPs, miR319 could also target MYB33 and MYB65 and caused anther defects similar to miR159 [6]. However, after WGT in B. campestris, homologs of MYB33 were lost [6,21]. In this study, we confirmed that Bra-miR319a could target homologs of MYB101 (Figure 7).…”

“…The methods for scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observation were previously described [20]. Semithin section observations of leaf and anther were previously described [21]. Image-Pro software was used to measure the size of epidermal cells at 1 K magnification.…”

BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis

“…The only difference between A/B lines is that the male sterile plant (‘ Bcajh97-01A ’) undergoes an aberrant meiotic cytokinesis at the microsporogenesis stage and thus could not produce any functional mature pollen [ 42 , 43 ]. Therefore, we used the RNA-seq data of ‘ Bcajh97-01A/B ’ to identify the male fertility-related CCCH genes in B. campestris [ 44 ]. When analyzing the expression of these genes in five pollen development stages of ‘ Bcajh97-01A/B ’, 11 genes were significantly differentially expressed in at least at one stage between the fertile plant ‘ Bcajh97-01B ’ and the sterile plant ‘ Bcajh97-01A ’, and all genes were downregulated in the sterile plant except Bra007205 ( Figure 1 A).…”

“…In our previous study, we have obtained RNA-Seq data of ‘ Bcajh97-01A/B ’ at five typical flower bud development stages [ 44 ]. Since the only difference between the fertile line ‘ Bcajh97-01B ’ and sterile line ‘ Bcajh97-01A ’ is that ‘ Bcajh97-01A ’ is a male meiotic cytokinesis mutant that cannot produce any viable mature pollen grains, it is an ideal strategy to identify the CCCH zinc-finger protein genes that may be involved in male fertility by comparing the expression levels of these genes in ‘ Bcajh97-01A/B ’.…”

Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.

“…In B. rapa , H3K9me2 was associated with transcriptional repression of genes and was overrepresented in transposable elements (TEs) ( Takahashi et al, 2018 ). H3K27me3 also showed an association with transcriptional repression of genes and a role in tissue- or developmental stage-specific transcriptional regulation ( Akter et al, 2019 ; Payá-Milans et al, 2019 ; Shen et al, 2019 ).…”