Dataset Information

Comparative transcriptome analysis in Chinese cabbage (Brassica rapa ssp. pekinesis) for DEGs of Ogura-, Polima-CMS and their shared maintainer.

ABSTRACT: Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to produce viable pollen in plants. It serves as a useful tool for hybrid seed production via exploiting heterosis in crops. The molecular mechanism of CMS and fertility restoration has been investigated in different crops. However, limited number of reports is available on comparison of Ogura- and Polima-CMS with their shared maintainer in Chinese cabbage. We performed transcript profiling of sterile Ogura CMS (Tyms), Polima CMS (22m2) and their shared maintainer line (231-330) with an aim to identify genes associated with male sterility. In this work, we identified 912, 7199 and 6381 DEGs (Differentially Expressed Genes) in 22m2 Vs Tyms, 231-330 VS 22m2 and 231-330 Vs Tyms, respectively. The GO (Gene Ontology) annotation and KEGG pathway analysis suggested that most of the DEGs were involved in pollen development, carbon metabolism, lipase activity, lipid binding, penta-tricopeptide repeat (PPR), citrate cycle and oxidative phosphorylation, which were down-regulated in both CMS lines. This result will provide an important resource for further understanding of functional pollen development, the CMS mechanism and to improve molecular breeding in Chinese cabbage.

SUBMITTER: Wei X

PROVIDER: S-EPMC7113364 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length of the largest leaf, plant spread angle, single head weight, head width and stem diameter showed stronger performance in Ogura-CMS broccoli than in DGMS line or maintainer fertile line. However, the Ogura-CMS broccoli was poorer in the seed yield and seed germination than in the DGMS line and maintainer fertile line. Additionally, the DGMS broccoli had longer maturation and flowering periods than the Ogura-CMS and maintainer fertile lines. There were obvious differences in the honey gland, happening in the male sterility and fertile lines of broccoli. Additionally, the mechanism regulating Ogura-CMS and DGMS in broccoli was investigated using florets transcriptome analyses of the Ogura-CMS, DGMS and maintainer fertile lines. As a result, a total of 2670 differentially expressed genes (DEGs) were detected, including 1054 up- and 1616 downregulated genes in the Ogura-CMS and DGMS lines compared to the maintainer fertile line. A number of functionally known genes involved in plant hormones (auxin, salicylic acid and brassinosteroid), five Mitochondrial Oxidative Phosphorylation (OXPHOS) genes of atp8, LOC106319879, LOC106324734, LOC106314622 and LOC106298585, and three upregulated genes (Lhcb1, Lhcb3 and Lhcb5) associated with the photosynthesis-antenna protein pathway, were obviously detected to be highly associated with reproductive development including flowering time, maturity and reproductive period in the Ogura-CMS and DGMS broccoli comparing to their maintainer fertile line. Our research would provide a comprehensive foundation for understanding the differences of electrophysiological, morphological and transcriptomic profiles in the Ogura-CMS, DGMS and maintainer broccoli, and as well as being beneficial to exploring the mechanism of male sterility in Brassica crops.

Project description:BACKGROUND: Chinese cabbage (Brassica rapa ssp. pekinensis) is a member of one of the most important leaf vegetables grown worldwide, which has experienced thousands of years in cultivation and artificial selection. The entire Chinese cabbage genome sequence, and more than forty thousand proteins have been obtained to date. The genome has undergone triplication events since its divergence from Arabidopsis thaliana (13 to 17 Mya), however a high degree of sequence similarity and conserved genome structure remain between the two species. Arabidopsis is therefore a viable reference species for comparative genomics studies. Variation in the number of members in gene families due to genome triplication may contribute to the broad range of phenotypic plasticity, and increased tolerance to environmental extremes observed in Brassica species. Transcription factors are important regulators involved in plant developmental and physiological processes. The AP2/ERF proteins, one of the most important families of transcriptional regulators, play a crucial role in plant growth, and in response to biotic and abiotic stressors. Our analysis will provide resources for understanding the tolerance mechanisms in Brassica rapa ssp. pekinensis. RESULTS: In the present study, 291 putative AP2/ERF transcription factor proteins were identified from the Chinese cabbage genome database, and compared with proteins from 15 additional species. The Chinese cabbage AP2/ERF superfamily was classified into four families, including AP2, ERF, RAV, and Soloist. The ERF family was further divided into DREB and ERF subfamilies. The AP2/ERF superfamily was subsequently divided into 15 groups. The identification, classification, phylogenetic reconstruction, conserved motifs, chromosome distribution, functional annotation, expression patterns, and interaction networks of the AP2/ERF transcription factor superfamily were predicted and analyzed. Distribution mapping results showed AP2/ERF superfamily genes were localized on the 10 Chinese cabbage chromosomes. AP2/ERF transcription factor expression levels exhibited differences among six tissue types based on expressed sequence tags (ESTs). In the AP2/ERF superfamily, 214 orthologous genes were identified between Chinese cabbage and Arabidopsis. Orthologous gene interaction networks were constructed, and included seven CBF and four AP2 genes, primarily involved in cold regulatory pathways and ovule development, respectively. CONCLUSIONS: The evolution of the AP2/ERF transcription factor superfamily in Chinese cabbage resulted from genome triplication and tandem duplications. A comprehensive analysis of the physiological functions and biological roles of AP2/ERF superfamily genes in Chinese cabbage is required to fully elucidate AP2/ERF, which provides us with rich resources and opportunities to understand crop stress tolerance mechanisms.

Dataset Information

Comparative transcriptome analysis in Chinese cabbage (Brassica rapa ssp. pekinesis) for DEGs of Ogura-, Polima-CMS and their shared maintainer.

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