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The use of male sterile lines is one of the ideal means in hybrid seed production. Despite the widespread application of Ogura cytoplasmic male sterile (CMS) lines, the molecular mechanisms remain largely unknown. In this study, histological analyses of floral buds from a CMS line 40MA and its corresponding maintainer line 40MB were conducted, which indicate that microspore abortion was initiated shortly after the tetrad stage. RNA sequencing was performed to analyze the transcriptomes of floral buds from the tetrad stage and the early microspore stages of these two lines. More than 39 million clean reads were generated for each library, and the portions mapped to the reference genome were all above 70.60%. To further analyze the differentially expressed genes (DEGs), the samples were grouped into four pairs, of which the pair of 40MA and 40MB at the early microspore stage showed the most DEGs (5100 members). According to the abnormal appearance of the tapetum cells in 40MA, a series of tapetum development related genes were screened and analyzed. In addition, a total of 623 genes with differential expressions in the tetrad stage, but not in the early microspore stage between the two lines were filtered as the microspore abortion initiation related candidates. Twelve genes were selected to validate the sequencing result by quantitative RT-PCR. In this study, we identified a number of candidate genes involved in the initiation of microspore degeneration, which may provide a new perspective to unravel the molecular mechanism of Ogura CMS.

High-throughput small RNA sequencing and degradome analysis were used in this study to thoroughly investigate the role of miRNA-mediated regulatory network in tuberous root development of radish. Samples from the early seedling stage (RE) and the cortex splitting stage (RL) were used for the construction of six small RNA libraries and one degradome library. A total of 518 known and 976 novel miRNAs were identified, of which, 338 known and 18 novel miRNAs were expressed in all six libraries, respectively. A total of 52 known and 57 novel miRNAs were identified to be significantly differentially expressed between RE and RL, and 195 mRNAs were verified to be the targets of 194 miRNAs by degradome sequencing. According to the degradome analysis, 11 differentially expressed miRNAs had miRNA-mRNA targets, and 13 targets were identified for these 11 miRNAs. Of the 13 miRNA-mRNA targets, 4 genes (RSG11079.t1, RSG11844.t1, RSG16775.t1, and RSG42419.t1) were involved in hormone-mediated signaling pathway, 2 gens (RSG11079.t1 and RSG16775.t1) were related to post-embryonic root development, and 1 gene (RSG23799.t1) was involved in anatomical structure morphogenesis, according to the GO function analysis for biological process. Target Genes participated in these processes are important candidates for further studies. This study provides valuable information for a better understanding of the molecular mechanisms involved in radish tuberous root formation and development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1330-z) contains supplementary material, which is available to authorized users.

We aimed to identify Turnip mosaic virus (TuMV) resistance genes in Chinese cabbage by analysing the TuMV resistance of 43 P1 (resistant), 88 P2 (susceptible), 26 F1, 104 B1 (F1 × P1), 108 B2 (F1 × P2) and 509 F2 individuals. All parents and progeny populations were mechanically inoculated with TuMV-C4. Both F1 and B1 populations showed TuMV resistance. Resistant: susceptible ratios in the B2 and F2 populations were 1 : 1 and 3 : 1, respectively. TuMV resistance in P1 was controlled by a dominant gene, TuRBCS01. Bulked segregation analysis was performed to identify simple sequence repeat or insertion or deletion markers linked to TuRBCS01. Data from 108 B2 individuals with resistant or susceptible phenotypes were analysed using mapmaker/exp 3.0. Polymorphic marker sequences were blast searched on http://brassicadb.org/brad/. TuRBCS01 was found to be linked to eight markers: SAAS_mDN192117a_159 (3.3 cM), SAAS_mDN192117b_196 (4.0 cM), SAAS_mDN192403_148 (13.0 cM), SAAS_mGT084561_233 (6.8 cM), BrID10723 (3.3 cM), mBr4041 (3.3 cM), SAAS_mBr4055_194 (2.6 cM) and mBr4068 (4.0 cM). Further, TuRBCS01 was mapped to a 1.98-Mb region on chromosome A04 between markers BrID10723 and SAAS_mBr4055_194.

Two genes coding for eukaryotic translation initiation factors, eIF4E.a and eIF4E.c, were isolated from twelve accessions of Chinese cabbage (Brassica rapa L. ssp. pekinensis). Polymorphism analysis revealed that 94 and 142 polymorphic sites were characterized from allele of BraeIF4E.a and BraeIF4E.c which produced complex haplotype structures. Six novel haplotypes were characterized from the two alleles respectively. Among the six novel haplotypes of BraeIF4E.a, three loss-of-function mutations were identified in which a conserved single nucleotide deletion mutation cause the early termination of BraeIF4E.a coding product; while for six new BraeIF4E.c haplotypes, their coding product show amino acid substitution mutations on non-conservative amino acid residues which might affect TuMV infection in Chinese cabbage.

Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish.

The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish. De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.