Upregulation of the AT-hook DNA binding gene BoMF2 in OguCMS anthers of Brassica oleracea suggests that it encodes a transcriptional regulatory factor for anther development

QTL mapping for seed density per silique in Brassica napus

Seed density per silique (SDPS) and valid silique length (VSL) are two important yield-influencing traits in rapeseed. SDPS has a direct or indirect effect on rapeseed yield through its effect on seed per silique. In this study, a quantitative trait locus (QTL) for SDPS was detected on chromosome A09 using the QTL-seq approach and confirmed via linkage analysis in the mapping population obtained from 4263 × 3001 cross. Furthermore, one major QTL for SDPS (qSD.A9-1) was mapped to a 401.8 kb genomic interval between SSR markers Nys9A190 and Nys9A531. In the same genomic region, a QTL (qSL.A9) linked to VSL was also detected. The phenotypic variation of qSD.A9-1 and qSL.A9 was 53.1% and 47.6%, respectively. Results of the additive and dominant effects demonstrated that the expression of genes controlling SDPS and VSL were derived from a different parent in this population. Subsequently, we identified 56 genes that included 45 specific genes with exonic (splicing) variants. Further analysis identified specific genes containing mutations that may be related to seed density as well as silique length. These genes could be used for further studies to understand the details of these traits of rapeseed.

Mechanism and Utilization of Ogura Cytoplasmic Male Sterility in Cruciferae Crops

Hybrid production using lines with cytoplasmic male sterility (CMS) has become an important way to utilize heterosis in vegetables. Ogura CMS, with the advantages of complete pollen abortion, ease of transfer and a progeny sterility rate reaching 100%, is widely used in cruciferous crop breeding. The mapping, cloning, mechanism and application of Ogura CMS and fertility restorer genes in Brassica napus, Brassica rapa, Brassica oleracea and other cruciferous crops are reviewed herein, and the existing problems and future research directions in the application of Ogura CMS are discussed.

Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development

Male-sterile mutants are useful materials to study the anther and pollen development. Here, whole transcriptome sequencing was performed for inflorescences in three sterile lines of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis), the genic male-sterile line (A line), the Polima cytoplasmic male-sterile (CMS) line (P line), and the Ogura CMS line (O line) along with their maintainer line (B line). In total, 7,136 differentially expressed genes (DEGs), 361 differentially expressed long non-coding RNAs (lncRNAs) (DELs), 56 differentially expressed microRNAs (miRNAs) (DEMs) were selected out. Specific regulatory networks related to anther cell differentiation, meiosis cytokinesis, pollen wall formation, and tapetum development were constructed based on the abortion characteristics of male-sterile lines. Candidate genes and lncRNAs related to cell differentiation were identified in sporocyteless P line, sixteen of which were common to the DEGs in Arabidopsis spl/nzz mutant. Genes and lncRNAs concerning cell plate formation were selected in A line that is defected in meiosis cytokinesis. Also, the orthologs of pollen wall formation and tapetum development genes in Arabidopsis showed distinct expression patterns in the three different sterile lines. Among 361 DELs, 35 were predicted to interact with miRNAs, including 28 targets, 47 endogenous target mimics, and five precursors for miRNAs. Two lncRNAs were further proved to be functional precursors for bra-miR156 and bra-miR5718, respectively. Overexpression of bra-miR5718HG in B. campestris slowed down the growth of pollen tubes, caused shorter pollen tubes, and ultimately affected the seed set. Our study provides new insights into molecular regulation especially the ncRNA interaction during pollen development in Brassica crops.

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.

RESULTS

To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.

CONCLUSION

Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

Advances in Research and Application of Male Sterility in Brassica oleracea

Brassica oleracea is an important vegetable species which belongs to the genus Brassica and the mustard family Brassicaceae Burnett. Strong heterosis in B. oleracea is displayed in yield, quality, disease resistance, and stress tolerance. Heterosis breeding is the main way to improve B. oleracea varieties. Male sterile mutants play an important role in the utilization of heterosis and the study of development and regulation in plant reproduction. In this paper, advances in the research and application of male sterility in B. oleracea were reviewed, including aspects of the genetics, cytological characteristics, discovery of genes related to male sterility, and application of male sterility in B. oleracea. Moreover, the main existing problems and prospect of male sterility application in B. oleracea were addressed and a new hybrids’ production strategy with recessive genic male sterility is introduced.

Genetic and signalling pathways of dry fruit size: targets for genome editing-based crop improvement

Fruit is seed-bearing structures specific to angiosperm that form from the gynoecium after flowering. Fruit size is an important fitness character for plant evolution and an agronomical trait for crop domestication/improvement. Despite the functional and economic importance of fruit size, the underlying genes and mechanisms are poorly understood, especially for dry fruit types. Improving our understanding of the genomic basis for fruit size opens the potential to apply gene-editing technology such as CRISPR/Cas to modulate fruit size in a range of species. This review examines the genes involved in the regulation of fruit size and identifies their genetic/signalling pathways, including the phytohormones, transcription and elongation factors, ubiquitin-proteasome and microRNA pathways, G-protein and receptor kinases signalling, arabinogalactan and RNA-binding proteins. Interestingly, different plant taxa have conserved functions for various fruit size regulators, suggesting that common genome edits across species may have similar outcomes. Many fruit size regulators identified to date are pleiotropic and affect other organs such as seeds, flowers and leaves, indicating a coordinated regulation. The relationships between fruit size and fruit number/seed number per fruit/seed size, as well as future research questions, are also discussed.

Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformatics

Ogura-type cytoplasmic male sterility (Ogura-CMS) has been widely used in the hybrid breeding industry for cruciferous vegetables. Turnip (Brassica rapa ssp. rapifera) is one of the most important local cruciferous vegetables in China, cultivated for its fleshy root as a flat disc. Here, morphological characteristics of an Ogura-CMS line ‘BY10-2A’ and its maintainer fertile (MF) line ‘BY10-2B’ of turnip were investigated. Ogura-CMS turnip showed a reduction in the size of the fleshy root, and had distinct defects in microspore development and tapetum degeneration during the transition from microspore mother cells to tetrads. Defective microspore production and premature tapetum degeneration during microgametogenesis resulted in short filaments and withered white anthers, leading to complete male sterility of the Ogura-CMS line. Additionally, the mechanism regulating Ogura-CMS in turnip was investigated using inflorescence transcriptome analyses of the Ogura-CMS and MF lines. The de novo assembly resulted in a total of 84,132 unigenes. Among them, 5,117 differentially expressed genes (DEGs) were identified, including 1,339 up- and 3,778 down-regulated genes in the Ogura-CMS line compared to the MF line. A number of functionally known members involved in anther development and microspore formation were addressed in our DEG pool, particularly genes regulating tapetum programmed cell death (PCD), and associated with pollen wall formation. Additionally, 185 novel genes were proposed to function in male organ development based on GO analyses, of which 26 DEGs were genotype-specifically expressed. Our research provides a comprehensive foundation for understanding anther development and the CMS mechanism in turnip.

Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

Yellow seed is a desirable trait in Brassica oilseed crops. The B. rapa var. Yellow Sarson carry unique yellow seed color genes which are not only important for the development of yellow-seeded oilseed B. rapa cultivars but this variant can also be used to develop yellow-seeded B. napus. In this study, we developed near-isogenic lines (NILs) of Yellow Sarson for the major seed coat color QTL SCA9-2 of the chromosome A9 and used the NILs to fine map this QTL region and to identify the candidate genes through linkage mapping and transcriptome sequencing of the developing seeds. From the 18.4 to 22.79 Mb region of SCA9-2, six SSR markers showing 0.63 to 5.65% recombination were developed through linkage analysis and physical mapping. A total of 55 differentially expressed genes (DEGs) were identified in the SCA9-2 region through transcriptome analysis; these included three transcription factors, Bra028039 (NAC), Bra023223 (C2H2 type zinc finger), Bra032362 (TIFY), and several other genes which encode unknown or nucleic acid binding protein; these genes might be the candidates and involved in the regulation of seed coat color in the materials used in this study. Several biosynthetic pathways, including the flavonoid, phenylpropanoid and suberin biosynthetic pathways were significantly enriched through GO and KEGG enrichment analysis of the DEGs. This is the first comprehensive study to understand the yellow seed trait of Yellow Sarson through employing linkage mapping and global transcriptome analysis approaches.

Integrated analysis of transcriptome and proteome changes related to the Ogura cytoplasmic male sterility in cabbage

Cabbage (Brassica oleracea L. var. capitata), an important vegetable crop in the Brassicaceae family, is economically important worldwide. In the process of hybrid seed production, Ogura cytoplasmic male sterility (OguCMS), controlled by the mitochondrial gene orf138, has been extensively used for cabbage hybrid production with complete and stable male sterility. To identify the critical genes and pathways involved in the sterility and to better understand the underlying molecular mechanisms, the anther of OguCMS line R2P2CMS and the fertile line R2P2 were used for RNA-seq and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) proteome analysis. RNA-seq analysis generated 13,037,109 to 13,066,594 SE50-clean reads, from the sterile and fertile lines, which were assembled into 36,890 unigenes. Among them, 1,323 differentially expressed genes (DEGs) were identified, consisting of 307 up- and 1016 down-regulated genes. For ITRAQ analysis, a total of 7,147 unique proteins were identified, and 833 were differentially expressed including 538 up- and 295 down-regulated proteins. These were mainly annotated to the ribosome, spliceosome and mRNA surveillance pathways. Combined transcriptomic and proteomic analyses identified 22 and 70 genes with the same and opposite expression profiles, respectively. Using KEGG analysis of DEGs, gibberellin mediated signaling pathways regulating tapetum programmed cell death and four different pathways involved in sporopollenin synthesis were identified. Secretion and translocation of the sporopollenin precursors were identified, and the key genes participating in these pathways were all significantly down-regulated in R2P2CMS. Light and transmission electron (TE) microscopy revealed fat abnormal tapetum rather than vacuolization and degradation at the tetrad and microspore stages of the OguCMS line. This resulted in the failed deposition of sporopollenin on the pollen resulting in sterility. This study provides a comprehensive understanding of the mechanism underlying OguCMS in cabbage.