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In higher plants, the structure of a flower is precisely controlled by a series of genes. An aberrance flower results in abnormal fruit morphology. Previously, we reported multi-silique rapeseed (Brassica napus) line zws-ms. We identified two associated regions and investigated differentially expressed genes (DEGs); thus, some candidate genes underlying the multi-silique phenotype in warm area Xindu were selected. However, this phenotype was switched off by lower temperature, and the responsive genes, known as thermomorphogenesis-related genes, remained elusive. So, based on that, in this study, we further investigated the transcriptome data from buds of zws-ms and its near-isogenic line zws-217 grown in colder area Ma’erkang, where both lines showed normal siliques only, and the DEGs between them analyzed. We compared the 129 DEGs from Xindu to the 117 ones from Ma’erkang and found that 33 of them represented the same or similar expression trends, whereas the other 96 DEGs showed different expression trends, which were defined as environment-specific. Furthermore, we combined this with the gene annotations and ortholog information and then selected BnaA09g45320D (chaperonin gene CPN10-homologous) and BnaC08g41780D [Seryl-tRNA synthetase gene OVULE ABORTION 7 (OVA7)-homologous] the possible thermomorphogenesis-related genes, which probably switched off the multi-silique under lower temperature. This study paves a way to a new perspective into flower/fruit development in Brassica plants.

Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F2:3 family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.

Background Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecular mechanism underlying this beneficial trait remains unclear. Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines (NILs) zws-ms (multi-silique) and zws-217 (single-silique). We used the Euclidean Distance (ED) to identify genomic regions associated with this trait based on both SNPs and InDels. We also conducted transcriptome sequencing to identify differentially expressed genes (DEGs) between zws-ms and zws-217. Results Genetic analysis using the ED algorithm identified three SNP- and two InDel-associated regions for the multi-silique trait. Two highly overlapped parts of the SNP- and InDel-associated regions were identified as important intersecting regions, which are located on chromosomes A09 and C08, respectively, including 2044 genes in 10.20-MB length totally. Transcriptome sequencing revealed 129 DEGs between zws-ms and zws-217 in buds, including 39 DEGs located in the two abovementioned associated regions. We identified candidate genes involved in multi-silique formation in rapeseed based on the results of functional annotation. Conclusions This study identified the genomic regions and candidate genes related to the multi-silique trait in rapeseed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5675-4) contains supplementary material, which is available to authorized users.

Plant height is a vital agronomic trait for crops, including oilseed crops such as rapeseed (Brassica napus L.). It affects the crop yield, oil content, and lodging resistance in rapeseed. In this study, we investigated a dwarf trait controlled by a semi-dominant allele in rapeseed. A dwarf line, YA2016-12, was crossed with a tall line, G184-189, and an F2 population was established. Forty of the tallest plants and 40 of the shortest plants from the F2 population were selected and two DNA pools (tall and dwarf) were constructed by the bulked segregant analysis (BSA) method. The two DNA pools and two parental DNAs were then re-sequenced. A sliding window analysis was used to calculate the &Delta, (SNP-index) and discover an association region on chromosome A03 with a length of 12.4 Mb. Within this region, we found 1225 genes, including 811 genes with non-synonymous or frameshift mutations between YA2016-12 and G184-189. Alignment to known plant height-related orthologs in Arabidopsis thaliana, as well as KEGG pathway and gene ontology annotations, was used to identify nine candidate genes (BnaA03g31770D, BnaA03g37960D, BnaA03g24740D, BnaA03g40550D, BnaA03g26120D, BnaA03g35130D, BnaA03g42350D, BnaA03g25610D, and BnaA03g39850D) involved in gibberellin or cytokinin signaling. Identification of the causal gene for this trait, and of genetic markers linked to favorable alleles, has potential utility for marker-assisted selection to breed rapeseed varieties with improved height.

Plants constantly suffer from simultaneous infection by multiple pathogens, which can be divided into biotrophic, hemibiotrophic, and necrotrophic pathogens, according to their lifestyles. Many studies have contributed to improving our knowledge of how plants can defend against pathogens, involving different layers of defense mechanisms. In this sense, the review discusses: (1) the functions of PAMP (pathogen-associated molecular pattern)-triggered immunity (PTI) and effector-triggered immunity (ETI), (2) evidence highlighting the functions of salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET)-mediated signaling pathways downstream of PTI and ETI, and (3) other defense aspects, including many novel small molecules that are involved in defense and phenomena, including systemic acquired resistance (SAR) and priming. In particular, we mainly focus on SA and (JA)/ET-mediated signaling pathways. Interactions among them, including synergistic effects and antagonistic effects, are intensively explored. This might be critical to understanding dynamic disease regulation.

Ubiquitin-mediated protein degradation plays a crucial role in enabling plants to effectively and efficiently cope with environmental stresses. The E3 ligases have emerged as a central component of the ubiquitination pathway and modulate plant response to abiotic stresses. However, few such studies have been reported in maize. In this study, a C3HC4-type RING finger E3 ligase in maize, ZmAIRP4 (Zea mays Abscisic acid [ABA]-Insensitive RING Protein 4), which is an ortholog of AtAIRP4, was isolated by reverse transcription polymerase chain reaction with specific primers, and its functions in tolerance to drought stress were described. ZmAIRP4 was upregulated by ABA, polyethylene glycol and sodium chloride. In vitro ubiquitination assays and subcellular localization indicated that ZmAIRP4 was an active E3 ligase predominantly localized in the cytoplasm and nucleus. Compared to wild type, ZmAIRP4-overexpressing Arabidopsis plants were hypersensitive to ABA during early seedling development, and showed enhanced drought tolerance. Moreover, the transcript levels of several drought-related downstream genes in transgenic plants were dramatically increased compared with wild type plants. Our results suggested that E3 ligase ZmAIRP4 is a positive regulator in the drought tolerance response pathway.