BnA10.RCO, a homeobox gene, positively regulates leaf lobe formation in Brassica napus L

BnaC06.WIP2-BnaA09.STM transcriptional regulatory module promotes leaf lobe formation in Brassica napus

The lobed leaves of rapeseed (Brassica napus L.) offer significant advantages in dense planting, leading to increased yield. Although AtWIP2, a C2H2 zinc finger transcription factor, acts as a regulator of leaf development in Arabidopsis thaliana, the function and regulatory mechanisms of BnaWIP2 in B. napus remain unclear. Here, constitutive expression of the BnaC06.WIP2 paralog, predominantly expressed in leaf serrations, produced lobed leaves in both A. thaliana and B. napus. We demonstrated that BnaC06.WIP2 directly repressed the expression of BnaA01.TCP4, BnaA03.TCP4, and BnaC03.TCP4 and indirectly inhibited the expression of BnaA05.BOP1 and BnaC02.AS2 to promote leaf lobe formation. On the other hand, we discovered that BnaC06.WIP2 modulated the levels of endogenous gibberellin, cytokinin, and auxin, and controlled the auxin distribution in B. napus leaves, thus accelerating leaf lobe formation. Meanwhile, we revealed that BnaA09.STM physically interacted with BnaC06.WIP2, and ectopic expression of BnaA09.STM generated smaller and lobed leaves in B. napus. Furthermore, we found that BnaC06.WIP2 and BnaA09.STM synergistically promoted leaf lobe formation through forming transcriptional regulatory module. Collectively, our findings not only facilitate in-depth understanding of the regulatory mechanisms underlying lobed leaf formation, but also are helpful for guiding high-density breeding practices through improving leaf morphology in B. napus.

BrrA02.LMI1 Encodes a Homeobox Protein That Affects Leaf Margin Development in Brassica rapa

Leaf margin morphology is an important quality trait affecting the commodity and environmental adaptability of crops. Brassica rapa is an ideal research material for exploring the molecular mechanisms underlying leaf lobe development. Here, we identified BrrA02.LMI1 to be a promising gene underlying the QTL qBrrLLA02 controlling leaf lobe formation in B. rapa, which was detected in our previous study. Sequence comparison analysis showed that the promoter divergences were the most obvious variations of BrrA02.LMI1 between parental lines. The higher expression level and promoter activity of BrrA02.LMI1 in the lobe-leafed parent indicated that promoter variations of BrrA02.LMI1 were responsible for elevating expression and ultimately causing different allele effects. Histochemical GUS staining indicated that BrrA02.LMI1 is mainly expressed at the leaf margin, with the highest expression at the tip of each lobe. Subcellular localization results showed that BrrA02.LMI1 was in the nucleus. The ectopic expression of BrrA02.LMI1 in A. thaliana resulted in a deep leaf lobe in the wild-type plants, and lobed leaf formation was disturbed in BrrA02.LMI11-downregulated plants. Our findings revealed that BrrA02.LMI1 plays a vital role in regulating the formation of lobed leaves, providing a theoretical basis for the selection and breeding of leaf-shape-diverse varieties of B. rapa.

Promoter variations in a homeobox gene, BrLMI1, contribute to leaf lobe formation in Brassica rapa ssp. chinensis Makino

Key message BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage, and cis-regulatory variations lead to the phenotype of lobed or entire leaf margins.Abstract Leaves are the main consumed organ in leafy non-heading Chinese cabbage (Brassica rapa L. ssp. chinensis Makino), and the shape of the leaves is an important economic trait. However, the molecular regulatory mechanism underlying the lobed-leaf trait in non-heading Chinese cabbage remains unclear. Here, we identified a stable incompletely dominant major locus, qLLA10, for lobed leaf formation in non-heading Chinese cabbage. Based on map-based cloning strategies, BrLMI1, a LATE MERISTEM IDENTITY1 (LMI1)-like gene, was predicted as the candidate gene for qLLA10. Genotyping analysis showed that promoter variations of BrLMI1 in the two parents are responsible for elevating the expression in the lobed-leaf parent and ultimately causing the difference in leaf shape between the two parents, and the promoter activity of BrLMI1 was significantly affected by the promoter variations. BrLMI1 was exclusively localized in the nucleus and expressed mainly at the tip of each lobe. Leaf lobe development was perturbed in BrLMI1-silenced plants produced by virus-induced gene silencing assays, and ectopic overexpression of BrLMI1 in Arabidopsis led to deeply lobed leaves never seen in the wild type, which indicates that BrLMI1 is required for leaf lobe formation in non-heading Chinese cabbage. These findings suggested that BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage and that cis-regulatory variations lead to the phenotype of lobed or entire leaf margins, thus providing a theoretical basis for unraveling the molecular mechanism underlying the lobed leaf phenotype in Brassica crops.

The HD-ZIP Gene Family in Watermelon: Genome-Wide Identification and Expression Analysis under Abiotic Stresses

Homeodomain-leucine zipper (HD-ZIP) transcription factors are one of the plant-specific gene families involved in plant growth and response to adverse environmental conditions. However, little information is available on the HD-ZIP gene family in watermelon. In this study, forty ClHDZs were systemically identified in the watermelon genome, which were subsequently divided into four distinctive subfamilies (I-IV) based on the phylogenetic topology. HD-ZIP members in the same subfamily generally shared similar gene structures and conserved motifs. Syntenic analyses revealed that segmental duplications mainly contributed to the expansion of the watermelon HD-ZIP family, especially in subfamilies I and IV. HD-ZIP III was considered the most conserved subfamily during the evolutionary history. Moreover, expression profiling together with stress-related cis-elements in the promoter region unfolded the divergent transcriptional accumulation patterns under abiotic stresses. The majority (13/23) of ClHDZs in subfamilies I and II were downregulated under the drought condition, e.g., ClHDZ4, ClHDZ13, ClHDZ18, ClHDZ19, ClHDZ20, and ClHDZ35. On the contrary, most HD-ZIP genes were induced by cold and salt stimuli with few exceptions, such as ClHDZ3 and ClHDZ23 under cold stress and ClHDZ14 and ClHDZ15 under the salt condition. Notably, the gene ClHDZ14 was predominantly downregulated by three stresses whereas ClHDZ1 was upregulated, suggesting their possible core roles in response to these abiotic stimuli. Collectively, our findings provide promising candidates for the further genetic improvement of abiotic stress tolerance in watermelon.

Precise A∙T to G∙C base editing in the allotetraploid rapeseed (Brassica napus L.) genome

Rapeseed is an important source of oilseed crop in the world. Achieving genetic improvement has always been the major goal in rapeseed production. Single nucleotide substitution is the basis of most genetic variation underpinning important agronomic traits. Nowadays, Cas-base editing acts as an efficient tool to mediate single-base substitution at the target site. In this study, four adenine base editors (ABE) were modified to achieve adenosine base editing at different genome sites in allotetraploid Brassica napus. We designed 18 small guide RNAs to target phytoene desaturase (PDS), acetolactate synthase (ALS), CLAVATA3 (CLV3), CLV2, TRANSPARENT TESTA12 (TT12), carotenoid isomerase (CRTISO), designated de-etiolated-2 (DET2), BRANCHED1 (BRC1), zeaxanthin epoxidase (ZEP) genes, respectively. Among the four ABE systems, pBGE17 had the highest base-editing efficiency, with an average editing efficiency of 3.51%. Target sequencing results revealed that the editing window ranged from A5 to A8 of the protospacer-adjacent motif (PAM) sequence. Moreover, the ABEmax-nCas9NG system with NG PAM was developed, with a base-editing efficiency of 1.22%. These results revealed that ABE system developed in this study could efficiently induce A to G substitution and the ABE-nCas9NG system could broaden editing window in oilseed rape.

BoALG10, an α-1,2 glycosyltransferase, plays an essential role in maintaining leaf margin shape in ornamental kale

The morphological diversity of leaf margin shapes is an identifying characteristic of many plant species. In our previous work, BoALG10 (α-1,2 glycosyltransferase) was predicted to be a key regulator of leaf margin shape in ornamental kale (Brassica oleracea var. acephala). An alanine and a leucine residue in the conserved domain of the smooth-margined S0835 were replaced by an aspartate and a phenylalanine, respectively, in the corresponding positions of the feathered-margined F0819. However, the expression pattern and function of this gene remain unclear. Here, we examined the expression patterns of BoALG10 using quantitative real-time PCR, and found that statistically significant differences in expression existed between F0819 and S0835 in nine developmental stages. The BoALG10 protein localized to the endoplasmic reticulum. The function of BoALG10 was then examined using complementary mutant assays. The overexpression strains phenocopied the smooth leaf margin after introduction of BoALG10 ^S0835 into the feathered-margined inbred line F0819. Simultaneously, irregular dissections appeared in the leaf margins of knockout mutants KO-1 and KO-2, which were generated by CRISPR/Cas9 technology from the smooth-margined inbred line S0835. Microscopic observation showed that the leaf margin cells of the smooth-margined plants S0835 and OE-3 were arranged regularly, while the cells of the feathered-margined plants F0819 and KO-1 were of inconsistent size and distributed in an irregular manner, particularly around the indentations of the leaf. This elucidation of BoALG10 function provides a novel insight into the morphological regulation of leaf margin shape.

Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L

CpDll, encoding an HD-Zip I transcription factor, positively regulates formation of deeply lobed leaf shape in zucchini, Cucurbita pepo, which is associated with sequence variation in its promoter region. Leaf shape is an important horticultural trait in zucchini (Cucurbita pepo L.). Deeply lobed leaves have potential advantages for high-density planting and hybrid production. However, little is known about the molecular basis of deeply lobed leaf formation in this important vegetable crop. Here, we conducted QTL analysis and fine mapping of the deeply lobed leaf (CpDll) locus using recombinant inbred lines and large F₂ populations developed from crosses between the deeply lobed leaf HM-S2, and entire leaf Jin-GL parental lines. We show that CpDll exhibited incomplete dominance for the deeply lobed leaf shape in HM-S2. Map-based cloning provided evidence that CpCll encodes a type I homeodomain (HD)- and Leu zipper (Zip) element-containing transcription factor. Sequence analysis between HM-S2 and Jin-GL revealed no sequence variations in the coding sequences, whereas a number of variations were identified in the promoter region between them. DUAL-LUC assays revealed significantly stronger promoter activity in HM-S2 than that in Jin-GL. There was also significantly higher expression of CpDll in the leaf base of deeply lobed leaves of HM-S2 compared with entire leaf Jin-GL. Comparative analysis of CpDll gene homologs in nine cucurbit crop species (family Cucurbitaceae) revealed conservation in both structure and function of this gene in regulation of deeply lobed leaf formation. Our work provides new insights into the molecular basis of leaf lobe formation in pumpkin/squash and other cucurbit crops. This work also facilitates marker-assisted selection for leaf shape in zucchini breeding.