Sequence and expression variations suggest an adaptive role for the DA1-like gene family in the evolution of soybeans

Genome-Wide Identification and Expression Analysis of the DA1 Gene Family in Sweet Potato and Its Two Diploid Relatives

The DA1-like gene family plays a crucial role in regulating seed and organ size in plants. The DA1 gene family has been identified in several species but has not yet been reported in sweet potatoes. In this study, nine, eleven, and seven DA1s were identified in cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid wild relatives, I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively. The DA1 genes were classified into three subgroups based on their phylogenetic relationships with Arabidopsis thaliana and Oryza sativa (rice). Their protein physiological properties, chromosomal localization, phylogenetic relationships, gene structure, promoter cis-elements, and expression patterns were systematically analyzed. The qRT-PCR results showed that the expression levels of four genes, IbDA1-1, IbDA1-3, IbDA1-6, and IbDA1-7, were higher in the sweet potato leaves than in the roots, fiber roots, and stems. In our study, we provide a comprehensive comparison and further the knowledge of DA1-like genes in sweet potatoes, and provide a theoretical basis for functional studies.

Oat AsDA1-2D enhances heat stress tolerance and negatively regulates seed-storage globulin

The importance of oats has increased because of their high nutritional value and health benefits in the human diet. High-temperature stress during the reproductive growth period has a detrimental effect on grain morphology by changing the structure and concentration of several seed-storage proteins. DA1, a conserved ubiquitin-proteasome pathway component, plays an important role in regulating grain size by controlling cell proliferation in maternal integuments during the grain-filling stage. However, there have been no reports or studies on oat DA1 genes. In this study, we identified three DA1-like genes (AsDA1-2D, AsDA1-5A, and AsDA1-1D) using genome-wide analysis. Among these, AsDA1-2D was found to be responsible for high-temperature stress tolerance via a yeast thermotolerance assay. The physical interaction of AsDA1-2D with oat-storage-globulin (AsGL-4D) and a protease inhibitor (AsPI-4D) was observed using yeast two-hybrid screening. A subcellular localization assay revealed that AsDA1-2D and its interacting proteins are localized in the cytosol and plasma membrane. An in vitro pull-down assay showed that AsDA1-2D forms a complex with both AsPI-4D and AsGL-4D. An in vitro cell-free degradation assay showed that AsGL-4D was degraded by AsDA1-2D under high-temperature conditions and that AsPI-4D inhibited the function of AsDA1-2D. These results suggest that AsDA1-2D acts as a cysteine protease and negatively regulates oat-grain-storage-globulin under heat stress.

Modulation of the DA1 pathway in maize shows that translatability of information from Arabidopsis to crops is complex

Modern agriculture is struggling to meet the increasing food, silage and raw material demands due to the rapid growth of population and climate change. In Arabidopsis, DA1 and DAR1 are proteases that negatively regulate cell proliferation and control organ size. DA1 and DAR1 are activated by ubiquitination catalyzed by the E3 ligase BIG BROTHER (BB). Here, we characterized the DA1, DAR1 and BB gene families in maize and analyzed whether perturbation of these genes regulates organ size similar to what was observed in Arabidopsis. We generated da1_dar1a_dar1b triple CRISPR maize mutants and bb1_bb2 double mutants. Detailed phenotypic analysis showed that the size of leaf, stem, cob, and seed was not consistently enlarged in these mutants. Also overexpression of a dominant-negative DA1^R333K allele, resembling the da1-1 allele of Arabidopsis which has larger leaves and seeds, did not alter the maize phenotype. The mild negative effects on plant height of the DA1^R333K_bb1_bb2 mutant indicate that the genes in the DA1 pathway may control organ size in maize, albeit less obvious than in Arabidopsis.

A 24,482-bp deletion is associated with increased seed weight in Brassica napus L

A major QTL for seed weight was fine-mapped in rapeseed, and a 24,482-bp deletion likely mediates the effect through multiple pathways. Exploration of the genes controlling seed weight is critical to the improvement of crop yield and elucidation of the mechanisms underlying seed formation in rapeseed (Brassica napus L.). We previously identified the quantitative trait locus (QTL) qSW.C9 for the thousand-seed weight (TSW) in a double haploid population constructed from F₁ hybrids between the parental accessions HZ396 and Y106. Here, we confirmed the phenotypic effects associated with qSW.C9 in BC₃F₂ populations and fine-mapped the candidate causal locus to a 266-kb interval. Sequence and expression analyses revealed that a 24,482-bp deletion in HZ396 containing six predicted genes most likely underlies qSW.C9. Differential gene expression analysis and cytological observations suggested that qSW.C9 affects both cell proliferation and cell expansion through multiple signaling pathways. After genotyping of a rapeseed diversity panel to define the haplotype structure, it could be concluded that the selection of germplasm with two specific markers may be effective in improving the seed weight of rapeseed. This study provides a solid foundation for the identification of the causal gene of qSW.C9 and offers a promising target for the breeding of higher-yielding rapeseed.

Genome-Wide Analysis of DA1-Like Genes in Gossypium and Functional Characterization of GhDA1-1A Controlling Seed Size

Cotton (Gossypium spp.) is an economically important crop grown for natural fiber and seed oil production. DA1 is a ubiquitin receptor that determines final seed and organ size by restricting the period of cell proliferation. In the present study, we identified 7 DA1-like genes each in cultivated tetraploid (AADD) G. hirsutum and G. barbadense, and 4 and 3 DA1-like genes in their ancestral diploid G. arboreum (A2A2) and G. raimondii (D5D5), respectively. The 7 GhDA1 genes were confirmed to be distributed on four At and three Dt subgenome chromosomes in G. hirsutum. GhDA1-1A showed a high sequence similarity to AtDA1 in Arabidopsis, and they possessed the same functional domains, suggesting conserved functions. The overexpression of GhDA1-1A ^R301K in Arabidopsis significantly increased seed size and seed weight, indicating that GhDA1-1A is a promising target for cotton improvement. This study provides information on the molecular evolutionary properties of DA1-like genes in cotton, which will be useful for the genetic improvement of cotton.

Post-translational modifications regulate the activity of the growth-restricting protease DA1

Plants are a primary food source and can form the basis for renewable energy resources. The final size of their organs is by far the most important trait to consider when seeking increased plant productivity. Being multicellular organisms, plant organ size is mainly determined by the coordination between cell proliferation and cell expansion. The protease DA1 limits the duration of cell proliferation and thereby restricts final organ size. Since its initial identification as a negative regulator of organ growth, various transcriptional regulators of DA1, but also interacting proteins, have been identified. These interactors include cleavage substrates of DA1, and also proteins that modulate the activity of DA1 through post-translational modifications, such as ubiquitination, deubiquitination, and phosphorylation. In addition, many players in the DA1 pathway display conserved phenotypes in other dicot and even monocot species. In this review, we provide a timely overview of the complex, but intriguing, molecular mechanisms that fine-tune the activity of DA1 and therefore final organ size. Moreover, we lay out a roadmap to identify and characterize substrates of proteases and frame the substrate cleavage events in their biological context.

The PHOSPHATE1 genes participate in salt and Pi signaling pathways and play adaptive roles during soybean evolution

BACKGROUND

The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poorly understood.

RESULTS

Cultivated soybean (Glycine max) was domesticated from wild soybean (Glycine soja). To illuminate their roles in this evolutionary process, we comparatively investigated the G. max PHO1 genes (GmPHO1) in Suinong 14 (SN14) and G. soja PHO1 genes (GsPHO1) in ZYD00006 (ZYD6). The sequences of the orthologous Gm-GsPHO1 pairs were grouped into two Classes. The expression of Class I in both SN14 and ZYD6 was widely but relatively high in developing fruits, whereas Class II was predominantly expressed in the roots. The whole family displayed diverse response patterns to salt stresses and Pi-starvation in roots. Between SN14 and ZYD6, most PHO1 genes responded similarly to salinity stresses, and half had sharp contrasts in response to Pi-starvation, which corroborated the differential response capacities to salinity and low-Pi stress between SN14 and ZYD6. Furthermore, in transgenic Arabidopsis plants, most Class II members and GmPHO1;H9 from Class I could enhance salt tolerance, while only two Class II genes (GmPHO1;H4 and GmPHO1;H8) differently altered sensitivity to Pi-starvation. The expression of critical genes was accordingly altered in either salt or Pi signaling pathways in transgenic Arabidopsis plants.

CONCLUSIONS

Our work identifies some PHO1 genes as promising genetic materials for soybean improvement, and suggests that expression variation is decisive to functional divergence of the orthologous Gm-GsPHO1 pairs, which plays an adaptive role during soybean evolution.

Over-expression of mutated ZmDA1 or ZmDAR1 gene improves maize kernel yield by enhancing starch synthesis

Grain weight and grain number are important crop yield determinants. DA1 and DAR1 are the ubiquitin receptors that function as the negative regulators of cell proliferation during development in Arabidopsis. An arginine to lysine mutant at amino acid site 358 could lead to the da1-1 phenotype, which results in an increased organ size and larger seeds. In this study, the mutated ZmDA1 (Zmda1) and mutated ZmDAR1 (Zmdar1) driven by the maize ubiquitin promoter were separately introduced into maize elite inbred line DH4866. The grain yield of the transgenic plants was 15% greater than that of the wild-type in 3 years of field trials due to improvements in the grain number, weight and starch content. Interestingly, the over-expression of Zmda1 and Zmdar1 promoted kernel development, resulting in a more developed basal endosperm transfer cell layer (BETL) than WT and enhanced expression of starch synthase genes. This study suggests that the over-expression of the mutated ZmDA1 or ZmDAR1 genes improves the sugar imports into the sink organ and starch synthesis in maize kernels.

Down-regulation of BnDA1, whose gene locus is associated with the seeds weight, improves the seeds weight and organ size in Brassica napus

Brassica napus L. is an important oil crop worldwide and is the main raw material for biofuel. Seed weight and seed size are the main contributors to seed yield. DA1 (DA means big in Chinese) is an ubiquitin receptor and negatively regulates seed size. Down-regulation of AtDA1 in Arabidopsis leads to larger seeds and organs by increasing cell proliferation in integuments. In this study, BnDA1 was down-regulated in B. napus by over expressed of AtDA1^R358K , which is a functional deficiency of DA1 with an arginine-to-lysine mutation at the 358th amino acid. The results showed that the biomass and size of the seeds, cotyledons, leaves, flowers and siliques of transgenic plants all increased significantly. In particular, the 1000 seed weight increased 21.23% and the seed yield per plant increased 13.22% in field condition. The transgenic plants had no negative traits related to yield. The candidate gene association analysis demonstrated that the BnDA1 locus was contributed to the seeds weight. Therefore, our study showed that regulation of DA1 in B. napus can increase the seed yield and biomass, and DA1 is a promising target for crop improvement.

Genome Wide Identification of LIM Genes in Cicer arietinum and Response of Ca-2LIMs in Development, Hormone and Pathogenic Stress

The eukaryotic lineage-specific LIM protein (LIN11, ISL1, and MEC3) family play pivotal role in modulation of actin dynamics and transcriptional regulation. The systematic investigation of this family has not been carried in detail and rare in legumes. Current study involves the mining of Cicer arietinum genome for the genes coding for LIM domain proteins and displayed significant homology with LIM genes of other species. The analysis led to the identification of 15 members, which were positioned on chickpea chromosomes. The phylogenetic and motif analysis suggested their categorization into two sub-families i.e., Ca-2LIMs and Ca-DA1/DAR, which comprised of nine and six candidates, respectively. Further sub-categories of Ca-2LIMs were recognised as αLIM, βLIM, δLIM and γLIM. The LIM genes within their sub-families displayed conserved genomic and motif organization. The expression pattern of Ca-2LIMs across developmental and reproductive tissues demonstrated strong correlation with established consensus. The Ca-2LIM belongs to PLIM and GLIM (XLIM) was found highly expressed in floral tissue. Others showed ubiquitous expression pattern with their dominance in stem. Under hormonal and pathogenic conditions these LIMs were found to up-regulate during salicylic acid, abscisic acid and Ascochyta rabiei treatment or infection; and down-regulated in response to jasmonic acid treatment. The findings of this work, particularly in terms of modulation of LIM genes under biotic stress will open up the way to further explore and establish the role of chickpea LIMs in plant defense response.