D-type cyclin OsCYCD3;1 is involved in the maintenance of meristem activity to regulate branch formation in rice

Functional characterization of D-type cyclins involved in cell division in rice

BACKGROUND

D-type cyclins (CYCD) regulate the cell cycle G1/S transition and are thus closely involved in cell cycle progression. However, little is known about their functions in rice.

RESULTS

We identified 14 CYCD genes in the rice genome and confirmed the presence of characteristic cyclin domains in each. The expression of the OsCYCD genes in different tissues was investigated. Most OsCYCD genes were expressed at least in one of the analyzed tissues, with varying degrees of expression. Ten OsCYCD proteins could interact with both retinoblastoma-related protein (RBR) and A-type cyclin-dependent kinases (CDKA) forming holistic complexes, while OsCYCD3;1, OsCYCD6;1, and OsCYCD7;1 bound only one component, and OsCYCD4;2 bound to neither protein. Interestingly, all OsCYCD genes except OsCYCD7;1, were able to induce tobacco pavement cells to re-enter mitosis with different efficiencies. Transgenic rice plants overexpressing OsCYCD2;2, OsCYCD6;1, and OsCYCD7;1 (which induced cell division in tobacco with high-, low-, and zero-efficiency, respectively) were created. Higher levels of cell division were observed in both the stomatal lineage and epidermal cells of the OsCYCD2;2- and OsCYCD6;1-overexpressing plants, with lower levels seen in OsCYCD7;1-overexpressing plants.

CONCLUSIONS

The distinct expression patterns and varying effects on the cell cycle suggest different functions for the various OsCYCD proteins. Our findings will enhance understanding of the CYCD family in rice and provide a preliminary foundation for the future functional verification of these genes.

Study on the Interactions of Cyclins with CDKs Involved in Auxin Signal during Leaf Development by WGCNA in Populus alba

Cell division plays an indispensable role in leaf morphogenesis, which is regulated via the complexes formed by cyclin and cyclin-dependent kinase (CDK). In this study, gene family analysis, exogenous auxin stimulation, RNA-seq and WGCNA analysis were all used to investigate the molecular mechanisms by which cell-cycle-related factors participated in the auxin signaling pathway on leaf morphogenesis. Sixty-three cyclin members and seventeen CDK members in Populus alba were identified and systematically analyzed. During the evolution, WGD was the main reason that resulted in the expansion of cyclin and CDK genes. Firstly, after a short time treating with auxin to matured leaves of seedlings, genes related to cell division including GRF and ARGOS were both upregulated to restart the transition of cells from G1-to-S phase. Secondly, with three days of continuous auxin stimulation to leaves at different developmental stages, leaves area variation, transcriptomes and hormones were analyzed. By PCA, PCoA and WGCNA analyses, the turquoise module was both positively related to leaf development and auxin. Based on the co-expression analysis and Y2H experiment, PoalbCYCD1;4, PoalbCYCD3;3 and PoalbCYCD3;5 were supposed to interact with PoalbCDKA;1, which could be the trigger to promote the G1-to-S phase transition. The ARF transcription factor might play the key role of connecting the auxin signaling pathway and cell division in leaf morphogenesis by affecting CYC-CDK complexes.

The Secrets of Meristems Initiation: Axillary Meristem Initiation and Floral Meristem Initiation

The branching phenotype is an extremely important agronomic trait of plants, especially for horticultural crops. It is not only an important yield character of fruit trees, but also an exquisite ornamental trait of landscape trees and flowers. The branching characteristics of plants are determined by the periodic initiation and later development of meristems, especially the axillary meristem (AM) in the vegetative stage and the floral meristem (FM) in the reproductive stage, which jointly determine the above-ground plant architecture. The regulation of meristem initiation has made great progress in model plants in recent years. Meristem initiation is comprehensively regulated by a complex regulatory network composed of plant hormones and transcription factors. However, as it is an important trait, studies on meristem initiation in horticultural plants are very limited, and the mechanism of meristem initiation regulation in horticultural plants is largely unknown. This review summarizes recent research advances in axillary meristem regulation and mainly reviews the regulatory networks and mechanisms of AM and FM initiation regulated by transcription factors and hormones. Finally, considering the existing problems in meristem initiation studies and the need for branching trait improvement in horticulture plants, we prospect future studies to accelerate the genetic improvement of the branching trait in horticulture plants.

The selection and application of peduncle length QTL QPL_6D.1 in modern wheat (Triticum aestivum L.) breeding

QPL_6D.1b displayed an additive effect with Rht-B1b and Rht-D1b in reducing wheat plant height and peduncle length, which confers shorter peduncle length and more kernels per spike, and had been broadly selected by Chinese modern wheat cultivars. Peduncle length (PL), as the key component of wheat plant height (PH), plays critical role in determining wheat lodging resistance and wheat pathogen resistance; then, its breeding selection and genetic basis remain largely unclear. Here the PH and PL were investigated in 406 wheat accessions in eight environments. In this study, a PL preferentially QTL QPL_6D.1 was identified in six environments by GWAS, which explained 13.6-24.2% of wheat PL variations in natural population. The allele QPL_6D.1b displayed a significantly additive effect with Rht-B1b and Rht-D1b in controlling PH and PL and could freely combined with Rht-B1b and Rht-D1b in current wheat cultivars. Haplotypic analysis demonstrates the QPL_6D.1b has been selected by Chinese modern wheat cultivar and confers shorter PL and more kernels per spike, highlighting its potentials in wheat breeding.

Genome-Wide Identification, Characterization, and Transcriptomic Analysis of the Cyclin Gene Family in Brassica rapa

Cyclins are involved in cell division and proliferation by activating enzymes required for the cell cycle progression. Our genome-wide analysis identified 76 cyclin genes in Brassica rapa, which were divided into nine different types (A-, B-, C-, D-, H-, L-, P-, T-, and SDS-type). Cyclin genes were unevenly scattered on all chromosomes, with a maximum of 10 on A08 and a minimum of 2 on A04. The gene structure and conserved motif analysis showed that the cyclins which belonged to the same type or subgroup have a comparable intron/exon pattern or motif. A total of 14 collinear gene pairs suggested that the B. rapa cyclin genes experienced a mass of segmental duplication. The Ka/Ks analysis revealed that the Brcyclin gene family has undergone an extensive purifying pressure. By analyzing the cis-elements in the promoters, we identified 11 cis-elements and five of them are related to the hormone response. We observed 48 potential miRNAs targeting 44 Brcyclin genes, which highlighted the involvement of miRNAs in the regulation of cyclin genes. An association analysis between the leaf size and SNPs in mutants and a transcriptome analysis of two Chinese cabbage-cabbage translocation lines also showed that the Brcyclin gene family was involved in the development of the leaves. The functional characterization of the B. rapa cyclin gene family will provide the foundation for future physiological and genetic studies in the regulation of leaf growth.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

BACKGROUND

Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development.

RESULTS

In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation.

CONCLUSIONS

Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Using a high density bin map to analyze quantitative trait locis of germination ability of maize at low temperatures

Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using R/qtl software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10-202.30 Mb segment on chromosome 1. The primary segment was named cQTL1-2, with a phenotypic variation of 5.18-25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to cQTL1-2. The physical distance of cQTL1-2 was reduced to approximately 1.9 Mb. The consistent meta-QTL mQTL1 was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with cQTL1-2. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and mQTL1 found the consistent QTL to be LtQTL1-1. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes GRMZM2G082630 and GRMZM2G115730 were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (P < 0.01).