Biology subjects

Jia, Z.

Publications and source records attributed to Jia, Z..

97 records · Page 6Linked to original sources

bioRxiv2019

Assessment of gibberellin (GA4+7) mediated changes on grain filling, hormonal behaviour and antioxidants in high-density maize (Zea Mays L.)

Dense plant cultivation is an efficient approach to improve the maize production by maximizing the utilization of energy and nutrient. However, dense plant populations may aggravate the abortion rate of young grains and result in fewer number of kernels per ear. Grain filling rate and duration play a decisive role in maize grain yield. Therefore, increasing plant density, consideration of enhancing the grain filling rate and duration of individual maize plant and regulating crop senescence would be the first priority. In this study, we examined the regulatory effects of GA4+7 under two application methods (shank-smearing and silk-smearing). Shank-soaking with GA4+7 at the rate of 0 (CK1), 10 (T1), 60 (T2), and 120 (T3) mg L-1, while silk-smearing at the rate of 0 (CK2), 10 (S1), 60 (S2), and 120 (S3) mg L-1 were used. The results showed that GA4+7 improved the grain filling rate by increasing the content of auxin, gibberellin and zeatin and abscisic acid in grains compared to control plants. In addition, The auxin, gibberellin and zeatin contents in the grains were positively and significantly correlated with the maximum grain weight and the maximum and mean grain-filling rates; the abscisic acid level was positively correlated with the maximum grain weight and the maximum and mean grain-filling rates. Moreover, GA4+7 increased the activities of superoxide dismutases, catalases, peroxidases, and reduced the malondialdehyde content in leaves compared with untreated plants. At the rate of 60 mg L-1, GA4+7 showed the greatest effect for shank-smearing and silk-smearing (T2 and S2), followed by 10 mg L-1 (T1) for shank-smearing and 120 mg L-1 (S3) for silk-smearing. Our results suggest that application of 60 mg L-1 GA4+7 for smearing application could efficiently be used for changed the level of hormones in grains and antioxidant enzymes in ear leaf, would be useful for enhancing grain filling rate and delaying leaves senescence, and resulting in an increasing of maize grain yield.

plant biology↗

bioRxiv2018

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

genomics↗

bioRxiv2018

Inference of Chromosome-length Haplotypes Using Genomic Data of Three to Five Single Gametes

Knowledge of chromosome-length haplotypes will not only advance our understanding of the relationship between DNA and phenotypes, but also promote a variety of genetic applications. Here we present Hapi, an innovative method for chromosomal haplotype inference using only 3 to 5 gametes. Hapi outperformed all existing haploid-based phasing methods in terms of accuracy, reliability, and cost efficiency in both simulated and real gamete datasets. This highly cost-effective phasing method will make large-scale haplotype studies feasible to facilitate human disease studies and plant/animal breeding. In addition, Hapi can detect meiotic crossovers in gametes, which has promise in the diagnosis of abnormal recombination activity in human reproductive cells.

bioinformatics↗

bioRxiv2018

Structure-guided disruption of pseudopilus tip inhibits Type II secretion in Pseudomonas aeruginosa

Pseudomonas aeruginosa utilizes the Type II secretion system (T2SS) to translocate a wide range of large, structured protein virulence factors through the periplasm to the extracellular environment for infection. In the T2SS, five pseudopilins assemble into the pseudopilus that acts as a piston to extrude exoproteins out of cells. Through structure determination of the pseudopilin complexes of XcpVWX and XcpVW and function analysis, we have confirmed that two minor pseudopilins, XcpV and XcpW, constitute a core complex indispensable to the pseudopilus tip. The absence of either XcpV or -W resulted in the non-functional T2SS. Our small-angle X-ray scattering experiment for the first time revealed the architecture of the entire pseudopilus tip and established the working model. Based on the interaction interface of complexes, we have developed inhibitory peptides. The structure-based peptides not only disrupted of the XcpVW core complex and the entire pseudopilus tip in vitro but also inhibited the T2SS in vivo. More importantly, these peptides effectively reduced the virulence of P. aeruginosa towards Caenorhabditis elegans.

microbiology↗

bioRxiv2018

Optimizing Trait Predictability in Hybrid Rice Using Superior Prediction Models and Selective Omic Datasets

Hybrid breeding has dramatically boosted yield and its stability in rice. Genomic prediction further benefits rice breeding by increasing selection intensity and accelerating breeding cycles. With the rapid advancement of technology, other omic data, such as metabolomic data and transcriptomic data, are readily available for predicting genetic values (or breeding values) for agronomically important traits. In the current study, we searched for the best prediction strategy for four traits (yield, 1000 grain weight, number of grains per panicle and number of tillers per plant) of hybrid rice by evaluating all possible combinations of omic datasets with different prediction methods. We conclude that, in rice, the predictions using the combination of genomic and metabolomic data generally produce better results than single-omics predictions or predictions based on other combined omic data. Inclusion of transcriptomic data does not improve predictability possibly because transcriptome does not provide more information for the trait than the sum of genome and metabolome; rather, the computational complexity is substantially increased if transcriptomic data is included in the models. Best linear unbiased prediction (BLUP) appears to be the most efficient prediction method compared to the other commonly used approaches, including LASSO, SSVS, SVM-RBF, SVP-POLY and PLS. Our study has provided a guideline for selection of hybrid rice in terms of which types of omic datasets and which method should be used to achieve higher trait predictability.

genetics↗

bioRxiv2017

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC

The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, to facilitate downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.\n\nAvailabilityGDCRNATools is an R/Bioconductor package that is freely available at https://github.com/Jialab-UCR/GDCRNATools

bioinformatics↗

bioRxiv2017

Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes

The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Interspecific hybrids between C. maxima and C. moschata are widely used as rootstocks for other cucurbit crops. We report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), and the allotetraploidization happened earlier than 3 Mya, when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization is uncommon in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima x C. moschata interspecific F1 hybrid and the two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into plant genome evolution and valuable resources for genetic improvement of cucurbit crops.

genomics↗