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Genome-wide identification, evolution, and expression analysis of RNA-binding glycine-rich protein family in maize

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Journal of Integrative Plant Biology 2014年第10期56卷 1020-1031页

作者： Jianhua Zhangy Yanxin Zhaoy Hailin Xiao Yonglian Zheng Bing Yue national key laboratory of crop genetic improvement Huazhong Agricultural University

The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB‐GRPs distributed on 10 chromosomes were identified in maize（Zea mays L.）, and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified,while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB‐GRPs in maize. Comparative analysis of RB‐GRPs in maize, Arabidopsis（Arabidopsis thaliana L.）, rice（Oryza sativa L.）, and wheat（Triticum aestivum）revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB‐GRPs was significantly regulated by at least two kinds of stresses. In addition, cis‐elements predicted in the promoter regions of the ZmRB‐GRPs also indicated that these ZmRB‐GRPs would be involved in stress response of maize. The preliminary genome‐wide analysis of the RB‐GRPs in maize would provide useful information for further study on the function of the ZmRB‐GRPs.

关键词： Gene expression maize motif prediction phylogenetic analysis RNA‐binding glycine‐rich proteins

Genome-wide association study of callus induction variation to explore the callus formation mechanism of rice

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Journal of Integrative Plant Biology 2019年第11期61卷 1134-1150页

作者： Zhaoyang Zhang Hu Zhao Wei Li Jiemin Wu Zaihui Zhou Fei Zhou Hao Chen Yongjun Lin national key laboratory of crop genetic improvement Huazhong Agricultural University

Rice(Oryza sativa) is one of the most widely cultivated food crops, worldwide. Tissue culture is extensively used in rice breeding and functional genome research. The ability to induce callus determines whether a particular rice variety can be subjected to tissue culture and Agrobacterium-mediated transformation. Over the past two decades, many quantitative trait loci(QTLs)related to callus induction traits have been identified;however, individual genes associated with rice callus induction have not been reported. In this study, we characterized three callus-induction traits in a global collection of 510 rice accessions. A genome-wide association study of the rice population in its entirety as well as subpopulations revealed 21 significant loci located in rice callus induction QTLs. We identified three candidate callus induction genes, namely CRL1, Os BMM1, and Os SET1, which Rese are orthologs of Arabidopsis LBD17/LBD29, BBM, and SWN,respectively, which are known to affect callus ***, we predicted that 14 candidate genes might be involved in rice callus induction and showed that RNA interference(RNAi)-mediated disruption of Os IAA10 inhibited callus formation on tissue culture *** growth in the Os IAA10 RNAi line was not inhibited by synthetic auxin(2,4-D) treatment, suggesting that Os IAA10 may perceive auxin and activate the expression of downstream genes, such as CRL1, to induce callus formation. The significant loci and candidate genes identified here may provide insight into the mechanism underlying callus formation in rice.

关键词： breeding crops

Genome-wide Association Analysis of Ten Chilling Tolerance Indices at the Germination and Seedling Stages in Maize

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Journal of Integrative Plant Biology 2013年第8期55卷 735-744页

作者： Juan Huang Jianhua Zhang Wenzhen Li Wei Hu Lichao Duan Yang Feng Fazhan Qiu Bing Yue national key laboratory of crop genetic improvement Huazhong Agricultural University

Maize seedlings are very sensitive to chilling, especially during the transition phase from heterotrophic to autotrophic growth. genetic dissection of the genetic basis of chilling tolerance would provide useful information for genetic improvement of maize inbreds. In this study, genome-wide association analysis was conducted to explore the genetic architecture of maize chilling tolerance at the seed germination and seedling stages with an association panel of 125 inbreds. Ten tolerance indices （ratios of the performance of 10 germination rates and seedling growth-related traits under chilling stress and control conditions） were investigated to assess the ability of chilling tolerance of the inbreds, and a total of 43 single nucleotide polymorphisms associated with chilling tolerance were detected, with none of them being related to chilling tolerance at both the germination and seedling stages simultaneously. Correlation analysis also revealed that the genetic basis of chilling tolerance at the seed germination stage is generally different from that at the seedling stage. In addition, a total of 40 candidate genes involving 31 of the 43 single nucleotide polymorphisms were predicted, and were grouped into five categories according to their functions. The possible roles of these candidate genes in chilling tolerance were also discussed.

关键词： Association mapping chilling tolerance germination and seedling stage maize.

Identification and characterization of Argonaute gene family and meiosis-enriched Argonaute during sporogenesis in maize

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Journal of Integrative Plant Biology 2014年第11期56卷 1042-1052页

作者： Lihong Zhai Wei Sun Ke Zhang Haitao Jia Lei Liu Zhijie Liu Feng Teng Zuxin Zhang national key laboratory of crop genetic improvement Huazhong Agricultural University

Argonaute（AGO） proteins play a key role in regulation of gene expression through small RNA‐directed RNA cleavage and translational repression, and are essential for multiple developmental processes. In the present study, 17 AGO genes of maize（Zea mays L., ZmAGOs） were identified using a Hidden Markov Model and validated by rapid amplification of cDNA ends assay. Subsequently, quantitative PCR revealed that expressions of these genes were higher in reproductive than in vegetative tissues. AGOs presented five temporal and spatial expression patterns, which were likely modulated by DNA methylation, 50‐untranslated exons and microRNA‐mediated feedback loops. Intriguingly, ZmAGO18 b was highly expressed in tassels during meiosis. Furthermore, in situ hybridization and immunofluorescence showed that ZmAResearchGO18b was enriched in the tapetum and germ cells in meiotic anthers. We hypothesized that ZmAGOs are highly expressed in reproductive tissues, and that ZmAGO18 b is a tapetum and germ cell‐specific member of the AGO family in maize.

关键词： Anther Argonaute gene expression immunochemistry meiosis

Maize orthologs of rice GS5 and their transregulator are associated with kernel development

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Journal of Integrative Plant Biology 2015年第11期57卷 943-953页

作者： Jie Liu Min Deng Huan Guo Sharif Raihan Jingyun Luo Yuancheng Xu Xiaofei Dong Jianbing Yan national key laboratory of crop genetic improvement Huazhong Agricultural University

Genome information from model species such as rice can assist in the cloning of genes in a complex genome, such as maize. Here, we identified a maize ortholog of rice GS5 that contributes to kernel development in maize. The genome- wide association analysis of the expression levels of ZmGSs, and 15 of its 26 paralogs, identified a trans-regulator on chromosome 7, which was a BAK1-1ike gene. This gene that we named as ZmBAK1-7 could regulate the expression of ZmGS5 and three of the paralogs. Candidate-gene association analyses revealed that these five genes were associated with maize kernel development-related traits. Linkage analyses also detected that ZINGS5 and ZmI3AK1-7 co-localized with mapped QTLs. A transgenic analysis of ZINGS5 in Arabidopsis thaliana L. showed a significant increase in seed weight and cell number, suggesting that 2mG55 may have a conserved function among different plant species that affects seed development.

关键词： Association analysis kernel development maize ZmBAK1-7 ZmGS5

Discovery of MicroRNAs Associated with the S Type Cytoplasmic Male Sterility in Maize

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Journal of Integrative Agriculture 2013年第2期12卷 229-238页

作者： YU Jiang-hua ZHAO Yan-xin QIN Ya-ting YUE Bing ZHENG Yong-lian XIAO Hai-lin national key laboratory of crop genetic improvement/Huazhong Agricultural University

MicroRNAs （miRNAs） are endogenous small RNAs that play important regulatory roles in the growth and development processes of plants and animals. In this study, we examined the expression profiles of pollen miRNAs from a maize S type cytoplasmic male sterile line and its fertility restored line. In total, 100 known miRNAs belonging to 20 families and 81 novel miRNAs belonging to 44 families were identified. Two and seven known miRNAs had significant expression difference between the two lines at the level of P-value〈0.01 and 0.01〈P-value〈0.05, respectively. Four miRNAs showing 〉1.5 fold expression difference were verified by stem-loop RT-qPCR. Gene Ontology analysis of miRNA target genes revealed that these genes mainly participated in the transcriptional regulation processes.

关键词： CMS-S microRNAs real-time PCR Solexa sequencing target gene maize

New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize

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Journal of Integrative Plant Biology 2019年第4期61卷 394-405页

作者： Linqian Han Zhenna Mu Zi Luo Qingchun Pan Lin Li national key laboratory of crop genetic improvement Huazhong Agricultural University

Long non-coding RNAs(lncRNAs), whose sequences are approximately 200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize(Zea mays L.) reference genome provides an essential genomic resource, genome-wide annotations of maize lncRNAs have not been updated. Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte. We identified 18,165 high-confidence lncRNAs in maize, of which 6,873 are conserved between maize and teosinte. We uncovered distinct genomic characteristics of conserved lncRNAs,non-conserved lncRNAs, and protein-coding ***, Shannon entropy analysis showed that conserved lncRNAs are likely to be expressed similarly to protein-coding transcripts. Co-expression network analysis revealed significant variation in the degree of co-expression. Furthermore, selection analysis indicated that conserved lncRNAs are more likely than non-conserved lncRNAs to be located in regions subject to recent selection, indicating evolutionary differentiation. Our results provide the latest genomewide annotation and analysis of maize lncRNAs and uncover potential functional divergence between proteincoding, conserved lncRNA, and non-conserved lncRNA genes, demonstrating the high complexity of the maize transcriptome.

关键词： lncRNA maize

Transgenic Bt cotton driven by the green tissue-specific promoter shows strong toxicity to lepidopteran pests and lower Bt toxin accumulation in seeds

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Science China(Life Sciences) 2016年第2期59卷 172-182页

作者： Qing Wang Yi Zhu Lin Sun Lebin Li Shuangxia Jin Xianlong Zhang national key laboratory of crop genetic improvement Huazhong Agricultural University

A promoter of the PNZIP （Pharbitis nil leucine zipper） gene （1.459 kb） was cloned from Pharbitis nil and fused to the GUS（^-glucuronidase） and Bacillus thuringiensis endotoxin （Cry9C） genes. Several transgenic PNZIP：：GUS and PNZIP：：Cry9C cotton lines were developed by Agrobacterium-mediated transformation. Strong GUS staining was detected in the green tissues of the transgenic PNZIP：：GUS cotton plants. In contrast, GUS staining in the reproductive structures such as petals, anther, and immature seeds of PNZIP：：GUS cotton was very faint. Two transgenic PNZIP：：Cry9C lines and one trans- genic cauliflower mosaic virus （CaMV） 35S：：Cry9C line were selected for enzyme-linked immunosorbent assay （ELISA） and insect bioassays. Expression of the Cry9C protein in the 35S：：Cry9C line maintained a high level in most tissues ranging from 24.6 to 45.5 ~tg g-I fresh weight. In green tissues such as the leaves, boll rinds, and bracts of the PNZIP：：Cry9C line, the Cry9C protein accumulated up to 50.2, 39.7, and 48.3 jag g-a fresh weight respectively. In contrast, seeds of the PNZIP：：Cry9C line （PZ1.3） accumulated only 0.26 ~ag g-~ fresh weight of the Cry9C protein, which was 100 times lower than that recorded for the seeds of the CaMV 35S：：Cry9C line. The insect bioassay showed that the transgenic PNZIP：：Cry9C cotton plant exhibited strong resistance to both the cotton bollworm and the pink bollworm. The PNZIP promoter could effectively drive Bt toxin ex- pression in green tissues of cotton and lower accumulated levels of the Bt protein in seeds. These features should allay public concerns about the safety of transgenic foods. We propose the future utility of PNZIP as an economical, environmentally friendly promoter in cotton biotechnology.

关键词： tissue-specific promoter GUS expression Bt toxin transgenic cotton plants

Structural variation in complex genome: detection, integration and function

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Science China(Life Sciences) 2019年第8期62卷 1098-1100页

作者： Ning Yang Shenshen Wu Jianbing Yan national key laboratory of crop genetic improvement Huazhong Agricultural University

Structural variations (SVs) are mutations with large-scale changes (generally>50 bp) in the genome. SVs are major sources of the genetic diversity of organisms and thus are of high relevance to phenotype variations, gene dosage and evolutionary genetics. Except detecting SVs through comparative genetic analyses, dozens of software had been developed based on the alignment of short-reads to a single linear genome in the past decades (Guan and Sung, 2016).

关键词： pro Structural variation in complex genome integration and function