Guangtang Pan

Sichuan Agricultural University

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Co-Authors

Yaou Shen

Sichuan Agricultural University

102

Haijian Lin

Sichuan Agricultural University

Langlang Ma

Sichuan Agricultural University

Guangsheng Yuan

Sichuan Agricultural University

Shibin Gao

Sichuan Agricultural University

Chaoying Zou

Sichuan Agricultural University

Tingzhao Rong

Sichuan Agricultural University

Zhiming Zhang

Shandong Agricultural University

Zhiming Zhang

Shandong Agricultural University

Thomas Lübberstedt

Iowa State University

Cooperative Institutions

Sichuan Agricultural University

222

Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

University of Chinese Academy of Sciences

Institute of Crop Sciences

Shandong Agricultural University

Chinese Academy of Medical Sciences & Peking Union Medical College

Zhejiang University

Ministry of Agriculture and Rural Affairs

Peking University

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Quantitative Genetic Analysis of Seed Dormancy in Maize(Zea mays L.)

ACTA AGRONOMICA SINICA (2006)

Hai Lan Shibin Gao Qingqi Fan Moju Cao Qilin Tang

Inheritance of seed dormancy in the cross R08 × A318 in Zea rnays L. was detected by applying the major gene plus poly-gene model of quantitative traits to a joint analysis of multi-generations （P_(1), P_(2), F_(1), B_(1:2), B_(2:2) and F_(2:3)）. The results indicated that seed dormancy in the cross R08 × A318 was controlled by one major gene with entirely dominance effects plus polygene with additive-dominance effects（the D-4 model）. Genetic variance values of the major gene in B_(1:2), B_(2:2) and F_(2:3) populations were estimated as 0.5863, 0.9260 and 1.4176, while those of polygene were 0.4623, 0.1184 and 0.1022, respectively. And the additive effects values and dominance effects values of major gene was estimated as 1.2172 and -1.2172, while those of polygene were 1.5028 and 1.4334. Heritability values of the major gene in B_(1:2), B_(2:2) and F_(2:3) populations were estimated as 79.65%, 44.8% and 71% while those of polygene were 5.74%, 35.33% and 9.07% ,respectively. There was the maximum value of heritability in the B_(1:2) population.

Polygene

Major gene

Dominance (genetics)

Genetic Analysis

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Transcriptional responses of maize seedling root to phosphorus starvation

Molecular Biology Reports (2013)

Haijian Lin Jian Gao Zhiming Zhang Yaou Shen Hai Lan

MYB

Phytase

Phosphorus deficiency

10.1007/s11033-013-2636-x

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Citations (43)

Additional file 10: of Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation

Figshare (2019)

Xiaoling Zhang Yanli Wang Yuanyuan Yan Hua Peng Yun Long

Table S16. List of enriched pathways for specific common DEGs of ZYDH381â 1 and DH3732 at three stages (stage I II and III). (XLSX 44 kb)

Callus

10.6084/m9.figshare.7782212

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Structural and Functional Characterization of a PollenSpecific Promoter NTPp13 in Tobacco 1

Genetika (2010)

Aiguo Yang S. Zhang Shing‐Hwa Liu Qian Zhao Guangtang Pan

A novel 407 bp nucleotide sequence NTPp13 was isolated from tobacco (Nicotiana tabacum L.) by PCR, its structure and function were characterized. The NTPp13 sequence was highly homologous with the pollen-specific expression promoter Zm13 from maize (Zea mays L.) and contained some key motifs which controlled pollen-specific expression. The NTPp 13 was fused to the β-glucuronidase (G US) reporter gene and transferred into tobacco. Analysis of the transgenic plants revealed that this putative promoter fragment was sufficient to direct GUS expression specifically in the anther, exactly in the pollen and pollen tube, and that G US activity reached the maximum at the stage of pollen grain began to separate. Further study showed that the expression of NTPp13 sequence at pollen was stable at the range of temperature measured. These data suggested that the NTPp13 sequence was likely the essential element of promoter region of an unknown pollen-specific gene from tobacco.

Sequence (biology)

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Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

BMC Genomics (2014)

Hongjun Liu Cheng Qin Zhe Chen Tao Zuo Xuerong Yang

Abstract Background In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana . In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. Results We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. Conclusions This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.

Piwi-interacting RNA

10.1186/1471-2164-15-25

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Citations (96)

Genome expression profile analysis of the maize sheath in response to inoculation to R. solani

Molecular Biology Reports (2014)

Jian Gao Zhe Chen Mao Luo Hua Peng Haijian Lin

Currently, the molecular regulation mechanisms of disease-resistant involved in maize leaf sheaths infected by banded leaf and sheath blight (BLSB) are poorly known. To gain insight into the transcriptome dynamics that are associated with their disease-resistant, genome-wide gene expression profiling was conducted by Solexa sequencing. More than four million tags were generated from sheath tissues without any leaf or development leaf, including 193,222 and 204,824 clean tags in the two libraries, respectively. Of these, 82,864 (55.4 %) and 91,678 (51.5 %) tags were matched to the reference genes. The most differentially expressed tags with log2 ratio >2 or <-2 (P < 0.001) were further analyzed, representing 1,476 up-regulated and 1,754 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Next, the expression patterns of 12 genes were assessed by quantitative real-time PCR, and it is showed the results were general agreement with the Solexa analysis, although the degree of change was lower in amplitude. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize sheath infected by BLSB and provide a comprehensive set of data that are essential for understanding its molecular regulation mechanism.

10.1007/s11033-014-3103-z

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The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection

PLoS ONE (2015)

Hongjun Liu Huangkai Zhou WU Yong-sheng Xiao Li Jing Zhao

Genomic selection is a promising research area due to its practical application in breeding. In this study, impact of realized genetic relationship and linkage disequilibrium (LD) on marker density and training population size required was investigated and their impact on practical application was further discussed. This study is based on experimental data of two populations derived from the same two founder lines (B73, Mo17). Two populations were genotyped with different marker sets at different density: IBM Syn4 and IBM Syn10. A high-density marker set in Syn10 was imputed into the Syn4 population with low marker density. Seven different prediction scenarios were carried out with a random regression best linear unbiased prediction (RR-BLUP) model. The result showed that the closer the real genetic relationship between training and validation population, the fewer markers were required to reach a good prediction accuracy. Taken the short-term cost for consideration, relationship information is more valuable than LD information. Meanwhile, the result indicated that accuracies based on high LD between QTL and markers were more stable over generations, thus LD information would provide more robust prediction capacity in practical applications.

Linkage Disequilibrium

Linkage (software)

Genomic Selection

10.1371/journal.pone.0132379

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Citations (44)

ZmbZIP54 and ZmFDX5 cooperatively regulate maize seedling tolerance to lead by mediating ZmPRP1 transcription

International Journal of Biological Macromolecules (2022)

Fengxia Hou Na Zhang Langlang Ma Lijun An Xun Zhou

Bimolecular fluorescence complementation

Transcription

Two-hybrid screening

10.1016/j.ijbiomac.2022.10.151

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Citations (11)

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Genomics (2015)

Hongjun Liu Xuerong Yang Xinhui Liao Tao Zuo Cheng Qin

10.1016/j.ygeno.2015.03.005

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Citations (16)

Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation

BMC Plant Biology (2017)

Hongjun Liu Langlang Ma Xuerong Yang Lin Zhang Xing Zeng

Maize (Zea mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos. Increased methylation at promoters was associated with down-regulated protein-coding gene expression; however, the correlation was not strong. Analysis of the callus and immature embryos indicated that the methylation increase was induced during induction of embryonic callus, suggesting phenotypic consequences may be caused by perturbations in genomic DNA methylation levels. The correlation between the 21-24nt small RNAs and DNA methylation regions were investigated but only a statistically significant correlation for 24nt small RNAs was observed. These data extend the significance of epigenetic changes during maize embryo callus formation, and the methylation changes might explain some of the observed embryonic callus variation in callus formation.

Callus

Epigenome

RNA-Directed DNA Methylation

Epigenomics

Differentially methylated regions

10.1186/s12870-017-1055-x

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Citations (17)