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Identification of Differentially Expressed bHLH Genes in Maize under Drought‑Rewatering Treatments

XIE Xiaowen, ZHANG Xinyue, FU Jiaxu, SHAO Jing, WEN Pengfei, WANG Tongchao, WEI Li

Journal of Henan Agricultural Sciences 2023, 52 (9): 33-44. DOI: 10.15933/j.cnki.1004-3268.2023.09.004

Abstract （1616）

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In order to explore bHLH transcription factors related to drought resistance in maize（ Zea mays），differentially expressed bHLH genes were identified under drought‑rewatering treatment，and physicochemical characteristics，phylogenetic evolution，chromosome distribution，gene duplication，gene structure，conserved motif，cis‑elements in promoter region and gene expression were analyzed.The results showed that a total of 51 differentially expressed bHLH genes were identified in maize under drought‑rewatering treatment，the amino acid number，molecular weight and isoelectric point of 51 bHLH proteins ranged from 80 to 705 aa，21.26 to 92.17 ku，and 4.54 to 12.41，respectively.bHLH genes were divided into 16 subgroups，Ⅺ subgroup was the largest，containing 9 bHLH proteins；Ⅵ，Ⅷ，Ⅸ and ⅩⅢ subgroups were the smallest，containing 1 bHLH protein each. bHLH genes were distributed unevenly on 10 chromosomes，among which 7 pairs of genes had replication relationships.The number of exons varied greatly，9 bHLH genes contained 1 exon，27 bHLH genes contained 2—5 exons，and 15 bHLH genes contained 6 or more exons；Motif 1 and Motif 2 appeared more frequently in the conserved motifs of bHLH protein，followed by Motif 3 and Motif 5，with Motif 6 and Motif 9 appeared least frequently.The promoter region of bHLH genes contained many cis‑acting elements related to plant hormones and abiotic stress，such as ABRE，GARE‑motif，P‑box，AuxRR‑core，MBS，TGACG‑motif，CGTCA‑motif，TCA‑rich，TGA‑element and TCA‑element. Under drought‑rewatering treatment，51 bHLH genes exhibited different expression patterns，among them，14 genes such as ZmbHLH20，ZmbHLH25，ZmbHLH9，ZmbHLH137and ZmbHLH178 positively responded to drought stress，and 14 genes such as ZmbHLH58，ZmbHLH87， ZmbHLH36 and ZmbHLH106 negatively responded to drought stress，which were candidate genes for further study of drought response in maize bHLH family.

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Analysis of Differentially Expressed Genes in Two Different Nitrogen Efficiency Maize Varieties in Response to Nitrogen Reduction

LI Chuan, ZHANG Panpan, ZHANG Meiwei, NIU Jun, ZHAO Xia, HE Guanhua, QIAO Jiangfang

Journal of Henan Agricultural Sciences 2022, 51 (9): 10-24. DOI: 10.15933/j.cnki.1004-3268.2022.09.002

Abstract （2019）

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In order to explore the differentially expressed genes（DEGs）in Weike 518（WK518）with high nitrogen efficiency and Nongda108（ND108） with low nitrogen efficiency under nitrogen reduction condition and their functions，the ear⁃leaf samples were collected from WK518 and ND108 at mid filling stage under normal nitrogen fertilizer application rate（225 kg/ha nitrogen,HN）and low nitrogen fertilizer application rate（0 kg/hanitrogen,LN）,and used for high⁃throughput RNA sequencing. Then the GO term and KEGG metabolic pathway of DEGs were analyzed from different compared groups，and the differentially expressed transcription factor families were analyzed. The results showed that 2 065 up⁃regulated DEGs and 2 319 down⁃regulated DEGs were detected between WK518 and ND108 under LN condition,2 368 up⁃regulated DEGs and 3 780 down⁃regulated DEGs were detected under HN condition;1 009 up⁃regulated DEGs and 2 268 down⁃regulated DEGs were detected in WK518 under different nitrogen application rates,and 364 up⁃regulated DEGs and 510 down⁃regulated DEGs were detected in ND108 under different nitrogen application rates.Under LN condition,DEGs between WK518 and ND108 were mainly enriched in uroporphyrin⁃Ⅲ C⁃methyltransferase activity,mannose⁃6⁃phosphate isomerase activity,oxidation⁃reduction process,mitochondrion organization,nuclear chromatin and other GO terms,and amino sugar and nucleotide sugar metabolism,phenylalaninemetabolism,monoterpenoid biosynthesis,glycine/serine and threonine metabolism,base excision repair and other KEGG pathways. Under HN condition，DEGs between WK518 and ND108 were mainly enriched in stomatal closure,transmembrane receptor protein serine/threonine kinase activity,chloroplast stroma，thylakoid,chloroplast envelope and other GO terms,and carbon fixation in photosynthetic organisms，amino sugar and nucleotide sugar metabolism,glycolysis/gluconeogenesis,β⁃alanine metabolism,photosynthesis⁃antenna proteins and other KEGG pathways.DEGs in WK518 were mainly enriched in response to chitin,protein phosphorylation，membrane，indole glucosinolate metabolic process，galactinol⁃sucrose galactosyltransferase and other GO terms,and carbon fixation in photosynthetic origination,plant hormone signal transduction,protein processing in endoplasmic reticulum,plant⁃pathogen interaction,MAPK signaling pathway⁃plant and other KEGG pathways under different nitrogen application rates.DEGs in ND108 were mainly enriched in response to water deprivation,toxin catabolic process,chitinase activity,trehalose biosynthetic process,trehalose⁃phosphatase activity and other GO terms,and glyoxylate and dicarboxylate metabolism,MAPK signaling pathway⁃plant，prodigiosin biosynthesis,zeatin biosynthesis,biotin metabolism and other KEGG pathways under different nitrogen application rates.Fifty⁃eight differentially expressed transcription factor families were detected in WK518 and ND108 under different nitrogen application rates,including GRAS,bHLH,MYB⁃related,NAC,C3H,ERF,C2H2,WRKY,FAR1 transcription factor families and so on,which were very important in plants growth,development and response to biotic and abiotic stresses.

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Identification and Analysis of WRKY Transcription Factors Differentially Expressed in Maize under Drought⁃Rewatering Treatment

FU Jiaxu, YAN Yali, XIE Xiaowen, ZHANG Xinyue, WEN Pengfei, GUAN Xiaokang, WANG Tongchao, WEI Li

Journal of Henan Agricultural Sciences 2022, 51 (8): 9-19. DOI: 10.15933/j.cnki.1004-3268.2022.08.002

Abstract （1852）

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In order to explore WRKY transcription factors related to drought resistance in maize（ Zea mays），differentially expressed WRKY genes were identified under drought⁃rewatering treatment，and their physicochemical characteristics，phylogenetic evolution，chromosome distribution，gene duplication，gene structure，conserved motif，cis⁃elements in promoter region and gene expression level were analyzed.The results showed that a total of 51 differentially expressed ZmWRKY genes were identified，the amino acid number，molecular weight and isoelectric point of 51 ZmWRKY proteins ranged from 99 to 729 aa，11.22 to 78.73 ku，and 4.58 to 12.26，respectively.ZmWRKY genes were divided into three groups Ⅰ，Ⅱ and Ⅲ，ZmWRKY genes of group Ⅱ were divided into Ⅱa，Ⅱb，Ⅱc，Ⅱd and Ⅱe.ZmWRKY genes were unequally distributed on 10 chromosomes，including 2 pairs of tandem duplication and 16 pairs of segmental duplication.The ZmWRKY genes contained 1—12 exons，most of ZmWRKY proteins（41）contained 2—4 conserved motifs，and WRKY members in the same group had similar motif compositions.Many cis⁃elements related to plant hormone and abiotic stress，such as ABRE，AuxRR⁃core，TCA⁃element，TC⁃rich repeats，TGACG⁃motif，LTR，MBS，TATC⁃box，P⁃box，CGTCA⁃motif，GC⁃motif，TGA⁃element and GARE⁃motif were identified in ZmWRKY gene promotor region.Under drought⁃rewatering treatment，51 ZmWRKY genes exhibited different expression patterns，among them，fifteen genes positively responded to drought stress，including ZmWRKY1，ZmWRKY10，ZmWRKY16， ZmWRKY28， ZmWRKY30， ZmWRKY33， ZmWRKY42， ZmWRKY65， ZmWRKY68， ZmWRKY78， ZmWRKY96，ZmWRKY99，ZmWRKY100，ZmWRKY102 and ZmWRKY111，and one gene negatively responded to drought stress，which were candidate genes for further study of drought response in
ZmWRKY family.

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Transcriptome and Metabolome Analysis of Mechanisms Responding to High Temperature Stress during Anthesis Stage in Zhengdan 309

LI Chuan, HUANG Lu, QIAO Jiangfang, ZHANG Meiwei, ZHANG Panpan, NIU Jun, LIU Jingbao, WANG Shufeng

Journal of Henan Agricultural Sciences 2021, 50 (2): 19-31. DOI: 10.15933/j.cnki.1004-3268.2021.02.003

Abstract （1197）

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The ear-leaf samples collected from Zhengdan 309 under normal condition(CK) and high temperature stress for 7 d and 14 d were used for RNA-sequencing using Illumina HiSeqTM2500 high-throughput sequencing technology and metabolome profiling analysis using liquid-chromatographymass spectrometry-based metabolomics. Differentially expressed genes (DEGs) and metabolites were explored to clarify the mechanism of maize responding to high temperature stress at the anthesis stage.The transcriptome sequencing results showed that 515 DEGs were detected in Zhengdan 309 under high temperature stress for 7 d compared with the control under normal growth condition, of which 75 genes were up-regulated,and 440 genes were down-regulated.There were 506 DEGs detected in Zhengdan 309 under high temperature stress for 14 d compared with the control under normal growth condition,including 114 up-regulated genes and 392 down-regulated genes. There were 2 050 DEGs detected in Zhengdan 309 under high temperature stress for 7 d compared with that under high temperature stress for 14 d, of which 790 genes were up-regulated,and 1 260 genes were down-regulated. The DEGs in Zhengdan 309 under high temperature stress for 7 d compared with that under the normal condition were concentrated in extracelluar region, molecular function regulator and other GO classification.The DEGs in Zhengdan 309 under high temperature stress for 14 d compared with that under the normal condition were mainly enriched in rhythmic process, extracelluar region and other GO classification.The DEGs in Zhengdan 309 under high temperature stress for 7 d compared with that under high temperature stress for 14 d were mainly enriched in cell part, single-organism process and other GO classification.The DEGs in Zhengdan 309 under high temperature stress for 7 d compared with that under the normal condition,Zhengdan 309 under high temperature stress for 14 d compared with that under the normal condition and Zhengdan 309 under high temperature stress for 7 d compared with that under high temperature stress for 14 d were mainly distributed in 5, 7 and 15 major KOG/COG classifications, respectively, and were mainly annotated into 6,7,20 KEGG metabolic pathways. There were 654 metabolites detected in Zhengdan 309,40 differentially expressed metabolites(DEMs) were detected in Zhengdan 309 under high temperature stress for 7 d compared with that under the normal condition, of which 8 metablites were up-regulated,and 32 metablites were down-regulated.There were also 40 DEMs detected in Zhengdan 309 under high temperature stress for 14 d compared with that under the normal condition, including 4 up-regulated metablites and 36 down-regulated metablites.There were 46 DEMs detected in Zhengdan 309 under high temperature stress for 7 d compared with that under high temperature stress for 14 d, of which 17 metablites were up-regulated,and 29 metablites were down-regulated.The 40 DEMs in Zhengdan 309 under high temperature stress for 7 d compared with that under the normal condition were concentrated in biosynthesis of secondary metabolites, arginine and proline metabolism and other KEGG pathways.The 40 DEMs in Zhengdan 309 under high temperature stress for 14 d compared with that under the normal condition were concentrated in biosynthesis of secondary metabolites, steroid biosynthesis and other KEGG pathways.The 46 DEMs in Zhengdan 309 under high temperature stress for 7 d compared with that under high temperature stress for 14 d were mainly enriched in aminoacyl-tRNA biosynthesis, alanine,aspartate and glutamate metabolism and other KEGG pathways.

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