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Progresses in Stress Tolerance and Field Cultivation Studies of Orphan Cereals in China DIAO XianMin Scientia Agricultura Sinica    2019, 52 (22): 3943-3949.   DOI: 10.3864/j.issn.0578-1752.2019.22.001 Abstract （634）   HTML （123）    PDF （378KB）（928）       Knowledge map    Save Small cereal crops, including foxtail millet (Setaria italica), sorghum (Sorghum bicolor) and broomcorn millet (Panicum miliaceum), are important in northern China’s arid and semi-arid dry land agriculture, which are main components for a diversified food system and considered as traditional healthy food. Because they are mainly cultivated in dry land and salinity soils, natural and human selection had made those crops with super capability for drought and salt tolerant. This issue of Scientia Agricultura Sinica published 20 papers focus on drought tolerance, salinity tolerance, disease resistance and cultivation of those orphan crops in China. Nearly all these papers were conducted by the scientific researcher of the Chinese Agricultural Research System, Millet and Sorghum Section. This is a brief introduction of these 20 papers, and some comparisons between conclusions of those researches with the known published ones are also included. Foxtail millet, sorghum and broomcorn millet are considered as models for drought and salinity study in the grasses family, the papers published here will push the progress of this system. Reference | Related Articles | Metrics

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Identification NADP-ME Gene of Foxtail Millet and Its Response to Stress ZHAO JinFeng,DU YanWei,WANG GaoHong,LI YanFang,ZHAO GenYou,WANG ZhenHua,CHENG Kai,WANG YuWen,YU AiLi Scientia Agricultura Sinica    2019, 52 (22): 3950-3963.   DOI: 10.3864/j.issn.0578-1752.2019.22.002 Abstract （388）   HTML （38）    PDF （6457KB）（422）       Knowledge map    Save 【Objective】 The objectives of this study are to identify the NADP-ME family genes (SiNADP-MEs) from foxtail millet (Setaria italica) genome, study the response of different members to abiotic stress, and to lay a theoretical foundation for revealing the role of SiNADP-ME genes in stress signal pathway of foxtail millet. 【Method】 The members of NADP-ME family in the foxtail millet genome were identified by bioinformatics methods. The protein and gene sequence of identified members were analyzed using software such as GSDS2.0, plantCARE, Clustalx, MEGA6.0 and the website ExPASy. Real-time quantitative PCR (qRT-PCR) was used to detect the expression levels of SiNADP-ME genes under different stresses at seedling stage, under drought and different light intensities stress at different growth stages. 【Result】 The NADP-ME family of foxtail millet consists of seven members, which were unevenly distributed on chromosomes 2, 3, 5, and 7 of foxtail millet. Conservative functional domain analysis revealed that all seven genes contain the conserved characteristic domains of NADP-ME. Amino acid sequence alignment revealed that the sequences were very conserved and the similarity was very high among the members. The sequence identity of 7 SiNADP-ME members was 77.30%, while the identity of NADP-MEs in different species was 56.52%. Sequence analysis showed that the sequences of SiNADP-ME1, 4, 5, and 6 were longer, encoding 576, 639, 652, and 636 amino acids residues respectively, while the sequences of SiNADP-ME2, 3, and 7 were shorter, encoding 213, 265 amino acids residues respectively. Gene structure analysis showed that SiNADP-ME1 has two alternative transcript, SiNADP-ME5 has three alternative transcript, and other genes have no alternative transcript. SiNADP-ME1, 2, 3 and 7 contain fewer introns, while SiNADP-ME4, 5 and 6 contain more introns. The prediction of protein parameters showed that the molecular weight span among members is large, ranging from 161.94 to 725.43 kD, the isoelectric point from 5.32 to 8.05, the instability index from 23.01 to 45.01, the aliphatic index from 89.19 to 107.77, and the grand average of hydropathicity from -0.218 to 0.004. Subcellular localization predictions show that SiNADP-ME members are mainly localized in chloroplasts, mitochondrial and cytoplasmic. Cis-elements analysis revealed that hormonal, stress, light, and other growth-related cis-elements are present in the promoter region of the SiNADP-ME members. Cluster analysis revealed that SiNADP-ME genes were present before the isolation of monocotyledonous and dicotyledonous plants. The homologous pairs of different species present in the phylogenetic tree revealed that they may evolve from a common ancestor, suggesting that they may have similar functions in certain signaling pathways. Stress expression analysis of seedling stage showed that the expression levels of all the SiNADP-ME family genes were significantly induced under the four stresses applied in this paper. The highest relative expression levels of SiNADP-ME1 under ABA, low temperature and NaCl treatment were 460.53, 411.50 and 15.24 folds than that of the control respectively, while the highest relative expression levels of SiNADP-ME6 under ABA, low temperature, PEG and NaCl treatment were 211.13, 15.21, 772.41 and 643.99 folds than that of the control respectively. Further analysis showed that the expression levels of SiNADP-ME1 and SiNADP-ME6 were up-regulated under drought stress at jointing, heading and filling stage.【Conclusion】 Seven members of NADP-ME gene family were identified from foxtail millet genome. All SiNADP-ME genes contain the typical characteristic domains of the NADP-ME, and their sequences are very conserved. All of the SiNADP-ME genes are involved in plant abiotic stress response, especially SiNADP-ME1 and SiNADP-ME6 may play an important role in response to abiotic stress. Table and Figures | Reference | Related Articles | Metrics

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Transcriptomics Analysis of NaCl Response in Foxtail Millet (Setaria italica L.) Seeds at Germination Stage PAN JiaoWen, LI Zhen, WANG QingGuo, GUAN YanAn, LI XiaoBo, DAI ShaoJun, DING GuoHua, LIU Wei Scientia Agricultura Sinica    2019, 52 (22): 3964-3975.   DOI: 10.3864/j.issn.0578-1752.2019.22.003 Abstract （574）   HTML （53）    PDF （2396KB）（546）       Knowledge map    Save 【Objective】 Foxtail millet (Setaria italica L.) remarkably adapts to adverse ecologies, including drought, barren regions and high soil salinity. These characteristics promote it as a very promising model crop for exploring basic biology processes of plants. Unveil of mechanisms of foxtail millet under salinity is of immense significance. 【Method】 In this research, 14 millet varieties at germination stage were used for resistance screening under 150 mmol·L -1 NaCl. The germination rate, root and bud length of each variety were measured after been treated for 7 d, and the salt tolerance variety Yugu 2 and salt susceptible variety An 04 were obtained. These two varieties before and after salt treatment were used for transcriptomes analysis by RNA-seq sequencing. The functional and pathway enrichments of differentially expressed genes (DEGs) were also performed by GO and KEGG analysis. Fifteen DEGs were randomly selected for further qRT-PCR analysis to verify the RNA-seq data.【Result】 Totally 2 786 and 4 413 DEGs were identified in Yugu 2 and An 04, and there were 1 470 and 3 826 DEGs within each cultivar before and after salt treatment, respectively. GO and KEGG enrichment analysis suggested that DEGs were mainly clustered into signaling, antioxidant system, organic acid biosynthesis and transport, and secondary metabolism, and the DEGs participated in response to stress, ion transmembrane transport, redox homeostasis, secondary metabolism, organic acid, polyamine and phenylpropanoid biosynthetic process. The qRT-PCR results showed high correlation coefficient of 0.8817 with the data of RNA-seq. Especially the genes such as cation transporter (HKT8), peroxidase (POD), flavanone 3-dioxygenase (FL3H) and MYB transcription factors, which displayed higher vary degrees in Yugu2 under salinity may play key roles in salt response process of foxtail millet. 【Conclusion】There was difference in the response degree of salt tolerance variety and salt sensitive variety of millet under salinity. Moreover, the resistance trait formation and function to salt was mainly depends on the response degree instead of the number of DEGs under stress. Table and Figures | Reference | Related Articles | Metrics

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Response of Receptor-Like Protein Kinase Gene SiRLK35 of Foxtail Millet to Salt in Heterologous Transgenic Rice LI XiaoBo,LI Zhen,DAI ShaoJun,PAN JiaoWen,WANG QingGuo,GUAN YanAn,DING GuoHua,LIU Wei Scientia Agricultura Sinica    2019, 52 (22): 3976-3986.   DOI: 10.3864/j.issn.0578-1752.2019.22.004 Abstract （348）   HTML （27）    PDF （1208KB）（257）       Knowledge map    Save 【Objective】Salt stress affects the crop yield and quality, while the crop salt tolerance is regulated by specific genes. Using heterogeneous over-expressed rice lines (OE-1, OE-2, and OE-3) of foxtail millet receptor-like protein kinase gene SiRLK35, the possible mechanisms of SiRLK35 under salinity will be dissected on phenotypic, physiological and molecular levels. 【Method】 The expressions of SiRLK35 in OE-1, OE-2, and OE-3 were analyzed by qRT-PCR. The phenotypes of three-leaf stage seedlings treated with 0, 150 and 200 mmol·L -1 NaCl were observed, and the lengths of seedlings and roots were measured after treated with 150 mmol·L -1 NaCl for 3 days. The dry weights, death rate and dead leaf rate of four-leaf stage seedlings that treated with 150 mmol·L -1 NaCl for 14 days were also measured. OE-1with the highest SiRLK35 expression was further used for DAB and NBT dyeing analysis. The activities of partial antioxidases, and expression patterns of marker genes were detected. 【Result】 There was the highest SiRLK35 expression level in OE-1. The growth of control and OE seedlings were all inhibited under 150 mmol·L -1 NaCl. The decreased levels of dry weight, the death rate and dead leaf rate of OE rice were all lower than those of the control, together with the less accumulation of O 2- and H2O2, and the higher activities of antioxidases under salinity. Partial of salt responsive genes were up-regulated in SiRLK35 OE lines, especially the OsLEA3 was induced about 1.9 times higher after treated with NaCl for 24 h. 【Conclusion】 SiRLK35 OE rice lines have tolerance under salinity, and the gene SiRLK35 of foxtail millet could participate in salt response by regulation the activities of antioxidases and related signal pathways. Table and Figures | Reference | Related Articles | Metrics

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Transcriptome Analysis and Gene Mining of Salt Tolerance in Sorghum Seedlings (Sorghum bicolor L. Moench) DONG Ming, KUERBAN Zaituniguli, Lü Peng, DU RuiHeng, YE Kai, HOU ShengLin, LIU GuoQing Scientia Agricultura Sinica    2019, 52 (22): 3987-4001.   DOI: 10.3864/j.issn.0578-1752.2019.22.005 Abstract （366）   HTML （36）    PDF （2300KB）（356）       Knowledge map    Save 【Object】The primary aim of this study was to identify salt tolerance genes and explore the tolerance response mechanism under salt stress in sorghum, which may provide a theoretical basis for sorghum salt tolerance breeding. 【Method】Two sorghum varieties, L-Tian, salt-sensitive and Shihong 137, salt-tolerant were employed as plant materials. The sorghum seedlings were treated with 2% NaCl solution at three-leaf and one heart stage. Three treatments including 0 h (CK), 1 h and 24 h were conducted. The plant height, root length, dry matter weight, Na + content and relative content of chlorophyll (SPAD value) were determined, and the transcriptome sequencing was performed on Illumina HiSeq 2000 platform. The FPKM method was employed to calculate the gene expression level. Both the differential expression fold (Fold Change) ≥ 2 and FDR<0.001 were used as screening criteria to detect the differentially expressed genes. The Gene Ontology and KEGG Pathway databases were used to analyze the differentially expressed genes involved in salt stress at different time points. 【Result】Salt stress had no significant effect on plant height, root length and dry matter weight of sorghum, but had significant effect on Na + content and SPAD value. The plant height, root length, Na + content and SPAD value of Shihong 137 were higher than those of L-tian. Totally 26628 known genes and 866 new genes have been identified from RNA-seq, of which, the number of differentially expressed genes from Shihong 137 is higher than that from L-tian. 375, 4206 and 3750 differentially expressed genes in 0 h VS 1 h, 0 h VS 24 h and 1 h VS 24 h groups had been identified from Shihong 137 respectively. The number of differentially expressed genes of 0 h VS 1 h, 0 h VS 24 h, and 1 h VS 24 h of L-tian was 167, 2534 and 1612, respectively. GO and KEGG analysis revealed that plant hormones such as abscisic acid, auxin, cytokinin, gibberellin and ethylene were involved in the salt tolerance of sorghum at an early stage of salt stress (1h), while Lhca, Lhcb, phosphoenolpyruvate carboxylase, and ribulose phosphate kinase were involved in the salt tolerance at a late stage of salt stress (24 h). The difference in salt tolerance between Shihong 137 and L-tian was mainly caused by the flavonoid biosynthetic metabolic pathway. 【Conclusion】The sorghum response to salt stress is a complex biological process that relies on the balanced expression of multiple genes in complex networks. Under salt stress, sorghum response to environmental stimuli was controlled by both hormonal signal transduction and photosynthesis. The flavonoid biosynthesis pathway played an important role in salt-tolerant varieties. Table and Figures | Reference | Related Articles | Metrics

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Comparative Transcriptome Analysis of Different Salt Tolerance Sorghum (Sorghum bicolor L. Moench) Under Salt Stress ZHANG Fei,WANG YanQiu,ZHU Kai,ZHANG ZhiPeng,ZHU ZhenXing,LU Feng,ZOU JianQiu Scientia Agricultura Sinica    2019, 52 (22): 4002-4015.   DOI: 10.3864/j.issn.0578-1752.2019.22.006 Abstract （429）   HTML （32）    PDF （2192KB）（423）       Knowledge map    Save 【Objective】Soil salinization is one of the important abiotic stress factors that restricts crop production. Understanding the salt-tolerant mechanism of sorghum may provide a novel avenue to utilize saline soil for sorghum production. The objective of this study was to explore gene regulation mechanisms and metabolic pathways that related to salt tolerance of sorghum by transcriptome sequencing. 【Method】 The salt-tolerant genotype Bayeqi and salt-sensitive genotype PL212 were planted in plastic pots. At five-leaf stage (20 days after sowing), plants were treated with 180 mmol L -1 NaCl. Forty-eight hours after treatment, leaves treated by NaCl and unstressed control were sampled and were used for RNA extraction and transcriptome sequencing. Sequencing results were verified by qRT-PCR. 【Result】 Results showed that a total of 1 338 deferentially expressed genes, including 819 up-regulated and 519 down-regulated genes were detected. Cluster analysis revealed that in response to salt stress, five dependent oxygenase superfamily proteins, four cysteine-rich RLKs, three Glutathione S-transferase and three heavy metal transport/detoxification superfamily protein-related genes were significant up-regulated and/or down-regulated, and one K + ion transporter gene was also found to play an important role in salt-tolerance regulation. GO analysis found that 4 528 valid GO annotation entries were obtained from 15 418 genes, and salt-tolerant and salt-sensitive materials showed significant difference in biological processes, cellular components and molecular functions under salt stress treatment. The salt-tolerant materials exhibited obviously higher metabolic processes and cellular processes than salt-sensitive materials. Compared with salt-sensitive materials, multiple biological processes and localization processes were increased in salt-tolerant genotype, which might be the reasons of salt-tolerance. KEGG analysis showed that the salt-tolerant and salt-sensitive materials had more differential gene expression in phenylpropanoid biosynthesis, phenylalanine metabolism and flavonoid biosynthesis under control and salt stress conditions, which may be an important reason for the weak salt tolerance of sensitive materials. 【Conclusion】 The expression of salt-tolerant genes in sorghum is involved in many aspects of biological processes, cellular components and molecular functions. The gene expression in multiple processes and localization processes contributes to the salt tolerance, while excessive gene expression in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis likely contributes to the damage under salt stress. Table and Figures | Reference | Related Articles | Metrics

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Identification and Expression Analysis of MYB Transcription Factors Related to Rust Resistance in Foxtail Millet BAI Hui, SONG ZhenJun, WANG YongFang, QUAN JianZhang, MA JiFang, LIU Lei, LI ZhiYong, DONG ZhiPing Scientia Agricultura Sinica    2019, 52 (22): 4016-4026.   DOI: 10.3864/j.issn.0578-1752.2019.22.007 Abstract （276）   HTML （29）    PDF （1303KB）（280）       Knowledge map    Save 【Objective】 Millet rust is one of the important factors affecting the yield and quality of foxtail millet. Identification of MYB transcription factors related to rust resistance in foxtail millet lays a foundation for the study of the mechanism of rust resistance in foxtail millet. 【Method】 In this study, we used real-time PCR to detect the expression patterns of 9 MYB transcription factors (1) in roots, stems, leaves and panicles at booting stage; (2) during 120 hours post-inoculated with Uromyces setariae-italicae urediniospores in resistance (R) and susceptible (S) reactions; (3) during 24 hours after treatment with salicylic acid (SA) and methyl jasmonate (MeJA) in foxtail millet. Then their expression patterns in four reactions of R, S, SA and MeJA were compared, and the resistance-related MYB transcription factors were selected for detection of transactivation activity and subcellular localization. 【Result】 The highest expression of SiMYB100 was in leaves, and the highest expression of the other eight genes, especially SiMYB074, was in roots. The expression of five genes was correlated with disease resistance. SiMYB074 and SiMYB202 were induced by rust fungus infection and their expression levels at early stage of disease resistance were significantly higher than that in the susceptible reaction. The expression of SiMYB041 and SiMYB177 was down-regulated in the early stage of resistance reaction and increased to pre-inoculation level in the later stage, while their expression remained low in susceptible reaction. SiMYB100 showed opposite expression pattern in resistance and susceptible responses. In response to exogenous SA and MeJA, the expression of SiMYBs gene changed in varying degrees. The expression patterns of four genes (SiMYB074, SiMYB100, SiMYB174 and SiMYB202) in the R, SA and MeJA reactions were identical, but different from the S reaction. Five resistance-related SiMYBs genes have the transactivation activity and their encoding proteins are located in the nucleus. 【Conclusion】 The expression of five genes, SiMYB041, SiMYB074, SiMYB100, SiMYB177 and SiMYB202, was identified to be associated with resistance to rust disease in foxtail millet. SiMYB074 and SiMYB100 play certain roles in the growth and disease resistance of foxtail millet. Four genes, SiMYB074, SiMYB100, SiMYB174 and SiMYB202, may participate in early disease resistance of foxtail millet through SA and JA signaling pathways. Table and Figures | Reference | Related Articles | Metrics

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