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Yoo YH, Cho SY, Lee I, Kim N, Lee SK, Cho KS, Kim EY, Jung KH, Hong WJ. Characterization of the Regulatory Network under Waterlogging Stress in Soybean Roots via Transcriptome Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:2538. [PMID: 39339513 PMCID: PMC11435190 DOI: 10.3390/plants13182538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024]
Abstract
Flooding stress caused by climate change is a serious threat to crop productivity. To enhance our understanding of flooding stress in soybean, we analyzed the transcriptome of the roots of soybean plants after waterlogging treatment for 10 days at the V2 growth stage. Through RNA sequencing analysis, 870 upregulated and 1129 downregulated differentially expressed genes (DEGs) were identified and characterized using Gene Ontology (GO) and MapMan software (version 3.6.0RC1). In the functional classification analysis, "alcohol biosynthetic process" was the most significantly enriched GO term in downregulated DEGs, and phytohormone-related genes such as ABA, cytokinin, and gibberellin were upregulated. Among the transcription factors (TFs) in DEGs, AP2/ERFs were the most abundant. Furthermore, our DEGs encompassed eight soybean orthologs from Arabidopsis and rice, such as 1-aminocyclopropane-1-carboxylate oxidase. Along with a co-functional network consisting of the TF and orthologs, the expression changes of those genes were tested in a waterlogging-resistant cultivar, PI567343. These findings contribute to the identification of candidate genes for waterlogging tolerance in soybean, which can enhance our understanding of waterlogging tolerance.
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Affiliation(s)
- Yo-Han Yoo
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Seung-Yeon Cho
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
| | - Inhye Lee
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Namgeol Kim
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Seuk-Ki Lee
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Kwang-Soo Cho
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea; (Y.-H.Y.); (I.L.); (N.K.); (S.-K.L.); (K.-S.C.)
| | - Eun Young Kim
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
| | - Ki-Hong Jung
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea; (S.-Y.C.); (E.Y.K.)
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea;
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2
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Cai H, Zhu Y, Liu Y, Yan Z, Shen H, Fang S, Wang D, Liao S, Li J, Lv M, Lin X, Hu J, Song Y, Chen X, Yin L, Zhang J, Qi N, Sun M. Selection of a suitable reference gene for gene-expression studies in Trichomonas gallinae under various biotic and abiotic stress conditions. Gene 2024; 920:148522. [PMID: 38703865 DOI: 10.1016/j.gene.2024.148522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Trichomonas gallinae, a globally distributed protozoan parasite, significantly affects the pigeon-breeding industry. T. gallinae infection mainly causes yellow ulcerative nodules on the upper respiratory tract and crop mucosa of pigeons, impeding normal breathing and feeding and ultimately causing death. Real-time quantitative PCR (qPCR) is a crucial technique for gene-expression analysis in molecular biology. Reference-gene selection for normalization is critical for ensuring this technique's accuracy. However, no systematic screening or validation of T. gallinae reference genes has been reported. This study quantified the transcript levels of ten candidate reference genes in T. gallinae isolates with different genotypes and culture conditions using qPCR. Using the geNorm, NormFinder, and BestKeeper algorithms, we assessed these reference genes' stabilities and ranked them using RankAggreg analysis. The most stable reference gene was tubulin beta chain (TUBB), while the widely used reference genes TUBG and GAPDH demonstrated poor stability. Additionally, we evaluated these candidate reference genes' stabilities using the T. gallinae TgaAtg8 gene. On using TUBB as a reference gene, TgaAtg8's expression profiles in T. gallinae isolates with different genotypes remained relatively consistent under various culture conditions. Conversely, using ACTB as a reference gene distorted the data. These findings provide valuable reference-gene-selection guidance for functional gene research and gene-expression analysis in T. gallinae.
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Affiliation(s)
- Haiming Cai
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yibin Zhu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yu Liu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhuanqiang Yan
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Hanqin Shen
- Guangdong Jingjie Inspection and Testing Co., Ltd., Xinxing, Guangdong 527400, China
| | - Siyun Fang
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Dingai Wang
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Shenquan Liao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Juan Li
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Minna Lv
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xuhui Lin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junjing Hu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yongle Song
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiangjie Chen
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lijun Yin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianfei Zhang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Nanshan Qi
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Mingfei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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Zhao G, Liu W, Lin G, Wen J. Evaluation of reference genes and expression patterns of CONSTANS-LIKE genes in Tetrastigma hemsleyanum under different photoperiods. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23218. [PMID: 39038159 DOI: 10.1071/fp23218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024]
Abstract
CONSTANS-LIKE (COL ) genes are a key signalling molecule that regulates plant growth and development during the photoperiod. Our preliminary experiments showed that the photoperiod greatly influence the formation of Tetrastigma hemsleyanum root tubers. In this study, we examined the oscillation patterns and expression characteristics of COL genes in leaves of T. hemsleyanum under different photoperiod conditions. Six genes were selected as candidate reference genes for further analyses: (1) 18S ribosomal RNA (18S rRNA ); (2) α-tubulin (TUBA ); (3) 30S ribosomal RNA (30S rRNA ); (4) TATA binding protein (TBP ); (5) elongation factor 1α (EF-1α ); and (6) RNA polymerase II (RPII ). The geNorm, NormFinder, and BestKeeper software programs were used to evaluate expression stability. Two ThCOL genes were screened in the T. hemsleyanum transcriptome library, and their expression patterns under different photoperiod conditions were analysed using quantitative reverse transcription PCR. The genes EF-1α , TUBA , and 18S rRNA were used to analyse the expression profiles of CONSTANS genes (ThCOL4 and ThCOL5 ) under different photoperiods. The expression peaks of ThCOL4 and ThCOL5 appeared at different times, demonstrating that their oscillation patterns were influenced by the photoperiod. We speculate that these two ThCOL genes may be involved in different biological processes.
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Affiliation(s)
- Gang Zhao
- Life and Science College, Shangrao Normal University, Shangrao 334000, P. R. China
| | - Wenling Liu
- Life and Science College, Shangrao Normal University, Shangrao 334000, P. R. China
| | - Guowei Lin
- Life and Science College, Shangrao Normal University, Shangrao 334000, P. R. China
| | - Jing Wen
- Life and Science College, Shangrao Normal University, Shangrao 334000, P. R. China
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4
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Ren H, Zhao K, Zhang C, Lamlom SF, Liu X, Wang X, Zhang F, Yuan R, Gao Y, Cao B, Zhang B. Genetic analysis and QTL mapping of seed hardness trait in a soybean (Glycine max) recombinant inbred line (RIL) population. Gene 2024; 905:148238. [PMID: 38316262 DOI: 10.1016/j.gene.2024.148238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Seed hardness is a critical quality trait impacting both the suitability of soybeans for consumption and their processing. The primary objective of this study was to explore the genetic foundations underlying seed hardness in soybeans. A 234 recombinant inbred line (RIL) population was evaluated for seed hardness across three years (2015 in Gansu, 2016, and 2017 in Hainan). Notably, the parent varieties, Zhonghuang35 and Jindou21, displayed significant differences in seed hardness. Also, the RIL population exhibited a wide range of genetic variation in seed hardness, with coefficients of variation between 70.53 % and 94.94 %. The frequency distribution of this trait conformed to a relatively normal distribution, making it suitable for QTL analysis. Six QTLs associated with seed hardness were identified with three located on chromosome 2 and three on chromosome 16. The major QTL, qHS-2-1, consistently exhibited the highest percentage of PVE and LOD in Gansu 2015, Hainan 2016, and Hainan 2017, suggesting its central role in determining seed hardness. Further investigation revealed four genes within the qHS-2-1 interval potentially related to seed hardness. GO enrichment analysis provided insights into their functions, including factors such as Glyma.02G307000, a pectin lyase-like superfamily protein, which could influence seed hardness through its role in pectin lyase enzyme activity. Expression analysis of these candidate genes demonstrated significant differences between the two parent varieties, further highlighting their potential role in seed coat hardness. This study offers valuable insights into the genetic mechanisms governing soybean seed coat hardness, providing a foundation for future research and crop improvement efforts.
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Affiliation(s)
- Honglei Ren
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China.
| | - Kezhen Zhao
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Chunlei Zhang
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Sobhi F Lamlom
- Plant Production Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt
| | - Xiulin Liu
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Xueyang Wang
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Fengyi Zhang
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Rongqiang Yuan
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China
| | - Yuan Gao
- Heilongjiang Seed Industry Technical Service Center, Harbin 150080, China
| | - Baoxiang Cao
- Nenjiang Agricultural Technology Promotion Center, Nenjiang 161400, China
| | - Bixian Zhang
- Soybean Research Institute, Northeastern Precocious Soybean Scientific Observation Station of Ministry of Agriculture and Rural Affairs, Heilongjiang Academy of Agriculture Sciences, Harbin Branch of National Soybean Improvement Center, Harbin 150086, China.
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5
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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Yeom WW, Kim HJ, Lee JH, Jeong Jeong Y, Choi HK, Jung HW, Heo JB, Kim CY, Chung YS. Overexpression of R2R3-MYB IbMYB1a induces anthocyanin pigmentation in soybean cotyledon. PLANT CELL REPORTS 2024; 43:56. [PMID: 38319432 DOI: 10.1007/s00299-024-03142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/31/2023] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE This is the first report showing anthocyanin accumulation in the soybean cotyledon via genetic transformation of a single gene. Soybean [Glycine max (L.) Merrill] contains valuable components, including anthocyanins. To enhance anthocyanin production in Korean soybean Kwangankong, we utilized the R2R3-type MYB gene (IbMYB1a), known for inducing anthocyanin pigmentation in Arabidopsis. This gene was incorporated into constructs using two promoters: the CaMV 35S promoter (P35S) and the β-conglycinin promoter (Pβ-con). Kwangankong was transformed using Agrobacterium, and the presence of IbMYB1a and Bar transgenes in T0 plants was confirmed through polymerase chain reaction (PCR), followed by gene expression validation. Visual inspection revealed that one P35S:IbMYB1a and three Pβ-con:IbMYB1a lines displayed seed color change. Pβ-con:IbMYB1a T1 seeds accumulated anthocyanins in cotyledon outer layers, whereas P35S:IbMYB1a and non-transgenic black soybean (Cheongja 5 and Seum) accumulated anthocyanins in the seed coat. During the germination and growth phase, T1 seedlings from Pβ-con:IbMYB1a lines exhibited anthocyanin pigmentation in cotyledons for up to 1 month without growth aberrations. High-performance liquid chromatography confirmed cyanidin-3-O-glucoside as the major anthocyanin in the Pβ-con:IbMYB1a line (#3). We analyzed the expression patterns of anthocyanin biosynthesis genes, chalcone synthase 7,8, chalcone isomerase 1A, flavanone 3-hydroxylase, flavanone 3'-hydroxylase, dihydroflavanol reductase 1, dihydroflavanol reductase 2, anthocyanidin synthase 2, anthocyanidin synthase 3, and UDP glucose flavonoid 3-O-glucosyltransferase in transgenic and control Kwangankong and black soybean (Cheongja 5 and Seum) seeds using quantitative real-time PCR. We conclude that the induction of gene expression in transgenic plants in comparison with Kwangankong was attributable to IbMYB1a transformation. Notably, flavanone 3-hydroxylase, flavanone 3'-hydroxylase, and dihydroflavanol reductase 1 were abundantly expressed in black soybean seed coat, distinguishing them from transgenic cotyledons.
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Affiliation(s)
- Wan Woo Yeom
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Hye Jeong Kim
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Jin Hwan Lee
- Department of Life Resources Industry, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup, 56212, Korea
| | - Hong Kyu Choi
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Ho Won Jung
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Jae Bok Heo
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup, 56212, Korea.
| | - Young-Soo Chung
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan, 49315, Korea.
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Kang BH, Chowdhury S, Kang SH, Shin SY, Lee WH, Lee HS, Ha BK. Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation. PLANTS (BASEL, SWITZERLAND) 2024; 13:254. [PMID: 38256807 PMCID: PMC10818854 DOI: 10.3390/plants13020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.
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Affiliation(s)
- Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
| | - Se-Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seo-Young Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Won-Ho Lee
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
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8
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Szeluga N, Baldrich P, DelPercio R, Meyers BC, Frank MH. Introduction of barnase/barstar in soybean produces a rescuable male sterility system for hybrid breeding. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2585-2596. [PMID: 37596734 PMCID: PMC10651147 DOI: 10.1111/pbi.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023]
Abstract
Hybrid breeding for increased vigour has been used for over a century to boost agricultural outputs without requiring higher inputs. While this approach has led to some of the most substantial gains in crop productivity, breeding barriers have fundamentally limited soybean (Glycine max) from reaping the benefits of hybrid vigour. Soybean flowers self-pollinate prior to opening and thus are not readily amenable to outcrossing. In this study, we demonstrate that the barnase/barstar male sterility/rescue system can be used in soybean to produce hybrid seeds. By expressing the cytotoxic ribonuclease, barnase, under a tapetum-specific promoter in soybean anthers, we are able to completely block pollen maturation, creating male sterile plants. We show that fertility can be rescued in the F1 generation of these barnase-expressing lines when they are crossed with pollen from plants that express the barnase inhibitor, barstar. Importantly, we found that the successful rescue of male fertility is dependent on the relative dosage of barnase and barstar. When barnase and barstar were expressed under the same tapetum-specific promoter, the F1 offspring remained male sterile. When we expressed barstar under a relatively stronger promoter than barnase, we were able to achieve a successful rescue of male fertility in the F1 generation. This work demonstrates the successful implementation of a biotechnology approach to produce fertile hybrid offspring in soybean.
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Affiliation(s)
- Nicole Szeluga
- Plant Biology Section, School of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | | | - Ryan DelPercio
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant Sciences and TechnologyUniversity of Missouri – ColumbiaColumbiaMOUSA
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Division of Plant Sciences and TechnologyUniversity of Missouri – ColumbiaColumbiaMOUSA
| | - Margaret H. Frank
- Plant Biology Section, School of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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9
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Wei S, Yong B, Jiang H, An Z, Wang Y, Li B, Yang C, Zhu W, Chen Q, He C. A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2469-2489. [PMID: 37635359 DOI: 10.1111/jipb.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development. Here, we present such a rare and potential case of "to gain by loss" as a neomorphic mutation during soybean domestication for increasing seed weight. Using a population derived from a chromosome segment substitution line of Glycine max (SN14) and Glycine soja (ZYD06), a quantitative trait locus (QTL) of 100-seed weight (qHSW) was mapped on chromosome 11, corresponding to a truncated β-1, 3-glucosidase (βGlu) gene. The novel gene hsw results from a 14-bp deletion, causing a frameshift mutation and a premature stop codon in the βGlu. In contrast to HSW, the hsw completely lost βGlu activity and function but acquired a novel function to promote cell expansion, thus increasing seed weight. Overexpressing hsw instead of HSW produced large soybean seeds, and surprisingly, truncating hsw via gene editing further increased the seed size. We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size. Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control. Moreover, the hsw allele underwent selection and expansion during soybean domestication and improvement. Our work cloned a likely domesticated QTL controlling soybean seed weight, revealed a novel genetic variation and mechanism in soybean domestication, and provided new insight into crop domestication and breeding, and plant evolution.
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Affiliation(s)
- Siming Wei
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
- Jilin Academy of Agricultural Sciences, Changchun, 130022, China
| | - Zhenghong An
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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10
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Yao K, Wang Y, Li X, Ji H. Genome-Wide Identification of the Soybean LysM-RLK Family Genes and Its Nitrogen Response. Int J Mol Sci 2023; 24:13621. [PMID: 37686427 PMCID: PMC10487828 DOI: 10.3390/ijms241713621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Lysin-Motif receptor-like kinase (LysM-RLK) proteins are widely distributed in plants and serve a critical role in defending against pathogens and establishing symbiotic relationships. However, there is a lack of comprehensive identification and analysis of LysM-RLK family members in the soybean genome. In this study, we discovered and named 27 LysM-RLK genes in soybean. The majority of LysM-RLKs were highly conserved in Arabidopsis and soybean, while certain members of subclades III, VI, and VII are unique to soybean. The promoters of these LysM-RLKs contain specific cis-elements associated with plant development and responses to environmental factors. Notably, all LysM-RLK gene promoters feature nodule specificity elements, while 51.86% of them also possess NBS sites (NIN/NLP binding site). The expression profiles revealed that genes from subclade V in soybean roots were regulated by both rhizobia and nitrogen treatment. The expression levels of subclade V genes were then validated by real-time quantitative PCR, and it was observed that the level of GmLYK4a and GmLYK4c in roots was inhibited by rhizobia but induced via varying concentrations of nitrate. Consequently, our findings provide a comprehensive understanding of the soybean LysM-RLK gene family and emphasize the role of subclade V in coupling soybean symbiotic nitrogen fixation and nitrogen response.
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Affiliation(s)
- Kaijie Yao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
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11
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Moon CY, Kang BH, Kim WJ, Chowdhury S, Kang S, Lee JD, Kwon SJ, Kim HY, Lee HS, Ha BK. Morpho-physiological and genetic characteristics of a salt-tolerant mutant line in soybean (Glycine max L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:166. [PMID: 37393202 DOI: 10.1007/s00122-023-04408-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
KEY MESSAGE One major quantitative trait loci and candidate gene for salt tolerance were identified on chromosome 3 from a new soybean mutant derived from gamma-ray irradiation, which will provide a new genetic resource for improving soybean salt tolerance. Soil salinity is a worldwide problem that reduces crop yields, but the development of salt-tolerant crops can help overcome this challenge. This study was conducted with the purpose of evaluating the morpho-physiological and genetic characteristics of a new salt-tolerant mutant KA-1285 developed using gamma-ray irradiation in soybean (Glycine max L.). The morphological and physiological responses of KA-1285 were compared with salt-sensitive and salt-tolerant genotypes after treatment with 150 mM NaCl for two weeks. In addition, a major salt tolerance quantitative trait locus (QTL) was identified on chromosome 3 in this study using the Daepung X KA-1285 169 F2:3 population, and a specific deletion was identified in Glyma03g171600 (Wm82.a2.v1) near the QTL region based on re-sequencing analysis. A kompetitive allele-specific PCR (KASP) marker was developed based on the deletion of Glyma03g171600 which distinguished the wild-type and mutant alleles. Through the analysis of gene expression patterns, it was confirmed that Glyma03g171700 (Wm82.a2.v1) is a major gene that controls salt tolerance functions in Glyma03g32900 (Wm82.a1.v1). These results suggest that the gamma-ray-induced mutant KA-1285 has the potential to be employed for the development of a salt-tolerant cultivar and provide useful information for genetic research related to salt tolerance in soybeans.
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Affiliation(s)
- Chang Yeok Moon
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Byeong Hee Kang
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Woon Ji Kim
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
| | - Sehee Kang
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Han-Yong Kim
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju, 55365, Republic of Korea.
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea.
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea.
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12
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Soltani Najafabadi M, Amirbakhtiar N. Evaluating and Validating Sunflower Reference Genes for Q-PCR Studies Under High Temperature Condition. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3357. [PMID: 37228632 PMCID: PMC10203189 DOI: 10.30498/ijb.2023.338375.3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/07/2023] [Indexed: 05/27/2023]
Abstract
Background Q-PCR is the method of choice for PCR- based transcriptomics and validating microarray-based and RNA-seq results. Proper application of this technology requires proper normalization to correct as much as possible errors propagating during RNA extraction and cDNA synthesis. Objectives The investigation was performed to find stable reference genes in sunflower under shifting in ambient temperature. Materials and Methods Sequences of five well-known reference genes of Arabidopsis (Actin, Ubiquitin, Elongation factor-1, GAPDH, and SAND) and one well-known reference gene inhuman, Importin, were subjected to BLASTX against sunflower databases and the relevant genes were subjected to primer designing for q-PCR. Two sunflower inbred lines were cultivated at two dates so that anthesis occurred at nearly 30 °C and 40 °C (heat stress). The experiment was repeated for two years. Q-PCR was run on samples taken for two planting date separately at the beginning of anthesis for each genotype from leaf, taproots, receptacle base, immature and mature disc flowers and on pooled samples comprising of the tissues for each genotype, planting dates and also all tissues for both genotypes and both planting dates. Basic statistical properties of each candidate gene across all the samples were calculated. Furthermore, gene expression stability analysis was done for six candidate reference genes on Cq mean of two years using three independent algorithms, geNorm, Bestkeeper, and Refinder. Results Designed primers for Actin2, SAND, GAPDH, Ubiquitin, EF-1a, and Importin yielded a single peak in melting curve analysis indicating specificity of the PCR reaction. Basic statistical analysis showed that Actin2 and EF-1a had the highest and lowest expression levels across all the samples, respectively. Actin2 appeared to be the most stable reference gene across all the samples based on the three used algorithms. Pairwise variation analysis revealed that for samples taken under ambient temperature of 30 °C, Actin2, EF-1a, SAND and for those taken under ambient temperature of 40 °C, Actin2, EF-1a, Importin and SAND have to be used for normalization in q-PCR studies. Moreover, it is suggested that normalization to be based on Actin2, SAND and EF-1a for vegetative tissues and Actin2, EF-1a, SAND and Importin for reproductive tissues. Conclusions In the present research, proper reference genes for normalization of gene expression studies under heat stress conditions were introduced. Moreover, the presence of genotype-by- planting date interaction effects and tissue specific gene expression pattern on the behavior of the most three stable reference genes was indicated.
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Affiliation(s)
- Masood Soltani Najafabadi
- National Plant Genebank, Seed and Plant Improvement Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Genebank, Seed and Plant Improvement Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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13
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Chen H, Liu C, Li Y, Wang X, Pan X, Wang F, Zhang Q. Developmental dynamic transcriptome and systematic analysis reveal the major genes underlying isoflavone accumulation in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1014349. [PMID: 36959940 PMCID: PMC10027745 DOI: 10.3389/fpls.2023.1014349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Soy isoflavone, a class of polyphenolic compounds exclusively occurred in legumes, is an important bioactive compound for both plants and human beings. The outline of isoflavones biosynthesis pathway has been drawn up basically in the previous research. However, research on the subject has been mostly restricted to investigate the static regulation of isoflavone content in soybean, rather than characterize its dynamic variation and modulation network in developing seeds. METHODS In this study, by using eight recombinant inbred lines (RIL), the contents of six isoflavone components in the different stages of developing soybean seeds were determined to characterize the dynamic variation of isoflavones, and the isoflavones accumulation pattern at physiological level was investigated. Meanwhile, we integrated and analyzed the whole genome expression profile of four lines and 42 meta-transcriptome data, based on the multiple algorithms. RESULTS This study: 1) obtained 4 molecular modules strongly correlated with isoflavone accumulation; 2) identified 28 novel major genes that could affect the accumulation of isoflavones in developing seeds free from the limitation of environments; 3) discussed the dynamic molecular patterns regulating isoflavones accumulation in developing seed; 4) expanded the isoflavone biosynthesis pathway. DISCUSSION The results not only promote the understandings on the biosynthesis and regulation of isoflavones at physiological and molecular level, but also facilitate to breed elite soybean cultivars with high isoflavone contents.
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Affiliation(s)
- Heng Chen
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Changkai Liu
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yansheng Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Xue Wang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Xiangwen Pan
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Feifei Wang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Qiuying Zhang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
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14
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Novel Seed Size: A Novel Seed-Developing Gene in Glycine max. Int J Mol Sci 2023; 24:ijms24044189. [PMID: 36835599 PMCID: PMC9967547 DOI: 10.3390/ijms24044189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans.
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15
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Zhang W, Hou H, Zhang D, Zhu B, Yuan H, Gao T. Transcriptomic and Metabolomic Analysis of Soybean Nodule Number Improvements with the Use of Water-Soluble Humic Materials. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:197-210. [PMID: 36573896 DOI: 10.1021/acs.jafc.2c06200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Water-soluble humic materials (WSHMs) can enhance the nodule numbers of soybean plants. In this study, targeted metabolomics and transcriptomics were used to understand this mechanism. Results showed that 500 mg/L WSHM increased the adsorption and colonization of rhizobia in soybean roots. High-performance liquid chromatography and targeted metabolomics showed that WSHMs could regulate the content and distribution of endogenous hormones of soybean plants at the initial stage of soybean nodulation. Transcriptomic analysis showed a total of 2406 differentially expressed genes (DEGs) by the 25th day, accounting for 4.89% of total annotation genes (49159). These DEGs were found to contribute primarily to the MAPK signaling pathway, glycolysis/gluconeogenesis, and plant hormone signal transduction according to the -log 10 (Padjust) value in the KEGG pathway. Subsequently, DEGs related to these hormones were selected for verification using quantity-PCR. The WSHM increased the number of nodules by regulating the expression of endogenous hormones in soybean plants.
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Affiliation(s)
- Wenhua Zhang
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Huiyun Hou
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Dongdong Zhang
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Baocheng Zhu
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tongguo Gao
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
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16
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Xu M, Kong K, Miao L, He J, Liu T, Zhang K, Yue X, Jin T, Gai J, Li Y. Identification of major quantitative trait loci and candidate genes for seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:22. [PMID: 36688967 PMCID: PMC9870841 DOI: 10.1007/s00122-023-04299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Four major quantitative trait loci for 100-seed weight were identified in a soybean RIL population under five environments, and the most likely candidate genes underlying these loci were identified. Seed weight is an important target of soybean breeding. However, the genes underlying the major quantitative trait loci (QTL) controlling seed weight remain largely unknown. In this study, a soybean population of 300 recombinant inbred lines (RILs) derived from a cross between PI595843 (PI) and WH was used to map the QTL and identify candidate genes for seed weight. The RIL population was genotyped through whole genome resequencing, and phenotyped for 100-seed weight under five environments. A total of 38 QTL were detected, and four major QTL, each explained at least 10% of the variation in 100-seed weight, were identified. Six candidate genes within these four major QTL regions were identified by analyses of their tissue expression patterns, gene annotations, and differential gene expression levels in soybean seeds during four developmental stages between two parental lines. Further sequence variation analyses revealed a C to T substitution in the first exon of the Glyma.19G143300, resulting in an amino acid change between PI and WH, and thus leading to a different predicted kinase domain, which might affect its protein function. Glyma.19G143300 is highly expressed in soybean seeds and encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the known LRR-RLK protein XIAO (LOC_Os04g48760), which is involved in controlling seed size. The major QTL and candidate genes identified in this study provide useful information for molecular breeding of new soybean cultivars with desirable seed weight.
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Affiliation(s)
- Mengge Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Long Miao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Tengfei Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Kai Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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17
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Transcriptome and Metabolome Analysis of a Late-Senescent Vegetable Soybean during Seed Development Provides New Insights into Degradation of Chlorophyll. Antioxidants (Basel) 2022; 11:antiox11122480. [PMID: 36552689 PMCID: PMC9774520 DOI: 10.3390/antiox11122480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Senescence represents the final stage of plant growth and development, which transfers nutrients to growing seeds and directly affects the yield and quality of crops. However, little is known about chlorophyll degradation in developing and maturing seeds, in contrast to leaf senescence; (2) Methods: RNA-Seq was used to analyze the differentially expressed genes of different late-senescent germplasms. A widely untargeted metabolic analysis was used to analyze differential metabolites. In addition, qRT-PCR was conducted to detect gene expression levels; (3) Results: Transcriptome analysis revealed that ZX12 seeds have a higher expression level of the chlorophyll synthesis genes in the early stage of maturity, compared with ZX4, and have a lower expression level of chlorophyll degradation genes in the late stage of maturity. Flavonoids were the primary differential metabolites, and ZX12 contains the unique and highest expression of three types of metabolites, including farrerol-7-O-glucoside, cyanidin-3-o-(6'-o-feruloyl) glucoside, and kaempferide-3-o-(6'-malonyl) glucoside. Among them, farrerol-7-O-glucoside and cyanidin-3-o-(6'-o-feruloyl) glucoside are flavonoid derivatives containing mono and dihydroxy-B-ring chemical structures, respectively; and (4) Conclusions: It is speculated that the two metabolites can slow down the degradation process of chlorophyll by scavenging oxygen-free radicals in the chloroplast.
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Wang W, Li J, Nadeem M, Wang J, Huang R, Liu Q, Fan W, Zheng H, Yan L, Wang X. The central role of GmGLP20.4 in root architecture modifications of soybean under low-nitrogen stress. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4083-4093. [PMID: 35616706 DOI: 10.1007/s00122-022-04123-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE The GmGLP20.4 candidate gene plays an important role to improve soybean root architecture under low-nitrogen stress. The results lay the foundation for breeding low-nitrogen-tolerant soybean. Roots are fundamentally important for plant growth and development, facilitating water and nutrient uptake. Various abiotic and biotic factors significantly affect the root system architecture, especially low nitrogen (LN), but the molecular mechanism remains unclear. In this study, we identified GmGLP20.4, a germin-like protein (ubiquitous plant glycoproteins belonging to the Cupin superfamily) crucial for lateral root development and highly induced by LN stress in lateral roots of soybean. GmGLP20.4 overexpression increased root biomass through development of an improved root system in soybean under LN, whereas a significant decrease in root biomass was observed in the gmglp20.4 knockout mutant. Overexpression of GmGLP20.4 improved plant growth and root architecture in transgenic tobacco (Nicotiana tabacum) under LN. Natural variation of the GT-1 cis-element in the promoter (T to A) of GmGLP20.4 was strongly associated with its expression level under LN, and significantly increased LN-sensitive variation (type A) was observed in wild soybean compared to that in elite cultivars. Thus, type A variation in the promoter of GmGLP20.4 may have been a site of artificial selection during domestication. The GmGT1-16g gene was highly expressed under LN and showed an expression pattern opposite to that of GmGLP20.4. A luciferase complementation imaging assay revealed that the GmGLP20.4 promoter specifically binds to GmGT1-16g. In conclusion, GmGLP20.4 is involved in soybean root development and the natural variation of its promoter will be useful in modern intercropping systems or to improve nitrogen-use efficiency.
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Affiliation(s)
- Wei Wang
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jianxin Wang
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ru Huang
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Qian Liu
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenqiao Fan
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Haowei Zheng
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Long Yan
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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19
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Zhang J, Ng C, Jiang Y, Wang X, Wang S, Wang S. Genome-wide identification and analysis of LOX genes in soybean cultivar “Zhonghuang 13”. Front Genet 2022; 13:1020554. [PMID: 36276975 PMCID: PMC9585170 DOI: 10.3389/fgene.2022.1020554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lipoxygenases (LOXs; EC1.13.11.12) are a family of iron- or manganese-containing dioxygenases that catalyze the oxygenation of polyunsaturated fatty acids (PUFAs) and play important roles in plant growth, development, and stress response. In this study, a total of 36 LOX gene family members were identified and annotated in Zhonghuang 13, a soybean cultivar bred by Chinese scientists in 2001. Sanger sequencing of the GmLOX1-coding sequence and colorimetric assays for the GmLOX1 protein showed that Zhonghuang 13 possessed the GmLOX1 gene. These LOX genes are divided into three subfamilies: 9-LOX, type Ⅰ 13-LOX and type II 13-LOX. In the 13-LOX group, the number of GmLOX members was the highest. These GmLOX genes are unevenly distributed on chromosomes 3, 7, 8, 10, 11, 12, 13, 15, 16, 19, and 20. Most of the 13-LOX genes exist in the form of gene clusters, indicating that these genes may originate from tandem duplications. The analysis of duplicated gene pairs showed that GmLOX genes underwent purifying selective pressure during evolution. The gene structures and conserved functional domains of these genes are quite similar. Compared to the orthologous gene pairs of LOX genes between wild soybean (Glycine soja W05) and Zhonghuang 13, the sequences of most gene pairs are relatively conserved. Many cis-elements are present in the promoter region and are involved in stress response, growth and development, hormone response and light response. The tissue-specific gene expression of GmLOX genes was evaluated. Represented by GmLOX1, GmLOX2, and GmLOX3, which were expressed at extremely high levels in seeds, they showed the characteristics of specific expression. This study provides detailed information on soybean lipoxygenase gene family members in Zhonghuang 13, which lays a foundation for further research.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Cheungchuk Ng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Yan Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xianxu Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- *Correspondence: Shaodong Wang, ; Sui Wang,
| | - Sui Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Shaodong Wang, ; Sui Wang,
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20
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Song JH, Shin G, Kim HJ, Lee SB, Moon JY, Jeong JC, Choi HK, Kim IA, Song HJ, Kim CY, Chung YS. Mutation of GmIPK1 Gene Using CRISPR/Cas9 Reduced Phytic Acid Content in Soybean Seeds. Int J Mol Sci 2022; 23:ijms231810583. [PMID: 36142495 PMCID: PMC9504718 DOI: 10.3390/ijms231810583] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Phytic acid (PA) acts as an antinutrient substance in cereal grains, disturbing the bioavailability of micronutrients, such as iron and zinc, in humans, causing malnutrition. GmIPK1 encodes the inositol 1,3,4,5,6-pentakisphosphate 2-kinase enzyme, which converts myo-inopsitol-1,3,4,5,6-pentakisphosphate (IP5) to myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP6) in soybean (Glycine max L.). In this study, for developing soybean with low PA levels, we attempted to edit the GmIPK1 gene using the CRISPR/Cas9 system to introduce mutations into the GmIPK1 gene with guide RNAs in soybean (cv. Kwangankong). The GmIPK1 gene was disrupted using the CRISPR/Cas9 system, with sgRNA-1 and sgRNA-4 targeting the second and third exon, respectively. Several soybean Gmipk1 gene-edited lines were obtained in the T0 generation at editing frequencies of 0.1–84.3%. Sequencing analysis revealed various indel patterns with the deletion of 1–9 nucleotides and insertions of 1 nucleotide in several soybean lines (T0). Finally, we confirmed two sgRNA-4 Gmipk1 gene-edited homozygote soybean T1 plants (line #21-2: 5 bp deletion; line #21-3: 1 bp insertion) by PPT leaf coating assay and PCR analysis. Analysis of soybean Gmipk1 gene-edited lines indicated a reduction in PA content in soybean T2 seeds but did not show any defects in plant growth and seed development.
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Affiliation(s)
- Ji Hyeon Song
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
| | - Gilok Shin
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup 56212, Korea
| | - Hye Jeong Kim
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
| | - Saet Buyl Lee
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup 56212, Korea
| | - Ju Yeon Moon
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup 56212, Korea
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup 56212, Korea
| | - Hong-Kyu Choi
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
| | - In Ah Kim
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
| | - Hyeon Jin Song
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup 56212, Korea
- Correspondence: (C.Y.K.); (Y.-S.C.); Tel.: +82-51-200-7510 (Y.-S.C.); Fax: +82-51-200-6536 (Y.-S.C.)
| | - Young-Soo Chung
- Department of Molecular Genetics, College of National Resources and Life Science, Dong-A University, Busan 49315, Korea
- Correspondence: (C.Y.K.); (Y.-S.C.); Tel.: +82-51-200-7510 (Y.-S.C.); Fax: +82-51-200-6536 (Y.-S.C.)
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21
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Bueno TV, Fontes PP, Abe VY, Utiyama AS, Senra RL, Oliveira LS, Brombini Dos Santos A, Ferreira EGC, Darben LM, de Oliveira AB, Abdelnoor RV, Whitham SA, Fietto LG, Marcelino-Guimarães FC. A Phakopsora pachyrhizi Effector Suppresses PAMP-Triggered Immunity and Interacts with a Soybean Glucan Endo-1,3-β-Glucosidase to Promote Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:779-790. [PMID: 35617509 DOI: 10.1094/mpmi-12-21-0301-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Asian soybean rust, caused by the fungus Phakopsora pachyrhizi, is one of the most important diseases affecting soybean production in tropical areas. During infection, P. pachyrhizi secretes proteins from haustoria that are transferred into plant cells to promote virulence. To date, only one candidate P. pachyrhizi effector protein has been characterized in detail to understand the mechanism by which it suppresses plant defenses to enhance infection. Here, we aimed to extend understanding of the pathogenic mechanisms of P. pachyrhizi based on the discovery of host proteins that interact with the effector candidate Phapa-7431740. We demonstrated that Phapa-7431740 suppresses pathogen-associated molecular pattern-triggered immunity (PTI) and that it interacts with a soybean glucan endo-1,3-β-glucosidase (GmβGLU), a pathogenesis-related (PR) protein belonging to the PR-2 family. Structural and phylogenetic characterization of the PR-2 protein family predicted in the soybean genome and comparison to PR-2 family members in Arabidopsis thaliana and cotton, demonstrated that GmβGLU is a type IV β-1,3-glucanase. Transcriptional profiling during an infection time course showed that the GmβGLU mRNA is highly induced during the initial hours after infection, coinciding with peak of expression of Phapa-7431740. The effector was able to interfere with the activity of GmβGLU in vitro, with a dose-dependent inhibition. Our results suggest that Phapa-7431740 may suppress PTI by interfering with glucan endo-1,3-β-glucosidase activity. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Thays V Bueno
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Patrícia P Fontes
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Valeria Y Abe
- Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil
| | - Alice Satiko Utiyama
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Renato L Senra
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
| | - Liliane S Oliveira
- Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil
- Department of Computer Science, Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Paraná 86300-000, Brazil
| | | | | | | | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Luciano G Fietto
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, Minas Gerais, CEP 36570-900, Brazil
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22
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Silva LCC, Mayrink DB, Bueno RD, Piovesan ND, Ribeiro C, Dal-Bianco M. Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. Biochem Genet 2022; 60:937-952. [PMID: 34554351 DOI: 10.1007/s10528-021-10135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.
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Affiliation(s)
- Luiz Cláudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil.
| | | | - Rafael Delmond Bueno
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Newton Deniz Piovesan
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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23
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Yu H, Wang Q, Zhang Z, Wu T, Yang X, Zhu X, Ye Y, Leng J, Yang S, Feng X. Genetic Mapping of the Gmpgl3 Mutant Reveals the Function of GmTic110a in Soybean Chloroplast Development. FRONTIERS IN PLANT SCIENCE 2022; 13:892077. [PMID: 35693168 PMCID: PMC9178232 DOI: 10.3389/fpls.2022.892077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The generation of oxygen and organic matter in plants mainly depends on photosynthesis, which directly affects plant growth and development. The chloroplast is the main organelle in which photosynthesis occurs. In this study, a Glycine max pale green leaf 3-1 (Gmpgl3-1) mutant was isolated from the soybean mutagenized population. The Gmpgl3-1 mutant presented with decreased chlorophyll contents, reduced chloroplast stroma thylakoids, reduced yields, and decreased numbers of pods per plant. Bulked segregant analysis (BSA) together with map-based cloning revealed a single-nucleotide non-synonymous mutation at the 341st nucleotide of the first exon of the chloroplast development-related GmTic110a gene. The phenotype of the knockout plants was the same as that of the mutant. The GmTic110a gene was highly expressed in the leaves at various developmental stages, and its protein was localized to the inner chloroplast membrane. Split luciferase complementation assays and coimmunoprecipitation (co-IP) experiments revealed that GmTic110a interacted with GmTic20, GmTic40a, and GmTic40b in tobacco leaves. These results indicated that the GmTic110a gene plays an important role in chloroplast development.
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Affiliation(s)
- Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Qiushi Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinjing Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yongheng Ye
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Zhejiang Lab, Hangzhou, China
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24
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Wang J, Fu X, Zhang S, Chen G, Li S, Shangguan T, Zheng Y, Xu F, Chen ZH, Xu S. Evolutionary and Regulatory Pattern Analysis of Soybean Ca 2+ ATPases for Abiotic Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:898256. [PMID: 35665149 PMCID: PMC9161174 DOI: 10.3389/fpls.2022.898256] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
P2-type Ca2+ ATPases are responsible for cellular Ca2+ transport, which plays an important role in plant development and tolerance to biotic and abiotic stresses. However, the role of P2-type Ca2+ ATPases in stress response and stomatal regulation is still elusive in soybean. In this study, a total of 12 P2-type Ca2+ ATPases genes (GmACAs and GmECAs) were identified from the genome of Glycine max. We analyzed the evolutionary relationship, conserved motif, functional domain, gene structure and location, and promoter elements of the family. Chlorophyll fluorescence imaging analysis showed that vegetable soybean leaves are damaged to different extents under salt, drought, cold, and shade stresses. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that most of the GmACAs and GmECAs are up-regulated after drought, cold, and NaCl treatment, but are down-regulated after shading stress. Microscopic observation showed that different stresses caused significant stomatal closure. Spatial location and temporal expression analysis suggested that GmACA8, GmACA9, GmACA10, GmACA12, GmACA13, and GmACA11 might promote stomatal closure under drought, cold, and salt stress. GmECA1 might regulate stomatal closure in shading stress. GmACA1 and GmECA3 might have a negative function on cold stress. The results laid an important foundation for further study on the function of P2-type Ca2+ ATPase genes GmACAs and GmECAs for breeding abiotic stress-tolerant vegetable soybean.
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Affiliation(s)
- Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xujun Fu
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sheng Zhang
- Taizhou Seed Administration Station, Taizhou, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tengwei Shangguan
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yuanting Zheng
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Xu
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Shengchun Xu
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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25
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Feng S, Shi J, Hu Y, Li D, Guo L, Zhao Z, Lee GS, Qiao Y. Genome-Wide Analysis of Soybean Lateral Organ Boundaries Domain Gene Family Reveals the Role in Phytophthora Root and Stem Rot. FRONTIERS IN PLANT SCIENCE 2022; 13:865165. [PMID: 35599907 PMCID: PMC9116278 DOI: 10.3389/fpls.2022.865165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific lateral organ boundaries (LOB) domain (LBD) proteins, a family of transcription factors, play important roles in plant growth and development, as well as in responses to various stresses. However, little is known about the functions of LBD genes in soybean (Glycine max). In this study, we investigated the evolution and classification of the LBD family in soybean by a phylogenetic tree of the LBD gene family from 16 species. Phylogenetic analysis categorized these proteins into two classes (Class I and Class II) with seven subgroups. Moreover, we found that all the 18 LBD ancestors in angiosperm were kept in soybean, common bean genomes, and genome-wide duplication, suggesting the main force for the expansion of LBD from common bean to soybean. Analysis of gene expression profiling data indicated that 16 GmLBD genes were significantly induced at different time points after inoculation of soybean plants (cv. Huachun 6) with Phytophthora sojae (P. sojae). We further assessed the role of four highly upregulated genes, GmLBD9, GmLBD16, GmLBD23, and GmLBD88, in plant defense in soybean hairy roots using the transient overexpression and knockdown assays. The results showed that GmLBD9 and GmLBD23 negatively regulate plant immunity against P. sojae, whereas GmLBD16 and GmLBD88 positively manipulate plant immunity against P. sojae. Collectively, our findings expand our knowledge of the origin and evolution of the GmLBD gene family in soybean and promote the potential application of these genes in soybean genetic improvement.
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Affiliation(s)
- Siqi Feng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongkang Hu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Gang-Seob Lee
- National Institute of Agricultural Science, Jeonju, South Korea
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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26
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Qu Y, Guan R, Yu L, Berkowitz O, David R, Whelan J, Ford M, Wege S, Qiu L, Gilliham M. Enhanced reactive oxygen detoxification occurs in salt-stressed soybean roots expressing GmSALT3. PHYSIOLOGIA PLANTARUM 2022; 174:e13709. [PMID: 35580210 PMCID: PMC9327525 DOI: 10.1111/ppl.13709] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Soybean (Glycine max) is an important crop globally for food and edible oil production. Soybean plants are sensitive to salinity (NaCl), with significant yield decreases reported under saline conditions. GmSALT3 is the dominant gene underlying a major QTL for salt tolerance in soybean. GmSALT3 encodes a transmembrane protein belonging to the plant cation/proton exchanger (CHX) family, and is predominately expressed in root phloem and xylem associated cells under both saline and non-saline conditions. It is currently unknown through which molecular mechanism(s) the ER-localised GmSALT3 contributes to salinity tolerance, as its localisation excludes direct involvement in ion exclusion. In order to gain insights into potential molecular mechanism(s), we used RNA-seq analysis of roots from two soybean NILs (near isogenic lines); NIL-S (salt-sensitive, Gmsalt3), and NIL-T (salt-tolerant, GmSALT3), grown under control and saline conditions (200 mM NaCl) at three time points (0 h, 6 h, and 3 days). Gene ontology (GO) analysis showed that NIL-T has greater responses aligned to oxidation reduction. ROS were less abundant and scavenging enzyme activity was greater in NIL-T, consistent with the RNA-seq data. Further analysis indicated that genes related to calcium signalling, vesicle trafficking and Casparian strip (CS) development were upregulated in NIL-T following salt treatment. We propose that GmSALT3 improves the ability of NIL-T to cope with saline stress through preventing ROS overaccumulation in roots, and potentially modulating Ca2+ signalling, vesicle trafficking and formation of diffusion barriers.
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Affiliation(s)
- Yue Qu
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil ScienceSchool of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe UniversityBundooraVictoriaAustralia
| | - Rakesh David
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - James Whelan
- Department of Animal, Plant and Soil ScienceSchool of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe UniversityBundooraVictoriaAustralia
| | - Melanie Ford
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Stefanie Wege
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
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Identification and Validation of Reliable Reference Genes for Gene Expression Studies in Koelreuteria paniculata. Genes (Basel) 2022; 13:genes13050714. [PMID: 35627099 PMCID: PMC9141280 DOI: 10.3390/genes13050714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
RT-qPCR is considered a rapid and reliable technique for analyzing gene expression. This technique is commonly used to analyze the expression of various genes at diverse transcriptional levels in different samples. However, few studies have characterized ornamental Koelreuteria species for reliable reference genes. In this study, eight reference genes were evaluated as controls in RT-qPCR with SYBR green to quantify gene expression in different Koelreuteria paniculata samples. All selected reference genes showed a broad range of Ct values in all samples, which was supportive of their variable expression. Our results showed significant variation in the stable expression of K. paniculata genes. Sample data, analyzed using geNorm, NormFinder, and BestKeeper, showed that phospholipase (PLA2) and β-actin (ACT) were the most suitable and statistically reliable reference genes, whereas ribosomal protein L13 (RPL13) and elongation factor 1-α (EF1α) were less stable and unsuitable for use as internal controls. To compare gene expression levels, two or more reference genes should be used for data normalization. Thus, the stability and expression of both PLA2 and ACT were believed to provide better normalization and quantification of the transcript levels for gene expression studies in K. paniculata.
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Aznar-Moreno JA, Mukherjee T, Morley SA, Duressa D, Kambhampati S, Chu KL, Koley S, Allen DK, Durrett TP. Suppression of SDP1 Improves Soybean Seed Composition by Increasing Oil and Reducing Undigestible Oligosaccharides. FRONTIERS IN PLANT SCIENCE 2022; 13:863254. [PMID: 35401590 PMCID: PMC8983916 DOI: 10.3389/fpls.2022.863254] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/22/2022] [Indexed: 06/01/2023]
Abstract
In developing soybean seeds, carbon is partitioned between oil, protein and carbohydrates. Here, we demonstrate that suppression of lipase-mediated turnover of triacylglycerols (TAG) during late seed development increases fatty acid content and decreases the presence of undigestible oligosaccharides. During late stages of embryo development, the fatty acid content of soybean seed decreases while the levels of the oligosaccharides raffinose and stachyose increase. Three soybean genes orthologous to the Arabidopsis lipase gene SUGAR-DEPENDENT1 (SDP1) are upregulated at this time. Suppression of these genes resulted in higher oil levels, with lipid levels in the best lines exceeding 24% of seed weight. In addition, lipase-suppressed lines produced larger seeds compared to wild-type plants, resulting in increases of over 20% in total lipid per seed. Levels of raffinose and stachyose were lower in the transgenic lines, with average reductions of 15% in total raffinose family oligosaccharides observed. Despite the increase in oil, protein content was not negatively impacted and trended higher in the transgenic lines. These results are consistent with a role for SDP1 in turning over TAG to supply carbon for other needs, including the synthesis of oligosaccharides, and offer new strategies to further improve the composition of soybean seeds.
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Affiliation(s)
- Jose A. Aznar-Moreno
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Thiya Mukherjee
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Stewart A. Morley
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Dechassa Duressa
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | | | - Kevin L. Chu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Timothy P. Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
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Alves da Silva A, Oliveira Silva C, do Rosario Rosa V, Silva Santos MF, Naomi Kuki K, Dal-Bianco M, Delmond Bueno R, Alves de Oliveira J, Santos Brito D, Costa AC, Ribeiro C. Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean. PeerJ 2022; 10:e13118. [PMID: 35321407 PMCID: PMC8935993 DOI: 10.7717/peerj.13118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.
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Affiliation(s)
- Adinan Alves da Silva
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cíntia Oliveira Silva
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | - Kacilda Naomi Kuki
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Maximiller Dal-Bianco
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Rafael Delmond Bueno
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Danielle Santos Brito
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alan Carlos Costa
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cleberson Ribeiro
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Xu Y, Yan F, Zong Y, Li J, Gao H, Liu Y, Wang Y, Zhu Y, Wang Q. Proteomic and lipidomics analyses of high fatty acid AhDGAT3 transgenic soybean reveals the key lipase gene associated with the lipid internal mechanism. Genome 2022; 65:153-164. [PMID: 34995159 DOI: 10.1139/gen-2021-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vegetable oil is one of the most important components of human nutrition. Soybean (Glycine max) is an important oil crop worldwide and contains rich unsaturated fatty acids. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in the Kennedy pathway from diacylglycerol (DAG) to triacylglycerol (TAG). In this study, we conducted further research using T3 AhDGAT3 transgenic soybean. A high-performance gas chromatography flame ionization detector showed that oleic acid (18:1) content and total fatty acid content of transgenic soybean were significantly higher than those of the wild type (WT). However, linoleic acid (18:2) was much lower than that in the WT. For further mechanistic studies, 20 differentially expressed proteins (DEPs) and 119 differentially expressed metabolites (DEMs) were identified between WT (JACK) and AhDGAT3 transgenic soybean mature seeds using proteomic and lipidomics analyses. Combined proteomic and lipidomics analyses showed that the upregulation of the key DEP (lipase GDSL domain-containing protein) in lipid transport and metabolic process induced an increase in the total fatty acid and 18:1 composition, but a decrease in the 18:2 composition of fatty acids. Our study provides new insights into the deep study of molecular mechanism underlying the enhancement of fatty acids in transgenic soybeans, especially oleic acid and total fatty acid, which are enhanced by over-expression of AhDGAT3.
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Affiliation(s)
- Yang Xu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Fan Yan
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yu Zong
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Jingwen Li
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Han Gao
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yajing Liu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Ying Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Youcheng Zhu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
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Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.
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32
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Evaluation of Reference Genes for Quantitative PCR in Eustoma grandiflorum under Different Experimental Conditions. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Eustoma grandiflorum, commonly known as prairie gentian or Texas bluebells, is among the most popular agriculturally propagated species of cut flowers. Due to its widespread appeal, there is increasing interest in understanding the molecular genetic factors underlying floral development and resistance to abiotic stresses. We analyzed 18 potential reference genes in different organs, at different floral developmental stages and under drought- and salt-stress treatments, for use in RT-qPCR analysis. A total of four analytical tool packages, including geNorm, NormFinder, BestKeeper, and RefFinder were employed to determine the most appropriate reference genes under each treatment condition. The results demonstrate that different reference genes should be used for normalization under different experimental treatments. EgPP and EgPP2A2 were the most stable internal control genes across different organ types, EgPP and Eg18S were the most stable under salt-stress, EgPP and EgACT1 were the most stable across different floral development stages, and EgEF1A and EgTUA were the most stable reference genes under drought-stress. Additional gene expression analyses of EgMIXTA1, EgTOE1, and EgP5CS1 further confirmed the applicability of these reference genes. The results represent a significant contribution to future studies of reference gene selection for the normalization of gene expression in Eustoma grandiflorum.
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Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening. Genes (Basel) 2022; 13:genes13010160. [PMID: 35052500 PMCID: PMC8775616 DOI: 10.3390/genes13010160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a powerful tool to detect and quantify transcription abundance, and the stability of the reference gene determines its success. However, the most suitable reference gene for different genotypes and tobacco rattle virus (TRV) infected fruits was unclear in peach (Prunus persica L. Batsch). In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable variability of gene expression in all experimental conditions. Furthermore, to confirm the validity of the reference genes, the expression levels of PpACO1, PpEIN2, and PpPL were normalized at different fruit storage periods. In summary, our results provide guidelines for selecting reliable reference genes in different genotypes and TRV-infected fruits and lay the foundation for accurate evaluation of gene expression for RT-qPCR analysis in peach.
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Link TI. Host-Induced Gene Silencing Using BPMV on Soybean to Study Genes in the Soybean Rust Fungus Phakopsora pachyrhizi. Methods Mol Biol 2022; 2523:79-91. [PMID: 35759192 DOI: 10.1007/978-1-0716-2449-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To obtain direct evidence for the influence of an effector on the virulence or pathogenicity of a pathogen, it is necessary to knock out, knock down, or silence the respective gene. Since genetic transformation is not yet possible for rust fungi, silencing the gene is the only option. Posttranscriptional gene silencing uses RNAi. RNAi in plant pathogens can be accomplished by introducing dsRNA either by direct application of in vitro synthesized dsRNA or through positive-strand or double-strand RNA plant viruses. For studying effectors in Phakopsora pachyrhizi, we have implemented a host-induced silencing procedure based on virus-induced gene silencing using the bean pod mottle virus system. Here, procedures and interpretations of results are described and limitations of the system are discussed.
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Affiliation(s)
- Tobias I Link
- Department of Phytopathology, University of Hohenheim, Stuttgart, Germany.
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35
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Liu YP, Zhang Y, Liu F, Liu T, Chen JY, Fu G, Zheng CY, Su DD, Wang YN, Zhou HK, Su X, Aj H, Wang XM. Establishment of reference (housekeeping) genes via quantitative real-time PCR for investigation of the genomic basis of abiotic stress resistance in Psammochloa villosa (Poaceae). JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153575. [PMID: 34837885 DOI: 10.1016/j.jplph.2021.153575] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
Psammochloa villosa is a desert plant growing in Northwest China with considerable resistance to abiotic stress, including drought, cold, and salt. To facilitate future studies of stress resistance in Psammochloa villosa, we sought to establish a suite of reference (or housekeeping) genes for utilization within future gene expression studies. Specifically, we selected nine candidate genes based on prior studies and new transcriptomic data for P. villosa, and we evaluated their expression stability in three different tissues of P. villosa under different treatments simulating abiotic stress conditions using four different bioinformatics assessments. Our results showed that TIP41 (TIP41-like family protein) was the most stable reference gene in drought- and salt-stressed leaves and salt-stressed stems, ELF-1α (elongation factor 1-α) was the most stable in cold-stressed leaves and drought- and salt-stressed roots, ACT (actin) was the most stable in drought-stressed stems, TUA (α-tubulin) was the most stable in cold-stressed stems, and 18S rRNA (18S ribosomal RNA) was the most stable in cold-stressed roots. Additionally, we tested the utility of these candidate reference genes to detect the expression pattern of P5CS (Δ1-pyrroline-5-carboxylate synthetase), which is a drought-related gene. This study is the first report on selecting and validating reference genes of P. villosa under various stress conditions and will benefit future investigations of the genomic mechanisms of stress resistance in this ecologically important species.
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Affiliation(s)
- Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - Yu Zhang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Feng Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Geography, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Gui Fu
- School of Geography, Qinghai Normal University, Xining, 810008, China
| | - Chang Yuan Zheng
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Dan Dan Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Ya Nan Wang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Hua Kun Zhou
- Key Laboratory of Cold Regions Restoration Ecology in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Harris Aj
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiu Mei Wang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
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Yu Q, Liu YL, Sun GZ, Liu YX, Chen J, Zhou YB, Chen M, Ma YZ, Xu ZS, Lan JH. Genome-Wide Analysis of the Soybean Calmodulin-Binding Protein 60 Family and Identification of GmCBP60A-1 Responses to Drought and Salt Stresses. Int J Mol Sci 2021; 22:13501. [PMID: 34948302 PMCID: PMC8708795 DOI: 10.3390/ijms222413501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin-binding protein 60 (CBP60) members constitute a plant-specific protein family that plays an important role in plant growth and development. In the soybean genome, nineteen CBP60 members were identified and analyzed for their corresponding sequences and structures to explore their functions. Among GmCBP60A-1, which primarily locates in the cytomembrane, was significantly induced by drought and salt stresses. The overexpression of GmCBP60A-1 enhanced drought and salt tolerance in Arabidopsis, which showed better state in the germination of seeds and the root growth of seedlings. In the soybean hairy roots experiment, the overexpression of GmCBP60A-1 increased proline content, lowered water loss rate and malondialdehyde (MDA) content, all of which likely enhanced the drought and salt tolerance of soybean seedlings. Under stress conditions, drought and salt response-related genes showed significant differences in expression in hairy root soybean plants of GmCBP60A-1-overexpressing and hairy root soybean plants of RNAi. The present study identified GmCBP60A-1 as an important gene in response to salt and drought stresses based on the functional analysis of this gene and its potential underlying mechanisms in soybean stress-tolerance.
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Affiliation(s)
- Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Ya-Li Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
| | - Guo-Zhong Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Yuan-Xia Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Yong-Bin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - You-Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Zhao-Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Jin-Hao Lan
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
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Zhang C, Gao H, Sun Y, Jiang L, He S, Song B, Liu S, Zhao M, Wang L, Liu Y, Wu J, Xu P, Zhang S. The BTB/POZ domain protein GmBTB/POZ promotes the ubiquitination and degradation of the soybean AP2/ERF-like transcription factor GmAP2 to regulate the defense response to Phytophthora sojae. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7891-7908. [PMID: 34338731 DOI: 10.1093/jxb/erab363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/30/2021] [Indexed: 05/20/2023]
Abstract
Phytophthora root and stem rot in soybean (Glycine max) is a destructive disease worldwide, and hence improving crop resistance to the causal pathogen, P. sojae, is a major target for breeders. However, it remains largely unclear how the pathogen regulates the various affected signaling pathways in the host, which consist of complex networks including key transcription factors and their targets. We have previously demonstrated that GmBTB/POZ enhances soybean resistance to P. sojae and the associated defense response. Here, we demonstrate that GmBTB/POZ interacts with the transcription factor GmAP2 and promotes its ubiquitination. GmAP2-RNAi transgenic soybean hairy roots exhibited enhanced resistance to P. sojae, whereas roots overexpressing GmAP2 showed hypersensitivity. GmWRKY33 was identified as a target of GmAP2, which represses its expression by directly binding to the promoter. GmWRKY33 acts as a positive regulator in the response of soybean to P. sojae. Overexpression of GmBTB/POZ released the GmAP2-regulated suppression of GmWRKY33 in hairy roots overexpressing GmAP2 and increased their resistance to P. sojae. Taken together, our results indicate that GmBTB/POZ-GmAP2 modulation of the P. sojae resistance response forms a novel regulatory mechanism, which putatively regulates the downstream target gene GmWRKY33 in soybean.
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Affiliation(s)
- Chuanzhong Zhang
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Hong Gao
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Yan Sun
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Liangyu Jiang
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Shengfu He
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Bo Song
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Shanshan Liu
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Ming Zhao
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Le Wang
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Yaguang Liu
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin, China
| | - Pengfei Xu
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Shuzhen Zhang
- Soybean Research Institute of Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
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Xun H, Zhang X, Yu J, Pang J, Wang S, Liu B, Dong Y, Jiang L, Guo D. Analysis of expression characteristics of soybean leaf and root tissue-specific promoters in Arabidopsis and soybean. Transgenic Res 2021; 30:799-810. [PMID: 34115286 DOI: 10.1007/s11248-021-00266-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
The characterization of tissue-specific promoters is critical for studying the functions of genes in a given tissue/organ. To study tissue-specific promoters in soybean, we screened tissue-specific expressed genes using published soybean RNA-Seq-based transcriptome data coupled with RT-PCR analysis. We cloned the promoters of three genes, GmADR1, GmBTP1, and GmGER1, and constructed their corresponding β-Glucuronidase (GUS) promoter-GUS reporter vectors. We generated transgenic Arabidopsis plants and examined the expression patterns of these promoters by GUS staining and RT-PCR analysis. We also transformed the promoter-GUS reporter vectors into soybean to obtain hairy roots, and examined promoter expression by GUS staining. We found a root-specific expression pattern of GmADR1 and GmBTP1 in both Arabidopsis and soybean, and the promoter of GmGER1 showed a leaf-specific pattern in transgenic Arabidopsis plants. To test the potential utility of these promoters in soybean improvement by transgenic means, we used the GmADR1 promoter to drive expression of a salt resistance gene in soybean, GmCaM4, by generating transgenic soybean plants. We found that the transgenic plants had significantly enhanced salt tolerance compared to non-transformed wild-type, suggesting that introducing endogenous promoters by transgenic means can drive the expression of functional genes in specific tissues and organs in soybean.
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Affiliation(s)
- Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, China
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China
| | - Xue Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China
| | - Jiamiao Yu
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, 276000, Linyi, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, 130024, Changchun, China.
| | - Dongquan Guo
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, China.
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Sinha R, Bala M, Prabha P, Ranjan A, Chahota RK, Sharma TR, Singh AK. Identification and validation of reference genes for qRT-PCR based studies in horse gram ( Macrotyloma uniflorum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2859-2873. [PMID: 35035141 PMCID: PMC8720121 DOI: 10.1007/s12298-021-01104-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED The quantitative real-time polymerase chain reaction (qRT-PCR) is the most sensitive and commonly used technique for gene expression studies in biological systems. However, the reliability of qRT-PCR results depends on the selection of reference gene(s) for data normalization. Horse gram (Macrotyloma uniflorum) is an important legume crop on which several molecular studies have been reported. However, the stability of reference genes has not been evaluated. In the present study, nine candidate reference genes were identified from horse gram RNA-seq data and evaluated in two horse gram genotypes, HPK4 and HPKM317 under six abiotic stresses viz. cold, drought, salinity, heat, abscisic acid and methyl viologen-induced oxidative stress. The results were evaluated using geNorm, Bestkeeper, Normfinder and delta-delta Ct methods and comprehensive ranking was assigned using RefFinder and RankAggreg software. The overall result showed that TCTP was one of the most stable genes in all samples and in genotype HPK4, while in HPKM317 profilin was most stably expressed. However, PSMA5 was identified as least stable in all the experimental conditions. Expression of target genes dehydrin and early response to dehydration 6 under drought stress was also validated using TCTP and profilin for data normalization, either alone or in combination, which confirmed their suitability for qRT-PCR data normalization. Thus, TCTP and profilin genes may be used for qRT-PCR data normalization for molecular and genomic studies in horse gram. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01104-0.
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Affiliation(s)
- Ragini Sinha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Pragya Prabha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Alok Ranjan
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Rakesh K. Chahota
- Department of Agricultural Biotechnology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176061 India
| | - Tilak Raj Sharma
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Xu Y, Yan F, Liu Y, Wang Y, Gao H, Zhao S, Zhu Y, Wang Q, Li J. Quantitative proteomic and lipidomics analyses of high oil content GmDGAT1-2 transgenic soybean illustrate the regulatory mechanism of lipoxygenase and oleosin. PLANT CELL REPORTS 2021; 40:2303-2323. [PMID: 34427748 DOI: 10.1007/s00299-021-02768-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Proteomic and lipidomics analyses of WT and GmDGAT1-2 transgenic soybeans showed that GmDGAT1-2 over-expression induced lipoxygenase down-regulatation and oleoin up-regulatation, which significantly changed the compositions and total fatty acid. The main goal of soybean breeding is to increase the oil content. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in fatty acid metabolism and may regulate oil content. Herein, 10 GmDGAT genes were isolated from soybean and transferred into wild-type (WT) Arabidopsis. The total fatty acid was 1.2 times higher in T3 GmDGAT1-2 transgenic Arabidopsis seeds than in WT. Therefore, GmDGAT1-2 was transferred into WT soybean (JACK), and four T3 transgenic soybean lines were obtained. The results of high-performance gas chromatography and Soxhlet extractor showed that, compared with those of JACK, oleic acid (18:1), and total fatty acid levels in transgenic soybean plants were much higher, but linoleic acid (18:2) was lower than WT. Palmitic acid (16:0), stearic acid (18:0), and linolenic acid (18:3) were not significantly different. For mechanistic studies, 436 differentially expressed proteins (DEPs) and 180 differentially expressed metabolites (DEMs) were identified between WT (JACK) and transgenic soybean pods using proteomic and lipidomics analyses. Four lipoxygenase proteins were down-regulated in linoleic acid metabolism while four oleosin proteins were up-regulated in the final oil formation. The results showed an increase in the total fatty acid and 18:1 composition, and a decrease in the 18:2 composition of fatty acid. Our study brings new insights into soybean genetic transformation and the deep study of molecular mechanism that changes the total fatty acid, 18:1, and 18:2 compositions in GmDGAT1-2 transgenic soybean.
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Affiliation(s)
- Yang Xu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Fan Yan
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yajing Liu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ying Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Han Gao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shihui Zhao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Youcheng Zhu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Qingyu Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Jingwen Li
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
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Zhu X, Wang B, Wang X, Wei X. Screening of stable internal reference gene of Quinoa under hormone treatment and abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2459-2470. [PMID: 34924704 PMCID: PMC8639980 DOI: 10.1007/s12298-021-01094-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Real-time quantitative polymerase chain reaction is the most commonly used method to accurately detect gene expression patterns. The method requires stable internal reference genes to standardize the data. However, studies have shown that there is no stable expression of internal reference genes in different tissues and under different treatments. Therefore, in order to study the optimal reference genes of quinoa under different hormones and abiotic stress, leaves and stems from quinoa seedlings treated with low temperature (4 °C), salt (200 mmol/L) and abscisic acid (200 mmol/L) were used as experimental materials. Using ACT-1, eIF, EF1α, GAPDH, TUA, TUB-9, TUB-1, H2A and L8-1 as candidate reference genes, the expression stability of these 9 quinoa candidate reference genes under different hormone treatment and abiotic stress was evaluated by using geNorm, NormFinder and BestKeeper software. The results showed that TUB-1 gene under salt stress, L8-1 gene under low temperature stress, EF-1α gene induced by ABA. PLIM2c WLIM1and WLIM2b were selected to verify the candidate internal reference genes, and finally the expression of GAPDH was most unstable under the three treatments, which was not suitable to be the internal reference gene of quinoa under specific conditions, while EF1α showed good stability under the three different treatments and was suitable to be used as the internal reference gene. In conclusion, the results of this study could provide an important reference for quantifying the expression level of reference genes in quinoa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01094-z.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xian Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
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42
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Wang R, Deng M, Yang C, Yu Q, Zhang L, Zhu Q, Guo X. A Qa-SNARE complex contributes to soybean cyst nematode resistance via regulation of mitochondria-mediated cell death. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7145-7162. [PMID: 34165531 DOI: 10.1093/jxb/erab301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/23/2021] [Indexed: 05/27/2023]
Abstract
The resistance to Heterodera glycines 1 (Rhg1) locus is widely used by soybean breeders to reduce yield loss caused by soybean cyst nematode (SCN). α-SNAP (α-soluble NSF attachment protein) within Rhg1 locus contributes to SCN resistance by modulation of cell status at the SCN feeding site; however, the underlying mechanism is largely unclear. Here, we identified an α-SNAP-interacting protein, GmSYP31A, a Qa-SNARE (soluble NSF attachment protein receptor) protein from soybean. Expression of GmSYP31A significantly induced cell death in Nicotiana benthamiana leaves, and co-expression of α-SNAP and GmSYP31A could accelerate cell death. Overexpression of GmSYP31A increased SCN resistance, while silencing or overexpression of a dominant-negative form of GmSYP31A increased SCN sensitivity. GmSYP31A expression also disrupted endoplasmic reticulum-Golgi trafficking, and the exocytosis pathway. Moreover, α-SNAP was also found to interact with GmVDAC1D (voltage-dependent anion channel). The cytotoxicity induced by the expression of GmSYP31A could be relieved either with the addition of an inhibitor of VDAC protein, or by silencing the VDAC gene. Taken together, our data not only demonstrate that α-SNAP works together with GmSYP31A to increase SCN resistance through triggering cell death, but also highlight the unexplored link between the mitochondrial apoptosis pathway and vesicle trafficking.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Miaomiao Deng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chao Yang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qianqian Yu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lei Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qun Zhu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoli Guo
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Hosseini B, Voegele RT, Link TI. Establishment of a quadruplex real-time PCR assay to distinguish the fungal pathogens Diaporthe longicolla, D. caulivora, D. eres, and D. novem on soybean. PLoS One 2021; 16:e0257225. [PMID: 34506590 PMCID: PMC8432765 DOI: 10.1371/journal.pone.0257225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 08/27/2021] [Indexed: 11/18/2022] Open
Abstract
Diaporthe species are fungal plant pathogens of many important crops. Seed decay is one of the most important diseases on soybean. It is caused by various species of the genus Diaporthe and responsible for significant economic damage. In central Europe the four species D. longicolla, D. caulivora, D. eres, and D. novem are considered the principal species of Diaporthe on soybean. Fast and accurate detection of these pathogens is of utmost importance. In this study four species-specific TaqMan primer-probe sets that can be combined into a quadruplex assay were designed based on TEF sequences. The specificity and efficiency of the primer-probe sets were tested using PCR products and genomic DNA from pure cultures of the four Diaporthe species and other soybean fungal pathogens. Our results indicate that the primer-probe sets DPCL, DPCC, DPCE, and DPCN allow discrimination of D. longicolla, D. caulivora, D. eres, and D. novem, respectively, and can be used to detect and quantify these four Diaporthe species in parallel using quadruplex real-time PCR. In addition, the quadruplex real-time PCR assay was evaluated on different plant materials including healthy and infected soybean seeds or seed lots, soybean stems, and soybean leaves. This assay is a rapid and effective method to detect and quantify Diaporthe species from samples relevant for disease control.
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Affiliation(s)
- Behnoush Hosseini
- Faculty of Agricultural Sciences, Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Ralf T. Voegele
- Faculty of Agricultural Sciences, Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Tobias I. Link
- Faculty of Agricultural Sciences, Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
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Xu K, Zhang XM, Chen H, Zhang C, Zhu J, Cheng Z, Huang P, Zhou X, Miao Y, Feng X, Fu YF. Fine-Tuning Florigen Increases Field Yield Through Improving Photosynthesis in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:710754. [PMID: 34484271 PMCID: PMC8415793 DOI: 10.3389/fpls.2021.710754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/28/2021] [Indexed: 05/29/2023]
Abstract
Crop yield has been maintaining its attraction for researchers because of the demand of global population growth. Mutation of flowering activators, such as florigen, increases plant biomass at the expense of later flowering, which prevents crop maturity in the field. As a result, it is difficult to apply flowering activators in agriculture production. Here, we developed a strategy to utilize florigen to significantly improve soybean yield in the field. Through the screening of transgenic lines of RNAi-silenced florigen homologs in soybean (Glycine-max-Flowering Locus T Like, GmFTL), we identified a line, GmFTL-RNAi#1, with minor changes in both GmFTL expression and flowering time but with notable increase in soybean yield. As expected, GmFTL-RNAi#1 matured normally in the field and exhibited markedly high yield over multiple locations and years, indicating that it is possible to reach a trade-off between flowering time and high yield through the fine-tuning expression of flowering activators. Further studies uncovered an unknown mechanism by which GmFTL negatively regulates photosynthesis, a substantial source of crop yield, demonstrating a novel function of florigen. Thus, because of the highly conserved functions of florigen in plants and the classical RNAi approach, the findings provide a promising strategy to harness early flowering genes to improve crop yield.
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Affiliation(s)
- Kun Xu
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Xiao-Mei Zhang
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haifeng Chen
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Chanjuan Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Jinlong Zhu
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Zhiyuan Cheng
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Penghui Huang
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinan Zhou
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Yuchen Miao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xianzhong Feng
- CAS Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yong-Fu Fu
- MOA Key Laboratory of Soybean Biology, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Selection and Optimization of Reference Genes for MicroRNA Expression Normalization by qRT-PCR in Chinese Cedar ( Cryptomeria fortunei) under Multiple Stresses. Int J Mol Sci 2021; 22:ijms22147246. [PMID: 34298866 PMCID: PMC8304282 DOI: 10.3390/ijms22147246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 01/22/2023] Open
Abstract
MicroRNA (miRNA) expression analysis is very important for investigating its functions. To date, no research on reference genes (RGs) for miRNAs in gymnosperms, including Cryptomeria fortunei, has been reported. Here, ten miRNAs (i.e., pab-miR159a, cln-miR162, cas-miR166d, pab-miR395b, ppt-miR894, cln-miR6725, novel1, novel6, novel14 and novel16) and three common RGs (U6, 5S and 18S) were selected as candidate RGs. qRT-PCR was used to analyse their expressions in C. fortunei under various experimental conditions, including multiple stresses (cold, heat, drought, salt, abscisic acid and gibberellin) and in various tissues (roots, stems, tender needles, cones and seeds). Four algorithms (delta Ct, geNorm, NormFinder and BestKeeper) were employed to assess the stability of candidate RG expression; the geometric mean and RefFinder program were used to comprehensively evaluate RG stability. According to the results, novel16, cln-miR6725, novel1 and U6 were the most stable RGs for studying C. fortunei miRNA expression. In addition, the expression of three target miRNAs (aly-miR164c-5p, aly-miR168a-5p and smo-miR396) was examined to verify that the selected RGs are suitable for miRNA expression normalisation. This study may aid further investigations of miRNA expression/function in the response of C. fortunei to abiotic stress and provides an important basis for the standardisation of miRNA expression in other gymnosperm species.
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Kambhampati S, Aznar-Moreno JA, Bailey SR, Arp JJ, Chu KL, Bilyeu KD, Durrett TP, Allen DK. Temporal changes in metabolism late in seed development affect biomass composition. PLANT PHYSIOLOGY 2021; 186:874-890. [PMID: 33693938 PMCID: PMC8195533 DOI: 10.1093/plphys/kiab116] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/13/2021] [Indexed: 05/23/2023]
Abstract
The negative association between protein and oil production in soybean (Glycine max) seed is well-documented. However, this inverse relationship is based primarily on the composition of mature seed, which reflects the cumulative result of events over the course of soybean seed development and therefore does not convey information specific to metabolic fluctuations during developmental growth regimes. In this study, we assessed maternal nutrient supply via measurement of seed coat exudates and metabolite levels within the cotyledon throughout development to identify trends in the accumulation of central carbon and nitrogen metabolic intermediates. Active metabolic activity during late seed development was probed through transient labeling with 13C substrates. The results indicated: (1) a drop in lipid contents during seed maturation with a concomitant increase in carbohydrates, (2) a transition from seed filling to maturation phases characterized by quantitatively balanced changes in carbon use and CO2 release, (3) changes in measured carbon and nitrogen resources supplied maternally throughout development, (4) 13C metabolite production through gluconeogenic steps for sustained carbohydrate accumulation as the maternal nutrient supply diminishes, and (5) oligosaccharide biosynthesis within the seed coat during the maturation phase. These results highlight temporal engineering targets for altering final biomass composition to increase the value of soybeans and a path to breaking the inverse correlation between seed protein and oil content.
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Affiliation(s)
| | - Jose A Aznar-Moreno
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Sally R Bailey
- United States Department of Agriculture, Agricultural Research Service, St. Louis, Missouri 63132, USA
| | - Jennifer J Arp
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Kevin L Chu
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- United States Department of Agriculture, Agricultural Research Service, St. Louis, Missouri 63132, USA
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Kristin D Bilyeu
- United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Timothy P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- United States Department of Agriculture, Agricultural Research Service, St. Louis, Missouri 63132, USA
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Zhang Y, Zhu L, Xue J, Yang J, Hu H, Cui J, Xu J. Selection and Verification of Appropriate Reference Genes for Expression Normalization in Cryptomeria fortunei under Abiotic Stress and Hormone Treatments. Genes (Basel) 2021; 12:genes12060791. [PMID: 34064253 PMCID: PMC8224294 DOI: 10.3390/genes12060791] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Cryptomeria fortunei has become one of the main timber afforestation species in subtropical high-altitude areas of China due to its fast growth, good material quality, and strong adaptability, showing broad application prospects. Quantitative real-time PCR (qRT-PCR) is the most accurate and widely used gene expression evaluation technique, and selecting appropriate reference genes (RGs) is essential for normalizing qRT-PCR results. However, suitable RGs for gene expression normalization in C. fortunei have not been reported. Here, we tested the expression stability for 12 RGs in C. fortunei under various experimental conditions (simulated abiotic stresses (cold, heat, drought, and salinity) and hormone treatments (methyl jasmonate, abscisic acid, salicylic acid, and gibberellin) and in different tissues (stems, tender needles, needles, cones, and seeds) using four algorithms (delta Ct, geNorm, NormFinder, and BestKeeper). Then, geometric mean rankings from these algorithms and the RefFinder program were used to comprehensively evaluate RG stability. The results indicated CYP, actin, UBC, and 18S as good choices for studying C. fortunei gene expression. qRT-PCR analysis of the expression patterns of three target genes (CAT and MAPK1/6) further verified that the selected RGs were suitable for gene expression normalization. This study provides an important basis for C. fortunei gene expression standardization and quantification.
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Affiliation(s)
- Yingting Zhang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Lijuan Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jinyu Xue
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Junjie Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Hailiang Hu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Xu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (L.Z.); (J.X.); (J.Y.); (H.H.); (J.C.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-25-8542-7319
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Identification and validation of miRNA reference genes in poplar under pathogen stress. Mol Biol Rep 2021; 48:3357-3366. [PMID: 33948852 DOI: 10.1007/s11033-021-06369-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression. However, few universal genes, especially miRNAs, have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using geNorm, NormFinder and Bestkeeper reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g, miR156a and 5.8S rRNA were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a and 5.8S rRNA were used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different length between detected miRNAs and traditional reference genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.
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Garzón-Martínez GA, García-Arias FL, Enciso-Rodríguez FE, Soto-Suárez M, González C, Bombarely A, Barrero LS, Osorio Guarín JA. Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana- Fusarium oxysporum pathosystem. PeerJ 2021; 9:e11135. [PMID: 33828924 PMCID: PMC7993016 DOI: 10.7717/peerj.11135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/01/2021] [Indexed: 11/20/2022] Open
Abstract
Vascular wilt, caused by the pathogen Fusarium oxysporum f. sp. physali (Foph), is a major disease of cape gooseberry (Physalis peruviana L.) in Andean countries. Despite the economic losses caused by this disease, there are few studies related to molecular mechanisms in the P. peruviana—Foph pathosystem as a useful tool for crop improvement. This study evaluates eight candidate genes associated with this pathosystem, using real-time quantitative PCR (RT-qPCR). The genes were identified and selected from 1,653 differentially expressed genes (DEGs) derived from RNA-Seq analysis and from a previous genome-wide association study (GWAS) of this plant-pathogen interaction. Based on the RT-qPCR analysis, the tubuline (TUB) reference gene was selected for its highly stable expression in cape gooseberry. The RT-qPCR validation of the candidate genes revealed the biological variation in their expression according to their known biological function. Three genes related to the first line of resistance/defense responses were highly expressed earlier during infection in a susceptible genotype, while three others were overexpressed later, mostly in the tolerant genotype. These genes are mainly involved in signaling pathways after pathogen recognition, mediated by hormones such as ethylene and salicylic acid. This study provided the first insight to uncover the molecular mechanism from the P. peruviana—Foph pathosystem. The genes validated here have important implications in the disease progress and allow a better understanding of the defense response in cape gooseberry at the molecular level. Derived molecular markers from these genes could facilitate the identification of tolerant/susceptible genotypes for use in breeding schemes.
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Affiliation(s)
- Gina A Garzón-Martínez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Francy L García-Arias
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Felix E Enciso-Rodríguez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Mauricio Soto-Suárez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Carolina González
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | | | - Luz Stella Barrero
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Jaime A Osorio Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria Agrosavia, Mosquera, Cundinamarca, Colombia
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Selection and Evaluation of Potential Reference Genes for Quantitative Real-Time PCR in Agaricus blazei Based on Transcriptome Sequencing Data. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6661842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely used to detect gene expression due to its high sensitivity, high throughput, and convenience. The accurate choice of reference genes is required for normalization of gene expression in qRT-PCR analysis. In order to identify the optimal candidates for gene expression analysis using qRT-PCR in Agaricus blazei, we studied the potential reference genes in this economically important edible fungus. In this study, transcriptome datasets were used as source for identification of candidate reference genes. And 27 potential reference genes including 21 newly stable genes, three classical housekeeping genes, and homologous genes of three ideal reference genes in Volvariella volvacea, were screened based on transcriptome datasets of A. blazei and previous studies. The expression stability of these genes was investigated by qRT-PCR analysis and further evaluated by four software packages, geNorm, NormFinder, BestKeeper, and RefFinder. Among these candidates, α-TUB (Tubulin alpha) and Cox5a (COX5A subunit VA of cytochrome c oxidase) were revealed as the most stable in fruit body, and suitable for 5 different developmental stages. α-TUB and ATP3 (ATP3 gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase) showed the most stable expression in stipe tissues and, Uqcrc (core subunit of the ubiquinol-cytochrome c reductase complex) and PUP3 (20S proteasome subunit beta 3) performed well in pileus tissues during the process of A. blazei development, while GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was among the least stable genes in all sample sets. Finally, the Ableln3 (homology of eln3 gene of Coprinus cinereus) was adopted to validate the reliability of these stable and unstable reference genes, indicating that the use of unsuitable reference genes as internal controls could change the target gene’s expression pattern. This study can provide guidance for choosing reference genes for analyzing the expression pattern of target genes and facilitate the functional genomic investigation on fruit body formation and development, as well as stipe elongation and pileus expansion in A. blazei.
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