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Sun R, Han A, Wang H, Wang C, Lu Y, Ni D, Guo N, Xing H, Zhao J. Integrated Transcriptome and Metabolome Analysis Reveals Molecular Mechanisms Underlying Resistance to Phytophthora Root Rot. PLANTS (BASEL, SWITZERLAND) 2024; 13:1705. [PMID: 38931137 DOI: 10.3390/plants13121705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.
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Affiliation(s)
- Ruidong Sun
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Anan Han
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitang Wang
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Congcong Wang
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Lu
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Danqing Ni
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Guo
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Xing
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinming Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory, National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Luo T, Ma C, Fan Y, Qiu Z, Li M, Tian Y, Shang Y, Liu C, Cao Q, Peng Y, Zhang S, Liu S, Song B. CRISPR-Cas9-mediated editing of GmARM improves resistance to multiple stresses in soybean. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112147. [PMID: 38834106 DOI: 10.1016/j.plantsci.2024.112147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/06/2024]
Abstract
The growth and development of soybean plants can be affected by both abiotic and biotic stressors, such as saline-alkali stress and Phytophthora root rot. In this study, we identified a stress-related gene-GmARM-whose promoter contained several hormone-response and stress-regulatory elements, including ABRE, TCA element, STRE, and MBS. qRT-PCR analysis showed that the expression of GmARM was the highest in seeds at 55 days after flowering. Furthermore, this gene was upregulated after exposure to saline-alkali stress and Phytophthora root rot infection at the seedling stage. Thus, we generated GmARM mutants using the CRISPR-Cas9 system to understand the role of this gene in stress response. T3 plants showed significantly improved salt tolerance, alkali resistance, and disease resistance, with a significantly higher survival rate than the wildtype plants. Moreover, mutations in GmARM affected the expression of related stress-resistance genes, indicating that GmARM mutants achieved multiple stress tolerance. Therefore, this study provides a foundation for further exploration of the genes involved in resistance to multiple stresses in soybean that can be used for breeding multiple stress-resistance soybean varieties.
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Affiliation(s)
- Tingting Luo
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Chongxuan Ma
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuanhang Fan
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Zhendong Qiu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Ming Li
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161000, China
| | - Yusu Tian
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuzhuo Shang
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Chang Liu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Qingqian Cao
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuhan Peng
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Shuzhen Zhang
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Shanshan Liu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China.
| | - Bo Song
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China; Key Laboratory of Molecular and Cytogenetics, College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China.
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Heo SV, Park HR, Jang YW, Park J, Kang BK, Seo JH, Kim JH, Lee JY, Choi MS, Ko JY, Kim CS, Lee S, Jun TH. Identification of New Isolates of Phytophthora sojae and Selection of Resistant Soybean Genotypes. THE PLANT PATHOLOGY JOURNAL 2024; 40:329-335. [PMID: 38835304 PMCID: PMC11162861 DOI: 10.5423/ppj.nt.12.2023.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 06/06/2024]
Abstract
Phytophthora root and stem rot (PRR), caused by Phytophthora sojae, can occur at any growth stage under poorly drained and humid conditions. The expansion of soybean cultivation in South Korean paddy fields has increased the frequency of PRR outbreaks. This study aimed to identify four P. sojae isolates newly collected from domestic fields and evaluate race-specific resistance using the hypocotyl inoculation technique. The four isolates exhibited various pathotypes, with GJ3053 exhibiting the highest virulence complexity. Two isolates, GJ3053 and AD3617, were screened from 205 soybeans, and 182 and 190 genotypes (88.8 and 92.7%, respectively) were susceptible to each isolate. Among these accessions, five genotypes resistant to both isolates were selected. These promising genotypes are candidates for the development of resistant soybean cultivars that can effectively control PRR through gene stacking.
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Affiliation(s)
- Su Vin Heo
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Hye Rang Park
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Yun Woo Jang
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Jihee Park
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Beom Kyu Kang
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Jeong Hyun Seo
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Jun Hoi Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Ji Yoon Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Man Soo Choi
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Jee Yeon Ko
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Choon Song Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Sungwoo Lee
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea
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Antwi-Boasiako A, Jia S, Liu J, Guo N, Chen C, Karikari B, Feng J, Zhao T. Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population. PLANTS (BASEL, SWITZERLAND) 2024; 13:940. [PMID: 38611470 PMCID: PMC11013609 DOI: 10.3390/plants13070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.
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Affiliation(s)
- Augustine Antwi-Boasiako
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
- Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Fumesua, Kumasi P.O. Box 3785, Ghana
| | - Shihao Jia
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Jiale Liu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Na Guo
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale P.O. Box TL 1882, Ghana;
- Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jianying Feng
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
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Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? FRONTIERS IN PLANT SCIENCE 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
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Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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Yao D, Zhou J, Zhang A, Wang J, Liu Y, Wang L, Pi W, Li Z, Yue W, Cai J, Liu H, Hao W, Qu X. Advances in CRISPR/Cas9-based research related to soybean [ Glycine max (Linn.) Merr] molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1247707. [PMID: 37711287 PMCID: PMC10499359 DOI: 10.3389/fpls.2023.1247707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.
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Affiliation(s)
- Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Junming Zhou
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Aijing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yixuan Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Lixue Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zihao Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenjun Yue
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jinliang Cai
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyuan Hao
- Jilin Provincial Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiangchun Qu
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
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