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Liu H, Zhang X, Shang Y, Zhao S, Li Y, Zhou X, Huo X, Qiao P, Wang X, Dai K, Li H, Guo J, Shi W. Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:186. [PMID: 39017920 DOI: 10.1007/s00122-024-04690-1] [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: 05/10/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
KEY MESSAGE One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.
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Affiliation(s)
- Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Zhang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Shaoxing Zhao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yingjia Li
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xutao Zhou
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Huixia Li
- Millet Research Institute, Shanxi Agricultural University, Changzhi, 046000, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
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Sun Y, Wang X, Di Y, Li J, Li K, Wei H, Zhang F, Su Z. Systematic Analysis of DNA Demethylase Gene Families in Foxtail Millet ( Setaria italica L.) and Their Expression Variations after Abiotic Stresses. Int J Mol Sci 2024; 25:4464. [PMID: 38674049 PMCID: PMC11050331 DOI: 10.3390/ijms25084464] [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: 03/12/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. DNA demethylase (DNA-deMTase) genes have been identified in some plant species; however, there are no reports on the identification and analysis of DNA-deMTase genes in Foxtail millet (Setaria italica L.). In this study, seven DNA-deMTases were identified in S. italica. These DNA-deMTase genes were divided into four subfamilies (DML5, DML4, DML3, and ROS1) by phylogenetic and gene structure analysis. Further analysis shows that the physical and chemical properties of these DNA-deMTases proteins are similar, contain the typical conserved domains of ENCO3c and are located in the nucleus. Furthermore, multiple cis-acting elements were observed in DNA-deMTases, including light responsiveness, phytohormone responsiveness, stress responsiveness, and elements related to plant growth and development. The DNA-deMTase genes are expressed in all tissues detected with certain tissue specificity. Then, we investigated the abundance of DNA-deMTase transcripts under abiotic stresses (cold, drought, salt, ABA, and MeJA). The results showed that different genes of DNA-deMTases were involved in the regulation of different abiotic stresses. In total, our findings will provide a basis for the roles of DNA-deMTase in response to abiotic stress.
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Affiliation(s)
- Yingying Sun
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Xin Wang
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Yunfei Di
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Jinxiu Li
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Keyu Li
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Huanhuan Wei
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Fan Zhang
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Zhenxia Su
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
- Xinghuacun College (Shanxi Institute of Brewing Technology and Industry), Shanxi University, Taiyuan 030006, China
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Glison N, Gaiero P, Monteverde E, Speranza PR. Breeding for reduced seed dormancy to domesticate new grass species. Genet Mol Biol 2024; 47Suppl 1:e20230262. [PMID: 38666746 PMCID: PMC11046443 DOI: 10.1590/1678-4685-gmb-2023-0262] [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: 09/01/2023] [Accepted: 03/01/2024] [Indexed: 04/29/2024] Open
Abstract
Introducing new grass species into cultivation has long been proposed as beneficial to increase the sustainability and diversity of productive systems. However, wild species with potential tend to show high seed dormancy, causing slow, poor, and unsynchronized seedling emergence. Meanwhile, domesticated species, such as cereals, show lower seed dormancy, facilitating their successful establishment. In this work, we conduct a review of phenotypic variation on seed dormancy and its genetic and molecular basis. This quantitative and highly heritable trait shows phenotype plasticity which is modulated by environmental factors. The level of dormancy depends on the expression of genes associated with the metabolism and sensitivity to the hormones abscisic acid (ABA) and gibberellins (GA), along with other dormancy-specific genes. The genetic regulation of these traits is highly conserved across species. The low seed dormancy observed in cereals and some temperate forages was mostly unconsciously selected during various domestication processes. Emphasis is placed on selecting materials with low seed dormancy for warm-season forage grasses to improve their establishment and adoption. Finally, we review advances in the domestication of dallisgrass, where seed dormancy was considered a focus trait throughout the process.
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Affiliation(s)
- Nicolás Glison
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Paola Gaiero
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Eliana Monteverde
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
- University of Illinois, Department of Crop Sciences, Urbana, IL, USA
| | - Pablo R. Speranza
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
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Dai K, Wang X, Liu H, Qiao P, Wang J, Shi W, Guo J, Diao X. Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:18. [PMID: 38206376 DOI: 10.1007/s00122-023-04522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE Eleven QTLs for agronomic traits were identified by RTM- and MLM-GWAS, putative candidate genes were predicted and two markers for grain weight were developed and validated. Foxtail millet (Setaria italica), the second most cultivated millet crop after pearl millet, is an important grain crop in arid regions. Seven agronomic traits of 408 diverse foxtail millet accessions from 15 provinces in China were evaluated in three environments. They were clustered into two divergent groups based on genotypic data using ADMIXTURE, which was highly consistent with their geographical distribution. Two models for genome-wide association studies (GWAS), namely restricted two-stage multi-locus multi-allele (RTM)-GWAS and mixed linear model (MLM)-GWAS, were used to dissect the genetic architecture of the agronomic traits based on 13,723 SNPs. Eleven quantitative trait loci (QTLs) for seven traits were identified using two models (RTM- and MLM-GWAS). Among them, five were considered stable QTLs that were identified in at least two environments using MLM-GWAS. One putative candidate gene (SETIT_006045mg, Chr4: 744,701-746,852) that can enhance grain weight per panicle was identified based on homologous gene comparison and gene expression analysis and was validated by haplotype analysis of 330 accessions with high-depth (10×) resequencing data (unpublished). In addition, homologous gene comparison and haplotype analysis identified one putative foxtail millet ortholog (SETIT_032906mg, Chr2: 5,020,600-5,029,771) with rice affecting the target traits. Two markers (cGWP6045 and kTGW2906) were developed and validated and can be used for marker-assisted selection of foxtail millet with high grain weight. The results provide a fundamental resource for foxtail millet genetic research and breeding and demonstrate the power of integrating RTM- and MLM-GWAS approaches as a complementary strategy for investigating complex traits in foxtail millet.
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Affiliation(s)
- Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Jiaxue Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Knoshaug EP, Sun P, Nag A, Nguyen H, Mattoon EM, Zhang N, Liu J, Chen C, Cheng J, Zhang R, St. John P, Umen J. Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis. PLANT DIRECT 2023; 7:e527. [PMID: 38044962 PMCID: PMC10690477 DOI: 10.1002/pld3.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome-wide protein-coding gene annotation. A substantial fraction of protein-coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high-value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.
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Affiliation(s)
- Eric P. Knoshaug
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Peipei Sun
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Ambarish Nag
- Computational Sciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Huong Nguyen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil ScienceTexas Tech UniversityLubbockTexasUSA
| | - Erin M. Mattoon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical SciencesWashington University in Saint LouisSt. LouisMissouriUSA
| | | | - Jian Liu
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Chen Chen
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Ru Zhang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Peter St. John
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - James Umen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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He Q, Tang S, Zhi H, Chen J, Zhang J, Liang H, Alam O, Li H, Zhang H, Xing L, Li X, Zhang W, Wang H, Shi J, Du H, Wu H, Wang L, Yang P, Xing L, Yan H, Song Z, Liu J, Wang H, Tian X, Qiao Z, Feng G, Guo R, Zhu W, Ren Y, Hao H, Li M, Zhang A, Guo E, Yan F, Li Q, Liu Y, Tian B, Zhao X, Jia R, Feng B, Zhang J, Wei J, Lai J, Jia G, Purugganan M, Diao X. A graph-based genome and pan-genome variation of the model plant Setaria. Nat Genet 2023:10.1038/s41588-023-01423-w. [PMID: 37291196 DOI: 10.1038/s41588-023-01423-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023]
Abstract
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.
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Affiliation(s)
- Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Lihe Xing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Hongpo Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Xing
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Hongshan Yan
- Anyang Academy of Agriculture Sciences, Anyang, China
| | | | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Xiang Tian
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Guojun Feng
- Research Institute of Cereal Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ruifeng Guo
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Wenjuan Zhu
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Yuemei Ren
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Hongbo Hao
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Mingzhe Li
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Aiying Zhang
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Feng Yan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yanli Liu
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Bohong Tian
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Xiaoqin Zhao
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Ruiling Jia
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Baili Feng
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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7
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Ermakova M, Woodford R, Taylor Z, Furbank RT, Belide S, von Caemmerer S. Faster induction of photosynthesis increases biomass and grain yield in glasshouse-grown transgenic Sorghum bicolor overexpressing Rieske FeS. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1206-1216. [PMID: 36789455 DOI: 10.1111/pbi.14030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/08/2023] [Indexed: 05/27/2023]
Abstract
Sorghum is one of the most important crops providing food and feed in many of the world's harsher environments. Sorghum utilizes the C4 pathway of photosynthesis in which a biochemical carbon-concentrating mechanism results in high CO2 assimilation rates. Overexpressing the Rieske FeS subunit of the Cytochrome b6 f complex was previously shown to increase the rate of photosynthetic electron transport and stimulate CO2 assimilation in the model C4 plant Setaria viridis. To test whether productivity of C4 crops could be improved by Rieske overexpression, we created transgenic Sorghum bicolor Tx430 plants with increased Rieske content. The transgenic plants showed no marked changes in abundances of other photosynthetic proteins or chlorophyll content. The steady-state rates of electron transport and CO2 assimilation did not differ between the plants with increased Rieske abundance and control plants, suggesting that Cytochrome b6 f is not the only factor limiting electron transport in sorghum at high light and high CO2 . However, faster responses of non-photochemical quenching as well as an elevated quantum yield of Photosystem II and an increased CO2 assimilation rate were observed from the plants overexpressing Rieske during the photosynthetic induction, a process of activation of photosynthesis upon the dark-light transition. As a consequence, sorghum with increased Rieske content produced more biomass and grain when grown in glasshouse conditions. Our results indicate that increasing Rieske content has potential to boost productivity of sorghum and other C4 crops by improving the efficiency of light utilization and conversion to biomass through the faster induction of photosynthesis.
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Affiliation(s)
- Maria Ermakova
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, ACT, Australia
- School of Biological Sciences, Monash University, Melbourne, Vic, Australia
| | - Russell Woodford
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Zachary Taylor
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Robert T Furbank
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | | | - Susanne von Caemmerer
- Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, ACT, Australia
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8
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Gai W, Yang F, Yuan L, ul Haq S, Wang Y, Wang Y, Shang L, Li F, Ge P, Dong H, Tao J, Wang F, Zhang X, Zhang Y. Multiple-model GWAS identifies optimal allelic combinations of quantitative trait loci for malic acid in tomato. HORTICULTURE RESEARCH 2023; 10:uhad021. [PMID: 37035859 PMCID: PMC10076212 DOI: 10.1093/hr/uhad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/10/2023] [Indexed: 06/19/2023]
Abstract
Malic acid (MA) is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways. It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes. However, the metabolic accumulation of MA is controlled by complex heredity and environmental factors, making it difficult to predict and regulate the metabolism of MA. In this study, we carried out a genome-wide association study (GWAS) on MA using eight milestone models with two-environment repeats. A series of associated SNP variations were identified from the GWAS, and 15 high-confidence annotated genes were further predicted based on linkage disequilibrium and lead SNPs. The transcriptome data of candidate genes were explored within different tomato organs as well as various fruit tissues, and suggested specific expression patterns in fruit pericarp. Based on the genetic parameters of population differentiation and SNP distribution, tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding. In addition, genotype × environment interaction might contribute to the difference in domestication phenotypic data under different environments. This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.
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Affiliation(s)
- Wenxian Gai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Liangdan Yuan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China
- Department of Horticulture, The University of Agriculture Peshawar, Peshawar 25130, Pakistan
| | - Yaru Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Lele Shang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangman Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingfei Ge
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiqiang Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinbao Tao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
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9
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Hjertaas AC, Preston JC, Kainulainen K, Humphreys AM, Fjellheim S. Convergent evolution of the annual life history syndrome from perennial ancestors. FRONTIERS IN PLANT SCIENCE 2023; 13:1048656. [PMID: 36684797 PMCID: PMC9846227 DOI: 10.3389/fpls.2022.1048656] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.
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Affiliation(s)
- Ane C. Hjertaas
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, United States
| | - Kent Kainulainen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Aelys M. Humphreys
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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10
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Wang H, Jia G, Zhang N, Zhi H, Xing L, Zhang H, Sui Y, Tang S, Li M, Zhang H, Feng B, Wu C, Diao X. Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant. THE NEW PHYTOLOGIST 2022; 236:1809-1823. [PMID: 36178253 DOI: 10.1111/nph.18493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C4 model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.
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Affiliation(s)
- Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712000, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ning Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihe Xing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haoshan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingzhe Li
- Institute of Dry-land Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, Hebei, 053000, China
| | - Haijin Zhang
- Institute of Dry Land Agroforestry, Liaoning Academy of Agricultural Sciences, Chaoyang, Liaoning, 122000, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712000, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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Li X, Gao J, Song J, Guo K, Hou S, Wang X, He Q, Zhang Y, Zhang Y, Yang Y, Tang J, Wang H, Persson S, Huang M, Xu L, Zhong L, Li D, Liu Y, Wu H, Diao X, Chen P, Wang X, Han Y. Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. MOLECULAR PLANT 2022; 15:1367-1383. [PMID: 35808829 DOI: 10.1016/j.molp.2022.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/22/2022] [Accepted: 07/06/2022] [Indexed: 05/12/2023]
Abstract
Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail millet grains, we generated and analyzed the datasets encompassing the genomes, transcriptomes, metabolomes, and anti-inflammatory indices from 398 foxtail millet accessions. We identified hundreds of common variants that influence numerous secondary metabolites. We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet. Furthermore, we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones. Using CRISPR-mediated genome editing we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile. The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites, laying the foundations for future millet genetic research and metabolome-assisted improvement.
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Affiliation(s)
- Xukai Li
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Jianhua Gao
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Jingyi Song
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Siyu Hou
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Xingchun Wang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yakun Zhang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Yulu Yang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Jiaoyan Tang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Hailang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Staffan Persson
- Copenhagen Plant Science Centre, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark; Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Minhang, Shanghai 200240, China
| | - Mingquan Huang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Lishuai Xu
- College of Resources and Environment, Shanxi Agricultural University, Taigu, China
| | - Linlin Zhong
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongming Liu
- Grandomics Biosciences Company Limited, Beijing, China
| | - Hua Wu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Peng Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Xiaowen Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, China.
| | - Yuanhuai Han
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taigu, China.
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12
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Dangol A, Shavit R, Yaakov B, Strickler SR, Jander G, Tzin V. Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids. PLANT MOLECULAR BIOLOGY 2022; 109:533-549. [PMID: 35020104 DOI: 10.1007/s11103-021-01239-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.
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Affiliation(s)
- Anuma Dangol
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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13
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Xing G, Jin M, Qu R, Zhang J, Han Y, Han Y, Wang X, Li X, Ma F, Zhao X. Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv). BMC PLANT BIOLOGY 2022; 22:292. [PMID: 35701737 PMCID: PMC9199193 DOI: 10.1186/s12870-022-03676-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/01/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Modification of histone acetylation is a ubiquitous and reversible process in eukaryotes and prokaryotes and plays crucial roles in the regulation of gene expression during plant development and stress responses. Histone acetylation is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT plays an essential regulatory role in various growth and development processes by modifying the chromatin structure through interactions with other histone modifications and transcription factors in eukaryotic cells, affecting the transcription of genes. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana and Oryza sativa. However, little information is available on the HAT genes in foxtail millet (Setaria italica [L.] P. Beauv). RESULTS In this study, 24 HAT genes (SiHATs) were identified and divided into four groups with conserved gene structures via motif composition analysis. Phylogenetic analysis of the genes was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa, and foxtail millet; 19 and 2 orthologous gene pairs were individually identified. Moreover, all identified HAT gene pairs likely underwent purified selection based on their non-synonymous/synonymous nucleotide substitutions. Using published transcriptome data, we found that SiHAT genes were preferentially expressed in some tissues and organs. Stress responses were also examined, and data showed that SiHAT gene transcription was influenced by drought, salt, low nitrogen, and low phosphorus stress, and that the expression of four SiHATs was altered as a result of infection by Sclerospora graminicola. CONCLUSIONS Results indicated that histone acetylation may play an important role in plant growth and development and stress adaptations. These findings suggest that SiHATs play specific roles in the response to abiotic stress and viral infection. This study lays a foundation for further analysis of the biological functions of SiHATs in foxtail millet.
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Affiliation(s)
- Guofang Xing
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, 030031, Taiyuan, China
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Minshan Jin
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Ruifang Qu
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Jiewei Zhang
- Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, 100097, Beijing, China
| | - Yuanhuai Han
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Yanqing Han
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Xingchun Wang
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Xukai Li
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China
| | - Fangfang Ma
- College of Agricultural, Shanxi Agricultural University, 030801, Jinzhong, China.
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China.
| | - Xiongwei Zhao
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, 030031, Taiyuan, China.
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
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14
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Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim YM, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, Callister SJ. Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil. PLoS One 2021; 16:e0259937. [PMID: 34879068 PMCID: PMC8654227 DOI: 10.1371/journal.pone.0259937] [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: 06/13/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.
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Affiliation(s)
- Matthew J. Peterson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pubudu P. Handakumbura
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Allison M. Thompson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Zachary R. Russell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Sarah J. Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Montana L. Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason G. Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rosey K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bryan A. Stanfill
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Steven C. Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington, United States of America
| | - Vanessa L. Bailey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
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15
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Zhi H, He Q, Tang S, Yang J, Zhang W, Liu H, Jia Y, Jia G, Zhang A, Li Y, Guo E, Gao M, Li S, Li J, Qin N, Zhu C, Ma C, Zhang H, Chen G, Zhang W, Wang H, Qiao Z, Li S, Cheng R, Xing L, Wang S, Liu J, Liu J, Diao X. Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3023-3036. [PMID: 34081150 DOI: 10.1007/s00122-021-03875-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Multi-environment QTL mapping identified 23 stable loci and 34 co-located QTL clusters for panicle architecture and grain yield-related traits, which provide a genetic basis for foxtail millet yield improvement. Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line (RIL) population of 333 lines of foxtail millet, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) controlling nine agronomic traits related to panicle architecture and grain yield. We found that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits. Of the 159 QTL, 34 were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod and/or other environmental factors. Eighty-eight QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, which was detected 23 times in 13 environments. Several candidate genes, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700, were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters. Using available phenotypic and genotype data, we conducted haplotype analysis for Seita.2G002300 and Seita.9G064000,which showed high correlations with panicle weight and panicle exsertion length, respectively. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of traits related to panicle architecture in foxtail millet, but also provide information for comparative genomics analyses of cereal crops.
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Affiliation(s)
- Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Junjun Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Huifang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Yanchao Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Aiying Zhang
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Yuhui Li
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Erhu Guo
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Ming Gao
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Shujie Li
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Junxia Li
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Na Qin
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Cancan Zhu
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Chunye Ma
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Haijin Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Guoqiu Chen
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Wenfei Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Shunguo Li
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lu Xing
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Suying Wang
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinrong Liu
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China.
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Ma K, Zhang W, Zhang L, He X, Fan Y, Alam S, Yuan X. Effect of Pyrazosulfuron-Methyl on the Photosynthetic Characteristics and Antioxidant Systems of Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:696169. [PMID: 34421947 PMCID: PMC8375152 DOI: 10.3389/fpls.2021.696169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Foxtail millet (Setaria Italica L.) plays a principal role in food security in Africa and Asia, but it is sensitive to a variety of herbicides. This study was performed to clarify whether pyrazosulfuron-methyl can be used in foxtail millet fields and the effect of pyrazosulfuron-methyl on the photosynthetic performance of foxtail millet. Two foxtail millet varieties (Jingu 21 and Zhangzagu 10) were subjected to five doses (0, 15, 30, 60, and 120 g ai ha-1) of pyrazosulfuron-methyl in pot and field experiments. The plant height, leaf area, stem diameter, photosynthetic pigment contents, gas exchange parameters, chlorophyll fluorescence parameters, antioxidant enzyme activities, and antioxidant contents at 7 and 15 days after pyrazosulfuron-methyl application, and the yield of foxtail millet were measured. The results suggested that pyrazosulfuron-methyl inhibited the growth of foxtail millet and reduced the photosynthetic pigment contents, photosynthetic rate, and photosynthetic system II activity. Similarly, pyrazosulfuron-methyl decreased the antioxidant enzyme activities and antioxidant contents. These results also indicated that the toxicity of pyrazosulfuron-methyl to foxtail millet was decreased gradually with the extension of time after application; however, the foxtail millet yield was still significantly reduced. Therefore, pyrazosulfuron-methyl is not recommended for application in foxtail millet fields.
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Affiliation(s)
| | | | | | | | | | | | - Xiangyang Yuan
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Shanxi, China
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17
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Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J. Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 2021; 22:556. [PMID: 34281524 PMCID: PMC8290542 DOI: 10.1186/s12864-021-07882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07882-x.
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Affiliation(s)
- Huifang Xie
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Junliang Hou
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Nan Fu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Menghan Wei
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Yunfei Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China.
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China.
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18
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Zhao Z, Tang S, Zhang Y, Yue J, Xu J, Tang W, Sun Y, Wang R, Diao X, Zhang B. Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet. BMC PLANT BIOLOGY 2021; 21:291. [PMID: 34167462 PMCID: PMC8223282 DOI: 10.1186/s12870-021-03081-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Brassinosteroids (BRs) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, those in foxtail millet remain largely unknown. Here, we show that the BR signaling function of BRASSINOSTEROID INSENSITIVE 1 (BRI1) is conserved between Arabidopsis and foxtail millet, a new model species for C4 and Panicoideae grasses. We identified four putative BR receptor genes in the foxtail millet genome: SiBRI1, SiBRI1-LIKE RECEPTOR KINASE 1 (SiBRL1), SiBRL2 and SiBRL3. Phylogenetic analysis was used to classify the BR receptors in dicots and monocots into three branches. Analysis of their expression patterns by quantitative real-time PCR (qRT-PCR) showed that these receptors were ubiquitously expressed in leaves, stems, dark-grown seedlings, roots and non-flowering spikelets. GFP fusion experiments verified that SiBRI1 localized to the cell membrane. We also explored the SiBRI1 function in Arabidopsis through complementation experiments. Ectopic overexpression of SiBRI1 in an Arabidopsis BR receptor loss-of-function mutant, bri1-116, mostly reversed the developmental defects of the mutant. When SiBRI1 was overexpressed in foxtail millet, the plants showed a drooping leaf phenotype and root development inhibition, lateral root initiation inhibition, and the expression of BR synthesis genes was inhibited. We further identified BRI1-interacting proteins by immunoprecipitation (IP)-mass spectrometry (MS). Our results not only demonstrate that SiBRI1 plays a conserved role in BR signaling in foxtail millet but also provide insight into the molecular mechanism of SiBRI1.
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Affiliation(s)
- Zhiying Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yiming Zhang
- College of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Jingjing Yue
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Jiaqi Xu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Yanxiang Sun
- College of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Ruiju Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Foxtail Millet Improvement Center of China, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Science, Shijiazhuang, 050031, China.
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China.
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19
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Li C, Wang G, Li H, Wang G, Ma J, Zhao X, Huo L, Zhang L, Jiang Y, Zhang J, Liu G, Liu G, Cheng R, Wei J, Yao L. High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1303-1317. [PMID: 33566123 DOI: 10.1007/s00122-020-03760-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 05/20/2023]
Abstract
Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.
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Affiliation(s)
- Congcong Li
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Genping Wang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Haiquan Li
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Ma
- Beijing Vegetable Research Center, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xin Zhao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Linhe Huo
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Liquan Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jiewei Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guoqing Liu
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lei Yao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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20
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Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.
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Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
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21
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Bhatnagar N, Pandey S. Heterotrimeric G-Protein Interactions Are Conserved Despite Regulatory Element Loss in Some Plants. PLANT PHYSIOLOGY 2020; 184:1941-1954. [PMID: 33082269 PMCID: PMC7723102 DOI: 10.1104/pp.20.01309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 05/31/2023]
Abstract
Heterotrimeric G-proteins are key modulators of multiple signaling and development pathways in plants and regulate many agronomic traits, including architecture and grain yield. Regulator of G-protein signaling (RGS) proteins are an integral part of the G-protein networks; however, these are lost in many monocots. To assess if the loss of RGS in specific plants has resulted in altered G-protein networks and the extent to which RGS function is conserved across contrasting monocots, we explored G-protein-dependent developmental pathways in Brachypodium distachyon and Setaria viridis, representing species without or with a native RGS, respectively. Artificial microRNA-based suppression of Gα in both species resulted in similar phenotypes. Moreover, overexpression of Setaria italica RGS in B. distachyon resulted in phenotypes similar to the suppression of BdGα This effect of RGS overexpression depended on its ability to deactivate Gα, as overexpression of a biochemically inactive variant protein resulted in plants indistinguishable from the wild type. Comparative transcriptome analysis of B. distachyon plants with suppressed levels of Gα or overexpression of RGS showed significant overlap of differentially regulated genes, corroborating the phenotypic data. These results suggest that despite the loss of RGS in many monocots, the G-protein functional networks are maintained, and Gα proteins have retained their ability to be deactivated by RGS.
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Affiliation(s)
| | - Sona Pandey
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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22
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Cesarino I, Dello Ioio R, Kirschner GK, Ogden MS, Picard KL, Rast-Somssich MI, Somssich M. Plant science's next top models. ANNALS OF BOTANY 2020; 126:1-23. [PMID: 32271862 PMCID: PMC7304477 DOI: 10.1093/aob/mcaa063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.
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Affiliation(s)
- Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão 277, Butantã, São Paulo, Brazil
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Gwendolyn K Kirschner
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, Bonn, Germany
| | - Michael S Ogden
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kelsey L Picard
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Madlen I Rast-Somssich
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, VIC, Australia
| | - Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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23
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Qi H, Yang J, Yin C, Zhao J, Ren X, Jia S, Zhang G. Analysis of Pyricularia oryzae and P. grisea from Different Hosts Based on Multilocus Phylogeny and Pathogenicity Associated with Host Preference in China. PHYTOPATHOLOGY 2019; 109:1433-1440. [PMID: 30973308 DOI: 10.1094/phyto-10-18-0383-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pyricularia oryzae and P. grisea are important agents of major diseases on a wide range of gramineous hosts. Whereas P. oryzae is the most important pathogen causing outbreaks of rice blast, P. grisea is mainly a pathogen of crabgrass. In this study, 103 P. oryzae and 20 P. grisea isolates were collected from seven species of plants, and we analyzed their phylogeny, pathogenicity, and relationship with host preferences to investigate the differences among them from different hosts. Based on phylogenetic analysis of multilocus sequences, 16 isolates from crabgrass and four isolates from green bristlegrass were identified as P. grisea and another 103 isolates from crabgrass, green bristlegrass, goose grass, foxtail millet, wild millet, rice, and sedge belonged to P. oryzae. Results of pathogenicity tests by artificial inoculation demonstrated that six of 10 P. oryzae isolates from rice and three of 44 P. oryzae isolates from green bristlegrass showed cross-infectivity on green bristlegrass and rice, respectively. Taken together, our results demonstrated that isolates from green bristlegrass and crabgrass consist of both P. oryzae and P. grisea and that P. oryzae isolates showed cross-infectivity between rice and green bristlegrass, suggesting that host shifts may occur for P. oryzae and P. grisea.
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Affiliation(s)
- Hexing Qi
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Changfa Yin
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jian Zhao
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xianxian Ren
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shishuang Jia
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guozhen Zhang
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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