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Moustafa K. Maize's origin to be revisited. PLANT SIGNALING & BEHAVIOR 2024; 19:2332017. [PMID: 38513059 PMCID: PMC10962592 DOI: 10.1080/15592324.2024.2332017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
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Yan Z, Li K, Li Y, Wang W, Leng B, Yao G, Zhang F, Mu C, Liu X. The ZmbHLH32-ZmIAA9-ZmARF1 module regulates salt tolerance in maize. Int J Biol Macromol 2023; 253:126978. [PMID: 37741480 DOI: 10.1016/j.ijbiomac.2023.126978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/02/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
The growth and productivity of maize (Zea mays), along with other crop plants, can be significantly hindered by salt stress. Nevertheless, the precise molecular mechanism underlying salt tolerance in maize has yet to be fully elucidated. Hence, it was attempted to identify ZmIAA9, a member of the maize Aux/IAA gene family, as a positive regulator of salt tolerance in maize, which was accompanied by the increased ROS detoxification and elevated transcript abundances of ROS scavenging genes. Molecular and biochemical assays have provided compelling evidence that ZmbHLH32, a transcription factor belonging to the bHLH family, was capable of binding directly to the promoter region of ZmIAA9, thereby activating its expression. This interaction between ZmbHLH32 and ZmIAA9 could be critical for the regulation of salt tolerance in maize. As expected, overexpression of ZmbHLH32 led to the enhanced salt tolerance. In contrast, decreased salt tolerance was attained after application of knockout mutants of ZmbHLH32. Furthermore, ZmARF1, which could act as a downstream of ZmIAA9, was found to physically interact with ZmIAA9 and repress the expression levels of ROS scavenging genes. Thus, our work uncovers a novel mechanism of ZmbHLH32-ZmIAA9-ZmARF1 module-mediated salt tolerance in maize, which can be exploited for breeding salt-tolerant maize varieties.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Ke Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Yanli Li
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Wenli Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
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3
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Hu Y, Li C, Zhou R, Song Y, Lv Z, Wang Q, Dong X, Liu S, Feng C, Zhou Y, Zeng X, Zhang L, Wang Z, Di H. The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize ( Zea mays L.). Int J Mol Sci 2023; 24:15099. [PMID: 37894780 PMCID: PMC10606073 DOI: 10.3390/ijms242015099] [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: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The NAC gene family has transcription factors specific to plants, which are involved in development and stress response and adaptation. In this study, ZmNAC89, an NAC gene in maize that plays a role in saline-alkaline tolerance, was isolated and characterized. ZmNAC89 was localized in the nucleus and had transcriptional activation activity during in vitro experiments. The expression of ZmNAC89 was strongly upregulated under saline-alkaline, drought and ABA treatments. Overexpression of the ZmNAC89 gene in transgenic Arabidopsis and maize enhanced salt tolerance at the seedling stage. Differentially expressed genes (DEGs) were then confirmed via RNA-sequencing analysis with the transgenic maize line. GO analyses showed that oxidation-reduction process-regulated genes were involved in ZmNAC89-mediated salt-alkaline stress. ZmNAC89 may regulate maize saline-alkali tolerance through the REDOX pathway and ABA signal transduction pathway. From 140 inbred maize lines, 20 haplotypes and 16 SNPs were found in the coding region of the ZmNAC89 gene, including the excellent haplotype HAP20. These results contribute to a better understanding of the response mechanism of maize to salt-alkali stress and marker-assisted selection during maize breeding.
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Affiliation(s)
- Yingying Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chunxiang Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Runyu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yongfeng Song
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhichao Lv
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Qi Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xiaojie Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
- Institute of Crop Resources Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shan Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chenchen Feng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
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Zhang X, Wang H, Yang M, Liu R, Zhang X, Jia Z, Li P. Natural variation in ZmNAC087 contributes to total root length regulation in maize seedlings under salt stress. BMC PLANT BIOLOGY 2023; 23:392. [PMID: 37580686 PMCID: PMC10424409 DOI: 10.1186/s12870-023-04393-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Soil salinity poses a significant challenge to crop growth and productivity, particularly affecting the root system, which is vital for water and nutrient uptake. To identify genetic factors that influence root elongation in stressful environments, we conducted a genome-wide association study (GWAS) to investigate the natural variation associated with total root length (TRL) under salt stress and normal conditions in maize seedlings. Our study identified 69 genetic variants associated with 38 candidate genes, among which a specific single nucleotide polymorphism (SNP) in ZmNAC087 was significantly associated with TRL under salt stress. Transient expression and transactivation assays revealed that ZmNAC087 encodes a nuclear-localized protein with transactivation activity. Further candidate gene association analysis showed that non-coding variations in ZmNAC087 promoter contribute to differential ZmNAC087 expression among maize inbred lines, potentially influencing the variation in salt-regulated TRL. In addition, through nucleotide diversity analysis, neutrality tests, and coalescent simulation, we demonstrated that ZmNAC087 underwent selection during maize domestication and improvement. These findings highlight the significance of natural variation in ZmNAC087, particularly the favorable allele, in maize salt tolerance, providing theoretical basis and valuable genetic resources for the development of salt-tolerant maize germplasm.
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Affiliation(s)
- Xiaomin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Mengling Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Runxiao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Baldauf JA, Hochholdinger F. Molecular dissection of heterosis in cereal roots and their rhizosphere. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:173. [PMID: 37474870 PMCID: PMC10359381 DOI: 10.1007/s00122-023-04419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
Heterosis is already manifested early in root development. Consistent with the dominance model of heterosis, gene expression complementation is a general mechanism that contributes to phenotypic heterosis in maize hybrids. Highly heterozygous F1-hybrids outperform their parental inbred lines, a phenomenon known as heterosis. Utilization of heterosis is of paramount agricultural importance and has been widely applied to increase yield in many crop cultivars. Plant roots display heterosis for many traits and are an important target for further crop improvement. To explain the molecular basis of heterosis, several genetic hypotheses have been proposed. In recent years, high-throughput gene expression profiling techniques have been applied to investigate hybrid vigor. Consistent with the classical genetic dominance model, gene expression complementation has been demonstrated to be a general mechanism to contribute to phenotypic heterosis in diverse maize hybrids. Functional classification of these genes supported the notion that gene expression complementation can dynamically promote hybrid vigor under fluctuating environmental conditions. Hybrids tend to respond differently to available nutrients in the soil. It was hypothesized that hybrid vigor is promoted through a higher nutrient use efficiency which is linked to an improved root system performance of hybrids in comparison to their inbred parents. Recently, the interaction between soil microbes and their plant host was added as further dimension to disentangle heterosis in the belowground part of plants. Soil microbes influenced the performance of maize hybrids as illustrated in comparisons of sterile soil and soil inhabited by beneficial microorganisms.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany.
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6
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Qin R, Hu Y, Chen H, Du Q, Yang J, Li WX. MicroRNA408 negatively regulates salt tolerance by affecting secondary cell wall development in maize. PLANT PHYSIOLOGY 2023; 192:1569-1583. [PMID: 36864608 PMCID: PMC10231460 DOI: 10.1093/plphys/kiad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/09/2023] [Indexed: 06/01/2023]
Abstract
Although microRNA408 (miR408) is a highly conserved miRNA, the miR408 response to salt stress differs among plant species. Here, we show that miR408 transcripts are strongly repressed by salt stress and methyl viologen treatment in maize (Zea mays). Application of N, N1-dimethylthiourea partly relieved the NaCl-induced down-regulation of miR408. Transgenic maize overexpressing MIR408b is hypersensitive to salt stress. Overexpression of MIR408b enhanced the rate of net Na+ efflux, caused Na+ to locate in the inter-cellular space, reduced lignin accumulation, and reduced the number of cells in vascular bundles under salt stress. We further demonstrated that miR408 targets ZmLACCASE9 (ZmLAC9). Knockout of MIR408a or MIR408b or overexpression of ZmLAC9 increased the accumulation of lignin, thickened the walls of pavement cells, and improved salt tolerance of maize. Transcriptome profiles of the wild-type and MIR408b-overexpressing transgenic maize with or without salt stress indicated that miR408 negatively regulates the expression of cell wall biogenesis genes under salt conditions. These results indicate that miR408 negatively regulates salt tolerance by regulating secondary cell wall development in maize.
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Affiliation(s)
- Ruidong Qin
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yumei Hu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Chen
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Juan Yang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yin P, Liang X, Zhao H, Xu Z, Chen L, Yang X, Qin F, Zhang J, Jiang C. Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize. MOLECULAR PLANT 2023:S1674-2052(23)00109-0. [PMID: 37101396 DOI: 10.1016/j.molp.2023.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/18/2023] [Accepted: 04/23/2023] [Indexed: 05/26/2023]
Abstract
Excessive accumulation of chloride (Cl-) in the aboveground tissues under saline conditions is harmful to crops. Increasing the exclusion of Cl- from shoots promotes salt tolerance in various crops. However, the underlying molecular mechanisms remain largely unknown. In this study, we demonstrated that a type A response regulator (ZmRR1) modulates Cl- exclusion from shoots and underlies natural variation of salt tolerance in maize. ZmRR1 negatively regulates cytokinin signaling and salt tolerance, likely by interacting with and inhibiting His phosphotransfer (HP) proteins that are key mediators of cytokinin signaling. A naturally occurring non-synonymous SNP variant enhances the interaction between ZmRR1 and ZmHP2, conferring maize plants with a salt-hypersensitive phenotype. We found that ZmRR1 undergoes degradation under saline conditions, leading to the release of ZmHP2 from ZmRR1 inhibition, and subsequently ZmHP2-mediated signaling improves salt tolerance primarily by promoting Cl- exclusion from shoots. Furthermore, we showed that ZmMATE29 is transcriptionally upregulated by ZmHP2-mediated signaling under highly saline conditions and encodes a tonoplast-located Cl- transporter that promotes Cl- exclusion from shoots by compartmentalizing Cl- into the vacuoles of root cortex cells. Collectively, our study provides an important mechanistic understanding of the cytokinin signaling-mediated promotion of Cl- exclusion from shoots and salt tolerance and suggests that genetic modification to promote Cl- exclusion from shoots is a promising route for developing salt-tolerant maize.
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Affiliation(s)
- Pan Yin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hanshu Zhao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Zhipeng Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Limei Chen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100094, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100094, China; Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Jingbo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100094, China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100094, China; Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China; Outstanding Discipline Program for the Universities in Beijing, Beijing 100094, China.
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [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: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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Zhu Y, Ren Y, Liu J, Liang W, Zhang Y, Shen F, Ling J, Zhang C. New Genes Identified as Modulating Salt Tolerance in Maize Seedlings Using the Combination of Transcriptome Analysis and BSA. PLANTS (BASEL, SWITZERLAND) 2023; 12:1331. [PMID: 36987019 PMCID: PMC10053919 DOI: 10.3390/plants12061331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
(1) Background: Salt stress is an abiotic factor that limits maize yield and quality. A highly salt-tolerance inbred AS5 and a salt-sensitive inbred NX420 collected from Ningxia Province, China, were used to identify new genes for modulating salt resistance in maize. (2) Methods: To understand the different molecular bases of salt tolerance in AS5 and NX420, we performed BSA-seq using an F2 population for two extreme bulks derived from the cross between AS5 and NX420. Transcriptomic analysis was also conducted for AS5 and NX420 at the seedling stage after treatment with 150 mM of NaCl for 14 days. (3) Results: AS5 had a higher biomass and lower Na+ content than NX420 in the seedling stage after treatment with 150 mM NaCl for 14 days. One hundred and six candidate regions for salt tolerance were mapped on all of the chromosomes through BSA-seq using F2 in an extreme population. Based on the polymorphisms identified between both parents, we detected 77 genes. A large number of differentially expressed genes (DEGs) at the seedling stage under salt stress between these two inbred lines were detected using transcriptome sequencing. GO analysis indicated that 925 and 686 genes were significantly enriched in the integral component of the membrane of AS5 and NX420, respectively. Among these results, two and four DEGs were identified as overlapping in these two inbred lines using BSA-seq and transcriptomic analysis, respectively. Two genes (Zm00001d053925 and Zm00001d037181) were detected in both AS5 and NX420; the transcription level of Zm00001d053925 was induced to be significantly higher in AS5 than in NX420 (41.99 times versus 6.06 times after 150 mM of NaCl treatment for 48 h), while the expression of Zm00001d037181 showed no significant difference upon salt treatment in both lines. The functional annotation of the new candidate genes showed that it was an unknown function protein. (4) Conclusions: Zm00001d053925 is a new functional gene responding to salt stress in the seedling stage, which provides an important genetic resource for salt-tolerant maize breeding.
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Affiliation(s)
- Yongxing Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
- Agricultural Biotechnology Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Ying Ren
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Ji’an Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Wenguang Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Yuanyuan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Fengyuan Shen
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Jiang Ling
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
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10
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Strable J, Unger-Wallace E, Aragón Raygoza A, Briggs S, Vollbrecht E. Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture. PLANT PHYSIOLOGY 2023; 191:1084-1101. [PMID: 36508348 PMCID: PMC9922432 DOI: 10.1093/plphys/kiac559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/26/2022] [Indexed: 06/18/2023]
Abstract
Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.
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11
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Baldauf JA, Liu M, Vedder L, Yu P, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids. PLANT PHYSIOLOGY 2022; 189:1625-1638. [PMID: 35522211 PMCID: PMC9237695 DOI: 10.1093/plphys/kiac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The dominance model of heterosis explains the superior performance of F1-hybrids via the complementation of deleterious alleles by beneficial alleles in many genes. Genes active in one parent but inactive in the second lead to single-parent expression (SPE) complementation in maize (Zea mays L.) hybrids. In this study, SPE complementation resulted in approximately 700 additionally active genes in different tissues of genetically diverse maize hybrids on average. We established that the number of SPE genes is significantly associated with mid-parent heterosis (MPH) for all surveyed phenotypic traits. In addition, we highlighted that maternally (SPE_B) and paternally (SPE_X) active SPE genes enriched in gene co-expression modules are highly correlated within each SPE type but separated between these two SPE types. While SPE_B-enriched co-expression modules are positively correlated with phenotypic traits, SPE_X-enriched modules displayed a negative correlation. Gene ontology term enrichment analyses indicated that SPE_B patterns are associated with growth and development, whereas SPE_X patterns are enriched in defense and stress response. In summary, these results link the degree of phenotypic MPH to the prevalence of gene expression complementation observed by SPE, supporting the notion that hybrids benefit from SPE complementation via its role in coordinating maize development in fluctuating environments.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | | | - Lucia Vedder
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Hans-Peter Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210, USA
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12
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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13
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Genome-Wide Identification and Characterization of PRR Gene Family and their Diurnal Rhythmic Expression Profile in Maize. Int J Genomics 2022; 2022:6941607. [PMID: 35615408 PMCID: PMC9126661 DOI: 10.1155/2022/6941607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
As essential components of the circadian clock, the pseudo-response regulator (PRR) gene family plays critical roles in plant photoperiod pathway. In this study, we performed a genome-wide identification and a systematic analysis of the PRR gene family in maize. Nine ZmPRRs were identified, and the gene structure, conserved motif, evolution relationship, and expression pattern of ZmPRRs were analyzed comprehensively. Phylogenetic analysis indicated that the nine ZmPRR genes were divided into three groups, except for ZmPRR73, two of which were highly homologous to each of the AtPRR or OsPRR quintet members. Promoter cis-element analysis of ZmPRRs demonstrated that they might be involved in multiple signaling transduction pathways, such as light response, biological or abiotic stress response, and hormone response. qRT-PCR analysis revealed that the levels of ZmPRRs transcripts varied considerably and exhibited a diurnal rhythmic oscillation expression pattern in the given 24-h period under both SD and LD conditions, which indicated that the level of transcription of ZmPRRs expression is subjected to a circadian rhythm and modulated by light and the circadian clock. The present study will provide an insight into further exploring the biological function and regulatory mechanism of ZmPRR genes in circadian rhythm and response to photoperiod in maize.
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14
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A dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize. Nat Commun 2022; 13:2222. [PMID: 35468878 PMCID: PMC9038930 DOI: 10.1038/s41467-022-29809-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/31/2022] [Indexed: 01/01/2023] Open
Abstract
Plant salt-stress response involves complex physiological processes. Previous studies have shown that some factors promote salt tolerance only under high transpiring condition, thus mediating transpiration-dependent salt tolerance (TDST). However, the mechanism underlying crop TDST remains largely unknown. Here, we report that ZmSTL1 (Salt-Tolerant Locus 1) confers natural variation of TDST in maize. ZmSTL1 encodes a dirigent protein (termed ZmESBL) localized to the Casparian strip (CS) domain. Mutants lacking ZmESBL display impaired lignin deposition at endodermal CS domain which leads to a defective CS barrier. Under salt condition, mutation of ZmESBL increases the apoplastic transport of Na+ across the endodermis, and then increases the root-to-shoot delivery of Na+ via transpiration flow, thereby leading to a transpiration-dependent salt hypersensitivity. Moreover, we show that the ortholog of ZmESBL also mediates CS development and TDST in Arabidopsis. Our study suggests that modification of CS barrier may provide an approach for developing salt-tolerant crops. Most crops are farmed under high transpiring environments, but our understanding of transpiration-dependent salt tolerance (TDST) remains limited. Here, the authors report a dirigent family protein is responsible for TDST by affecting lignin deposition at Casparian strip barrier and transportation of Na+ across the endodermis.
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15
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Liu X, Zhang S, Jiang Y, Yan T, Fang C, Hou Q, Wu S, Xie K, An X, Wan X. Use of CRISPR/Cas9-Based Gene Editing to Simultaneously Mutate Multiple Homologous Genes Required for Pollen Development and Male Fertility in Maize. Cells 2022; 11:cells11030439. [PMID: 35159251 PMCID: PMC8834288 DOI: 10.3390/cells11030439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Male sterility represents an important trait for hybrid breeding and seed production in crops. Although the genes required for male fertility have been widely studied and characterized in many plant species, most of them are single genic male-sterility (GMS) genes. To investigate the role of multiple homologous genes in anther and pollen developments of maize, we established the CRISPR/Cas9-based gene editing method to simultaneously mutate the homologs in several putative GMS gene families. By using the integrated strategies of multi-gene editing vectors, maize genetic transformation, mutation-site analysis of T0 and F1 plants, and genotyping and phenotyping of F2 progenies, we further confirmed gene functions of every member in ZmTGA9-1/-2/-3 family, and identified the functions of ZmDFR1, ZmDFR2, ZmACOS5-1, and ZmACOS5-2 in controlling maize male fertility. Single and double homozygous gene mutants of ZmTGA9-1/-2/-3 did not affect anther and pollen development, while triple homozygous gene mutant resulted in complete male sterility. Two single-gene mutants of ZmDFR1/2 displayed partial male sterility, but the double-gene mutant showed complete male sterility. Additionally, only the ZmACOS5-2 single gene was required for anther and pollen development, while ZmACOS5-1 had no effect on male fertility. Our results show that the CRISPR/Cas9 gene editing system is a highly efficient and convenient tool for identifying multiple homologous GMS genes. These findings enrich GMS genes and mutant resources for breeding of maize GMS lines and promote deep understanding of the gene family underlying pollen development and male fertility in maize.
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Affiliation(s)
- Xinze Liu
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
| | - Shaowei Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
| | - Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
| | - Tingwei Yan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
| | - Chaowei Fang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Ke Xie
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
- Correspondence: (X.A.); (X.W.); Tel.: +86-137-1768-5330 (X.A.); +86-186-0056-1850 (X.W.)
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China; (X.L.); (S.Z.); (Y.J.); (T.Y.); (C.F.); (Q.H.); (S.W.); (K.X.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
- Correspondence: (X.A.); (X.W.); Tel.: +86-137-1768-5330 (X.A.); +86-186-0056-1850 (X.W.)
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16
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Huqe MAS, Haque MS, Sagar A, Uddin MN, Hossain MA, Hossain AKMZ, Rahman MM, Wang X, Al-Ashkar I, Ueda A, EL Sabagh A. Characterization of Maize Hybrids ( Zea mays L.) for Detecting Salt Tolerance Based on Morpho-Physiological Characteristics, Ion Accumulation and Genetic Variability at Early Vegetative Stage. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112549. [PMID: 34834912 PMCID: PMC8623748 DOI: 10.3390/plants10112549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 05/22/2023]
Abstract
Increasing soil salinity due to global warming severely restricts crop growth and yield. To select and recommend salt-tolerant cultivars, extensive genotypic screening and examination of plants' morpho-physiological responses to salt stress are required. In this study, 18 prescreened maize hybrid cultivars were examined at the early growth stage under a hydroponic system using multivariate analysis to demonstrate the genotypic and phenotypic variations of the selected cultivars under salt stress. The seedlings of all maize cultivars were evaluated with two salt levels: control (without NaCl) and salt stress (12 dS m-1 simulated with NaCl) for 28 d. A total of 18 morpho-physiological and ion accumulation traits were dissected using multivariate analysis, and salt tolerance index (STI) values of the examined traits were evaluated for grouping of cultivars into salt-tolerant and -sensitive groups. Salt stress significantly declined all measured traits except root-shoot ratio (RSR), while the cultivars responded differently. The cultivars were grouped into three clusters and the cultivars in Cluster-1 such as Prabhat, UniGreen NK41, Bisco 51, UniGreen UB100, Bharati 981 and Star Beej 7Star exhibited salt tolerance to a greater extent, accounting for higher STI in comparison to other cultivars grouped in Cluster-2 and Cluster-3. The high heritability (h2bs, >60%) and genetic advance (GAM, >20%) were recorded in 13 measured traits, indicating considerable genetic variations present in these traits. Therefore, using multivariate analysis based on the measured traits, six hybrid maize cultivars were selected as salt-tolerant and some traits such as Total Fresh Weight (TFW), Total Dry Weight (TDW), Total Na+, Total K+ contents and K+-Na+ Ratio could be effectively used for the selection criteria evaluating salt-tolerant maize genotypes at the early seedling stage.
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Affiliation(s)
- Md Al Samsul Huqe
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - Md Sabibul Haque
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
- Correspondence: (M.S.H.); (X.W.); (A.E.S.)
| | - Ashaduzzaman Sagar
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - Md Nesar Uddin
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - Md Alamgir Hossain
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - AKM Zakir Hossain
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - Md Mustafizur Rahman
- Department of Crop Botany, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.H.); (A.S.); (M.N.U.); (M.A.H.); (A.Z.H.); (M.M.R.)
| | - Xiukang Wang
- Department of Biology, College of Life Sciences, Yan’an University, Yan’an 716000, China
- Correspondence: (M.S.H.); (X.W.); (A.E.S.)
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Akihiro Ueda
- Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan;
| | - Ayman EL Sabagh
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Correspondence: (M.S.H.); (X.W.); (A.E.S.)
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17
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Garibay-Hernández A, Kessler N, Józefowicz AM, Türksoy GM, Lohwasser U, Mock HP. Untargeted metabotyping to study phenylpropanoid diversity in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:680-697. [PMID: 33963574 DOI: 10.1111/ppl.13458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Plant genebanks constitute a key resource for breeding to ensure crop yield under changing environmental conditions. Because of their roles in a range of stress responses, phenylpropanoids are promising targets. Phenylpropanoids comprise a wide array of metabolites; however, studies regarding their diversity and the underlying genes are still limited for cereals. The assessment of barley diversity via genotyping-by-sequencing is in rapid progress. Exploring these resources by integrating genetic association studies to in-depth metabolomic profiling provides a valuable opportunity to study barley phenylpropanoid metabolism; but poses a challenge by demanding large-scale approaches. Here, we report an LC-PDA-MS workflow for barley high-throughput metabotyping. Without prior construction of a species-specific library, this method produced phenylpropanoid-enriched metabotypes with which the abundance of putative metabolic features was assessed across hundreds of samples in a single-processed data matrix. The robustness of the analytical performance was tested using a standard mix and extracts from two selected cultivars: Scarlett and Barke. The large-scale analysis of barley extracts showed (1) that barley flag leaf profiles were dominated by glycosylation derivatives of isovitexin, isoorientin, and isoscoparin; (2) proved the workflow's capability to discriminate within genotypes; (3) highlighted the role of glycosylation in barley phenylpropanoid diversity. Using the barley S42IL mapping population, the workflow proved useful for metabolic quantitative trait loci purposes. The protocol can be readily applied not only to explore the barley phenylpropanoid diversity represented in genebanks but also to study species whose profiles differ from those of cereals: the crop Helianthus annuus (sunflower) and the model plant Arabidopsis thaliana.
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Affiliation(s)
| | | | | | - Gözde Merve Türksoy
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Ulrike Lohwasser
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Hans-Peter Mock
- Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
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18
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Liang X, Liu S, Wang T, Li F, Cheng J, Lai J, Qin F, Li Z, Wang X, Jiang C. Metabolomics-driven gene mining and genetic improvement of tolerance to salt-induced osmotic stress in maize. THE NEW PHYTOLOGIST 2021; 230:2355-2370. [PMID: 33666235 DOI: 10.1111/nph.17323] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 05/06/2023]
Abstract
The farmland of the world's main corn-producing area is increasingly affected by salt stress. Therefore, the breeding of salt-tolerant cultivars is necessary for the long-term sustainability of global corn production. Previous studies have shown that natural maize varieties display a large diversity of salt tolerance, yet the genetic variants underlying such diversity remain poorly discovered and applied, especially those mediating the tolerance to salt-induced osmotic stress (SIOS). Here we report a metabolomics-driven understanding and genetic improvement of maize SIOS tolerance. Using a LC-MS-based untargeted metabolomics approach, we profiled the metabolomes of 266 maize inbred lines under control and salt conditions, and then identified 37 metabolite biomarkers of SIOS tolerance (METO1-37). Follow-up metabolic GWAS (mGWAS) and genotype-to-phenotype modeling identified 10 candidate genes significantly associating with the SIOS tolerance and METO abundances. Furthermore, we validated that a citrate synthase, a glucosyltransferase and a cytochrome P450 underlie the genotype-METO-SIOS tolerance associations, and showed that their favorable alleles additively improve the SIOS tolerance of elite maize inbred lines. Our study provides a novel insight into the natural variation of maize SIOS tolerance, which boosts the genetic improvement of maize salt tolerance, and demonstrates a metabolomics-based approach for mining crop genes associated with this complex agronomic trait.
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Affiliation(s)
- Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Songyu Liu
- Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Tao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Fenrong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiangfeng Wang
- Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
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19
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Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genet 2021; 17:e1009491. [PMID: 33830994 PMCID: PMC8057601 DOI: 10.1371/journal.pgen.1009491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/20/2021] [Accepted: 03/15/2021] [Indexed: 11/19/2022] Open
Abstract
Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.
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Anderson SN, Zhou P, Higgins K, Brandvain Y, Springer NM. Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genet 2021. [PMID: 33830994 DOI: 10.1371/journal.pgen.100949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.
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Affiliation(s)
- Sarah N Anderson
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, Iowa, United States of America
| | - Peng Zhou
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
| | - Kaitlin Higgins
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, Iowa, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
| | - Nathan M Springer
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
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21
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Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. Gene capture by transposable elements leads to epigenetic conflict in maize. MOLECULAR PLANT 2021; 14:237-252. [PMID: 33171302 DOI: 10.1016/j.molp.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.
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Affiliation(s)
- Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Danelle Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA; Department of Botany and Plant Sciences, UC Riverside, Riverside, CA 92521, USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA.
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Zhang Y, Lai X, Yang S, Ren H, Yuan J, Jin H, Shi C, Lai Z, Xia G. Functional analysis of tomato CHIP ubiquitin E3 ligase in heat tolerance. Sci Rep 2021; 11:1713. [PMID: 33462308 PMCID: PMC7814054 DOI: 10.1038/s41598-021-81372-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023] Open
Abstract
Plants have evolved genetic and physiological mechanisms to mitigate the adverse effects of high temperature. CARBOXYL TERMINUS OF THE HSC70-INTERACTING PROTEINS (CHIP) is a conserved chaperone-dependent ubiquitin E3 ligase that targets misfolded proteins. Here, we report functional analysis of the SlCHIP gene from tomato (Solanum lycopersicum) in heat tolerance. SlCHIP encodes a CHIP protein with three tandem tetracopeptide repeat (TPR) motifs and a C-terminal U box domain. Phylogenetic analysis of CHIP homologs from animals, spore-bearing and seed plants revealed a tree topology similar to the evolutionary tree of the organisms. Expression of SlCHIP was induced under high temperature and was also responsive to plant stress hormones. Silencing of SlCHIP in tomato reduced heat tolerance based on increased heat stress symptoms, reduced photosynthetic activity, elevated electrolyte leakage and accumulation of insoluble protein aggregates. The accumulated protein aggregates in SlCHIP-silenced plants were still highly ubiquitinated, suggesting involvement of other E3 ligases in ubiquitination. SlCHIP restored the heat tolerance of Arabidopsis chip mutant to the wild type levels. These results indicate that tomato SlCHIP plays a critical role in heat stress responses most likely by targeting degradation of misfolded proteins that are generated during heat stress.
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Affiliation(s)
- Yan Zhang
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China.
| | - Xiaodong Lai
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Siqing Yang
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Huan Ren
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Jingya Yuan
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Huanchun Jin
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Chengchen Shi
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gengshou Xia
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, 323000, Zhejiang, China
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Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O'Connor C, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Hirsch CD, Buell CR, Kaeppler SM, Springer NM, Hirsch CN. Single-parent expression drives dynamic gene expression complementation in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:93-107. [PMID: 33098691 DOI: 10.1111/tpj.15042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
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Bian Z, Gao H, Wang C. NAC Transcription Factors as Positive or Negative Regulators during Ongoing Battle between Pathogens and Our Food Crops. Int J Mol Sci 2020; 22:E81. [PMID: 33374758 PMCID: PMC7795297 DOI: 10.3390/ijms22010081] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/13/2023] Open
Abstract
The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in crop-pathogen interactions, as positive or negative regulators of the downstream defense-related genes. NAC TFs link signaling pathways between plant hormones, including salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), or other signals, such as reactive oxygen species (ROS), to regulate the resistance against pathogens. Remarkably, NAC TFs can also contribute to hypersensitive response and stomatal immunity or can be hijacked as virulence targets of pathogen effectors. Here, we review recent progress in understanding the structure, biological functions and signaling networks of NAC TFs in response to pathogens in several main food crops, such as rice, wheat, barley, and tomato, and explore the directions needed to further elucidate the function and mechanisms of these key signaling molecules.
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Affiliation(s)
| | | | - Chongying Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (Z.B.); (H.G.)
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Schnable JC. Genes and gene models, an important distinction. THE NEW PHYTOLOGIST 2020; 228:50-55. [PMID: 31241760 DOI: 10.1111/nph.16011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/07/2019] [Indexed: 05/22/2023]
Abstract
Genome sequencing has fundamentally changed how plant biologists think about genes. All or nearly all genes can ultimately be associated with a gene model. However, many gene models appear to play little or no role in the traits of an organism. A range of structural, molecular, population and evolutionary features all show a separation between genes with known phenotypes and the overall set of annotated gene models. These different features could be combined to develop models to distinguish the genes that determine the traits of plants from the subset gene other annotated gene models which are unlikely to play a role in doing so. Efforts to identify the subset of annotated gene models likely involved in specifying the characteristics of plants would help aid a wide range of researchers.
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Affiliation(s)
- James C Schnable
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Baldauf JA, Vedder L, Schoof H, Hochholdinger F. Robust non-syntenic gene expression patterns in diverse maize hybrids during root development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:865-876. [PMID: 31638701 DOI: 10.1093/jxb/erz452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations. For instance, differentially expressed genes with preferential expression in hybrids were highly conserved during development in comparison to their parental counterparts. Similarly, in hybrids a major proportion of non-additively expressed genes with expression levels between the parental values were particularly conserved during development. Importantly, in these expression patterns non-syntenic genes that evolved after the separation of the maize and sorghum lineages were systemically enriched. Furthermore, non-syntenic genes were substantially linked to the conservation of all surveyed gene expression patterns during primary root development. Among all F1-hybrids, between ~40% of the non-syntenic genes with unexpected allelic expression ratios and ~60% of the non-syntenic differentially and non-additively expressed genes were conserved and therefore robust to developmental changes. Hence, the enrichment of non-syntenic genes during primary root development might be involved in the developmental adaptation of maize roots and thus the superior performance of hybrids.
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Affiliation(s)
- Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Lucia Vedder
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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Fan K, Yuan S, Chen J, Chen Y, Li Z, Lin W, Zhang Y, Liu J, Lin W. Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays. PLANTA 2019; 250:1521-1538. [PMID: 31346803 DOI: 10.1007/s00425-019-03243-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
97 ZmPP2Cs were clustered into 10 subfamilies with biased subfamily evolution and lineage-specific expansion. Segmental duplication after the divergence of maize and sorghum might have led to primary expansion of ZmPP2Cs. The protein phosphatase 2C (PP2C) enzymes control many stress responses and developmental processes in plants. In Zea mays, a comprehensive understanding of the evolution and expansion of the PP2C family is still lacking. In the current study, 97 ZmPP2Cs were identified and clustered into 10 subfamilies. Through the analysis of the PP2C family in monocots, the ZmPP2C subfamilies displayed biased subfamily molecular evolution and lineage-specific expansion, as evidenced by their differing numbers of member genes, expansion and evolutionary rates, conserved subdomains, chromosomal distributions, expression levels, responsive-regulatory elements and regulatory networks. Moreover, while segmental duplication events have caused the primary expansion of the ZmPP2Cs, the majority of their diversification occurred following the additional whole-genome duplication that took place after the divergence of maize and sorghum (Sorghum bicolor). After this event, the PP2C subfamilies showed asymmetric evolutionary rates, with the D, F2 and H subfamily likely the most closely to resemble its ancestral subfamily's genes. These findings could provide novel insights into the molecular evolution and expansion of the PP2C family in maize, and lay the foundation for the functional analysis of these enzymes in maize and related monocots.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Shuna Yuan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences/Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou, 571737, China
| | - Jie Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yunrui Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Zhaowei Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yongqiang Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Jianping Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Wenxiong Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China.
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Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF. Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics 2019; 213:143-160. [PMID: 31320409 PMCID: PMC6727801 DOI: 10.1534/genetics.119.302378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Abstract
In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon "hybrid decay" and present ideas on the mechanism that may underlie it.
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Affiliation(s)
- Wei Xue
- College of Agronomy, Shenyang Agricultural University, 110866 Liaoning Province, China
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
| | - Liyan Yang
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Life Science College, Shanxi Normal University, 041004 Shanxi Province, China
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Paul Bilinski
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Sherry Flint-Garcia
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
- Agricultural Research Service, United States Department of Agriculture, Columbia, Missouri 65211
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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30
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Cao Y, Liang X, Yin P, Zhang M, Jiang C. A domestication-associated reduction in K + -preferring HKT transporter activity underlies maize shoot K + accumulation and salt tolerance. THE NEW PHYTOLOGIST 2019; 222:301-317. [PMID: 30461018 DOI: 10.1111/nph.15605] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/10/2018] [Indexed: 05/26/2023]
Abstract
Maize was domesticated from Balsas teosinte c. 10 000 yr ago. Previous studies have suggested that increased tolerance to environmental stress occurred during maize domestication. However, the underlying genetic basis remains largely unknown. We used a maize (W22)-teosinte recombinant inbred line (RIL) to investigate the salt wild-type tolerance aspects of maize domestication. We revealed that ZmHKT2 is a major QTL that regulates K+ homeostasis in saline soils. ZmHKT2 encodes a K+ -preferring HKT family transporter and probably reduces shoot K+ content by removing K+ ions from root-to-shoot flowing xylem sap, ZmHKT2 deficiency increases xylem sap and shoot K+ concentrations, and increases salt tolerance. A coding sequence polymorphism in the ZmHKT2W22 allele (SNP389-G) confers an amino acid variant ZmHKT2 that increases xylem sap K+ concentration, thereby increasing shoot K+ content and salt tolerance. Additional analyses showed that SNP389-G first existed in teosinte (allele frequency 56% in assayed accessions), then swept through the maize population (allele frequency 98%), and that SNP389-G probably underwent positive selection during maize domestication. We conclude that a domestication-associated reduction in K+ transport activity in ZmHKT2 underlies maize shoot K+ content and salt tolerance, and propose that CRISPR-based editing of ZmHKT2 might provide a feasible strategy for improving maize salt tolerance.
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Affiliation(s)
- Yibo Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Pan Yin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
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Zhou P, Hirsch CN, Briggs SP, Springer NM. Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development. MOLECULAR PLANT 2019; 12:410-425. [PMID: 30593858 DOI: 10.1016/j.molp.2018.12.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 05/26/2023]
Abstract
Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their F1 hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into ∼30 000 genes that are expressed in at least one tissue of one inbred and an additional ∼10 000 ″silent" genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (∼74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single parent expression. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis- and trans-regulatory variation. Genes with cis-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-regulatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understanding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Steven P Briggs
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D. The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:751-766. [PMID: 30343386 DOI: 10.1007/s00122-018-3212-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 05/20/2023]
Abstract
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.
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Affiliation(s)
- Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia.
| | - David Innes
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, 4102, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Jared Baxter
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Michael Hassall
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
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33
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Rife TW, Graybosch RA, Poland JA. Genomic Analysis and Prediction within a US Public Collaborative Winter Wheat Regional Testing Nursery. THE PLANT GENOME 2018; 11:180012. [PMID: 30512033 DOI: 10.3835/plantgenome2018.02.0012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly unbalanced datasets that are common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat ( L.) varieties from breeding programs in the US Central Plains. New entries are submitted annually and can be re-entered only once. The trial is grown at >30 locations each year and lines are evaluated for grain yield, disease resistance, and agronomic traits. Overall genetic gain is measured across years by including common check cultivars for comparison. We have generated whole-genome profiles via genotyping-by-sequencing (GBS) for 939 SPRN entries dating back to 1992 to explore the potential use of the nursery as a genomic selection (GS) training population (TP). The GS prediction models across years (average = 0.33) outperformed year-to-year phenotypic correlation for yield ( = 0.27) for a majority of the years evaluated, suggesting that genomic selection has the potential to outperform low heritability selection on yield in these highly variable environments. We also examined the predictability of programs using both program-specific and whole-set TPs. Generally, the predictability of a program was similar with both approaches. These results suggest that wheat breeding programs can collaboratively leverage the immense datasets that are generated from regional testing networks.
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Liu S, Schnable JC, Ott A, Yeh CTE, Springer NM, Yu J, Muehlbauer G, Timmermans MCP, Scanlon MJ, Schnable PS. Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels. Mol Biol Evol 2018; 35:2762-2772. [PMID: 30184112 PMCID: PMC6231493 DOI: 10.1093/molbev/msy174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10−5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS.,Department of Agronomy, Iowa State University, Ames, IA
| | - James C Schnable
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE
| | - Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA.,Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI
| | | | - Nathan M Springer
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN
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35
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The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet 2018; 50:1282-1288. [PMID: 30061736 DOI: 10.1038/s41588-018-0158-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/17/2018] [Indexed: 11/08/2022]
Abstract
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.
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36
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Lai X, Yan L, Lu Y, Schnable JC. Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:843-855. [PMID: 29265526 DOI: 10.1111/tpj.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 05/14/2023]
Abstract
The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as 'domestication syndrome'. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many 'classic' domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Yan
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang College, Liangshan, 615000, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
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37
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Zhang M, Cao Y, Wang Z, Wang ZQ, Shi J, Liang X, Song W, Chen Q, Lai J, Jiang C. A retrotransposon in an HKT1 family sodium transporter causes variation of leaf Na + exclusion and salt tolerance in maize. THE NEW PHYTOLOGIST 2018; 217:1161-1176. [PMID: 29139111 DOI: 10.1111/nph.14882] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/07/2017] [Indexed: 05/20/2023]
Abstract
Soil salinity is one of several major abiotic stresses that constrain maize productivity worldwide. An improved understanding of salt-tolerance mechanisms will thus enhance the breeding of salt-tolerant maize and boost productivity. Previous studies have indicated that the maintenance of leaf Na+ concentration is essential for maize salt tolerance, and the difference in leaf Na+ exclusion has previously been associated with variation in salt tolerance between maize varieties. Here, we report the identification and functional characterization of a maize salt-tolerance quantitative trait locus (QTL), Zea mays Na+ Content1 (ZmNC1), which encodes an HKT-type transporter (designated as ZmHKT1). We show that a natural ZmHKT1 loss-of-function allele containing a retrotransposon insertion confers increased accumulation of Na+ in leaves, and salt hypersensitivity. We next show that ZmHKT1 encodes a plasma membrane-localized Na+ -selective transporter, and is preferentially expressed in root stele (including the parenchyma cells surrounding the xylem vessels). We also show that loss of ZmHKT1 function increases xylem sap Na+ concentration and causes increased root-to-shoot Na+ delivery, indicating that ZmHKT1 promotes leaf Na+ exclusion and salt tolerance by withdrawing Na+ from the xylem sap. We conclude that ZmHKT1 is a major salt-tolerance QTL and identifies an important new gene target in breeding for improved maize salt tolerance.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yibo Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhiping Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhi-Qiang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qijun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Baldauf JA, Marcon C, Lithio A, Vedder L, Altrogge L, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids. Curr Biol 2018; 28:431-437.e4. [PMID: 29358068 DOI: 10.1016/j.cub.2017.12.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022]
Abstract
Maize (Zea mays L.) displays an exceptional degree of structural genomic diversity [1, 2]. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids. The classical dominance model of heterosis explains the superiority of hybrid plants by the complementation of deleterious parental alleles by superior alleles of the second parent at many loci [3]. Genes active in one inbred line but inactive in another represent an extreme instance of allelic diversity defined as single-parent expression [4]. We observed on average ∼1,000 such genes in all inbred line combinations during primary root development. These genes consistently displayed expression complementation (i.e., activity) in their hybrid progeny. Consequently, extreme expression complementation is a general mechanism that results on average in ∼600 additionally active genes and their encoded biological functions in hybrids. The modern maize genome is complemented by a set of non-syntenic genes, which emerged after the separation of the maize and sorghum lineages and lack syntenic orthologs in any other grass species [5]. We demonstrated that non-syntenic genes are the driving force of gene expression complementation in hybrids. Among those, the highly diversified families of bZIP and bHLH transcription factors [6] are systematically overrepresented. In summary, extreme gene expression complementation extensively shapes the transcriptomic plasticity of maize hybrids and might therefore be one factor controlling the developmental plasticity of hybrids.
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Affiliation(s)
- Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Caroline Marcon
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, 2438 Osborne Dr., Ames, IA 50011-1210, USA
| | - Lucia Vedder
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Lena Altrogge
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstraße 23, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, 2438 Osborne Dr., Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
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39
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Díaz ML, Cuppari S, Soresi D, Carrera A. In Silico Analysis of Fatty Acid Desaturase Genes and Proteins in Grasses. Appl Biochem Biotechnol 2017; 184:484-499. [PMID: 28755245 DOI: 10.1007/s12010-017-2556-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/13/2017] [Indexed: 02/03/2023]
Abstract
Fatty acid desaturases (FADs) catalyze the introduction of a double bond into acyl chains. Two FAD groups have been identified in plants: acyl-acyl carrier proteins (ACPs) and acyl-lipid or membrane-bound FAD. The former catalyze the conversion of 18:0 to 18:1 and to date have only been identified in plants. The latter are found in eukaryotes and bacteria and are responsible for multiple desaturations. In this study, we identified 82 desaturase gene and protein sequences from 10 grass species deposited in GenBank that were analyzed using bioinformatic approaches. Subcellular localization predictions of desaturase family revealed their localization in plasma membranes, chloroplasts, endoplasmic reticula, and mitochondria. The in silico mapping showed multiple chromosomal locations in most species. Furthermore, the presence of the characteristic histidine domains, the predicted motifs, and the finding of transmembrane regions strongly support the protein functionality. The identification of putative regulatory sites in the promotor and the expression profiles revealed the wide range of pathways in which fatty acid desaturases are involved. This study is an updated survey on desaturases of grasses that provides a comprehensive insight into diversity and evolution. This characterization is a necessary first step before considering these genes as candidates for new biotechnological approaches.
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Affiliation(s)
- Marina Lucía Díaz
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina.
- Comisión de Investigaciones Científicas, Buenos Aires, Argentina.
| | - Selva Cuppari
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - Daniela Soresi
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - Alicia Carrera
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, San Andrés 800, Bahía Blanca, Argentina
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40
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Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F. Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:403-414. [PMID: 28204533 PMCID: PMC5444478 DOI: 10.1093/jxb/erw422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise comparisons of rtcs and wild-type embryo transcriptomes identified 131 transcription factors among 3526 differentially expressed genes [false discovery rate (FDR) <5% and |log2Fc|≥1]. Among those, functional annotation highlighted genes involved in cell cycle control and phytohormone action, particularly auxin signaling. Moreover, in silico promoter analyses identified putative RTCS target genes associated with transcription factor action and hormone metabolism and signaling. Significantly, non-syntenic genes that emerged after the separation of maize and sorghum were over-represented among genes displaying RTCS-dependent expression during seminal root primordia formation. This might suggest that these non-syntenic genes came under the transcriptional control of the syntenic gene rtcs during seminal root evolution. Taken together, this study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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41
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Salvi S. An evo-devo perspective on root genetic variation in cereals. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:351-354. [PMID: 28204583 PMCID: PMC5444473 DOI: 10.1093/jxb/erw505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Italy
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42
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Scully ED, Donze-Reiner T, Wang H, Eickhoff TE, Baxendale F, Twigg P, Kovacs F, Heng-Moss T, Sattler SE, Sarath G. Identification of an orthologous clade of peroxidases that respond to feeding by greenbugs (Schizaphis graminum) in C 4 grasses. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:1134-1148. [PMID: 32480533 DOI: 10.1071/fp16104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/29/2016] [Indexed: 06/11/2023]
Abstract
Knowledge of specific peroxidases that respond to aphid herbivory is limited in C4 grasses, but could provide targets for improving defence against these pests. A sorghum (Sorghum bicolor (L.) Moench) peroxidase (SbPrx-1; Sobic.002G416700) has been previously linked to biotic stress responses, and was the starting point for this study. Genomic analyses indicated that SbPrx-1 was part of a clade of five closely related peroxidase genes occurring within a ~30kb region on chromosome 2 of the sorghum genome. Comparison of this ~30-kb region to syntenic regions in switchgrass (Panicum virgatum L.) and foxtail millet (Setaria italica L.) identified similar related clusters of peroxidases. Infestation of a susceptible sorghum cultivar with greenbugs (Shizaphis graminum Rondani) induced three of the five peroxidases. Greenbug infestation of switchgrass and foxtail millet plants showed similar inductions of peroxidases. SbPrx-1 was also induced in response to aphid herbivory in a greenbug-resistant sorghum line, Cargill 607E. These data indicate that this genomic region of C4 grasses could be valuable as a marker to assess potential insect resistance in C4 grasses.
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Affiliation(s)
- Erin D Scully
- Stored Product Insect and Engineering Research Unit, Center for Grain and Animal Health Research USDA-ARS, Manhattan, KS 66502, USA
| | | | - Haichuan Wang
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Thomas E Eickhoff
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Frederick Baxendale
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Paul Twigg
- Department of Biology, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Frank Kovacs
- Department of Chemistry, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Tiffany Heng-Moss
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Scott E Sattler
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583, USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583, USA
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43
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Li Q, Hu L, Guo J, Yang T, Chen L. Molecular characterization of two type I acyl-CoA: diacylglycerol acyltransferase genes in maize. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1157036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Qingzhi Li
- Department of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, P.R. China
| | - Lizong Hu
- Department of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, P.R. China
| | - Jinjie Guo
- Key Laboratory constructed by Ministry of Education and Hebei province, Hebei sub-center for National Maize Improvement Center, Hebei Agricultural University, Baoding, P.R. China
| | - Tongwen Yang
- Department of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, P.R. China
| | - Long Chen
- Department of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, P.R. China
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44
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Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biol Evol 2015; 7:3286-98. [PMID: 26560340 PMCID: PMC4700967 DOI: 10.1093/gbe/evv219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind
using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Matthew D Bomhoff
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Evan Briones
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona
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45
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Wu X, Li Y, Li X, Li C, Shi Y, Song Y, Zheng Z, Li Y, Wang T. Analysis of genetic differentiation and genomic variation to reveal potential regions of importance during maize improvement. BMC PLANT BIOLOGY 2015; 15:256. [PMID: 26496865 PMCID: PMC4620006 DOI: 10.1186/s12870-015-0646-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Exploring genetic differentiation and genomic variation is important for both the utilization of heterosis and the dissection of the genetic bases of complex traits. METHODS We integrated 1857 diverse maize accessions from America, Africa, Europe and Asia to investigatetheir genetic differentiation, genomic variation using 43,252 high-quality single-nucleotide polymorphisms(SNPs),combing GWAS and linkage analysis strategy to exploring the function of relevant genetic segments. RESULTS We uncovered many more subpopulations that recently or historically formed during the breeding process. These patterns are represented by the following lines: Mo17, GB, E28, Ye8112, HZS, Shen137, PHG39, B73, 207, A634, Oh43, Reid Yellow Dent, and the Tropical/subtropical (TS) germplasm. A total of 85 highly differentiated regions with a DEST of more than 0.2 were identified between the TS and temperate subpopulations. These regions comprised 79% of the genetic variation, and most were significantly associated with adaptive traits. For example, the region containing the SNP tag PZE.108075114 was highly differentiated, and this region was significantly associated with flowering time (FT)-related traits, as supported by a genome-wide association study (GWAS) within the interval of FT-related quantitative trait loci (QTL). This region was also closely linked to zcn8 and vgt1, which were shown to be involved in maize adaptation. Most importantly, 197 highly differentiated regions between different subpopulation pairs were located within an FT- or plant architecture-related QTL. CONCLUSIONS Here we reported that 700-1000 SNPs were necessary needed to robustly estimate the genetic differentiation of a naturally diverse panel. In addition, 13 subpopulations were observed in maize germplasm, 85 genetic regions with higher differentiation between TS and temperate maize germplasm, 197 highly differentiated regions between different subpopulation pairs, which contained some FT- related QTNs/QTLs/genes supported by GWAS and linkage analysis, and these regions were expected to play important roles in maize adaptation.
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Affiliation(s)
- Xun Wu
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China.
- Nanchong Academy of Agricultural Sciences, Nanchong, Sichuan, China.
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China.
| | - Xin Li
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China.
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Zuping Zheng
- Nanchong Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China.
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing, China.
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