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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2024; 62:27-46. [PMID: 37739122 DOI: 10.1016/j.jare.2023.09.016] [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: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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Ji Y, Hewavithana T, Sharpe AG, Jin L. Understanding grain development in the Poaceae family by comparing conserved and distinctive pathways through omics studies in wheat and maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1393140. [PMID: 39100085 PMCID: PMC11295249 DOI: 10.3389/fpls.2024.1393140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success.
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Affiliation(s)
- Yuanyuan Ji
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thulani Hewavithana
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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Wang M, Wang L, Wang S, Zhang J, Fu Z, Wu P, Yang A, Wu D, Sun G, Wang C. Identification and Analysis of lncRNA and circRNA Related to Wheat Grain Development. Int J Mol Sci 2024; 25:5484. [PMID: 38791522 PMCID: PMC11122269 DOI: 10.3390/ijms25105484] [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: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA-circRNA-miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA-miRNA and circRNA-miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains.
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Affiliation(s)
- Meng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Lu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Shuanghong Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Junli Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Panpan Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
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Tsardakas Renhuldt N, Bentzer J, Ahrén D, Marmon S, Sirijovski N. Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat ( Avena sativa). FRONTIERS IN PLANT SCIENCE 2024; 15:1358490. [PMID: 38736447 PMCID: PMC11082396 DOI: 10.3389/fpls.2024.1358490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.
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Affiliation(s)
- Nikos Tsardakas Renhuldt
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Johan Bentzer
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Dag Ahrén
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Biology, Lund University, Lund, Sweden
| | - Sofia Marmon
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
| | - Nick Sirijovski
- ScanOats Industrial Research Centre, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
- CropTailor AB, Department of Chemistry, Division of Pure and Applied Biochemistry, Lund University, Lund, Sweden
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Yu Z, Cui B, Xiao J, Jiao W, Wang H, Wang Z, Sun L, Song Q, Yuan J, Wang X. Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid. J Genet Genomics 2024:S1673-8527(24)00081-X. [PMID: 38670432 DOI: 10.1016/j.jgg.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.
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Affiliation(s)
- Zhongyu Yu
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Baofeng Cui
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jingya Yuan
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
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Zhang J, Li S, Gao X, Liu Y, Fu B. Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress. BMC Genomics 2024; 25:382. [PMID: 38637768 PMCID: PMC11025244 DOI: 10.1186/s12864-024-10313-2] [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: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown. RESULT A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1-4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein-protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa. CONCLUSION This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.
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Affiliation(s)
- Jinqing Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
| | - Shuxia Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China
| | - Xueqin Gao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China
| | - Yaling Liu
- Inner Mongolia Pratacultural Technology Innovation Center Co, Ltd, Hohhot, 010000, China
| | - BingZhe Fu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China.
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Xixia District, Yinchuan, Ningxia Hui Autonomous Region, Yinchuan, 750021, China.
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Yinchuan, 750021, China.
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Sehgal D, Rathan ND, Özdemir F, Keser M, Akin B, Dababat AA, Koc E, Dreisigacker S, Morgounov A. Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Sci Rep 2024; 14:8431. [PMID: 38600135 PMCID: PMC11006659 DOI: 10.1038/s41598-024-57469-1] [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: 06/26/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico.
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
| | | | - Fatih Özdemir
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Mesut Keser
- International Center for Agricultural Research in Dry Areas (ICARDA), Ankara, Turkey
| | - Beyhan Akin
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | | | - Emrah Koc
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico
| | - Alexey Morgounov
- Scientific Production Center of Grain, Shortandy, Astana reg., 010000, Kazakhstan.
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Mei H, Cui C, Liu Y, Du Z, Wu K, Jiang X, Zheng Y, Zhang H. QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.). PLoS One 2023; 18:e0293155. [PMID: 37917626 PMCID: PMC10621824 DOI: 10.1371/journal.pone.0293155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
Seed size and shape are important traits that determine seed yield in sesame. Understanding the genetic basis of seed size and shape is essential for improving the yield of sesame. In this study, F2 and BC1 populations were developed by crossing the Yuzhi 4 and Bengal small-seed (BS) lines for detecting the quantitative trait loci (QTLs) of traits related to seed size and shape. A total of 52 QTLs, including 13 in F2 and 39 in BC1 populations, for seed length (SL), seed width (SW), and length to width ratio (L/W) were identified, explaining phenotypic variations from 3.68 to 21.64%. Of these QTLs, nine stable major QTLs were identified in the two populations. Notably, three major QTLs qSL-LG3-2, qSW-LG3-2, and qSW-LG3-F2 that accounted for 4.94-16.34% of the phenotypic variations were co-localized in a 2.08 Mb interval on chromosome 1 (chr1) with 279 candidate genes. Three stable major QTLs qSL-LG6-2, qLW-LG6, and qLW-LG6-F2 that explained 8.14-33.74% of the phenotypic variations were co-localized in a 3.27 Mb region on chr9 with 398 candidate genes. In addition, the stable major QTL qSL-LG5 was co-localized with minor QTLs qLW-LG5-3 and qSW-LG5 to a 1.82 Mb region on chr3 with 195 candidate genes. Gene annotation, orthologous gene analysis, and sequence analysis indicated that three genes are likely involved in sesame seed development. These results obtained herein provide valuable in-formation for functional gene cloning and improving the seed yield of sesame.
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Affiliation(s)
- Hongxian Mei
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Chengqi Cui
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhenwei Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Ke Wu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xiaolin Jiang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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Luo X, Yang Y, Lin X, Xiao J. Deciphering spike architecture formation towards yield improvement in wheat. J Genet Genomics 2023; 50:835-845. [PMID: 36907353 DOI: 10.1016/j.jgg.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.
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Affiliation(s)
- Xumei Luo
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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10
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Yang L, Yang L, Ding Y, Chen Y, Liu N, Zhou X, Huang L, Luo H, Xie M, Liao B, Jiang H. Global Transcriptome and Co-Expression Network Analyses Revealed Hub Genes Controlling Seed Size/Weight and/or Oil Content in Peanut. PLANTS (BASEL, SWITZERLAND) 2023; 12:3144. [PMID: 37687391 PMCID: PMC10490140 DOI: 10.3390/plants12173144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/21/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important economic and oilseed crop worldwide, providing high-quality edible oil and high protein content. Seed size/weight and oil content are two important determinants of yield and quality in peanut breeding. To identify key regulators controlling these two traits, two peanut cultivars with contrasting phenotypes were compared to each other, one having a larger seed size and higher oil content (Zhonghua16, ZH16 for short), while the second cultivar had smaller-sized seeds and lower oil content (Zhonghua6, ZH6). Whole transcriptome analyses were performed on these two cultivars at four stages of seed development. The results showed that ~40% of the expressed genes were stage-specific in each cultivar during seed development, especially at the early stage of development. In addition, we identified a total of 5356 differentially expressed genes (DEGs) between ZH16 and ZH6 across four development stages. Weighted gene co-expression network analysis (WGCNA) based on DEGs revealed multiple hub genes with potential roles in seed size/weight and/or oil content. These hub genes were mainly involved in transcription factors (TFs), phytohormones, the ubiquitin-proteasome pathway, and fatty acid synthesis. Overall, the candidate genes and co-expression networks detected in this study could be a valuable resource for genetic breeding to improve seed yield and quality traits in peanut.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430000, China; (L.Y.); (L.Y.); (Y.D.); (Y.C.); (N.L.); (X.Z.); (L.H.); (H.L.); (M.X.); (B.L.)
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11
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Chen H, Song Z, Wang L, Lai X, Chen W, Li X, Zhu X. Auxin-responsive protein MaIAA17-like modulates fruit ripening and ripening disorders induced by cold stress in 'Fenjiao' banana. Int J Biol Macromol 2023; 247:125750. [PMID: 37453644 DOI: 10.1016/j.ijbiomac.2023.125750] [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: 06/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Cold stress severely affects the banana fruit softening and de-greening, significantly inhibiting the ripening processes. However, the mechanism of ripening disorder caused by chilling injury (CI) in banana fruit remains largely unknown. Herein, MaIAA17-like, an Auxin/Indole-3-Acetic Acid (Aux/IAA) family member, was found to be highly related to the softening and de-greening in 'Fenjiao' banana. Its expression was rapidly increased with fruit ripening and then gradually decreased under normal ripening conditions (22 °C). Notably, cold storage severely repressed MaIAA17-like expression but was rapidly increased following ethephon treatment for ripening in fruits without CI. However, the expression repression was not reverted in fruits with serious CI symptoms after 12 days of storage at 7 °C. AtMaIAA17-like bound and regulated the activities of promoters of chlorophyll (MaNOL and MaSGR1), starch (MaBAM6 and MaBAM8), and cell wall (MaSUR14 and MaPL8) degradation-related genes. MaIAA17-like also interacted with ethylene-insensitive 3-binding F-box protein (MaEBF1), further activating the expression of MaNOL, MaBAM8, MaPL8, and MaSUR14. Generally, the transient overexpression of MaIAA17-like promoted fruit ripening by inducing the expression of softening and de-greening related genes. However, silencing MaIAA17-like inhibited fruit ripening by reducing the expression of softening and de-greening related genes. These results imply that MaIAA17-like modulates fruit ripening by transcriptionally upregulating the key genes related to fruit softening and de-greening.
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Affiliation(s)
- Hangcong Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zunyang Song
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China; Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Lihua Wang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiuhua Lai
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Weixin Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xueping Li
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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12
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Elsharawy H, Refat M. CRISPR/Cas9 genome editing in wheat: enhancing quality and productivity for global food security-a review. Funct Integr Genomics 2023; 23:265. [PMID: 37541970 DOI: 10.1007/s10142-023-01190-1] [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: 07/12/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Wheat (Triticum aestivum L.) is an important cereal crop that is grown all over the world for food and industrial purposes. Wheat is essential to the human diet due to its rich content of necessary amino acids, minerals, vitamins, and calories. Various wheat breeding techniques have been utilized to improve its quality, productivity, and resistance to biotic and abiotic stress impairing production. However, these techniques are expensive, demanding, and time-consuming. Additionally, these techniques need multiple generations to provide the desired results, and the improved traits could be lost over time. To overcome these challenges, researchers have developed various genome editing tools to improve the quality and quantity of cereal crops, including wheat. Genome editing technologies evolve quickly. Nowadays, single or multiple mutations can be enabled and targeted at specific loci in the plant genome, allowing controlled removal of undesirable features or insertion of advantageous ones. Clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) is a powerful genome editing tool that can be effectively used for precise genome editing of wheat and other crops. This review aims to provide a comprehensive understanding of this technology's potential applications to enhance wheat's quality and productivity. It will first explore the function of CRISPR/Cas9 in preserving the adaptive immunity of prokaryotic organisms, followed by a discussion of its current applications in wheat breeding.
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Affiliation(s)
- Hany Elsharawy
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
| | - Moath Refat
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong, University, Xi'an, 710061, China
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14
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Chen LN, Dou PT, Chen YK, Yang HQ. Mutant IAA21 genes from Dendrocalamus sinicus Chia et J. L. Sun inhibit stem and root growth in transgenic tobacco by interacting with ARF5. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107827. [PMID: 37329689 DOI: 10.1016/j.plaphy.2023.107827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023]
Abstract
Woody bamboos are important resource of industrial fibres. Auxin signaling plays a key role in multiple plant developmental processes, as yet the role of auxin/indole acetic acid (Aux/IAA) in culm development of woody bamboos has not been previously characterized. Dendrocalamus sinicus Chia et J. L. Sun is the largest woody bamboo documented in the world. Here, we identified two alleles of DsIAA21 gene (sIAA21 and bIAA21) from the straight- and bent-culm variants of D. sinicus, respectively, and studied how the domains I, i, and II of DsIAA21 affect the gene transcriptional repression. The results showed that bIAA21 expression was rapidly induced by exogenous auxin in D. sinicus. In transgenic tobacco, sIAA21 and bIAA21 mutated in domains i, and II significantly regulated plant architecture and root development. Stem cross sections revealed that parenchyma cells were smaller in transgenic plants than that in wild type plants. Domain i mutation changed the leucine and proline at position 45 to proline and leucine (siaa21L45P and biaa21P45L) strongly repressed cell expansion and root elongation by reducing the gravitropic response. Substitution of isoleucine with valine in domain II of the full length DsIAA21 resulted in dwarf stature in transgenic tobacco plants. Furthermore, the DsIAA21 interacted with auxin response factor 5 (ARF5) in transgenic tobacco plants, suggesting that DsIAA21 might inhibit stem and root elongation via interacting with ARF5. Taken together, our data indicated that DsIAA21 was a negative regulator of plant development and suggested that amino acid differences in domain i of sIAA21 versus bIAA21 affected their response to auxin, and might play a key role in the formation of the bent culm variant in D. sinicus. Our results not only shed a light on the morphogenetic mechanism in D. sinicus, but also provided new insights into versatile function of Aux/IAAs in plants.
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Affiliation(s)
- Ling-Na Chen
- College of Life Science, Xinjiang Normal University, Xinyi Road, Shayibake District, Urumqi, 830054, PR China; Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China
| | - Pei-Tong Dou
- Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China
| | - Yong-Kun Chen
- College of Life Science, Xinjiang Normal University, Xinyi Road, Shayibake District, Urumqi, 830054, PR China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Xinyi Road, Shayibake District, Urumqi, 830054, PR China
| | - Han-Qi Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China.
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Zhang J, Zhang X, Liu X, Pai Q, Wang Y, Wu X. Molecular Network for Regulation of Seed Size in Plants. Int J Mol Sci 2023; 24:10666. [PMID: 37445843 DOI: 10.3390/ijms241310666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are an important way of improving the ultimate "sink strength" of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, and phytohormone regulatory pathways including the auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and microRNA (miRNA) regulatory pathways. This article summarizes the seed size regulatory network and prospective ways of improving yield. We expect that it will provide a valuable reference to researchers in related fields.
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Affiliation(s)
- Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xueman Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaofeng Pai
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yahui Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
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16
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Tang H, Dong H, Guo X, Cheng M, Li M, Chen Q, Yuan Z, Pu Z, Wang J. Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1173861. [PMID: 37342127 PMCID: PMC10277647 DOI: 10.3389/fpls.2023.1173861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/03/2023] [Indexed: 06/22/2023]
Abstract
Wheat is a significant source of protein and starch worldwide. The defective kernel (Dek) mutant AK-3537, displaying a large hollow area in the endosperm and shrunken grain, was obtained through ethyl methane sulfonate (EMS) treatment of the wheat cultivar Aikang 58 (AK58). The mode of inheritance of the AK-3537 grain Dek phenotype was determined to be recessive with a specific statistical significance level. We used bulked segregant RNA-seq (BSR-seq), BSA-based exome capture sequencing (BSE-seq), and the ΔSNP-index algorithm to identify candidate regions for the grain Dek phenotype. Two major candidate regions, DCR1 (Dek candidate region 1) and DCR2, were identified on chromosome 7A between 279.98 and 287.93 Mb and 565.34 and 568.59 Mb, respectively. Based on transcriptome analysis and previous reports, we designed KASP genotyping assays based on SNP variations in the candidate regions and speculated that the candidate gene is TraesCS7A03G0625900 (HMGS-7A), which encodes a 3-hydroxy-3-methylglutaryl-CoA synthase. One SNP variation located at position 1,049 in the coding sequence (G>A) causes an amino acid change from Gly to Asp. The research suggests that functional changes in HMGS-7A may affect the expression of key enzyme genes involved in wheat starch syntheses, such as GBSSII and SSIIIa.
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Affiliation(s)
- Hao Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiaojiang Guo
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Mengping Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Maolian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qian Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhongwei Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
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17
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Liu H, Si X, Wang Z, Cao L, Gao L, Zhou X, Wang W, Wang K, Jiao C, Zhuang L, Liu Y, Hou J, Li T, Hao C, Guo W, Liu J, Zhang X. TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar-ABA interaction. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1159-1175. [PMID: 36752567 DOI: 10.1111/pbi.14025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 05/27/2023]
Abstract
Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) and crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection of the two traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat grain TKW was detected on chromosome 7AS flanked by a simple sequence repeat marker of Wmc17 in Chinese wheat 262 mini-core collection by genome-wide association study. Combined with the bulked segregant RNA-sequencing (BSR-seq) analysis of an F2 genetic segregation population with extremely different TKW traits, a candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, was identified. This gene was specifically expressed in developing grains and strongly influenced grain filling and size. Overexpression (OE) of TaTPP-7A in wheat enhanced grain TKW and wheat yield greatly. Detailed analysis revealed that OE of TaTPP-7A significantly increased the expression levels of starch synthesis- and senescence-related genes involved in abscisic acid (ABA) and ethylene pathways. Moreover, most of the sucrose metabolism and starch regulation-related genes were potentially regulated by SnRK1. In addition, TaTPP-7A is a crucial domestication- and breeding-targeted gene and it feedback regulates sucrose lysis, flux, and utilization in the grain endosperm mainly through the T6P-SnRK1 pathway and sugar-ABA interaction. Thus, we confirmed the T6P signalling pathway as the central regulatory system for sucrose allocation and source-sink interactions in wheat grains and propose that the trehalose pathway components have great potential to increase yields in cereal crops.
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Affiliation(s)
- Hongxia Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xuemei Si
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Liangjing Cao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xiaolong Zhou
- Beijing Biomics Biotechnology Company limited, Beijing, China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Ke Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengzhi Jiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lei Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yunchuan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jian Hou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Tian Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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18
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Liu Y, Shen K, Yin C, Xu X, Yu X, Ye B, Sun Z, Dong J, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Wang Z, Wu H, Liu D, Zhang L, Shen L, Hao Y, Lu F, Guo Z. Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits. Genome Biol 2023; 24:114. [PMID: 37173729 PMCID: PMC10176713 DOI: 10.1186/s13059-023-02932-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 04/10/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits. RESULTS Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions. CONCLUSION This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Xiaowan Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiayu Dong
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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19
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Alex Mason G. Wheat AUXIN RESPONSE FACTOR 15 delays senescence through interaction at the TaNAM1 locus. PLANT PHYSIOLOGY 2023; 192:25-27. [PMID: 36788762 PMCID: PMC10152649 DOI: 10.1093/plphys/kiad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 05/03/2023]
Affiliation(s)
- G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
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20
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Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
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Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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21
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Zhao J, Li X, Qiao L, Zheng X, Wu B, Guo M, Feng M, Qi Z, Yang W, Zheng J. Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:37. [PMID: 36897407 DOI: 10.1007/s00122-023-04283-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Jiajia Zhao
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaohua Li
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Meijun Guo
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Jinzhong University, Jinzhong, China
| | - Meichen Feng
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wude Yang
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China.
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China.
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22
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Mason GA. Wheat AUXIN RESPONSE FACTOR 15 delays senescence through competitive interaction at the TaNAM1 locus. PLANT PHYSIOLOGY 2023; 191:834-836. [PMID: 36454670 PMCID: PMC9922424 DOI: 10.1093/plphys/kiac535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Affiliation(s)
- G Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
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23
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Genome-wide evolutionary analysis of AUX/IAA gene family in wheat identifies a novel gene TaIAA15-1A regulating flowering time by interacting with ARF. Int J Biol Macromol 2023; 227:285-296. [PMID: 36549029 DOI: 10.1016/j.ijbiomac.2022.12.175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Flowering time is a critical agronomic trait that has strong effects on crop yields. Auxin signaling pathway plays an important role in various development processes, such as flowering, grain development. However, no Aux/IAA gene had been reported to have functions involving in wheat flowering time. Here, we systematically performed genome-wide identification, classification, domain distribution, exon-intron structure, chromosome locations and global expression pattern of Aux/IAA gene family in 14 plant genomes (including Triticum aestivum). A phylogenetic model was proposed to infer the Aux/IAA evolutionary history involving in a central exon-intron structure "2121" during evolution. Overexpression of TaIAA15-1A caused an early flowering time in Brachypodium. RNA-seq analysis showed that TaIAA15-1A overexpression alters various pathways including phytohormone signaling pathway, flowering-related pathway, and polyamine biosynthesis pathway. Screening of auxin response factor (ARF) genes identified BdARF16 that interacted with TaIAA15-1A. Exogenous polyamine (spermidine and spermine) treatments promoted early flowering and (putrescine and DCHA) delayed flowering time of WT plants. Our finding will provide insights on mechanisms of Aux/IAAs gene family and TaIAA15-1A, illustrating the potential during crop improvement programs.
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24
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Zhao J, Sun L, Gao H, Hu M, Mu L, Cheng X, Wang J, Zhao Y, Li Q, Wang P, Li H, Zhang Y. Genome-wide association study of yield-related traits in common wheat ( Triticum aestivum L.) under normal and drought treatment conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1098560. [PMID: 36684753 PMCID: PMC9846334 DOI: 10.3389/fpls.2022.1098560] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.
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Affiliation(s)
- Jie Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Lijing Sun
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mengyun Hu
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Liming Mu
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Xiaohu Cheng
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Jianbing Wang
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Yun Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qianying Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Peinan Wang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hui Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yingjun Zhang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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25
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Zhang Y, Miao H, Wang C, Zhang J, Zhang X, Shi X, Xie S, Li T, Deng P, Wang C, Chen C, Zhang H, Ji W. Genetic identification of the pleiotropic gene Tasg-D1/2 affecting wheat grain shape by regulating brassinolide metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111392. [PMID: 35868348 DOI: 10.1016/j.plantsci.2022.111392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Improving yield potential is a major goal of wheat breeding that depends on identifying key genetic loci. In this study, two residual heterozygous line RHL351- and RHL78-derived populations were employed for genetic linkage map construction and QTL detection. Two genetic populations indicated a robust grain-size QTL between Marker6 and Marker10. It covered a 95.54-99.38 Mb physical interval and was named Qpleio.nwafu.3D, containing the candidate gene Tasg (TraesCS3D02G137200). Intriguingly, RNA-seq analysis and sequencing revealed two different allelic variants in Tasg, named Tasg-D1 (G>A) and Tasg-D2 (C>G), respectively. Although the relationship between Tasg-D1 and grain size had been demonstrated previously, here we provided the first genetic evidence that C/G allelic variation in Tasg-D2 was associated with grain shape and size through a newly developed dCAPS marker. In addition, transcriptome comparison indicated that Tasg-D1/2 might primarily contribute to significant expression differences in brassinolide (BR) metabolism-related genes rather than those related to BR responses in developing grains and spikes. Our study provided new evidence and a breeder-friendly dCAPS marker for improving grain size through the selection of Tasg, as well as a basis to understand Tasg function in the future.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiangyu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
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Zhang L, Chen L, Pang S, Zheng Q, Quan S, Liu Y, Xu T, Liu Y, Qi M. Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:849048. [PMID: 35310671 PMCID: PMC8931701 DOI: 10.3389/fpls.2022.849048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/02/2022] [Indexed: 05/26/2023]
Abstract
APETALA2/ethylene responsive factors (AP2/ERF) are unique regulators in the plant kingdom and are involved in the whole life activity processes such as development, ripening, and biotic and abiotic stresses. In tomato (Solanum lycopersicum), there are 140 AP2/ERF genes; however, their functionality remains poorly understood. In this work, the 14th and 19th amino acid differences in the AP2 domain were used to distinguish DREB and ERF subfamily members. Even when the AP2 domain of 68 ERF proteins from 20 plant species and motifs in tomato DREB and ERF proteins were compared, the binding ability of DREB and ERF proteins with DRE/CRT and/or GCC boxes remained unknown. During fruit development and ripening, the expressions of 13 DREB and 19 ERF subfamily genes showed some regular changes, and the promoters of most genes had ARF, DRE/CRT, and/or GCC boxes. This suggests that these genes directly or indirectly respond to IAA and/or ethylene (ET) signals during fruit development and ripening. Moreover, some of these may feedback regulate IAA or ET biosynthesis. In addition, 16 EAR motif-containing ERF genes in tomato were expressed in many organs and their total transcripts per million (TPM) values exceeded those of other ERF genes in most organs. To determine whether the EAR motif in EAR motif-containing ERF proteins has repression function, their EAR motifs were retained or deleted in a yeast one-hybrid (YIH) assay. The results indicate that most of EAR motif-containing ERF proteins lost repression activity after deleting the EAR motif. Moreover, some of these were expressed during ripening. Thus, these EAR motif-containing ERF proteins play vital roles in balancing the regulatory functions of other ERF proteins by completing the DRE/CRT and/or GCC box sites of target genes to ensure normal growth and development in tomato.
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Affiliation(s)
- Li Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - LiJing Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - ShengQun Pang
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - Qun Zheng
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - ShaoWen Quan
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - YuFeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - YuDong Liu
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - MingFang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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27
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Guan J, Wang Z, Liu S, Kong X, Wang F, Sun G, Geng S, Mao L, Zhou P, Li A. Transcriptome Analysis of Developing Wheat Grains at Rapid Expanding Phase Reveals Dynamic Gene Expression Patterns. BIOLOGY 2022; 11:biology11020281. [PMID: 35205147 PMCID: PMC8869726 DOI: 10.3390/biology11020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/30/2022] [Accepted: 02/06/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Understanding the regulatory mechanism underlying grain development is essential for wheat improvement. The early grain expanding phase boasts critical biological events like embryogenesis and initiation of grain filling. RNA sequencing analysis of this developmental stage revealed dynamic expressions of genes related to cell division, starch biosynthesis, and hormone biosynthesis. An unbalanced expression among triads may play critical roles as shown by multiple enriched metabolic pathways. Our work demonstrated complex regulation mechanisms in early grain development and provided useful information for future wheat improvement. Abstract Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. The wheat grain expanding phase is the early process involving the rapid morphological changes and initiation of grain filling. However, little is known about the molecular basis of grain development at this stage. Here, we provide a time-series transcriptome profile of developing wheat grain at 0, 2, 4, 6, 8, and 10 days after pollination of the wheat landrace Chinese Spring. A total of 26,892 differentially expressed genes, including 1468 transcription factors, were found between adjacent time points. Co-expression cluster analysis and Gene Ontology enrichment revealed dynamic expressions of cell division and starch biosynthesis related structural genes and transcription factors. Moreover, diverse, differential and drastically varied expression trends of the key genes related to hormone metabolism were identified. Furthermore, ~30% of triads showed unbalanced expression patterns enriching for genes in multiple pivotal metabolic pathways. Hormone metabolism related genes, such as YUC10 (YUCCA flavin-containing monooxygenase 10), AOS2 (allene oxide synthase 2), CYP90D2 (cytochrome P450 90D2), and CKX1 (cytokinin dehydrogenase 1), were dominantly contributed by A or D homoeologs of the triads. Our study provided a systematic picture of transcriptional regulation of wheat grains at the early grain expanding phase which should deepen our understanding of wheat grain development and help in wheat yield improvement.
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Affiliation(s)
- Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Shaoshuai Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Xingchen Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Sino-Agro Research Station for Salt Tolerant Crops, Yellow River Delta, Kenli District, Dongying 257500, China
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Sino-Agro Research Station for Salt Tolerant Crops, Yellow River Delta, Kenli District, Dongying 257500, China
- Correspondence: (L.M.); (P.Z.); (A.L.)
| | - Peng Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Correspondence: (L.M.); (P.Z.); (A.L.)
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.G.); (Z.W.); (S.L.); (X.K.); (F.W.); (G.S.); (S.G.)
- Correspondence: (L.M.); (P.Z.); (A.L.)
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