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Lorenzo CD, Blasco-Escámez D, Beauchet A, Wytynck P, Sanches M, Garcia Del Campo JR, Inzé D, Nelissen H. Maize mutant screens: from classical methods to new CRISPR-based approaches. THE NEW PHYTOLOGIST 2024. [PMID: 39212458 DOI: 10.1111/nph.20084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site-directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR-Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.
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Affiliation(s)
- Christian Damian Lorenzo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - David Blasco-Escámez
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Arthur Beauchet
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Pieter Wytynck
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Matilde Sanches
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Jose Rodrigo Garcia Del Campo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
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Kumar P, Gill HS, Singh M, Kaur K, Koupal D, Talukder S, Bernardo A, Amand PS, Bai G, Sehgal SK. Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:205. [PMID: 39141073 PMCID: PMC11324803 DOI: 10.1007/s00122-024-04701-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/27/2024] [Indexed: 08/15/2024]
Abstract
KEY MESSAGE Multi-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle. Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length-width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9-13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.
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Affiliation(s)
- Pradeep Kumar
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Mandeep Singh
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Karanjot Kaur
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Dante Koupal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Shyamal Talukder
- Department of Soil and Crop Sciences, Texas A&M University, Texas A&M AgriLife Research Center, Beaumont, TX, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA.
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Liu L, Zhao L, Liu Y, Zhu Y, Chen S, Yang L, Li X, Chen W, Xu Z, Xu P, Wang H, Yu D. Transcription factor OsWRKY72 controls rice leaf angle by regulating LAZY1-mediated shoot gravitropism. PLANT PHYSIOLOGY 2024; 195:1586-1600. [PMID: 38478430 DOI: 10.1093/plphys/kiae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/13/2024] [Indexed: 06/02/2024]
Abstract
Leaf angle is a major trait of ideal architecture, which is considered to influence rice (Oryza sativa) cultivation and grain yield. Although a few mutants with altered rice leaf inclination angles have been reported, the underlying molecular mechanism remains unclear. In this study, we showed that a WRKY transcription factor gene, OsWRKY72, was highly expressed in the leaf sheath and lamina joint. Phenotypic analyses showed that oswrky72 mutants had smaller leaf angles than the wild type, while OsWRKY72 overexpression lines exhibited an increased leaf angle. This observation suggests that OsWRKY72 functions as a positive regulator, promoting the enlargement of the leaf angle. Our bioinformatics analysis identified LAZY1 as the downstream gene of OsWRKY72. Electrophoretic mobility shift assays and dual-luciferase analysis revealed that OsWRKY72 directly inhibited LAZY1 by binding to its promoter. Moreover, knocking out OsWRKY72 enhanced shoot gravitropism, which contrasted with the phenotype of lazy1 plants. These results imply that OsWRKY72 regulates the leaf angle through gravitropism by reducing the expression of LAZY1. In addition, OsWRKY72 could directly regulate the expression of other leaf angle-related genes such as FLOWERING LOCUS T-LIKE 12 (OsFTL12) and WALL-ASSOCIATED KINASE 11 (OsWAK11). Our study indicates that OsWRKY72 contributes positively to the expansion of the leaf angle by interfering with shoot gravitropism in rice.
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Affiliation(s)
- Lei Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lirong Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunwei Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Yi Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Shidie Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Lu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Xia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Wanqin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Zhiyu Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
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4
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Jafari F, Wang B, Wang H, Zou J. Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:849-864. [PMID: 38131117 DOI: 10.1111/jipb.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Maize is a major staple crop widely used as food, animal feed, and raw materials in industrial production. High-density planting is a major factor contributing to the continuous increase of maize yield. However, high planting density usually triggers a shade avoidance response and causes increased plant height and ear height, resulting in lodging and yield loss. Reduced plant height and ear height, more erect leaf angle, reduced tassel branch number, earlier flowering, and strong root system architecture are five key morphological traits required for maize adaption to high-density planting. In this review, we summarize recent advances in deciphering the genetic and molecular mechanisms of maize involved in response to high-density planting. We also discuss some strategies for breeding advanced maize cultivars with superior performance under high-density planting conditions.
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Affiliation(s)
- Fereshteh Jafari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Junjie Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
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Dzievit MJ, Li X, Yu J. Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize. THE PLANT GENOME 2024; 17:e20423. [PMID: 38123363 DOI: 10.1002/tpg2.20423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/22/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Optimizing leaf angle and other canopy architecture traits has helped modern maize (Zea mays L.) become adapted to higher planting densities over the last 60 years. Traditional investigations into genetic control of leaf angle have focused on one leaf or the average of multiple leaves; as a result, our understanding of genetic control across multiple canopy levels is still limited. To address this, genetic mapping across four canopy levels was conducted in the present study to investigate the genetic control of leaf angle across the canopy. We developed two populations of doubled haploid lines derived from three inbreds with distinct leaf angle phenotypes. These populations were genotyped with genotyping-by-sequencing and phenotyped for leaf angle at four different canopy levels over multiple years. To understand how leaf angle changes across the canopy, the four measurements were used to derive three additional traits. Composite interval mapping was conducted with the leaf-specific measurements and the derived traits. A set of 59 quantitative trait loci (QTLs) were uncovered for seven traits, and two genomic regions were consistently detected across multiple canopy levels. Additionally, seven genomic regions were found to contain consistent QTLs with either relatively stable or dynamic effects at different canopy levels. Prioritizing the selection of QTLs with dynamic effects across the canopy will aid breeders in selecting maize hybrids with the ideal canopy architecture that continues to maximize yield on a per area basis under increasing planting densities.
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Affiliation(s)
| | - Xianran Li
- USDA-ARS, Wheat Health, Genetics, and Quality Research, Pullman, Washington, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
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Dougherty L, Borejsza-Wysocka E, Miaule A, Wang P, Zheng D, Jansen M, Brown S, Piñeros M, Dardick C, Xu K. A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus. PLANT PHYSIOLOGY 2023; 193:1142-1160. [PMID: 37394917 DOI: 10.1093/plphys/kiad373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Ewa Borejsza-Wysocka
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Alexandre Miaule
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
| | - Ping Wang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Desen Zheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Michael Jansen
- United States Department of Agriculture-Agricultural Research Service, Systematic Entomology Laboratory, Electron and Confocal Microscopy Unit, Beltsville, MD 20705, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Miguel Piñeros
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Christopher Dardick
- United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
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Clark CB, Ma J. The genetic basis of shoot architecture in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:55. [PMID: 37351274 PMCID: PMC10281916 DOI: 10.1007/s11032-023-01391-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2023] [Indexed: 06/24/2023]
Abstract
Shoot architecture refers to the three-dimensional body plan of the above ground organs of the plant. The patterning of this body plan results from the tight genetic control of the size and maintenance of meristems, the initiation of axillary growth, and the timing of developmental phase transition. Variation in shoot architecture can result in dramatic differences in plant productivity and/or grain yield due to their effects on light interception, photosynthetic efficiency, response to agronomic inputs, and environmental adaptation. The fine-tuning of shoot architecture has consequently been of great interest to plant breeders, driving the need for deeper understanding of the genes and molecular mechanisms governing these traits. In soybean, the world's most important oil and protein crop, major components of shoot architecture include stem growth habit, plant height, branch angle, branch number, leaf petiole angle, and the size and shape of leaves. Key genes underlying some of these traits have been identified to integrate hormonal, developmental, and environmental signals modulating the growth and orientation of shoot organs. Here we summarize the current knowledge and recent advances in the understanding of the genetic control of these important architectural traits in soybean.
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Affiliation(s)
- Chancelor B. Clark
- Department of Agronomy, Purdue University, 915 W Mitch Daniels Blvd, West Lafayette, 47907 IN USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, 915 W Mitch Daniels Blvd, West Lafayette, 47907 IN USA
- Center for Plant Biology, Purdue University, West Lafayette, IN USA
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Basu U, Parida SK. Restructuring plant types for developing tailor-made crops. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1106-1122. [PMID: 34260135 PMCID: PMC10214764 DOI: 10.1111/pbi.13666] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
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Affiliation(s)
- Udita Basu
- Genomics‐Assisted Breeding and Crop Improvement LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
| | - Swarup K. Parida
- Genomics‐Assisted Breeding and Crop Improvement LaboratoryNational Institute of Plant Genome Research (NIPGR)New DelhiIndia
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9
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Wang S, Li H, Dong Z, Wang C, Wei X, Long Y, Wan X. Genetic structure and molecular mechanism underlying the stalk lodging traits in maize ( Zea mays L.). Comput Struct Biotechnol J 2022; 21:485-494. [PMID: 36618981 PMCID: PMC9803694 DOI: 10.1016/j.csbj.2022.12.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/03/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Stalk lodging seriously affects yield and quality of crops, and it can be caused by several factors, such as environments, developmental stages, and internal chemical components of plant stalks. Breeding of stalk lodging-resistant varieties is thus an important task for maize breeders. To better understand the genetic basis underlying stalk lodging resistance, several methods such as quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) have been used to mine potential gene resources. Based on different types of genetic populations and mapping methods, many significant loci associated with stalk lodging resistance have been identified so far. However, few work has been performed to compare and integrate these reported genetic loci. In this study, we first collected hundreds of QTLs and quantitative trait nucleotides (QTNs) related to stalk lodging traits in maize. Then we mapped and integrated the QTLs and QTNs in maize genome to identify overlapped hotspot regions. Based on the genomic confidence intervals harboring these overlapped hotspot regions, we predicted candidate genes related to stalk lodging traits. Meanwhile, we mapped reported genes to these hotspot regions. Finally, we constructed molecular regulatory networks underlying stalk lodging resistance in maize. Collectively, this study provides not only useful genetic loci for deeply exploring molecular mechanisms of stalk lodging resistance traits, but also potential candidate genes and targeted strategies for improving stalk lodging resistance to increase crop yields in future.
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Affiliation(s)
- Shuai Wang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Huangai Li
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, 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, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Zhenying Dong
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, 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, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Cheng Wang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, 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, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, 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, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, School of Chemistry and Biological Engineering, 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, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
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Duan H, Li J, Sun Y, Xiong X, Sun L, Li W, Gao J, Li N, Zhang J, Cui J, Fu Z, Zhang X, Tang J. Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis. Front Genet 2022; 13:1004211. [PMID: 36437932 PMCID: PMC9691904 DOI: 10.3389/fgene.2022.1004211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10–6), and individual QTL explained 4.80%–24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wenlong Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Junli Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiangkuan Cui
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
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11
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Wang X, Wang X, Sun S, Tu X, Lin K, Qin L, Wang X, Li G, Zhong S, Li P. Characterization of regulatory modules controlling leaf angle in maize. PLANT PHYSIOLOGY 2022; 190:500-515. [PMID: 35758633 PMCID: PMC9434308 DOI: 10.1093/plphys/kiac308] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/01/2022] [Indexed: 05/12/2023]
Abstract
Leaf angle is an important agronomic trait determining maize (Zea mays) planting density and light penetration into the canopy and contributes to the yield gain in modern maize hybrids. However, little is known about the molecular mechanisms underlying leaf angle beyond the ZmLG1 (liguleless1) and ZmLG2 (Liguleless2) genes. In this study, we found that the transcription factor (TF) ZmBEH1 (BZR1/BES1 homolog gene 1) is targeted by ZmLG2 and regulates leaf angle formation by influencing sclerenchyma cell layers on the adaxial side. ZmBEH1 interacted with the TF ZmBZR1 (Brassinazole Resistant 1), whose gene expression was also directly activated by ZmLG2. Both ZmBEH1 and ZmBZR1 are bound to the promoter of ZmSCL28 (SCARECROW-LIKE 28), a third TF that influences leaf angle. Our study demonstrates regulatory modules controlling leaf angle and provides gene editing targets for creating optimal maize architecture suitable for dense planting.
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Affiliation(s)
| | | | - Shilei Sun
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kande Lin
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Lei Qin
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xingyun Wang
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Silin Zhong
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Pinghua Li
- Author for correspondence: (P.L.); (XL.W)
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12
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Chen X, Huang Z, Fu D, Fang J, Zhang X, Feng X, Xie J, Wu B, Luo Y, Zhu M, Qi Y. Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:841693. [PMID: 35693186 PMCID: PMC9185841 DOI: 10.3389/fpls.2022.841693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 06/09/2023]
Abstract
Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane are always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed genome-wide association studies (GWAS) with a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes with +2, +3, and +4 leaf at the seedling, elongation, and mature stages. A total of 288 significantly associated loci of sugarcane leaf angle at different developmental stages (eight phenotypes) were identified by GWAS with 4,027,298 high-quality SNP markers. Among them, one key locus and 11 loci were identified in all three stages and two stages, respectively. An InDel marker (SNP Ss6A_102766953) linked to narrow leaf angle was obtained. Overall, 4,089 genes were located in the confidence interval of significant loci, among which 3,892 genes were functionally annotated. Finally, 13 core parents and their derivatives tagged with SNPs were selected for marker-assisted selection (MAS). These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine protein kinases, etc. They are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.
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Affiliation(s)
- Xinglong Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenghui Huang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Danwen Fu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Junteng Fang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangbo Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaomin Feng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Jinfang Xie
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Bin Wu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yiji Luo
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Mingfeng Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongwen Qi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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13
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Tiller Angle Control 1 Is Essential for the Dynamic Changes in Plant Architecture in Rice. Int J Mol Sci 2022; 23:ijms23094997. [PMID: 35563391 PMCID: PMC9105778 DOI: 10.3390/ijms23094997] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
Plant architecture is dynamic as plants develop. Although many genes associated with specific plant architecture components have been identified in rice, genes related to underlying dynamic changes in plant architecture remain largely unknown. Here, we identified two highly similar recombinant inbred lines (RILs) with different plant architecture: RIL-Dynamic (D) and RIL-Compact (C). The dynamic plant architecture of RIL-D is characterized by ‘loosetiller angle (tillering stage)–compact (heading stage)–loosecurved stem (maturing stage)’ under natural long-day (NLD) conditions, and ‘loosetiller angle (tillering and heading stages)–loosetiller angle and curved stem (maturing stage)’ under natural short-day (NSD) conditions, while RIL-C exhibits a compact plant architecture both under NLD and NSD conditions throughout growth. The candidate locus was mapped to the chromosome 9 tail via the rice 8K chip assay and map-based cloning. Sequencing, complementary tests, and gene knockout tests demonstrated that Tiller Angle Control 1 (TAC1) is responsible for dynamic plant architecture in RIL-D. Moreover, TAC1 positively regulates loose plant architecture, and high TAC1 expression cannot influence the expression of tested tiller-angle-related genes. Our results reveal that TAC1 is necessary for the dynamic changes in plant architecture, which can guide improvements in plant architecture during the modern super rice breeding.
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Ji X, Gao Q, Chen F, Bai M, Zhuang Z, Peng Y. Mutant lpa1 Analysis of ZmLPA1 Gene Regulates Maize Leaf-Angle Development through the Auxin Pathway. Int J Mol Sci 2022; 23:ijms23094886. [PMID: 35563277 PMCID: PMC9102400 DOI: 10.3390/ijms23094886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Maize plant type is one of the main factors determining maize yield, and leaf angle is an important aspect of plant type. The rice Loose Plant Architecture1 (LPA1) gene and Arabidopsis AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene are related to their leaf angle. However, the homologous ZmLPA1 in maize has not been studied. In this study, the changing of leaf angle, as well as gene expression in leaves in maize mutant lpa1 and wild-type ‘B73’ under different IAA concentrations were investigated. The regulation effect of IAA on the leaf angle of lpa1 was significantly stronger than that of the wild type. Transcriptome analysis showed that different exogenous IAA treatments had a common enrichment pathway—the indole alkaloid biosynthesis pathway—and among the differentially expressed genes, four genes—AUX1, AUX/IAA, ARF and SAUR—were significantly upregulated. This study revealed the regulation mechanism of ZmLPA1 gene on maize leaf angle and provided a promising gene resource for maize breeding.
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Affiliation(s)
- Xiangzhuo Ji
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Qiaohong Gao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
| | - Fenqi Chen
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Mingxing Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Zelong Zhuang
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-138-9323-8528
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15
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Fei J, Lu J, Jiang Q, Liu Z, Yao D, Qu J, Liu S, Guan S, Ma Y. Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations. BMC PLANT BIOLOGY 2022; 22:110. [PMID: 35277127 PMCID: PMC8915473 DOI: 10.1186/s12870-022-03470-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The plant architecture traits of maize determine the yield. Plant height, ear position, leaf angle above the primary ear and internode length above the primary ear together determine the canopy structure and photosynthetic efficiency of maize and at the same time affect lodging and disease resistance. A flat and tall plant architecture confers an obvious advantage in the yield of a single plant but is not conducive to dense planting and results in high rates of lodging; thus, it has been gradually eliminated in production. Although using plants that are too compact, short and density tolerant can increase the yield per unit area to a certain extent, the photosynthetic efficiency of such plants is low, ultimately limiting yield increases. Genetic mapping is an effective method for the improvement of plant architecture to identify candidate genes for regulating plant architecture traits. RESULTS To find the best balance between the yield per plant and the yield per unit area of maize, in this study, the F2:3 pedigree population and a RIL population with the same male parent were used to identify QTL for plant height (PH), ear height (EH), leaf angle and internode length above the primary ear (LAE and ILE) in Changchun and Gongzhuling for 5 consecutive years (2016-2020). A total of 11, 13, 23 and 13 QTL were identified for PH, EH, LAE, and ILE, respectively. A pleiotropic consistent QTL for PH overlapped with that for EH on chromosome 3, with a phenotypic variation explanation rate from 6.809% to 21.96%. In addition, there were major consistent QTL for LAE and ILE, and the maximum phenotypic contribution rates were 24.226% and 30.748%, respectively. Three candidate genes were mined from the three consistent QTL regions and were involved in the gibberellin-activated signal pathway, brassinolide signal transduction pathway and auxin-activated signal pathway, respectively. Analysis of the expression levels of the three genes showed that they were actively expressed during the jointing stage of vigorous maize growth. CONCLUSIONS In this study, three consistent major QTL related to plant type traits were identified and three candidate genes were screened. These results lay a foundation for the cloning of related functional genes and marker-assisted breeding of related functional genes.
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Affiliation(s)
- Jianbo Fei
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Jianyu Lu
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Qingping Jiang
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Zhibo Liu
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Bioscience, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Qu
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China.
| | - Yiyong Ma
- College of Agriculture, Jilin Agricultural University, Changchun, 130118, China
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16
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Clark CB, Wang W, Wang Y, Fear GJ, Wen Z, Wang D, Ren B, Ma J. Identification and molecular mapping of a major quantitative trait locus underlying branch angle in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:777-784. [PMID: 34779894 DOI: 10.1007/s00122-021-03995-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/06/2021] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE A major quantitative trait locus (QTL) modulating soybean (Glycine max) branch angle was identified by linkage analysis using two bi-parental mapping populations with and without pedigree from wild soybean (Glycine soja). Soybean branch angle is a critical architectural trait that affects many other traits of agronomic importance associated with the plant's productivity and grain yield and is thus a vital consideration in soybean breeding. However, the genetic basis for modulating this important trait in soybean and many other crops remain unknown. Previously, we developed a recombinant inbred line (RIL) population derived from a cross between a domesticated soybean (Glycine max) variety, Williams 82, and a wild soybean (Glycine soja) accession, PI 479,752, and observed drastic variation in plant architecture including branch angle among individual RILs. In this study, one of the RILs possessing extremely wide branch angle (WBA) was crossed with an elite soybean cultivar (LD00-3309) possessing narrow branch angle (NBA) to produce an F2 population composed of 147 plants and F2-derived F3 families for inheritance analysis and QTL mapping. We found that branch angle is controlled by a major QTL located on chromosome 19, designated qGmBa1 and that WBA-derived from the wild soybean accession-is dominant over NBA. This locus was also detected as a major one underlying branch angle by QTL mapping using a subset of the soybean nested association mapping (SoyNAM) population composed of 140 RILs, which were derived from a cross between a landrace, PI 437169B, possessing WBA and an elite variety, IA3023, possessing NBA. Molecular markers located in the QTL region defined by both mapping populations can be used for marker-assisted selection of branch angle in soybean breeding.
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Affiliation(s)
- Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Plant Science, Jilin University, Changchun, Jilin, 130062, China
| | - Gabriel J Fear
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
- Syngenta, Research Triangle Park, Durham, NC, 27709, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Bo Ren
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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17
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Cao Y, Zhong Z, Wang H, Shen R. Leaf angle: a target of genetic improvement in cereal crops tailored for high-density planting. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:426-436. [PMID: 35075761 PMCID: PMC8882799 DOI: 10.1111/pbi.13780] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 05/12/2023]
Abstract
High-density planting is an effective measure for increasing crop yield per unit land area. Leaf angle (LA) is a key trait of plant architecture and a target for genetic improvement of crops. Upright leaves allow better light capture in canopy under high-density planting, thus enhancing photosynthesis efficiency, ventilation and stress resistance, and ultimately higher grain yield. Here, we summarized the latest progress on the cellular and molecular mechanisms regulating LA formation in rice and maize. We suggest several standing out questions for future studies and then propose some promising strategies to manipulate LA for breeding of cereal crops tailored for high-density planting.
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Affiliation(s)
- Yingying Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Zhuojun Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
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18
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Zhi X, Tao Y, Jordan D, Borrell A, Hunt C, Cruickshank A, Potgieter A, Wu A, Hammer G, George-Jaeggli B, Mace E. Genetic control of leaf angle in sorghum and its effect on light interception. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:801-816. [PMID: 34698817 DOI: 10.1093/jxb/erab467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Developing sorghum genotypes adapted to different light environments requires understanding of a plant's ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.
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Affiliation(s)
- Xiaoyu Zhi
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Andrew Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Alan Cruickshank
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Andries Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD, Australia
| | - Alex Wu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
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Liu S, Magne K, Daniel S, Sibout R, Ratet P. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development. PLANT PHYSIOLOGY 2022; 188:363-381. [PMID: 34662405 PMCID: PMC8774750 DOI: 10.1093/plphys/kiab456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2-4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats - CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR-Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Kévin Magne
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Sylviane Daniel
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Richard Sibout
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
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20
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Tross MC, Gaillard M, Zwiener M, Miao C, Grove RJ, Li B, Benes B, Schnable JC. 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. PeerJ 2022; 9:e12628. [PMID: 35036135 PMCID: PMC8710048 DOI: 10.7717/peerj.12628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/21/2021] [Indexed: 12/22/2022] Open
Abstract
Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
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Affiliation(s)
- Michael C Tross
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States of America.,Complex Biosystems Graduate Program, University of Nebraska - Lincoln, Lincoln, NE, United States of America
| | - Mathieu Gaillard
- Computer Science, Purdue University, West Lafayette, IN, United States of America
| | - Mackenzie Zwiener
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States of America
| | - Chenyong Miao
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States of America
| | - Ryleigh J Grove
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States of America.,Lincoln North Star High School, Lincoln, NE, United States of America
| | - Bosheng Li
- Computer Science, Purdue University, West Lafayette, IN, United States of America
| | - Bedrich Benes
- Computer Science, Purdue University, West Lafayette, IN, United States of America.,Department of Computer Graphics Technology, Purdue University, West Lafayette, IN, United States of America
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States of America.,Complex Biosystems Graduate Program, University of Nebraska - Lincoln, Lincoln, NE, United States of America
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21
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Wang S, Zhang F, Jiang P, Zhang H, Zheng H, Chen R, Xu Z, Ikram AU, Li E, Xu Z, Fan J, Su Y, Ding Y. SDG128 is involved in maize leaf inclination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1597-1608. [PMID: 34612535 DOI: 10.1111/tpj.15527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Maize leaf angle (LA) is a complex quantitative trait that is controlled by developmental signals, hormones, and environmental factors. However, the connection between histone methylation and LAs in maize remains unclear. Here, we reported that SET domain protein 128 (SDG128) is involved in leaf inclination in maize. Knockdown of SDG128 using an RNA interference approach resulted in an expanded architecture, less large vascular bundles, more small vascular bundles, and larger spacing of large vascular bundles in the auricles. SDG128 interacts with ZmGID2 both in vitro and in vivo. Knockdown of ZmGID2 also showed a larger LA with less large vascular bundles and larger spacing of vascular bundles. In addition, the transcription level of cell wall expansion family genes ZmEXPA1, ZmEXPB2, and GRMZM2G005887; transcriptional factor genes Lg1, ZmTAC1, and ZmCLA4; and auxin pathway genes ZmYUCCA7, ZmYUCCA8, and ZmARF22 was reduced in SDG128 and ZmGID2 knockdown plants. SDG128 directly targets ZmEXPA1, ZmEXPB2, LG1, and ZmTAC1 and is required for H3K4me3 deposition at these genes. Together, the results of the present study suggest that SDG128 and ZmGID2 are involved in the maize leaf inclination.
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Affiliation(s)
- Shiliang Wang
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Fei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Pengfei Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Heng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Han Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Rihong Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Zuntao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Aziz Ul Ikram
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Enze Li
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Zaoshi Xu
- Anhui Forestry High-Tech Development Center, Hefei, Anhui, 230041, China
| | - Jun Fan
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yanhua Su
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Yong Ding
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular Cell Biophysics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
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22
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Geldhof B, Pattyn J, Eyland D, Carpentier S, Van de Poel B. A digital sensor to measure real-time leaf movements and detect abiotic stress in plants. PLANT PHYSIOLOGY 2021; 187:1131-1148. [PMID: 34618089 PMCID: PMC8566216 DOI: 10.1093/plphys/kiab407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/02/2021] [Indexed: 05/31/2023]
Abstract
Plant and plant organ movements are the result of a complex integration of endogenous growth and developmental responses, partially controlled by the circadian clock, and external environmental cues. Monitoring of plant motion is typically done by image-based phenotyping techniques with the aid of computer vision algorithms. Here we present a method to measure leaf movements using a digital inertial measurement unit (IMU) sensor. The lightweight sensor is easily attachable to a leaf or plant organ and records angular traits in real-time for two dimensions (pitch and roll) with high resolution (measured sensor oscillations of 0.36 ± 0.53° for pitch and 0.50 ± 0.65° for roll). We were able to record simple movements such as petiole bending, as well as complex lamina motions, in several crops, ranging from tomato to banana. We also assessed growth responses in terms of lettuce rosette expansion and maize seedling stem movements. The IMU sensors are capable of detecting small changes of nutations (i.e. bending movements) in leaves of different ages and in different plant species. In addition, the sensor system can also monitor stress-induced leaf movements. We observed that unfavorable environmental conditions evoke certain leaf movements, such as drastic epinastic responses, as well as subtle fading of the amplitude of nutations. In summary, the presented digital sensor system enables continuous detection of a variety of leaf motions with high precision, and is a low-cost tool in the field of plant phenotyping, with potential applications in early stress detection.
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Affiliation(s)
- Batist Geldhof
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - Jolien Pattyn
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - David Eyland
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
| | - Sebastien Carpentier
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
- Bioversity International, Leuven, 3001, Belgium
| | - Bram Van de Poel
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
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23
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Peng B, Zhao X, Wang Y, Li C, Li Y, Zhang D, Shi Y, Song Y, Wang L, Li Y, Wang T. Genome-wide association studies of leaf angle in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:50. [PMID: 37309541 PMCID: PMC10236034 DOI: 10.1007/s11032-021-01241-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/04/2021] [Indexed: 06/14/2023]
Abstract
Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across 3 consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q + K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54-10.44% of phenotypic variation were significantly (P < 0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned into 43 QTLs for leaf angle. Seven major QTLs with R2 > 8% stably detected in at least 2 years, and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01241-0.
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Affiliation(s)
- Bo Peng
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Xiaolei Zhao
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Yi Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Wang
- Handan Academy of Agricultural Sciences, Handan, 056001 Hebei China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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24
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Jaikumar NS, Stutz SS, Fernandes SB, Leakey ADB, Bernacchi CJ, Brown PJ, Long SP. Can improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation in Sorghum bicolor. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4965-4980. [PMID: 33914063 PMCID: PMC8219039 DOI: 10.1093/jxb/erab176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/28/2021] [Indexed: 05/29/2023]
Abstract
Previous studies have found that maximum quantum yield of CO2 assimilation (Φ CO2,max,app) declines in lower canopies of maize and miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear whether the maladaptive shade response is a general property of this C4 grass tribe, the Andropogoneae. We explored the generality of this maladaptation by testing the hypothesis that erect leaf forms (erectophiles), which allow more light into the lower canopy, suffer less of a decline in photosynthetic efficiency than drooping leaf (planophile) forms. On average, Φ CO2,max,app declined 27% in lower canopy leaves across 35 accessions, but the decline was over twice as great in planophiles than in erectophiles. The loss of photosynthetic efficiency involved a decoupling between electron transport and assimilation. This was not associated with increased bundle sheath leakage, based on 13C measurements. In both planophiles and erectophiles, shaded leaves had greater leaf absorptivity and lower activities of key C4 enzymes than sun leaves. The erectophile form is considered more productive because it allows a more effective distribution of light through the canopy to support photosynthesis. We show that in sorghum, it provides a second benefit, maintenance of higher Φ CO2,max,app to support efficient use of that light resource.
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Affiliation(s)
- Nikhil S Jaikumar
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Samantha S Stutz
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carl J Bernacchi
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL 61801, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Stephen P Long
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 4YQ, UK
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25
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Imran. The bioavailability of phosphorus in composite vs. hybrid maize differ with phosphorus and boron fertilization. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.1920588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Imran
- Department of Agronomy, The University of Agriculture, Peshawar, Pakistan
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26
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Dou D, Han S, Cao L, Ku L, Liu H, Su H, Ren Z, Zhang D, Zeng H, Dong Y, Liu Z, Zhu F, Zhao Q, Xie J, Liu Y, Cheng H, Chen Y. CLA4 regulates leaf angle through multiple hormone signaling pathways in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1782-1794. [PMID: 33270106 DOI: 10.1093/jxb/eraa565] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Leaf angle is an important agronomic trait in cereals and shares a close relationship with crop architecture and grain yield. Although it has been previously reported that ZmCLA4 can influence leaf angle, the underlying mechanism remains unclear. In this study, we used the Gal4-LexA/UAS system and transactivation analysis to demonstrate in maize (Zea mays) that ZmCLA4 is a transcriptional repressor that regulates leaf angle. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmCLA4 mainly binds to promoters containing the EAR motif (CACCGGAC) as well as to two other motifs (CCGARGS and CDTCNTC) to inhibit the expression of its target genes. Further analysis of ZmCLA4 target genes indicated that ZmCLA4 functions as a hub of multiple plant hormone signaling pathways: ZmCLA4 was found to directly bind to the promoters of multiple genes including ZmARF22 and ZmIAA26 in the auxin transport pathway, ZmBZR3 in the brassinosteroid signaling pathway, two ZmWRKY genes involved in abscisic acid metabolism, ZmCYP genes (ZmCYP75B1, ZmCYP93D1) related to jasmonic acid metabolism, and ZmABI3 involved in the ethylene response pathway. Overall, our work provides deep insights into the ZmCLA4 regulatory network in controlling leaf angle in maize.
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Affiliation(s)
- Dandan Dou
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Shengbo Han
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Liru Cao
- Henan Academy of Agricultural Science, Zhengzhou, Henan, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huafeng Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Zhenzhen Ren
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Dongling Zhang
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Haixia Zeng
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yahui Dong
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Zhixie Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Fangfang Zhu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Qiannan Zhao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Jiarong Xie
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yajing Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Haiyang Cheng
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
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27
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Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize. PLoS One 2021; 16:e0245129. [PMID: 33406127 PMCID: PMC7787474 DOI: 10.1371/journal.pone.0245129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.
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28
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Kenchanmane Raju SK, Adkins M, Enersen A, Santana de Carvalho D, Studer AJ, Ganapathysubramanian B, Schnable PS, Schnable JC. Leaf Angle eXtractor: A high-throughput image processing framework for leaf angle measurements in maize and sorghum. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11385. [PMID: 32999772 PMCID: PMC7507698 DOI: 10.1002/aps3.11385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/17/2020] [Indexed: 05/08/2023]
Abstract
PREMISE Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment. METHODS High-throughput time series image data from water-deprived maize (Zea mays subsp. mays) and sorghum (Sorghum bicolor) were obtained using battery-powered time-lapse cameras. A MATLAB-based image processing framework, Leaf Angle eXtractor (LAX), was developed to extract and quantify leaf angles from images of maize and sorghum plants under drought conditions. RESULTS Leaf angle measurements showed differences in leaf responses to drought in maize and sorghum. Tracking leaf angle changes at intervals as short as one minute enabled distinguishing leaves that showed signs of wilting under water deprivation from other leaves on the same plant that did not show wilting during the same time period. DISCUSSION Automating leaf angle measurements using LAX makes it feasible to perform large-scale experiments to evaluate, understand, and exploit the spatial and temporal variations in plant response to water limitations.
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Affiliation(s)
- Sunil K. Kenchanmane Raju
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Miles Adkins
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | - Alex Enersen
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
| | - Daniel Santana de Carvalho
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of BioinformaticsFederal University of Minas GeraisBelo HorizonteMinas GeraisBrazil
| | | | | | | | - James C. Schnable
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Department of Agronomy and HorticultureUniversity of Nebraska–LincolnLincolnNebraskaUSA
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29
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Cao Y, Zeng H, Ku L, Ren Z, Han Y, Su H, Dou D, Liu H, Dong Y, Zhu F, Li T, Zhao Q, Chen Y. ZmIBH1-1 regulates plant architecture in maize. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2943-2955. [PMID: 31990030 PMCID: PMC7260713 DOI: 10.1093/jxb/eraa052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/25/2020] [Indexed: 05/20/2023]
Abstract
Leaf angle (LA) is a critical agronomic trait in maize, with more upright leaves allowing higher planting density, leading to more efficient light capture and higher yields. A few genes responsible for variation in LA have been identified by map-based cloning. In this study, we cloned maize ZmIBH1-1, which encodes a bHLH transcription factor with both a basic binding region and a helix-loop-helix domain, and the results of qRT-PCR showed that it is a negative regulator of LA. Histological analysis indicated that changes in LA were mainly caused by differential cell wall lignification and cell elongation in the ligular region. To determine the regulatory framework of ZmIBH1-1, we conducted RNA-seq and DNA affinity purification (DAP)-seq analyses. The combined results revealed 59 ZmIBH1-1-modulated target genes with annotations, and they were mainly related to the cell wall, cell development, and hormones. Based on the data, we propose a regulatory model for the control of plant architecture by ZmIBH1-1 in maize.
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Affiliation(s)
- Yingying Cao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Haixia Zeng
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
- Correspondence: or
| | - Zhenzhen Ren
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yun Han
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Dandan Dou
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huafeng Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yahui Dong
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Fangfang Zhu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Tianyi Li
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Qiannan Zhao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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Liu J, Fernie AR, Yan J. The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement. PLANT COMMUNICATIONS 2020; 1:100010. [PMID: 33404535 PMCID: PMC7747985 DOI: 10.1016/j.xplc.2019.100010] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 05/14/2023]
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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Maldonado C, Mora F, Scapim CA, Coan M. Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4. PLoS One 2019; 14:e0212925. [PMID: 30840677 PMCID: PMC6402688 DOI: 10.1371/journal.pone.0212925] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/12/2019] [Indexed: 11/18/2022] Open
Abstract
Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.
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Affiliation(s)
- Carlos Maldonado
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Freddy Mora
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Carlos A. Scapim
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
| | - Marlon Coan
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
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Dzievit MJ, Li X, Yu J. Dissection of Leaf Angle Variation in Maize through Genetic Mapping and Meta-Analysis. THE PLANT GENOME 2019; 12:180024. [PMID: 30951086 DOI: 10.3835/plantgenome2018.05.0024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maize ( L.) hybrids have transitioned to upright leaf angles (LAs) over the last 50 yr as maize yields and planting densities increased concurrently. Genetic mapping and a meta-analysis were conducted in the present study to dissect genetic factors controlling LA variation. We developed mapping populations using inbred lines B73 (Iowa Stiff Stalk Synthetic), PHW30 (Iodent, expired plant variety protection inbred), and Mo17 (Non-Stiff Stalk) that have distinct LA architectures and represent three important heterotic groups in the United States. These populations were genotyped using genotyping-by-sequencing (GBS), and phenotyped for LA in the F and F generation. Inclusive composite interval mapping across the two generations of the mapping populations revealed 12 quantitative trait loci (QTL), and a consistent QTL on chromosome 1 explained 10 to 17% of the phenotypic variance. To gain a comprehensive understanding of natural variations underlying LA variation, these detected QTL were compared with results from 19 previous studies. In total, 495 QTL were compiled and mapped into 143 genomic bins. A meta-analysis revealed that 58 genomic bins were associated with LA variation. Thirty-three candidate genes were identified in these genomic bins. Together, these results provide evidence of QTL controlling LA variation from inbred lines representing three important heterotic groups in the United States and a useful resource for future research into the molecular variants underlying specific regions of the genome associated with LA variation.
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Mantilla-Perez MB, Salas Fernandez MG. Differential manipulation of leaf angle throughout the canopy: current status and prospects. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5699-5717. [PMID: 29126242 DOI: 10.1093/jxb/erx378] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/01/2017] [Indexed: 05/20/2023]
Abstract
Leaf angle is defined as the inclination between the midrib of the leaf blade and the vertical stem of a plant. This trait has been identified as a key component in the development of high-yielding varieties of cereal species, particularly maize, rice, wheat, and sorghum. The effect of leaf angle on light interception efficiency, photosynthetic rate, and yield has been investigated since the 1960s, yet, significant knowledge gaps remain in understanding the genetic control of this complex trait. Recent advances in physiology and modeling have proposed a plant ideotype with varying leaf angles throughout the canopy. In this context, we present historical and recent evidence of: (i) the effect of leaf angle on photosynthetic efficiency and yield; (ii) the hormonal regulation of this trait; (iii) the current knowledge on its quantitative genetic control; and (iv) the opportunity to utilize high-throughput phenotyping methods to characterize leaf angle at multiple canopy levels. We focus on research conducted on grass species of economic importance, with similar plant architecture and growth patterns. Finally, we present the challenges and strategies plant breeders will need to embrace in order to manipulate leaf angle differentially throughout the canopy and develop superior crops for food, feed, and fuel production.
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35
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QTL analysis of ear leaf traits in maize ( Zea mays L.) under different planting densities. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. FRONTIERS IN PLANT SCIENCE 2017; 8:900. [PMID: 28659934 PMCID: PMC5465304 DOI: 10.3389/fpls.2017.00900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/12/2017] [Indexed: 05/21/2023]
Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Affiliation(s)
- Alexander Bucksch
- Department of Plant Biology, University of Georgia, AthensGA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, AthensGA, United States
- Institute of Bioinformatics, University of Georgia, AthensGA, United States
| | | | - Akomian F. Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-CalaviCotonou, Benin
| | - Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, BlacksburgVA, United States
| | - Aly Baumgartner
- Department of Geosciences, Baylor University, WacoTX, United States
| | - Brad M. Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | | | - Cynthia Chang
- Division of Biology, University of Washington, BothellWA, United States
| | - Viktoirya Coneva
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | - Thomas J. DeWitt
- Department of Wildlife and Fisheries Sciences–Department of Plant Pathology and Microbiology, Texas A&M University, College StationTX, United States
| | - Alexander G. Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of SheffieldSheffield, United Kingdom
| | - Malia A. Gehan
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | | | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, United States
| | - Anjali S. Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. LouisMO, United States
| | - Samuel Leiboff
- School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Mao Li
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University ParkPA, United States
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg UniversityHeidelberg, Germany
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - R. J. Cody Markelz
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - Ciera C. Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, BerkeleyCA, United States
| | - Laura A. Miller
- Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel HillNC, United States
| | - Washington Mio
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Wojtek Palubicki
- The Sainsbury Laboratory, University of CambridgeCambridge, United Kingdom
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, JülichGermany
| | | | - Charles A. Price
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Eetu Puttonen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland
- Centre of Excellence in Laser Scanning Research, National Land Survey of FinlandMasala, Finland
| | - John B. Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Rubén Rellán-Álvarez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)Irapuato, Mexico
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, MadisonWI, United States
| | - Erin E. Sparks
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, NewarkDE, United States
| | | | - Joseph H. Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
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37
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Kong F, Zhang T, Liu J, Heng S, Shi Q, Zhang H, Wang Z, Ge L, Li P, Lu X, Li G. Regulation of Leaf Angle by Auricle Development in Maize. MOLECULAR PLANT 2017; 10:516-519. [PMID: 28216423 DOI: 10.1016/j.molp.2017.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 05/09/2023]
Affiliation(s)
- Fanying Kong
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Tingting Zhang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jisheng Liu
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China; Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, Shandong 250200, China
| | - Siqi Heng
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qingbiao Shi
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Haisen Zhang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Zeli Wang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lei Ge
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Pinghua Li
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, Shandong 250200, China
| | - Gang Li
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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38
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 28659934 DOI: 10.3389/978-2-88945-297-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Affiliation(s)
- Alexander Bucksch
- Department of Plant Biology, University of Georgia, AthensGA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, AthensGA, United States
- Institute of Bioinformatics, University of Georgia, AthensGA, United States
| | | | - Akomian F Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-CalaviCotonou, Benin
| | - Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, BlacksburgVA, United States
| | - Aly Baumgartner
- Department of Geosciences, Baylor University, WacoTX, United States
| | - Brad M Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | | | - Cynthia Chang
- Division of Biology, University of Washington, BothellWA, United States
| | - Viktoirya Coneva
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | - Thomas J DeWitt
- Department of Wildlife and Fisheries Sciences-Department of Plant Pathology and Microbiology, Texas A&M University, College StationTX, United States
| | - Alexander G Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of SheffieldSheffield, United Kingdom
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. LouisMO, United States
| | | | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, United States
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, United States
| | - Laura L Klein
- Department of Biology, Saint Louis University, St. LouisMO, United States
| | - Samuel Leiboff
- School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Mao Li
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University ParkPA, United States
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg UniversityHeidelberg, Germany
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, DavisCA, United States
| | - Ciera C Martinez
- Department of Molecular and Cell Biology, University of California, Berkeley, BerkeleyCA, United States
| | - Laura A Miller
- Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel HillNC, United States
| | - Washington Mio
- Department of Mathematics, Florida State University, TallahasseeFL, United States
| | - Wojtek Palubicki
- The Sainsbury Laboratory, University of CambridgeCambridge, United Kingdom
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, JülichGermany
| | | | - Charles A Price
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Eetu Puttonen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland
- Centre of Excellence in Laser Scanning Research, National Land Survey of FinlandMasala, Finland
| | - John B Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
| | - Rubén Rellán-Álvarez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV)Irapuato, Mexico
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin-Madison, MadisonWI, United States
| | - Erin E Sparks
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, NewarkDE, United States
| | | | - Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, KnoxvilleTN, United States
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Chen L, Li YX, Li C, Wu X, Qin W, Li X, Jiao F, Zhang X, Zhang D, Shi Y, Song Y, Li Y, Wang T. Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize. BMC PLANT BIOLOGY 2016; 16:81. [PMID: 27068015 PMCID: PMC4828868 DOI: 10.1186/s12870-016-0768-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/06/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. RESULTS QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. CONCLUSION The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.
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Affiliation(s)
- Lin Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yong-xiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xun Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Weiwei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xin Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Fuchao Jiao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
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Wang Y, Xu J, Deng D, Ding H, Bian Y, Yin Z, Wu Y, Zhou B, Zhao Y. A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.). PLANTA 2016; 243:459-71. [PMID: 26474992 DOI: 10.1007/s00425-015-2419-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 10/07/2015] [Indexed: 05/09/2023]
Abstract
The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.
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Truong SK, McCormick RF, Rooney WL, Mullet JE. Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor. Genetics 2015; 201:1229-38. [PMID: 26323882 PMCID: PMC4649647 DOI: 10.1534/genetics.115.178608] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022] Open
Abstract
The efficiency with which a plant intercepts solar radiation is determined primarily by its architecture. Understanding the genetic regulation of plant architecture and how changes in architecture affect performance can be used to improve plant productivity. Leaf inclination angle, the angle at which a leaf emerges with respect to the stem, is a feature of plant architecture that influences how a plant canopy intercepts solar radiation. Here we identify extensive genetic variation for leaf inclination angle in the crop plant Sorghum bicolor, a C4 grass species used for the production of grain, forage, and bioenergy. Multiple genetic loci that regulate leaf inclination angle were identified in recombinant inbred line populations of grain and bioenergy sorghum. Alleles of sorghum dwarf-3, a gene encoding a P-glycoprotein involved in polar auxin transport, are shown to change leaf inclination angle by up to 34° (0.59 rad). The impact of heritable variation in leaf inclination angle on light interception in sorghum canopies was assessed using functional-structural plant models and field experiments. Smaller leaf inclination angles caused solar radiation to penetrate deeper into the canopy, and the resulting redistribution of light is predicted to increase the biomass yield potential of bioenergy sorghum by at least 3%. These results show that sorghum leaf angle is a heritable trait regulated by multiple loci and that genetic variation in leaf angle can be used to modify plant architecture to improve sorghum crop performance.
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Affiliation(s)
- Sandra K Truong
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - Ryan F McCormick
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - William L Rooney
- Soil and Crop Sciences Department, Texas A&M University, College Station, Texas 77843
| | - John E Mullet
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
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Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T, Li Y. Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations. PLoS One 2015; 10:e0121624. [PMID: 25807369 PMCID: PMC4373667 DOI: 10.1371/journal.pone.0121624] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/02/2015] [Indexed: 12/22/2022] Open
Abstract
Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.
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Affiliation(s)
- Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Gong F, Wu X, Zhang H, Chen Y, Wang W. Making better maize plants for sustainable grain production in a changing climate. FRONTIERS IN PLANT SCIENCE 2015; 6:835. [PMID: 26500671 PMCID: PMC4593952 DOI: 10.3389/fpls.2015.00835] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/23/2015] [Indexed: 05/20/2023]
Abstract
Achieving grain supply security with limited arable land is a major challenge in the twenty-first century, owing to the changing climate and increasing global population. Maize plays an increasingly vital role in global grain production. As a C4 plant, maize has a high yield potential. Maize is predicted to become the number one cereal in the world by 2020. However, maize production has plateaued in many countries, and hybrid and production technologies have been fully exploited. Thus, there is an urgent need to shape maize traits and architectures for increased stress tolerance and higher yield in a changing climate. Recent achievements in genomics, proteomics, and metabolomics have provided an unprecedented opportunity to make better maize. In this paper, we discuss the current challenges and potential of maize production, particularly in China. We also highlight the need for enhancing maize tolerance to drought and heat waves, summarize the elite shoot and root traits and phenotypes, and propose an ideotype for sustainable maize production in a changing climate. This will facilitate targeted maize improvement through a conventional breeding program combined with molecular techniques.
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Affiliation(s)
| | | | | | | | - Wei Wang
- *Correspondence: Wei Wang, State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China,
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