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Abraham‐Juárez MJ, Busche M, Anderson AA, Lunde C, Winders J, Christensen SA, Hunter CT, Hake S, Brunkard JO. Liguleless narrow and narrow odd dwarf act in overlapping pathways to regulate maize development and metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:881-896. [PMID: 36164819 PMCID: PMC9827925 DOI: 10.1111/tpj.15988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Narrow odd dwarf (nod) and Liguleless narrow (Lgn) are pleiotropic maize mutants that both encode plasma membrane proteins, cause similar developmental patterning defects, and constitutively induce stress signaling pathways. To investigate how these mutants coordinate maize development and physiology, we screened for protein interactors of NOD by affinity purification. LGN was identified by this screen as a strong candidate interactor, and we confirmed the NOD-LGN molecular interaction through orthogonal experiments. We further demonstrated that LGN, a receptor-like kinase, can phosphorylate NOD in vitro, hinting that they could act in intersecting signal transduction pathways. To test this hypothesis, we generated Lgn-R;nod mutants in two backgrounds (B73 and A619), and found that these mutations enhance each other, causing more severe developmental defects than either single mutation on its own, with phenotypes including very narrow leaves, increased tillering, and failure of the main shoot. Transcriptomic and metabolomic analyses of the single and double mutants in the two genetic backgrounds revealed widespread induction of pathogen defense genes and a shift in resource allocation away from primary metabolism in favor of specialized metabolism. These effects were similar in each single mutant and heightened in the double mutant, leading us to conclude that NOD and LGN act cumulatively in overlapping signaling pathways to coordinate growth-defense tradeoffs in maize.
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Affiliation(s)
- María Jazmín Abraham‐Juárez
- Laboratorio Nacional de Genómica para la BiodiversidadUnidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato36821Mexico
| | - Michael Busche
- Laboratory of GeneticsUniversity of WisconsinMadisonWisconsin53706USA
| | - Alyssa A. Anderson
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
- Plant Gene Expression CenterUSDA Agricultural Research ServiceAlbanyCalifornia94710USA
| | - China Lunde
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
| | - Jeremy Winders
- Genomics and Bioinformatics Research Unit, US Department of Agriculture‐Agricultural Research ServiceRaleighNorth CarolinaUSA
| | | | - Charles T. Hunter
- Chemistry Research Unit, USDA Agricultural Research ServiceGainesvilleFlorida32608USA
| | - Sarah Hake
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
- Plant Gene Expression CenterUSDA Agricultural Research ServiceAlbanyCalifornia94710USA
| | - Jacob O. Brunkard
- Laboratory of GeneticsUniversity of WisconsinMadisonWisconsin53706USA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
- Plant Gene Expression CenterUSDA Agricultural Research ServiceAlbanyCalifornia94710USA
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2
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Deng Y, Liu S, Zhang Y, Tan J, Li X, Chu X, Xu B, Tian Y, Sun Y, Li B, Xu Y, Deng XW, He H, Zhang X. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. MOLECULAR PLANT 2022; 15:1268-1284. [PMID: 35746868 DOI: 10.1016/j.molp.2022.06.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.
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Affiliation(s)
- Yun Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Shoucheng Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yilin Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Jingsheng Tan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiaopeng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiao Chu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Binghua Xu
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Yao Tian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yudong Sun
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yunbi Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| | - Xingping Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China.
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Filyushin MA, Khatefov EB, Kochieva EZ, Shchennikova AV. Comparative Analysis of Transcription Factor Genes liguleless1 and liguleless1-like in Teosinte and Modern Maize Accessions. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542203005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Swentowsky KW, Bell HS, Wills DM, Dawe RK. QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis. FRONTIERS IN PLANT SCIENCE 2021; 12:707839. [PMID: 34504508 PMCID: PMC8421791 DOI: 10.3389/fpls.2021.707839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Numerous climate change threats will necessitate a shift toward more sustainable agricultural practices during the 21st century. Conversion of annual crops to perennials that are capable of regrowing over multiple yearly growth cycles could help to facilitate this transition. Perennials can capture greater amounts of carbon and access more water and soil nutrients compared to annuals. In principle it should be possible to identify genes that confer perenniality from wild relatives and transfer them into existing breeding lines to create novel perennial crops. Two major loci controlling perennial regrowth in the maize relative Zea diploperennis were previously mapped to chromosome 2 (reg1) and chromosome 7 (reg2). Here we extend this work by mapping perennial regrowth in segregating populations involving Z. diploperennis and the maize inbreds P39 and Hp301 using QTL-seq and traditional QTL mapping approaches. The results confirmed the existence of a major perennial regrowth QTL on chromosome 2 (reg1). Although we did not observe the reg2 QTL in these populations, we discovered a third QTL on chromosome 8 which we named regrowth3 (reg3). The reg3 locus exerts its strongest effect late in the regrowth cycle. Neither reg1 nor reg3 overlapped with tiller number QTL scored in the same population, suggesting specific roles in the perennial phenotype. Our data, along with prior work, indicate that perennial regrowth in maize is conferred by relatively few major QTL.
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Affiliation(s)
- Kyle W. Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Harrison S. Bell
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - David M. Wills
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - R. Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Department of Genetics, University of Georgia, Athens, GA, United States
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Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
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Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
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Pan Z, Liu M, Xiao Z, Ren X, Zhao H, Gong D, Liang K, Tan Z, Shao Y, Qiu F. ZmSMK9, a pentatricopeptide repeat protein, is involved in the cis-splicing of nad5, kernel development and plant architecture in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110205. [PMID: 31521217 DOI: 10.1016/j.plantsci.2019.110205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/08/2019] [Accepted: 07/25/2019] [Indexed: 05/23/2023]
Abstract
Maize kernel size and weight are essential contributors to its yield. So the identification of the genes controlling kernel size and weight can give us a chance to gain the yield. Here, we identified a small kernel mutant, Zea mays small kernel 9 (Zmsmk9), in maize. Cytological observation showed that the development of the endosperm and embryo was delayed in Zmsmk9 mutants at the early stages, resulting in a small kernel phenotype. Interestingly, despite substantial variation in kernel size, the germination of Zmsmk9 seeds was comparable to that of WT, and could develop into normal plants with upright leaf architecture. We cloned Zmsmk9 via map-based cloning. ZmSMK9 encodes a P-type pentatricopeptide repeat protein that targets to mitochondria, and is involved in RNA splicing in mitochondrial NADH dehydrogenase5 (nad5) intron-1 and intron-4. Consistent with the delayed development phenotype, transcriptome analysis of 12-DAP endosperm showed that starch and zeins biosynthesis related genes were dramatically down regulated in Zmsmk9, while cell cycle and cell growth related genes were dramatically increased. As a result, ZmSMK9 is a novel gene required for the splicing of nad5 intron-1 and intron-4, kernel development, and plant architecture in maize.
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Affiliation(s)
- Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Min Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ziyi Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuemei Ren
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kun Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yangqing Shao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China.
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Anderson A, St Aubin B, Abraham-Juárez MJ, Leiboff S, Shen Z, Briggs S, Brunkard JO, Hake S. The Second Site Modifier, Sympathy for the ligule, Encodes a Homolog of Arabidopsis ENHANCED DISEASE RESISTANCE4 and Rescues the Liguleless narrow Maize Mutant. THE PLANT CELL 2019; 31:1829-1844. [PMID: 31217219 PMCID: PMC6713312 DOI: 10.1105/tpc.18.00840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/14/2019] [Accepted: 06/13/2019] [Indexed: 05/19/2023]
Abstract
Liguleless narrow1 encodes a plasma membrane-localized receptor-like kinase required for normal development of maize (Zea mays) leaves, internodes, and inflorescences. The semidominant Lgn-R mutation lacks kinase activity, and phenotypic severity is dependent on inbred background. We created near isogenic lines and assayed the phenotype in multiple environments. Lgn-R plants that carry the B73 version of Sympathy for the ligule (Sol-B) fail to grow under hot conditions, but those that carry the Mo17 version (Sol-M) survive at hot temperatures and are significantly taller at cool temperatures. To identify Sol, we used recombinant mapping and analyzed the Lgn-R phenotype in additional inbred backgrounds. We identified amino acid sequence variations in GRMZM2G075262 that segregate with severity of the Lgn-R phenotypes. This gene is expressed at high levels in Lgn-R B73, but expression drops to nonmutant levels with one copy of Sol-M An EMS mutation solidified the identity of SOL as a maize homolog of Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE4 (EDR4). SOL, like EDR4, is induced in response to pathogen-associated molecular patterns such as flg22. Integrated transcriptomic and phosphoproteomic analyses suggest that Lgn-R plants constitutively activate an immune signaling cascade that induces temperature-sensitive responses in addition to defects in leaf development. We propose that aspects of the severe Lgn-R developmental phenotype result from constitutive defense induction and that SOL potentially functions in repressing this response in Mo17 but not B73. Identification of LGN and its interaction with SOL provides insight into the integration of developmental control and immune responses.
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Affiliation(s)
- Alyssa Anderson
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
| | - Brian St Aubin
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
| | - María Jazmín Abraham-Juárez
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
| | - Samuel Leiboff
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Steve Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Jacob O Brunkard
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
| | - Sarah Hake
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California Berkeley, Albany, California 94710
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Fikas AA, Dilkes BP, Baxter I. Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome. PLANT DIRECT 2019; 3:e00139. [PMID: 31245778 PMCID: PMC6589523 DOI: 10.1002/pld3.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 04/02/2019] [Indexed: 05/06/2023]
Abstract
The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype-by-environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. QTL influencing trait covariation were detected at loci that were not found by mapping single-element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi-element traits that were determined by both genetic and environmental factors as well as genotype-by-environment interactions. Growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.
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Affiliation(s)
- Alexandra Asaro Fikas
- Donald Danforth Plant Science CenterSt. LouisMissouri
- Washington University in St. LouisSt. LouisMissouri
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
| | - Ivan Baxter
- Donald Danforth Plant Science CenterSt. LouisMissouri
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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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A Very Oil Yellow1 Modifier of the Oil Yellow1-N1989 Allele Uncovers a Cryptic Phenotypic Impact of Cis-regulatory Variation in Maize. G3-GENES GENOMES GENETICS 2019; 9:375-390. [PMID: 30518539 PMCID: PMC6385977 DOI: 10.1534/g3.118.200798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Forward genetics determines the function of genes underlying trait variation by identifying the change in DNA responsible for changes in phenotype. Detecting phenotypically-relevant variation outside protein coding sequences and distinguishing this from neutral variants is not trivial; partly because the mechanisms by which DNA polymorphisms in the intergenic regions affect gene regulation are poorly understood. Here we utilized a dominant genetic reporter to investigate the effect of cis and trans-acting regulatory variation. We performed a forward genetic screen for natural variation that suppressed or enhanced the semi-dominant mutant allele Oy1-N1989, encoding the magnesium chelatase subunit I of maize. This mutant permits rapid phenotyping of leaf color as a reporter for chlorophyll accumulation, and mapping of natural variation in maize affecting chlorophyll metabolism. We identified a single modifier locus segregating between B73 and Mo17 that was linked to the reporter gene itself, which we call very oil yellow1 (vey1). Based on the variation in OY1 transcript abundance and genome-wide association data, vey1 is predicted to consist of multiple cis-acting regulatory sequence polymorphisms encoded at the wild-type oy1 alleles. The vey1 locus appears to be a common polymorphism in the maize germplasm that alters the expression level of a key gene in chlorophyll biosynthesis. These vey1 alleles have no discernable impact on leaf chlorophyll in the absence of the Oy1-N1989 reporter. Thus, the use of a mutant as a reporter for magnesium chelatase activity resulted in the detection of expression-level polymorphisms not readily visible in the laboratory.
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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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