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Li Z, Li Z, Ji Y, Wang C, Wang S, Shi Y, Le J, Zhang M. The heat shock factor 20-HSF4-cellulose synthase A2 module regulates heat stress tolerance in maize. THE PLANT CELL 2024; 36:2652-2667. [PMID: 38573521 PMCID: PMC11218781 DOI: 10.1093/plcell/koae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/22/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Temperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms underlying the plant heat stress response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors (TFs) that may contribute to the maize heat stress response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the inbred line B73. Co-expression network analysis highlighted several TFs, including the class B2a heat shock factor (HSF) ZmHSF20. Zmhsf20 mutant seedlings exhibited enhanced tolerance to heat stress. Furthermore, DNA affinity purification sequencing and Cleavage Under Targets and Tagmentation assays demonstrated that ZmHSF20 binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three class A Hsf genes, including ZmHsf4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 promote the heat stress response, with ZmHSF4 directly activating ZmCesA2 transcription. In agreement with the transcriptome analysis, ZmHSF20 inhibited cellulose accumulation and repressed the expression of cell wall-related genes. Importantly, the Zmhsf20 Zmhsf4 double mutant exhibited decreased thermotolerance, placing ZmHsf4 downstream of ZmHsf20. We proposed an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers seedling heat tolerance by repressing ZmHsf4 and ZmCesA2, thus balancing seedling growth and defense.
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Affiliation(s)
- Ze Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zerui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Ji
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shufang Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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Maceda-López LF, Góngora-Castillo EB, Ibarra-Laclette E, Morán-Velázquez DC, Girón Ramírez A, Bourdon M, Villalpando-Aguilar JL, Toomer G, Tang JZ, Azadi P, Santamaría JM, López-Rosas I, López MG, Simpson J, Alatorre-Cobos F. Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111496. [PMID: 35684270 PMCID: PMC9182668 DOI: 10.3390/plants11111496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 05/08/2023]
Abstract
Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.
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Affiliation(s)
- Luis F. Maceda-López
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Elsa B. Góngora-Castillo
- CONACYT-Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico;
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico;
| | - Dalia C. Morán-Velázquez
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Amaranta Girón Ramírez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - José L. Villalpando-Aguilar
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Gabriela Toomer
- Division of Microbiology and Molecular Biology, IIT Research Institute, Chicago, IL 60616, USA;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Itzel López-Rosas
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Mercedes G. López
- Departmento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - Fulgencio Alatorre-Cobos
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence:
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Crane CF, Nemacheck JA, Subramanyam S, Williams CE, Goodwin SB. SLAG: A Program for Seeded Local Assembly of Genes in Complex Genomes. Mol Ecol Resour 2022; 22:1999-2017. [PMID: 34995394 PMCID: PMC9303413 DOI: 10.1111/1755-0998.13580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/11/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022]
Abstract
Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local Assembly of Genes) fulfils this need by performing iterative local assembly based on cycles of matching‐read retrieval with blast and assembly with cap3, phrap, spades, canu or unicycler. The target sequence can be nucleotide or protein. Read fragmentation allows slag to use phrap or cap3 to assemble long reads at lower coverage (e.g., 5×) than is possible with canu or unicycler. In simple, nonrepetitive genomes, a slag assembly can cover a whole chromosome, but in complex genomes the growth of target‐matching contigs is limited as additional reads are consumed by consensus contigs consisting of repetitive elements. Apart from genomic complexity, contig length and correctness depend on read length and accuracy. With pyrosequencing or Illumina reads, slag‐assembled contigs are accurate enough to allow design of PCR primers, while contigs assembled from Oxford Nanopore or pre‐HiFi Pacific Biosciences long reads are generally only accurate enough to design baiting sequences for further targeted sequencing. In an application with real reads, slag successfully extended sequences for four wheat genes, which were verified by cloning and Sanger sequencing of overlapping amplicons. slag is a robust alternative to atram2 for local assemblies, especially for read sets with less than 20× coverage. slag is freely available at https://github.com/cfcrane/SLAG.
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Affiliation(s)
- Charles F Crane
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
| | - Jill A Nemacheck
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Subhashree Subramanyam
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Christie E Williams
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA
| | - Stephen B Goodwin
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
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Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize. Proc Natl Acad Sci U S A 2020; 117:20908-20919. [PMID: 32778598 DOI: 10.1073/pnas.2005014117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Maintaining sufficient water transport during flowering is essential for proper organ growth, fertilization, and yield. Water deficits that coincide with flowering result in leaf wilting, necrosis, tassel browning, and sterility, a stress condition known as "tassel blasting." We identified a mutant, necrotic upper tips1 (nut1), that mimics tassel blasting and drought stress and reveals the genetic mechanisms underlying these processes. The nut1 phenotype is evident only after the floral transition, and the mutants have difficulty moving water as shown by dye uptake and movement assays. These defects are correlated with reduced protoxylem vessel thickness that indirectly affects metaxylem cell wall integrity and function in the mutant. nut1 is caused by an Ac transposon insertion into the coding region of a unique NAC transcription factor within the VND clade of Arabidopsis NUT1 localizes to the developing protoxylem of root, stem, and leaf sheath, but not metaxylem, and its expression is induced by flowering. NUT1 downstream target genes function in cell wall biosynthesis, apoptosis, and maintenance of xylem cell wall thickness and strength. These results show that maintaining protoxylem vessel integrity during periods of high water movement requires the expression of specialized, dynamically regulated transcription factors within the vasculature.
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