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Low Temperature Inhibits the Defoliation Efficiency of Thidiazuron in Cotton by Regulating Plant Hormone Synthesis and the Signaling Pathway. Int J Mol Sci 2022; 23:ijms232214208. [PMID: 36430686 PMCID: PMC9694417 DOI: 10.3390/ijms232214208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Thidiazuron (TDZ) is the main defoliant used in production to promote leaf abscission for machine-picked cotton. Under low temperatures, the defoliation rate of cotton treated with TDZ decreases and the time of defoliation is delayed, but there is little information about this mechanism. In this study, RNA-seq and physiological analysis are performed to reveal the transcriptome profiling and change in endogenous phytohormones upon TDZ treatment in abscission zones (AZs) under different temperatures (daily mean temperatures: 25 °C and 15 °C). Genes differentially expressed in AZs between TDZ treatment and control under different temperatures were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two temperature conditions. The results show that, compared with the corresponding control group, TDZ induces many differentially expressed genes (DEGs) in AZs, and the results of the GO and KEGG analyses show that the plant hormone signaling transduction pathway is significantly regulated by TDZ. However, under low temperature, TDZ induced less DEGs, and the enriched GO terms and KEGG pathways were different with those under normal temperature condition. Many genes in the plant hormone signal transduction pathway could not be induced by TDZ under low temperature conditions. In particular, the upregulated ethylene-signaling genes and downregulated auxin-signaling genes in AZs treated with TDZ were significantly affected by low temperatures. Furthermore, the expression of ethylene and auxin synthesis genes and their content in AZs treated with TDZ were also regulated by low temperature conditions. The upregulated cell wall hydrolase genes induced by TDZ were inhibited by low temperatures. However, the inhibition of low temperature on genes in AZs treated with TDZ was relieved with the extension of the treatment time. Together, these results indicate that the responses of ethylene and auxin synthesis and the signaling pathway to TDZ are inhibited by low temperatures, which could not induce the expression of cell wall hydrolase genes, and then inhibit the separation of AZ cells and the abscission of cotton leaves. This result provides new insights into the mechanism of defoliation induced by TDZ under low temperature conditions.
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Wang X, Chen S, Ma X, Yssel AEJ, Chaluvadi SR, Johnson MS, Gangashetty P, Hamidou F, Sanogo MD, Zwaenepoel A, Wallace J, Van de Peer Y, Bennetzen JL, Van Deynze A. Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). Gigascience 2021; 10:6168810. [PMID: 33710327 PMCID: PMC7953496 DOI: 10.1093/gigascience/giab013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/14/2020] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
Background Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement. Findings We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains. Conclusions We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.
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Affiliation(s)
- Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Shiyu Chen
- Department of Plant Sciences, Seed Biotechnology Center, University of California, 1 Shields Ave. Davis, CA 95616, USA
| | - Xiao Ma
- Bioinformatics & Systems Biology, VIB / Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium
| | - Anna E J Yssel
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa.,Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | | | - Matthew S Johnson
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, USA
| | - Prakash Gangashetty
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger
| | - Falalou Hamidou
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger
| | - Moussa D Sanogo
- Institut d'Economie Rurale, Ministere de l'Agriculture, Cinzana, BP 214, Ségou, Mali
| | - Arthur Zwaenepoel
- Bioinformatics & Systems Biology, VIB / Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium
| | - Jason Wallace
- Department of Crop and Soil Sciences, University of Georgia, 3111 Carlton St Bldg, Athens, GA 30602, USA
| | - Yves Van de Peer
- Bioinformatics & Systems Biology, VIB / Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa.,College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | | | - Allen Van Deynze
- Department of Plant Sciences, Seed Biotechnology Center, University of California, 1 Shields Ave. Davis, CA 95616, USA
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Cappai F, Amadeu RR, Benevenuto J, Cullen R, Garcia A, Grossman A, Ferrão LFV, Munoz P. High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry. FRONTIERS IN PLANT SCIENCE 2020; 11:562171. [PMID: 33304360 PMCID: PMC7701094 DOI: 10.3389/fpls.2020.562171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/21/2020] [Indexed: 05/21/2023]
Abstract
Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.
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Affiliation(s)
- Francesco Cappai
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rodrigo R. Amadeu
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Juliana Benevenuto
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Ryan Cullen
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Alexandria Garcia
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Adina Grossman
- Forage Breeding and Genetics Lab, Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Luís Felipe V. Ferrão
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Patricio Munoz
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- *Correspondence: Patricio Munoz
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Tranbarger TJ, Domonhédo H, Cazemajor M, Dubreuil C, Fischer U, Morcillo F. The PIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Enhances Populus Leaf and Elaeis guineensis Fruit Abscission. PLANTS (BASEL, SWITZERLAND) 2019; 8:E143. [PMID: 31151222 PMCID: PMC6630328 DOI: 10.3390/plants8060143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 01/18/2023]
Abstract
The programmed loss of a plant organ is called abscission, which is an important cell separation process that occurs with different organs throughout the life of a plant. The use of floral organ abscission in Arabidopsis thaliana as a model has allowed greater understanding of the complexities of organ abscission, but whether the regulatory pathways are conserved throughout the plant kingdom and for all organ abscission types is unknown. One important pathway that has attracted much attention involves a peptide ligand-receptor signalling system that consists of the secreted peptide IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and at least two leucine-rich repeat (LRR) receptor-like kinases (RLK), HAESA (HAE) and HAESA-LIKE2 (HSL2). In the current study we examine the bioactive potential of IDA peptides in two different abscission processes, leaf abscission in Populus and ripe fruit abscission in oil palm, and find in both cases treatment with IDA peptides enhances cell separation and abscission of both organ types. Our results provide evidence to suggest that the IDA-HAE-HSL2 pathway is conserved and functions in these phylogenetically divergent dicot and monocot species during both leaf and fruit abscission, respectively.
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Affiliation(s)
- Timothy John Tranbarger
- UMR DIADE, Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France.
- Ecology and Genetics Laboratory, Pontificia Universidad Católica del Ecuador (PUCE), 17-01-21-84 Quito, Ecuador.
| | | | - Michel Cazemajor
- CRAPP, INRAB, BP 1 Pobè, Benin.
- PalmElit SAS, F-34980 Montferrier-sur-Lez, France.
| | - Carole Dubreuil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
- DRT DPACA, CEA Tech Cadarache, 13108 Saint Paul Lez Durance, France.
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
- KWS SAAT SE, RD-BT, 37574 Einbeck, Germany.
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Fu Z, Song J, Zhao J, Jameson PE. Identification and expression of genes associated with the abscission layer controlling seed shattering in Lolium perenne. AOB PLANTS 2019; 11:ply076. [PMID: 30697405 PMCID: PMC6343819 DOI: 10.1093/aobpla/ply076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 05/09/2023]
Abstract
Perennial ryegrass (Lolium perenne) is one of the most important pasture grasses in the world. However, seed production is negatively impacted by the seed shattering (shedding) nature of this species. Recently, genes involved in the seed shattering process have been isolated and functionally characterized in several crop species. The aim of this study was to identify the genes playing critical roles in the seed shattering process in perennial ryegrass. DNA sequences of genes involved in seed shattering in the Poaceae were used to identify and isolate target genes in perennial ryegrass using a comparative genomics strategy. The candidate seed shattering genes were identified using an 'in-house' perennial ryegrass transcriptome database. The relative expression levels of the candidate ryegrass shattering genes were determined using RT-qPCR during different floret and seed developmental stages. Histological analysis of the abscission layer was also conducted. Homologues of seed shattering genes were identified and isolated from perennial ryegrass, and the relative gene expression results suggested that several genes, including LpqSH1 and LpSH1, might have a role in abscission layer formation during seed development. In addition, lignification of the abscission layer may play an important role in the abscission process. A genetic model for seed shattering in perennial ryegrass is suggested and may be useful for directing gene editing towards the production of a reduced-shattering ryegrass.
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Affiliation(s)
- Zeyu Fu
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- School of Life Sciences, Yantai University, Yantai 264005, China
- Corresponding authors’ e-mail addresses: ;
| | - Jiqiang Zhao
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Corresponding authors’ e-mail addresses: ;
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