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Wang SS, Tsai PH, Cheng SF, Chen RK, Chen KY. Identification of genomic regions controlling spikelet degeneration under FRIZZLE PANICLE (FZP) defect genetic background in rice. Sci Rep 2024; 14:12451. [PMID: 38816469 PMCID: PMC11139880 DOI: 10.1038/s41598-024-63362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts.
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Affiliation(s)
- Sheng-Shan Wang
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan.
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Pei-Hua Tsai
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Shu-Fang Cheng
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Rong-Kuen Chen
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Kai-Yi Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Hina A, Khan N, Kong K, Lv W, Karikari B, Abbasi A, Zhao T. Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation. PHYSIOLOGIA PLANTARUM 2024; 176:e14191. [PMID: 38351287 DOI: 10.1111/ppl.14191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/16/2023] [Accepted: 01/01/2024] [Indexed: 02/16/2024]
Abstract
F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.
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Affiliation(s)
- Aiman Hina
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Nadeem Khan
- Global Institute for Food Security, Saskatoon, SK, Canada
| | - Keke Kong
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wenhuan Lv
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, QC, Québec, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Pakistan
| | - Tuanjie Zhao
- Soybean Research Institute, Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), MOA National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Wang W, Chen W, Wang J. FRIZZLE PANICLE (FZP) regulates rice spikelets development through modulating cytokinin metabolism. BMC PLANT BIOLOGY 2023; 23:650. [PMID: 38102566 PMCID: PMC10724965 DOI: 10.1186/s12870-023-04671-4] [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: 09/07/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The number of grains per panicle is an important factor in determining rice yield. The DST-OsCKX2 module has been demonstrated to regulate panicle development in rice by controlling cytokinin content. However, to date, how the function of DST-OsCKX2 module is regulated during panicle development remains obscure. RESULT In this study, the ABNORMAL PANICLE 1 (ABP1), a severely allele of FRIZZY PANICLE (FZP), exhibits abnormal spikelets morphology. We show that FZP can repress the expression of DST via directly binding to its promotor. Consistently, the expression level of OsCKX2 increased and the cytokinin content decreased in the fzp mutant, suggesting that the FZP acts upstream of the DST-OsCKX2 to maintain cytokinin homeostasis in the inflorescence meristem. CONCLUSIONS Our results indicate that FZP plays an important role in regulating spikelet development and grain number through mediating cytokinin metabolism.
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Affiliation(s)
- Wei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wenqiang Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Junmin Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
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Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
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Saeed S, Usman B, Shim SH, Khan SU, Nizamuddin S, Saeed S, Shoaib Y, Jeon JS, Jung KH. CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111435. [PMID: 36031021 DOI: 10.1016/j.plantsci.2022.111435] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.
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Affiliation(s)
- Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Babar Usman
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University KPK, Pakistan
| | - Sabzoi Nizamuddin
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Sundus Saeed
- School of Engineering, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Yasira Shoaib
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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Deblieck M, Szilagyi G, Andrii F, Saranga Y, Lauterberg M, Neumann K, Krugman T, Perovic D, Pillen K, Ordon F. Dissection of a grain yield QTL from wild emmer wheat reveals sub-intervals associated with culm length and kernel number. Front Genet 2022; 13:955295. [DOI: 10.3389/fgene.2022.955295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat (Triticum turgidum ssp. dicoccoides), conferring high grain yield under well-watered and water-limited conditions, was transferred to the elite durum wheat cultivar Uzan (T. turgidum ssp. durum) by a marker-assisted backcross breeding approach. The 2B introgression line turned out to be higher yielding but also exhibited negative traits that likely result from trans-, cis-, or linkage drag effects from the wild emmer parent. In this study, the respective 2BS QTL was subjected to fine-mapping, and a set of 17 homozygote recombinants were phenotyped at BC4F5 generation under water-limited and well-watered conditions at an experimental farm in Israel and at a high-throughput phenotyping platform (LemnaTec-129) in Germany. In general, both experimental setups allowed the identification of sub-QTL intervals related to culm length, kernel number, thousand kernel weight, and harvest index. Sub-QTLs for kernel number and harvest index were detected specifically under either drought stress or well-watered conditions, while QTLs for culm length and thousand-kernel weight were detected in both conditions. Although no direct QTL for grain yield was identified, plants with the sub-QTL for kernel number showed a higher grain yield than the recurrent durum cultivar Uzan under well-watered and mild drought stress conditions. We, therefore, suggest that this sub-QTL might be of interest for future breeding purposes.
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Kellogg EA. Genetic control of branching patterns in grass inflorescences. THE PLANT CELL 2022; 34:2518-2533. [PMID: 35258600 PMCID: PMC9252490 DOI: 10.1093/plcell/koac080] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.
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Ding Y, Zhu J, Zhao D, Liu Q, Yang Q, Zhang T. Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:705834. [PMID: 34456947 PMCID: PMC8385297 DOI: 10.3389/fpls.2021.705834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 05/05/2023]
Abstract
Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.
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Affiliation(s)
- Yu Ding
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jiannan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Dongsheng Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qingqing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qingqing Yang
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Zhang
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