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Pandey S, Divakar S, Singh A. Genome editing prospects for heat stress tolerance in cereal crops. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108989. [PMID: 39094478 DOI: 10.1016/j.plaphy.2024.108989] [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: 01/04/2024] [Revised: 06/10/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
The world population is steadily growing, exerting increasing pressure to feed in the future, which would need additional production of major crops. Challenges associated with changing and unpredicted climate (such as heat waves) are causing global food security threats. Cereal crops are a staple food for a large portion of the world's population. They are mostly affected by these environmentally generated abiotic stresses. Therefore, it is imperative to develop climate-resilient cultivars to support the sustainable production of main cereal crops (Rice, wheat, and maize). Among these stresses, heat stress causes significant losses to major cereals. These issues can be solved by comprehending the molecular mechanisms of heat stress and creating heat-tolerant varieties. Different breeding and biotechnology techniques in the last decade have been employed to develop heat-stress-tolerant varieties. However, these time-consuming techniques often lack the pace required for varietal improvement in climate change scenarios. Genome editing technologies offer precise alteration in the crop genome for developing stress-resistant cultivars. CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeat/Cas9), one such genome editing platform, recently got scientists' attention due to its easy procedures. It is a powerful tool for functional genomics as well as crop breeding. This review will focus on the molecular mechanism of heat stress and different targets that can be altered using CRISPR/Cas genome editing tools to generate climate-smart cereal crops. Further, heat stress signaling and essential players have been highlighted to provide a comprehensive overview of the topic.
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Affiliation(s)
- Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - S Divakar
- Department of Agricultural Biotechnology Biotechnology and Molecular Biotechnology, CBSH, RPCAU, Pusa, Samastipur, Bihar, 8481253, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Bihar, 848125, India.
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2
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Ma L, Zhang T, Zhu QH, Zhang X, Sun J, Liu F. HSP70 and APX1 play important roles in cotton male fertility by mediating ROS homeostasis. Int J Biol Macromol 2024; 278:134856. [PMID: 39168224 DOI: 10.1016/j.ijbiomac.2024.134856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/22/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
Male sterility is used in the production of hybrid seeds and can improve the breeding efficiency of cotton hybrids. Reactive oxygen species is closely associated with the tapetum and pollen development, but their relationship in cotton male fertility remains unclear. In this study, we comprehensively compared the cytology and proteome of the anthers from an Upland cotton (Gossypium hirsutum) material, Shida 98 (WT), and its nearly-isogenic male sterile line Shida 98A (MS). Cytology indicated delayed PCD in the tapetum and defects in microspores in MS anthers. And further studies revealed disruption of ROS homeostasis. Proteomic analysis identified proteins with differential abundance mainly being related to redox homeostasis, protein folding, and apoptotic signaling pathways. GhAPX1 interacted with GhHSP70 and played a crucial role in the development of cotton anthers. Exogenous application of HSP70 inhibitor increased H2O2 content and decreased the activity of APX1 and pollen viability. The GhAPX1 mutants generated by CRISPR/Cas9-mediated gene editing exhibited premature degradation of the tapetum, significant decrease in pollen viability, and significant increase in H2O2 content. Altogether, our results imply HSP70 and APX1 being the key players jointly regulating male fertility by mediating ROS homeostasis. These results provide insights into the proteins associated with male fertility.
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Affiliation(s)
- Lihong Ma
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Tao Zhang
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra 2601, Australia
| | - Xinyu Zhang
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Feng Liu
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
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3
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Xiong J, Huang B, Peng D, Shen Q, Wu D, Zhang G. JAZ2 Negatively Regulates Drought Tolerance in Barley by Modulating PLT2 Expression. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39323024 DOI: 10.1111/pce.15149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/27/2024]
Abstract
Drought is an important abiotic factor constricting crop production globally. Although the roles of JAZ proteins in regulating jasmonic acid signalling and plant responses to environmental stress are well documented, their specific functions and underlying mechanisms remain little known. In this study, JAZ proteins in barley were thoroughly analyzed, revealing a total of 11 members classified into three phylogenetic subgroups. HvJAZ2, based on its distinct expression patterns, is considered a key candidate gene for regulating drought tolerance in barley. Using the HvJAZ2 knockout mutants, we revealed that the gene negatively regulates drought tolerance by inhibiting barley root growth. Notably, the jaz2 mutants upregulated the expression of root development genes, including SHR1, PLT1, PLT2 and PLT6. plt2 and plt1/plt2 mutants exhibited suppressed root development and reduced drought tolerance. Analysis of interactions between HvJAZ2 and other proteins showed that HvJAZ2 does not directly interact with HvPLT1/2/6, but interacts with some other proteins. BIFC and LCA assays further confirmed the nuclear interaction between HvJAZ2 and HvMYC2. Y1H and Dual-Luciferase experiments demonstrated that HvMYC2 can bind to and activate the HvPLT2 promoter. In summary, HvJAZ2 negatively regulates root development and drought tolerance in barley by suppressing HvPLT2 expression through interacting with HvMYC2.
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Affiliation(s)
- Jiangyan Xiong
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Binbin Huang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Di Peng
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Qiufang Shen
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - DeZhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, P.R. China
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4
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Wang ZZ, Cao MJ, Yan J, Dong J, Chen MX, Yang JF, Li JH, Ying RN, Gao YY, Li L, Leng YN, Tian Y, Hewage KAH, Pei RJ, Huang ZY, Yin P, Zhu JK, Hao GF, Yang GF. Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination. Nat Commun 2024; 15:8077. [PMID: 39277642 PMCID: PMC11401921 DOI: 10.1038/s41467-024-52426-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 09/04/2024] [Indexed: 09/17/2024] Open
Abstract
Abscisic acid (ABA) is the primary preventing factor of seed germination, which is crucial to plant survival and propagation. ABA-induced seed germination inhibition is mainly mediated by the dimeric PYR/PYL/RCAR (PYLs) family members. However, little is known about the relevance between dimeric stability of PYLs and seed germination. Here, we reveal that stabilization of PYL dimer can relieve ABA-induced inhibition of seed germination using chemical genetic approaches. Di-nitrobensulfamide (DBSA), a computationally designed chemical probe, yields around ten-fold improvement in receptor affinity relative to ABA. DBSA reverses ABA-induced inhibition of seed germination mainly through dimeric receptors and recovers the expression of ABA-responsive genes. DBSA maintains PYR1 in dimeric state during protein oligomeric state experiment. X-ray crystallography shows that DBSA targets a pocket in PYL dimer interface and may stabilize PYL dimer by forming hydrogen networks. Our results illustrate the potential of PYL dimer stabilization in preventing ABA-induced seed germination inhibition.
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Affiliation(s)
- Zhi-Zheng Wang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Min-Jie Cao
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Junjie Yan
- State Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin Dong
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Mo-Xian Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China
| | - Jing-Fang Yang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Jian-Hong Li
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China
| | - Rui-Ning Ying
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Yang-Yang Gao
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China
| | - Li Li
- State Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ya-Nan Leng
- State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Kamalani Achala H Hewage
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Rong-Jie Pei
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Zhi-You Huang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Ping Yin
- State Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Ge-Fei Hao
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China.
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China.
| | - Guang-Fu Yang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China.
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Yan B, Liu C, Sun J, Mao Y, Zhou C, Li J, Liu W, Li S, Yan W, Fu C, Qin P, Fu X, Zhao X, Song X, Nie J, Gao F, Yang Y, Chen Y, Cao X. Impaired 2',3'-cyclic phosphate tRNA repair causes thermo-sensitive genic male sterility in rice. Cell Res 2024:10.1038/s41422-024-01012-4. [PMID: 39251844 DOI: 10.1038/s41422-024-01012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/24/2024] [Indexed: 09/11/2024] Open
Abstract
Hybrid rice, widely planted in Asia, is pathogen resistant and has superior yields, making it a major contributor to global food security. The two-line hybrid rice system, which utilizes mutants exhibiting photo-/thermo-sensitive genic male sterility (P/TGMS), is the leading hybrid rice breeding technology. Mutations in THERMO-SENSITIVE GENIC MALE STERILE 5 (TMS5) accounts for over 95% of current TGMS lines. We previously found that tms5 carries a mutation in ribonuclease ZS1. Despite its importance for breeding robust rice lines, the mechanism underlying tms5-mediated TGMS remains elusive. Here, we demonstrate that TMS5 is a tRNA 2',3'-cyclic phosphatase. The tms5 mutation leads to accumulation of 2',3'-cyclic phosphate (cP)-ΔCCA-tRNAs (tRNAs without 3' CCA ended with cP), which is exacerbated by high temperatures, and reduction in the abundance of mature tRNAs, particularly alanine tRNAs (tRNA-Alas). Overexpression of tRNA-Alas in the tms5 mutant restores male fertility to 70%. Remarkably, male fertility of tms5 mutant is completely restored at high temperatures by knocking out OsVms1 which encodes the enzyme for cP-ΔCCA-tRNA generation. Our study reveals the mechanism underlying tms5-mediated TGMS in rice and provides mechanistic insight into the further improvement of TGMS in hybrid crop development.
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Affiliation(s)
- Bin Yan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chunyan Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Jing Sun
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Mao
- Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Can Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Ji Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shengdong Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Yan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Chenjian Fu
- Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China
| | - Peng Qin
- Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China
| | - Xingxue Fu
- Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China
| | - Xinghui Zhao
- Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China
| | - Xianwei Song
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Nie
- Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Feng Gao
- Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuanzhu Yang
- Yuan Longping High-tech Agriculture Co., Ltd., Changsha, Hunan, China.
- State Key Laboratory of Hybrid Rice, Changsha, Hunan, China.
- Key Laboratory of Rice Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Changsha, Hunan, China.
| | - Yuhang Chen
- Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of the Chinese Academy of Sciences, Beijing, China.
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of the Chinese Academy of Sciences, Beijing, China.
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Bhaduri A, Ha TJ. Biowaste-Derived Triboelectric Nanogenerators for Emerging Bioelectronics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405666. [PMID: 39248387 DOI: 10.1002/advs.202405666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/20/2024] [Indexed: 09/10/2024]
Abstract
Triboelectric nanogenerators (TENGs) combine contact electrification and electrostatic induction effects to convert waste mechanical energy into electrical energy. As conventional devices contribute to electronic waste, TENGs based on ecofriendly and biocompatible materials have been developed for various energy applications. Owing to the abundance, accessibility, low cost, and biodegradability of biowaste (BW), recycling these materials has gained considerable attention as a green approach for fabricating TENGs. This review provides a detailed overview of BW materials, processing techniques for BW-based TENGs (BW-TENGs), and potential applications of BW-TENGs in emerging bioelectronics. In particular, recent progress in material design, fabrication methods, and biomechanical and environmental energy-harvesting performance is discussed. This review is aimed at promoting the continued development of BW-TENGs and their adoption for sustainable energy-harvesting applications in the field of bioelectronics.
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Affiliation(s)
- Abhisikta Bhaduri
- Dept. of Electronic Materials Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Tae-Jun Ha
- Dept. of Electronic Materials Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
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Ganguly S, Nimitha K, Saha S, Sinha Mahapatra N, Bhattacharya K, Kundu R, Ganguly S, Sen P, Saha AK, Purkayastha S, Bhattacharyya PK, Biswas T, Bhattacharyya S. Identification and analysis of low light responsive yield enhancing QTLs in rice. Sci Rep 2024; 14:21011. [PMID: 39251768 PMCID: PMC11385566 DOI: 10.1038/s41598-024-71593-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
Rice is one of the major food crops grown globally. However, during the wet season, rice suffers significant yield loss due to reduced light intensity caused by overcast clouds when the light intensity is only around 450-500 µmol/m2/s, compared to 1400-1800 µmol/m2/s in summer. This reduction in light intensity leads to a decrease in seed yield, mainly by limiting tiller or panicle numbers. Yield and its attributing parameters were recorded in one hundred thirty RILs for four consecutive wet seasons in ambient light (AL) and low light (LL, 35% light-cut using white shade net). QTL analysis was performed using Inclusive Composite Interval Mapping (ICIM) with all the phenotypic data and 927 polymorphic SNPs identified by the 7 K Infinium chip. The study identified a large QTL influencing panicle numbers and yield exclusively in lowlight on chromosome 1 (qPNLL1.1, qGYLL1.1) in four consecutive seasons with LOD > 10 and PVE > 30%. The favourable alleles are from the tolerant parent, Swarnaprabha. Another grain yield improving QTL was identified on chromosome 6 (qGYLL6.1), with LOD > 3 in three consecutive seasons. In a diverse rice panel of one hundred seventeen genotypes with five different models, association analysis identified the associated marker for panicle numbers and grain yield in LL, which is also the left marker of the newly identified QTLs for the traits under LL condition. A shade-responsive gene, monoculm 2 (MOC2, LOC_Os01g64660) inside the QTL on chromosome 1, upregulated in the tolerant parent and its QTL-carrying RILs, whereas repressed in the susceptible one. Therefore, due to its significant additive effect and validation across various genotypes, the yield-improving QTL on chromosome 1 can be directly utilised in marker-assisted selection (MAS) for developing shade-tolerant rice. This can also help reduce the yield gap between wet and dry-season rice.
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Affiliation(s)
- Shamba Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - K Nimitha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Shoumik Saha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Nilanjan Sinha Mahapatra
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Kriti Bhattacharya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Rimpa Kundu
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Sebantee Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Poulomi Sen
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Arup Kumar Saha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Shampa Purkayastha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Prabir Kumar Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Tirthankar Biswas
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Somnath Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India.
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8
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Li C, Huang L, Huang Y, Kuang M, Wu Y, Ma Z, Fu X. Fine-mapping of a major QTL controlling plant height by BSA-seq and transcriptome sequencing in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:217. [PMID: 39249496 DOI: 10.1007/s00122-024-04714-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/04/2024] [Indexed: 09/10/2024]
Abstract
KEY MESSAGE GhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071000, China
| | - Longyu Huang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572025, China
| | - Yiwen Huang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Meng Kuang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuzhen Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, 071000, China.
| | - Xiaoqiong Fu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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9
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Aleem M, Razzaq MK, Aleem M, Yan W, Sharif I, Siddiqui MH, Aleem S, Iftikhar MS, Karikari B, Ali Z, Begum N, Zhao T. Genome-wide association study provides new insight into the underlying mechanism of drought tolerance during seed germination stage in soybean. Sci Rep 2024; 14:20765. [PMID: 39237583 PMCID: PMC11377444 DOI: 10.1038/s41598-024-71357-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
Drought is one of the major environmental issues that reduce crop yield. Seed germination is a crucial stage of plant development in all crop plants, including soybean. In soybean breeding, information about genetic mechanism of drought tolerance has great importance. However, at germination stage, there is relatively little knowledge on the genetic basis of soybean drought resistance. The objective of this work was to find the quantitative trait nucleotides (QTNs) linked to drought tolerance related three traits using a genome-wide association study (GWAS), viz., germination rate (GR), root length (RL), and whole seedling length (WSL), using germplasm population of 240 soybean PIs with 34,817 SNPs genotype data having MAF > 0.05. It was observed that heritability (H2) for GR, WSL, and RL across both environments (2020, and 2019) were high in the range of 0.76-0.99, showing that genetic factors play a vital role in drought tolerance as compared to environmental factors. A number of 23 and 27 QTNs were found to be linked to three traits using MLM and mrMLM, respectively. Three significant QTNs, qGR8-1, qWSL13-1, and qRL-8, were identified using both MLM and mrMLM methods among these QTNs. QTN8, located on chromosome 8 was consistently linked to two traits (GR and RL). The area (± 100 Kb) associated with this QTN was screened for drought tolerance based on gene annotation. Fifteen candidate genes were found by this screening. Based on the expression data, four candidate genes i.e. Glyma08g156800, Glyma08g160000, Glyma08g162700, and Glyma13g249600 were found to be linked to drought tolerance regulation in soybean. Hence, the current study provides evidence to understand the genetic constitution of drought tolerance during the germination stage and identified QTNs or genes could be utilized in molecular breeding to enhance the yield under drought stress.
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Affiliation(s)
- Muqadas Aleem
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationCollege of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | | | - Maida Aleem
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Wenliang Yan
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationCollege of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Iram Sharif
- Cotton Research Station, Faisalabad, Pakistan
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saba Aleem
- Barani Agricultural Research Station, Fatehjang, Pakistan
| | - Muhammad Sarmad Iftikhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, PO Box TL 1882, Tamale, Ghana
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Naheeda Begum
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationCollege of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationCollege of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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10
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Roy D, Vashisth A, Krishnan P, Mukherjee J, Meena MC, Biswakarma N, Rathore P, Bag K, Kumari S. Delayed sowing and its ramifications: biophysical, yield and quality analysis of wheat cultivars in the northwest Indo-Gangetic plains. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6831-6843. [PMID: 38597889 DOI: 10.1002/jsfa.13512] [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: 09/25/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The continuous cultivation of rice-wheat in the same field is a key element of double-cropping systems in the Indo-Gangetic plains. Yields of such cropping systems are increasingly challenged as climate change drives increases in temperature, terminal stress and uneven rainfall, delaying rice harvesting and subsequently delaying sowing of wheat. In this paper, we evaluate the optimum sowing dates to achieve high grain yield and quality of wheat cultivars in northwest India. Three cultivars of wheat, HD-2967, HD-3086 and PBW-723, were sown on three different dates at the research farm of ICAR-IARI, New Delhi, to generate different weather conditions at different phenological stages. Different biophysical attributes, photosynthetic rate, stomatal conductance and transpiration rate, were measured at different phenological stages. Yield and grain quality parameters such as protein, starch, amylopectin, amylose and gluten were measured in different cultivars sown on different dates. RESULTS Biophysical parameters were found to be higher in timely sown crops followed by late-sown and very late-sown crops. Further, the different sowing dates had a significant (P < 0.05) impact on the grain quality parameters such as protein, starch, amylopectin, amylose and gluten content. Percentage increases in the value of starch and amylose content under timely sown were ~7% and 11.6%, ~5% and 8.4%, compared to the very late-sown treatment. In contrast, protein and amylopectin contents were found to increase by ~9.7% and 7.5%, ~13.8% and 16.6% under very late-sown treatment. CONCLUSION High-temperature stress during the grain-filling periods significantly decreased the grain yield. Reduction in the grain yield was associated with a reduction in starch and amylose content in the grains. The protein content in the grains is less affected by terminal heat stress. Cultivar HD-3086 had higher growth, yield as well as quality parameters, compared to HD-2967 and PBW-723 in all treatments, hence could be adopted by farmers in northwest India. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Debasish Roy
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Ananta Vashisth
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Prameela Krishnan
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Joydeep Mukherjee
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Mahesh Chand Meena
- Division of Soil Science and Agricultural Chemistry, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Niraj Biswakarma
- Division of Agronomy, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Rathore
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Koushik Bag
- Division of Agricultural Physics, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Sweta Kumari
- Division of Biochemistry, ICAR - Indian Agricultural Research Institute, New Delhi, India
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11
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Moshelion M, Dietz KJ, Dodd IC, Muller B, Lunn JE. Guidelines for designing and interpreting drought experiments in controlled conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4671-4679. [PMID: 38957989 PMCID: PMC11350075 DOI: 10.1093/jxb/erae292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Affiliation(s)
- Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology, Faculty of Biology, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Ian C Dodd
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Bertrand Muller
- INRAE-LEPSE, Institut Agro, Université Montpellier, UMR 759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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12
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Masood A, Khan S, Mir IR, Anjum NA, Rasheed F, Al-Hashimi A, Khan NA. Ethylene Is Crucial in Abscisic Acid-Mediated Modulation of Seed Vigor, Growth, and Photosynthesis of Salt-Treated Mustard. PLANTS (BASEL, SWITZERLAND) 2024; 13:2307. [PMID: 39204743 PMCID: PMC11360230 DOI: 10.3390/plants13162307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/15/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
The current study explored the differential interaction between ethylene (ET) and abscisic acid (ABA) in relation to salt stress in mustard (Brassica juncea L.) plants. Significant reductions in seed germination, growth, and photosynthesis were observed with 100 mmol NaCl. Among the cultivars tested, the Pusa Vijay cultivar was noted as ET-sensitive. Pusa Vijay responded maximally to an application of 2.0 mmol ethephon (Eth; 2-chloethyl phosphonic acid-ethylene source), and exhibited the greatest growth, photosynthesis, activity of 1-aminocyclopropane carboxylic acid (ACC) synthase (ACS), and ET evolution. Notably, Eth (2.0 mmol) more significantly improved the seed germination percentage, germination and vigor index, amylase activity, and reduced H2O2 content under salt stress, while ABA (25 µmol) had negative effects. Moreover, the individual application of Eth and ABA on Pusa Vijay under both optimal and salt-stressed conditions increased the growth and photosynthetic attributes, nitrogen (N) and sulfur (S) assimilation, and antioxidant defense machinery. The addition of aminoethoxyvinylglycine (0.01 µmol AVG, ET biosynthesis inhibitor) to ABA + NaCl-treated plants further added to the effects of ABA on parameters related to seed germination and resulted in less effectiveness of growth and photosynthesis. In contrast, the effects of Eth were seen with the addition of fluoridone (25 µmol Flu, ABA biosynthesis inhibitor) to Eth + NaCl. Thus, it can be suggested that ET is crucial for alleviating salt-induced inhibition in seed germination, growth, and photosynthesis, while ABA collaborated with ET to offer protection by regulating nutrient assimilation and enhancing antioxidant metabolism. These findings provide insight into the complex regulatory processes involved in ET-ABA interaction, enhancing our understanding of plant growth and development and the mitigation of salt stress in mustard. It opens pathways for developing hormonal-based strategies to improve crop productivity and resilience, ultimately benefiting agricultural practices amidst a challenging environment.
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Affiliation(s)
- Asim Masood
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Sheen Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Iqbal R. Mir
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Naser A. Anjum
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Rasheed
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Abdulrahman Al-Hashimi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Nafees A. Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
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13
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Ryu JS, Park B, van Peer AF, Na KS, Lee SH. Quantitative trait loci analysis for molecular markers linked to agricultural traits of Pleurotus ostreatus. PLoS One 2024; 19:e0308832. [PMID: 39133731 PMCID: PMC11318876 DOI: 10.1371/journal.pone.0308832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Pleurotus ostreatus is a global mushroom crop with nutritional and medicinal benefits. However, the genetic basis of several commercial traits remains unknown. To address this, we analyzed the quantitative trait loci (QTLs) for two representative cultivars, "Heuktari" and "Miso," with apparently distinct alleles. A genetic map with 11 linkage groups was constructed, in which 27 QTLs were assigned to 14 traits. The explained phenotypic variations in QTLs ranged from 7.8% to 22.0%. Relatively high LOD values of 6.190 and 5.485 were estimated for the pinheading period and the number of valid stipes, respectively. Some QTL-derived molecular markers showed potential enhancement rates of selection precision in inbred lines, especially for cap shape (50%) and cap thickness (30%). Candidate genes were inferred from the QTL regions and validated using qRT-PCR, particularly for the cysteine and glutathione pathway, in relation to cap yellowness. The molecular markers in this study are expected to facilitate the breeding of the Heuktari and Miso lines and provide probes to identify related genes in P. ostreatus.
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Affiliation(s)
- Jae-San Ryu
- Department of Mushroom Science, Korea National University of Agriculture and Fisheries, Jeonju, Jeonju-si, Jeollabuk-do, South Korea
| | - Bokyung Park
- Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Arend F. van Peer
- Plant Breeding, Wageningen University and Research, PB Wageningen, The Netherlands
| | - Kyeong Sook Na
- Department of Mushroom Science, Korea National University of Agriculture and Fisheries, Jeonju, Jeonju-si, Jeollabuk-do, South Korea
| | - Song Hee Lee
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea
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14
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Jiang N, Zhu XG. Modern phenomics to empower holistic crop science, agronomy, and breeding research. J Genet Genomics 2024; 51:790-800. [PMID: 38734136 DOI: 10.1016/j.jgg.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales, representing a greater data collection throughput compared with traditional measurements. Most modern crop phenomics use different sensors to collect reflective, emitted, and fluorescence signals, etc., from plant organs at different spatial and temporal resolutions. Such multi-modal, high-dimensional data not only accelerates basic research on crop physiology, genetics, and whole plant systems modeling, but also supports the optimization of field agronomic practices, internal environments of plant factories, and ultimately crop breeding. Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection, management, sharing, and processing, developing capabilities to measure physiological parameters, and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.
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Affiliation(s)
- Ni Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xin-Guang Zhu
- Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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15
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Ruan B, Jiang Y, Ma Y, Zhou M, Chen F, Zhang Y, Yu Y, Wu L. Characterization of the ddt1 Mutant in Rice and Its Impact on Plant Height Reduction and Water Use Efficiency. Int J Mol Sci 2024; 25:7629. [PMID: 39062872 PMCID: PMC11277124 DOI: 10.3390/ijms25147629] [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: 06/04/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world's population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant's improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (B.R.); (Y.J.); (Y.M.); (M.Z.); (F.C.); (Y.Z.); (Y.Y.)
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16
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Adly M, Ezzat A, Awad A, El-Fiki A. Mutations induced in some Egyptian cowpea varieties with yield characteristics and high nutritional value using gamma rays and evaluation by microsatellite markers. Int J Radiat Biol 2024; 100:1117-1125. [PMID: 38991120 DOI: 10.1080/09553002.2024.2374912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024]
Abstract
PURPOSE In order to achieve mutations with enhanced economic, productive, and nutritional characteristics in the two Egyptian cowpea varieties, Dokki 331 and Kaha 1, the application of gamma irradiation at different doses is employed. Additionally, this method aids in distinguishing between these mutations using simple sequence repeat (SSR) analysis. MATERIALS AND METHODS Two different cowpea cultivars were subjected to varying doses of gamma radiation ranging from 50 to 300 Gy. In order to analyze the effects of radiation, both unirradiated and irradiated seeds from both cultivars were planted using a randomized complete block design. This experiment was conducted over a span of six generations, namely M1, M2, M3, M4, M5, and M6, starting from April 2017 and continuing until 2022. Among the various radiation doses, the cultivar Kaha 1 produced promising traits when exposed to a dose of 150 Gy, while the cultivar Dokki 331 showed favorable traits when exposed to a dose of 300 Gy. These traits were further cultivated and studied until the M6 generation. RESULTS Induced mutations in two Egyptian cowpea varieties, Kaha 1 and Dokki 331, are subjected to varying doses of gamma radiation (0, 50, 100, 150, 200, 250, and 300 Gy). Morphological and genetic variations were observed, with mutations being induced at doses of 150 Gy for Kaha 1 and 300 Gy for Dokki 331. The mutation in Kaha 1 (beam 1) resulted in dwarfism, altered leaf shape, early flowering, increased peduncles, pods, and pod seed numbers, ultimately leading to enhanced seed production and acreage productivity. In Dokki 331, the mutations primarily affected pod color, resulting in greenish-brown pods with mosaic seeds, segregating black and gray seeds from the mosaic ones. These mutations led to an increase in the nutritional value of the seeds, including higher nitrogen content, total free amino acids, crude protein, total carbohydrates, and total sugars. The genetic diversity of the seven cowpea mutations was assessed using 20 microsatellite markers. The analysis revealed a total of 60 alleles, with an average of three alleles per locus. The allele frequency ranged from 0.2857 to 1.0, with an average of 0.6036. Gene diversity varied from 0.0 to 0.8163, while the heterozygosity was mostly zero, except for one primer (VM 37) with an average of 0.0071. The polymorphic information content (PIC) ranged from 0.7913 to 0.0, with an average of 0.4323. The Marker Index value ranged from 0.36 to 0.0, with an average of 0.152. Overall, our findings demonstrate the successful induction of mutations in Egyptian cowpea varieties using gamma rays, resulting in improved yield characteristics and nutritional value. CONCLUSIONS Radiation as a physical mutagen is highly regarded for its effectiveness, affordability, speed, and safety in inducing mutations. Utilizing gamma rays, we successfully derived a novel cowpea variety called beam 1 mutation, which has gained approval from the Egyptian Ministry of Agriculture.
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Affiliation(s)
- M Adly
- Department of Natural Products, National Centre for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - A Ezzat
- Department of Horticulture, Faculty of Agriculture, Minia University, Minya, Egypt
| | - A Awad
- Department of Natural Products, National Centre for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - A El-Fiki
- Department of Natural Products, National Centre for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
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17
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Tu M, Wang R, Guo W, Xu S, Zhu Y, Dong J, Yao X, Jiang L. A CRISPR/Cas9-induced male-sterile line facilitating easy hybrid production in polyploid rapeseed ( Brassica napus). HORTICULTURE RESEARCH 2024; 11:uhae139. [PMID: 38988621 PMCID: PMC11233878 DOI: 10.1093/hr/uhae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Rapeseed is a globally significant oilseed crop cultivated to meet the increasing demand for vegetable oil. In order to enhance yield and sustainability, breeders have adopted the development of rapeseed hybrids as a common strategy. However, current hybrid production systems in rapeseed have various limitations, necessitating the development of a simpler and more efficient approach. In this study, we propose a novel method involving the targeted disruption of Defective in Anther Dehiscence1 of Brassica napus (BnDAD1), an essential gene in the jasmonic acid biosynthesis pathway, using CRISPR/Cas9 technology, to create male-sterile lines. BnDAD1 was found to be dominantly expressed in the stamen of rapeseed flower buds. Disrupting BnDAD1 led to decreased levels of α-linolenic acid and jasmonate in the double mutants, resulting in defects in anther dehiscence and pollen maturation. By crossing the double mutant male-sterile lines with male-fertile lines, a two-line system was demonstrated, enabling the production of F 1 seeds. The male-sterile trait of the bndad1 double mutant lines was maintainable by applying exogenous methyl jasmonate and subsequently self-pollinating the flowers. This breakthrough holds promising potential for harnessing heterosis in rapeseed and offers a simpler and more efficient method for producing hybrid seeds.
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Affiliation(s)
- Mengxin Tu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Ruisen Wang
- Institute of Economic Crops, Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Wenhui Guo
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Shiqi Xu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiangtan Yao
- Institute of Economic Crops, Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
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Ma H, Li C, Xiao N, Liu J, Li P, Xu J, Yan J, Zhang S, Xia T. Heterologous synthesis of poly-γ-glutamic acid enhanced drought resistance in maize (Zea mays L.). Int J Biol Macromol 2024; 273:133179. [PMID: 38880448 DOI: 10.1016/j.ijbiomac.2024.133179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/27/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Drought stress is the main factor restricting maize yield. Poly-γ-glutamic acid (γ-PGA), as a water-retaining agent and fertilizer synergist, could significantly improve the drought resistance and yield of many crops. However, its high production costs and unclear long-term impact on soil ecology limit its large-scale application. In this study, an environmentally friendly green material γ-PGA was heterologous synthesized in maize for the first time using the synthetic biology method. The genes (PgsA, PgsB, PgsC) participated in γ-PGA synthesis were cloned from Bacillus licheniformis and transformed into maize to produce γ-PGA for the first time. Under drought stress, transgenic maize significantly increased the ear length, ear weight and grain weight by 50 % compared to the control, whereas the yield characteristic of ear weight, grain number per ear, grain weight per ear and 100-grain weight increased by 1.67 %-2.33 %, 3.78 %-13.06 %, 8.41 %-22.06 %, 6.03 %-19.28 %, and 11.85 %-18.36 %, respectively under normal growth conditions. γ-PGA was mainly expressed in the mesophyll cells of maize leaf rosette structure and improved drought resistance and yield by protecting and increasing the expression of genes for the photosynthetic and carbon fixation. This study is an important exploration for maize drought stress molecular breeding and building resource-saving agriculture.
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Affiliation(s)
- Haizhen Ma
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China
| | - Can Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China
| | - Ning Xiao
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China
| | - Jiang Liu
- College of Life Science, Shanxi Agricultural University, Taiyuan 030031, PR China
| | - Panpan Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China
| | - Jieting Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Jianbin Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Shengkui Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China
| | - Tao Xia
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, PR China.
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Zhou L, Mao Y, Yang Y, Wang J, Zhong X, Han Y, Zhang Y, Shi Q, Huang X, Meyers BC, Zhu J, Yang Z. Temperature and light reverse the fertility of rice P/TGMS line ostms19 via reactive oxygen species homeostasis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2020-2032. [PMID: 38421616 PMCID: PMC11182586 DOI: 10.1111/pbi.14322] [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: 11/27/2023] [Revised: 01/30/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
P/TGMS (Photo/thermo-sensitive genic male sterile) lines are crucial resources for two-line hybrid rice breeding. Previous studies revealed that slow development is a general mechanism for sterility-fertility conversion of P/TGMS in Arabidopsis. However, the difference in P/TGMS genes between rice and Arabidopsis suggests the presence of a distinct P/TGMS mechanism in rice. In this study, we isolated a novel P/TGMS line, ostms19, which shows sterility under high-temperature conditions and fertility under low-temperature conditions. OsTMS19 encodes a novel pentatricopeptide repeat (PPR) protein essential for pollen formation, in which a point mutation GTA(Val) to GCA(Ala) leads to ostms19 P/TGMS phenotype. It is highly expressed in the tapetum and localized to mitochondria. Under high temperature or long-day photoperiod conditions, excessive ROS accumulation in ostms19 anthers during pollen mitosis disrupts gene expression and intine formation, causing male sterility. Conversely, under low temperature or short-day photoperiod conditions, ROS can be effectively scavenged in anthers, resulting in fertility restoration. This indicates that ROS homeostasis is critical for fertility conversion. This relationship between ROS homeostasis and fertility conversion has also been observed in other tested rice P/TGMS lines. Therefore, we propose that ROS homeostasis is a general mechanism for the sterility-fertility conversion of rice P/TGMS lines.
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Affiliation(s)
- Lei Zhou
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yi‐Chen Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yan‐Ming Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Jun‐Jie Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Xiang Zhong
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yu Han
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yan‐Fei Zhang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Qiang‐Sheng Shi
- Jiangxi Yangtze River Economic Zone Research InstituteJiujiang UniversityJiujiangJiangxiChina
| | - Xue‐hui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | | | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Zhong‐Nan Yang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
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20
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Sallam A, Dawood MFA, Jarquín D, Mohamed EA, Hussein MY, Börner A, Ahmed AAM. Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings. THE PLANT GENOME 2024; 17:e20444. [PMID: 38476036 DOI: 10.1002/tpg2.20444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.
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Affiliation(s)
- Ahmed Sallam
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Mona F A Dawood
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Diego Jarquín
- Department of Agronomy, University of Florida, Gainesville, Florida, USA
| | - Elsayed A Mohamed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Mohamed Y Hussein
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Asmaa A M Ahmed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
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21
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El Baouchi A, Ibriz M, Dreisigacker S, Lopes MS, Sanchez-Garcia M. Dissection of the Genetic Basis of Genotype by Environment Interactions for Morphological Traits and Protein Content in Winter Wheat Panel Grown in Morocco and Spain. PLANTS (BASEL, SWITZERLAND) 2024; 13:1477. [PMID: 38891286 PMCID: PMC11174427 DOI: 10.3390/plants13111477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 06/21/2024]
Abstract
To fulfill the growing demand for wheat consumption, it is important to focus on enhancement breeding strategies targeting key parameters such as yield, thousand kernel weight (TKW), quality characteristics including morphological traits, and protein content. These elements are key to the ongoing and future objectives of wheat breeding programs. Prioritizing these factors will effectively help meet the rising demand for wheat, especially given the challenges posed by unpredictable weather patterns. This study evaluated the morphological traits and protein content of 249 winter wheat varieties and advanced lines grown in eleven different environments in Morocco and Spain incorporating three varied sowing dates. The results showed considerable variability in morphological traits and protein content. Significant correlations were observed among various grain traits, with most grain morphological parameters exhibiting negative correlations with protein content. Differences across environments (p ≤ 0.01) in all traits, genotypes, and genotype by environment interaction were significant. A factorial regression analysis revealed significant impacts of environmental conditions on all grain morphological parameters, protein content, and TKW during the three growth stages. The study identified several high-performing and stable genotypes across diverse environments, providing valuable insights for wheat breeding programs such as genotypes 129, 234, 241, and 243. Genome-Wide Association Studies pinpointed 603 significant markers across 11 environments, spread across chromosomes. Among these, 400 markers were linked with at least two traits or observed in at least two different environments. Moreover, twelve marker-trait associations were detected that surpassed the Bonferroni correction threshold. These findings highlight the importance of targeted breeding efforts to enhance wheat quality and adaptability to different environmental conditions.
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Affiliation(s)
- Adil El Baouchi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco
- Plant, Animal, and Agro-Industry Production Laboratory, Faculty of Sciences, Ibn Tofail University, Kenitra BP. 242, Kenitra 14000, Morocco;
| | - Mohammed Ibriz
- Plant, Animal, and Agro-Industry Production Laboratory, Faculty of Sciences, Ibn Tofail University, Kenitra BP. 242, Kenitra 14000, Morocco;
| | - Susanne Dreisigacker
- The International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico;
| | - Marta S. Lopes
- The International Maize and Wheat Improvement Center (CIMMYT), Ankara 3906511, Turkey;
- Sustainable Field Crops Institute for Food and Agricultural Research and Technology (IRTA), 251981 Lleida, Spain
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10100, Morocco
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22
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Ahmed M, Marrez DA, Rizk R, Zedan M, Abdul-Hamid D, Decsi K, Kovács GP, Tóth Z. The Influence of Zinc Oxide Nanoparticles and Salt Stress on the Morphological and Some Biochemical Characteristics of Solanum lycopersicum L. Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:1418. [PMID: 38794488 PMCID: PMC11125107 DOI: 10.3390/plants13101418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024]
Abstract
Salinity reduces crop yields and quality, causing global economic losses. Zinc oxide nanoparticles (ZnO-NPs) improve plant physiological and metabolic processes and abiotic stress resistance. This study examined the effects of foliar ZnO-NPs at 75 and 150 mg/L on tomato Kecskeméti 549 plants to alleviate salt stress caused by 150 mM NaCl. The precipitation procedure produced ZnO-NPs that were characterized using UV-VIS, TEM, STEM, DLS, EDAX, Zeta potential, and FTIR. The study assessed TPCs, TFCs, total hydrolyzable sugars, total free amino acids, protein, proline, H2O2, and MDA along with plant height, stem width, leaf area, and SPAD values. The polyphenolic burden was also measured by HPLC. With salt stress, plant growth and chlorophyll content decreased significantly. The growth and development of tomato plants changed by applying the ZnO-NPs. Dosages of ZnO-NPs had a significant effect across treatments. ZnO-NPs also increased chlorophyll, reduced stress markers, and released phenolic chemicals and proteins in the leaves of tomatoes. ZnO-NPs reduce salt stress by promoting the uptake of minerals. ZnO-NPs had beneficial effects on tomato plants when subjected to salt stress, making them an alternate technique to boost resilience in saline soils or low-quality irrigation water. This study examined how foliar application of chemically synthesized ZnO-NPs to the leaves affected biochemistry, morphology, and phenolic compound synthesis with and without NaCl.
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Affiliation(s)
- Mostafa Ahmed
- Festetics Doctoral School, Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
- Department of Agricultural Biochemistry, Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
| | - Diaa Attia Marrez
- Food Toxicology and Contaminants Department, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Roquia Rizk
- Department of Agricultural Biochemistry, Faculty of Agriculture, Cairo University, Giza 12613, Egypt;
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Mostafa Zedan
- National Institute of Laser Enhanced Science, Cairo University, Giza 12613, Egypt;
| | - Donia Abdul-Hamid
- Heavy Metals Department, Central Laboratory for The Analysis of Pesticides and Heavy Metals in Food (QCAP), Dokki, Cairo 12311, Egypt;
| | - Kincső Decsi
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Gergő Péter Kovács
- Institute of Agronomy, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary;
| | - Zoltán Tóth
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
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23
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Gai W, Yuan L, Yang F, Ahiakpa JK, Li F, Ge P, Zhang X, Tao J, Wang F, Yang Y, Zhang Y. Genome-wide variants and optimal allelic combinations for citric acid in tomato. HORTICULTURE RESEARCH 2024; 11:uhae070. [PMID: 38725459 PMCID: PMC11079488 DOI: 10.1093/hr/uhae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/25/2024] [Indexed: 05/12/2024]
Abstract
Citric acid (CA) plays a crucial role as a fruit flavor enhancer and serves as a mediator in multiple metabolic pathways in tomato fruit development. Understanding factors influencing CA metabolism is essential for enhancing fruit flavor and CA-mediated biological processes. The accumulation of CA, however, is influenced by a complex interplay of genetic and environmental factors, leading to challenges in accurately predicting and regulating its levels. In this study, we conducted a genome-wide association study (GWAS) on CA, employing six landmark models based on genome-wide variations including structural variants, insertions and deletions, and single nucleotide polymorphisms. The identification of 11 high-confidence candidate genes was further facilitated by leveraging linkage disequilibrium and causal variants associated with CA. The transcriptome data from candidate genes were examined, revealing higher correlations between the expression of certain candidate genes and changes in CA metabolism. Three CA-associated genes exerted a positive regulatory effect on CA accumulation, while the remaining genes exhibited negative impacts based on gene cluster and correlation analyses. The CA content of tomatoes is primarily influenced by improvement sweeps with minimal influence from domestication sweeps in the long-term breeding history, as evidenced by population differentiation and variants distribution. The presence of various causal variants within candidate genes is implicated in the heterogeneity of CA content observed among the tomato accessions. This observation suggests a potential correlation between the number of alternative alleles and CA content. This study offers significant function-based markers that can be utilized in marker-assisted breeding, thereby enhancing their value and applicability.
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Affiliation(s)
- Wenxian Gai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangdan Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - John Kojo Ahiakpa
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangman Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingfei Ge
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinbao Tao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyang Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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Zhang TT, Lin YJ, Liu HF, Liu YQ, Zeng ZF, Lu XY, Li XW, Zhang ZL, Zhang S, You CX, Guan QM, Lang ZB, Wang XF. The AP2/ERF transcription factor MdDREB2A regulates nitrogen utilisation and sucrose transport under drought stress. PLANT, CELL & ENVIRONMENT 2024; 47:1668-1684. [PMID: 38282271 DOI: 10.1111/pce.14834] [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: 04/15/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
Drought stress is one of the main environmental factors limiting plant growth and development. Plants adapt to changing soil moisture by modifying root architecture, inducing stomatal closure, and inhibiting shoot growth. The AP2/ERF transcription factor DREB2A plays a key role in maintaining plant growth in response to drought stress, but the molecular mechanism underlying this process remains to be elucidated. Here, it was found that overexpression of MdDREB2A positively regulated nitrogen utilisation by interacting with DRE cis-elements of the MdNIR1 promoter. Meanwhile, MdDREB2A could also directly bind to the promoter of MdSWEET12, which may enhance root development and nitrogen assimilation, ultimately promoting plant growth. Overall, this regulatory mechanism provides an idea for plants in coordinating with drought tolerance and nitrogen assimilation to maintain optimal plant growth and development under drought stress.
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Affiliation(s)
- Ting-Ting Zhang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilisation, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Yu-Jing Lin
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao-Feng Liu
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Ya-Qi Liu
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Zhi-Feng Zeng
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Yan Lu
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilisation, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Xue-Wei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhen-Lu Zhang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Shuai Zhang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Chun-Xiang You
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Qing-Mei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhao-Bo Lang
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xiao-Fei Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
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25
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Sharma A, Verma K, Kumar A, Rani S, Chauhan K, Battan B, Kumar R. Delineating the role of host plants in regulating the water and salinity stress induced changes in sandalwood roots. 3 Biotech 2024; 14:133. [PMID: 38660477 PMCID: PMC11035507 DOI: 10.1007/s13205-024-03979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The interaction of root hemi-parasite (sandalwood) with its hosts is crucial for establishing successful plantations under abiotic stresses. In the present study, we explored the best possible host for sandalwood along with its effect on sandalwood physiology in terms of water and nutrients. Interactive effects of host species (Alternanthera sp., Azadirachta indica, Dalbergia sissoo, Melia dubia, and Aquilaria malaccensis) with sandalwood were observed under eight treatments {100% best available water (BAW); 100% BAW + nutrient medium; 50% water deficit; 50% water deficit + nutrient medium; 100% saline water (ECiw 8ds/m); 100% saline water (ECiw 8ds/m) + nutrient medium; 50% water deficit + saline water (ECiw 8ds/m); and 50% water deficit + saline water (ECiw 8ds/m) + nutrient medium}. A significant change in morpho-physiological traits of sandalwood roots was observed under different stress conditions, which were slightly improved through external supply of nutrient medium. Dalbergia sissoo (Shisham) and Melia dubia (Dek) seemed to be the best host plants providing better environment for sandalwood growth and development, i.e., higher plant height (59.7 and 53.68 cm) and collar diameter (3.24 and 3.07 mm) under stresses by maintaining water and ionic balance. Root length is an important parameter that was reduced by 27.58%, 19.22%, and 36.3% under water deficit, salinity, and combined stress of water deficit and salinity. Sandalwood grown with D. sissoo and M. dubia maintained the lowest Ψw (- 1.38 MPa) and Ψs (- 1.47 and - 1.48 MPa), respectively. In addition, sandalwood cultivated with D. sissoo and A. indica had higher accumulation of soluble proteins (0.48 and 0.42 mg/g) and soluble sugars (98.56 and 91.04 mg/g) in their roots. Results also showed that sandalwood roots had higher K+/Na+ with compatible host, i.e., with A. indica (1.85) and D. sissoo (1.83) than other studied hosts. It was also observed that sandalwood plants could not grow and survive alone under stress conditions even with application of nutrient medium. Based on the morphological traits, it was observed that sandalwood grown with hosts, Dalbergia sissoo and Melia dubia, was able to tolerate stress conditions better than other studied hosts. We can further recommend growing sandalwood with D. sissoo and M. dubia as a viable option to endure adverse environmental conditions.
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Affiliation(s)
- Aarju Sharma
- Kurukshetra University, Kurukshetra, 136119 India
- ICAR–Central Soil salinity Research Institute, Karnal, 132001 India
| | - Kamlesh Verma
- ICAR–Central Soil salinity Research Institute, Karnal, 132001 India
| | - Ashwani Kumar
- ICAR–Central Soil salinity Research Institute, Karnal, 132001 India
| | - Sulekha Rani
- Kurukshetra University, Kurukshetra, 136119 India
| | | | - Bindu Battan
- Kurukshetra University, Kurukshetra, 136119 India
| | - Raj Kumar
- ICAR–Central Soil salinity Research Institute, Karnal, 132001 India
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26
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Li G, Zhu W, Tian M, Liu R, Ruan Y, Liu C. Genome-Wide Identification of the SPP/SPPL Gene Family and BnaSPPL4 Regulating Male Fertility in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:3936. [PMID: 38612746 PMCID: PMC11012144 DOI: 10.3390/ijms25073936] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, the functions of SPP/SPPL in rapeseed (Brassica napus L.) have not been reported. In this study, 26 SPP/SPPLs were identified in rapeseed and categorized into three groups: SPP, SPPL2, and SPPL3. These members mainly contained the Peptidase_A22 and PA domains, which were distributed on 17 out of 19 chromosomes. Evolutionary analyses indicated that BnaSPP/SPPLs evolved with a large number of whole-genome duplication (WGD) events and strong purifying selection. Members are widely expressed and play a key role in the growth and development of rapeseed. The regulation of rapeseed pollen fertility by the BnaSPPL4 gene was further validated through experiments based on bioinformatics analysis, concluding that BnaSPPL4 silencing causes male sterility. Cytological observation showed that male infertility caused by loss of BnaSPPL4 gene function occurs late in the mononucleate stage due to microspore dysplasia.
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Affiliation(s)
- Guangze Li
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Wenjun Zhu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Minyu Tian
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Rong Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Ying Ruan
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
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Zhou W, Yan Z, Zhang L. A comparative study of 11 non-linear regression models highlighting autoencoder, DBN, and SVR, enhanced by SHAP importance analysis in soybean branching prediction. Sci Rep 2024; 14:5905. [PMID: 38467662 PMCID: PMC10928191 DOI: 10.1038/s41598-024-55243-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
To explore a robust tool for advancing digital breeding practices through an artificial intelligence-driven phenotype prediction expert system, we undertook a thorough analysis of 11 non-linear regression models. Our investigation specifically emphasized the significance of Support Vector Regression (SVR) and SHapley Additive exPlanations (SHAP) in predicting soybean branching. By using branching data (phenotype) of 1918 soybean accessions and 42 k SNP (Single Nucleotide Polymorphism) polymorphic data (genotype), this study systematically compared 11 non-linear regression AI models, including four deep learning models (DBN (deep belief network) regression, ANN (artificial neural network) regression, Autoencoders regression, and MLP (multilayer perceptron) regression) and seven machine learning models (e.g., SVR (support vector regression), XGBoost (eXtreme Gradient Boosting) regression, Random Forest regression, LightGBM regression, GPs (Gaussian processes) regression, Decision Tree regression, and Polynomial regression). After being evaluated by four valuation metrics: R2 (R-squared), MAE (Mean Absolute Error), MSE (Mean Squared Error), and MAPE (Mean Absolute Percentage Error), it was found that the SVR, Polynomial Regression, DBN, and Autoencoder outperformed other models and could obtain a better prediction accuracy when they were used for phenotype prediction. In the assessment of deep learning approaches, we exemplified the SVR model, conducting analyses on feature importance and gene ontology (GO) enrichment to provide comprehensive support. After comprehensively comparing four feature importance algorithms, no notable distinction was observed in the feature importance ranking scores across the four algorithms, namely Variable Ranking, Permutation, SHAP, and Correlation Matrix, but the SHAP value could provide rich information on genes with negative contributions, and SHAP importance was chosen for feature selection. The results of this study offer valuable insights into AI-mediated plant breeding, addressing challenges faced by traditional breeding programs. The method developed has broad applicability in phenotype prediction, minor QTL (quantitative trait loci) mining, and plant smart-breeding systems, contributing significantly to the advancement of AI-based breeding practices and transitioning from experience-based to data-based breeding.
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Affiliation(s)
- Wei Zhou
- Florida Agricultural and Mechanical University, Tallahassee, FL, 32307, USA.
| | - Zhengxiao Yan
- Florida State University, Tallahassee, FL, 32306, USA
| | - Liting Zhang
- Florida State University, Tallahassee, FL, 32306, USA
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Obunyali CO, Pillay K, Meisel B, Ndou EN, Mashingaidze K, Sserumaga JP, Asea G, Mwimali M, Tende R, Beyene Y, Mugo S, Okogbenin E, Oikeh SO. Efficacy of Event MON 87460 in drought-tolerant maize hybrids under optimal and managed drought-stress in eastern and southern africa. J Genet Eng Biotechnol 2024; 22:100352. [PMID: 38494265 PMCID: PMC10941202 DOI: 10.1016/j.jgeb.2024.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Frequent drought events due to climate change have become a major threat to maize (Zea mays L.) production and food security in Africa. Genetic engineering is one of the ways of improving drought tolerance through gene introgression to reduce the impact of drought stress in maize production. This study aimed to evaluate the efficacy of Event MON 87460 (CspB; DroughtGard®) gene in more than 120 conventional drought-tolerant maize hybrids in Kenya, South Africa, and Uganda for 3-6 years under managed drought-stress and optimal conditions and establish any additional yield contribution or yield penalties of the gene in traited hybrids relative to their non-traited isohybrids. Germplasm used in the study were either MON 87460 traited un-adapted (2008-2010), adapted traited DroughtTEGO® (2011-2013) or a mix of both under confined field trials. RESULTS Results showed significant yield differences (p < 0.001) among MON 87460 traited and non-traited hybrids across well-watered and managed drought-stress treatments. The gene had positive and significant effect on yield by 36-62% in three hybrids (CML312/CML445; WMA8101/CML445; and CML312/S0125Z) relative to non-traited hybrids under drought, and without significant yield penalty under optimum-moisture conditions in Lutzville, South Africa. Five traited hybrids (WMA2003/WMB4401; CML442/WMB4401; CML489/WMB4401; CML511/CML445; and CML395/WMB4401) had 7-13% significantly higher yield than the non-traited isohybrids out of 34 adapted DroughtTEGO® hybrids with same background genetics in the three countries for ≥ 3 years. The positive effect of MON 87460 was mostly observed under high drought-stress relative to low, moderate, or severe stress levels. CONCLUSION This study showed that MON 87460 transgenic drought tolerant maize hybrids could effectively tolerate drought and shield farmers against severe yield loss due to drought stress. The study signified that development and adoption of transgenic drought tolerant maize hybrids can cushion against farm yield losses due to drought stress as part of an integrated approach in adaptation to climate change effects.
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Affiliation(s)
- Caleb O Obunyali
- African Agricultural Technology Foundation (AATF), P.O Box 30709, 00100 Nairobi Kenya.
| | - Kiru Pillay
- Bayer Crop Science. 27 Wrench Rd, Isando, Johannesburg 1600, South Africa.
| | - Barbara Meisel
- Bayer Crop Science. 27 Wrench Rd, Isando, Johannesburg 1600, South Africa.
| | - Eric N Ndou
- Agricultural Research Council (ARC)-Grain Crops Institute Private Bag X1251, Potchefstroom 2520, South Africa; Present address: Bayer Crop Science. 27 Wrench Rd, Isando, Johannesburg, 1600, South Africa.
| | - Kingstone Mashingaidze
- Agricultural Research Council (ARC)-Grain Crops Institute Private Bag X1251, Potchefstroom 2520, South Africa.
| | - Julius Pyton Sserumaga
- National Agricultural Research Organization, National Livestock Resources Research Institute (NaLIRRI), P.O. Box 5704, Kampala, Uganda.
| | - Godfrey Asea
- National Agricultural Research Organization, National Crops Resources Research Institute, P.O Box 7084, Kampala, Uganda.
| | - Murenga Mwimali
- Kenya Agricultural and Livestock Research Organization (KALRO) Agricultural Mechanization Research Institute, P.O. Box 340-90100 Machakos, Kenya.
| | - Regina Tende
- Kenya Agricultural and Livestock Research Organization (KALRO) Agricultural Mechanization Research Institute, P.O. Box 340-90100 Machakos, Kenya.
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, 00621, Nairobi, Kenya.
| | - Stephen Mugo
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, 00621, Nairobi, Kenya; Present Address: Center for Resilient Agriculture for Africa (CRA-Africa), PO Box 286-00206 Kiserian, Kenya.
| | - Emmanuel Okogbenin
- African Agricultural Technology Foundation (AATF), P.O Box 30709, 00100 Nairobi Kenya.
| | - Sylvester O Oikeh
- African Agricultural Technology Foundation (AATF), P.O Box 30709, 00100 Nairobi Kenya.
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Chandran AEJ, Finkler A, Hait TA, Kiere Y, David S, Pasmanik-Chor M, Shkolnik D. Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress. PLANT PHYSIOLOGY 2024; 194:1834-1852. [PMID: 38057162 PMCID: PMC10904324 DOI: 10.1093/plphys/kiad651] [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: 08/22/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
Calcium is known to improve seed-germination rates under salt stress. We investigated the involvement of calcium ions (Ca2+) in regulating HIGH-AFFINITY K+ TRANSPORTER 1 (HKT1; 1), which encodes a Na+/K+ transporter, and its post-translational regulator TYPE 2C PROTEIN PHOSPHATASE 49 (PP2C49), in germinating Arabidopsis (Arabidopsis thaliana) seedlings. Germination rates of hkt1 mutant seeds under salt stress remained unchanged by CaCl2 treatment in wild-type Arabidopsis, whereas pp2c49 mutant seeds displayed improved salt-stress tolerance in the absence of CaCl2 supplementation. Analysis of HKT1;1 and PP2C49 promoter activity revealed that CaCl2 treatment results in radicle-focused expression of HKT1;1 and reduction of the native radicle-exclusive expression of PP2C49. Ion-content analysis indicated that CaCl2 treatment improves K+ retention in germinating wild-type seedlings under salt stress, but not in hkt1 seedlings. Transgenic seedlings designed to exclusively express HKT1;1 in the radicle during germination displayed higher germination rates under salt stress than the wild type in the absence of CaCl2 treatment. Transcriptome analysis of germinating seedlings treated with CaCl2, NaCl, or both revealed 118 upregulated and 94 downregulated genes as responsive to the combined treatment. Bioinformatics analysis of the upstream sequences of CaCl2-NaCl-treatment-responsive upregulated genes revealed the abscisic acid response element CACGTGTC, a potential CaM-binding transcription activator-binding motif, as most prominent. Our findings suggest a key role for Ca2+ in mediating salt-stress responses during germination by regulating genes that function to maintain Na+ and K+ homeostasis, which is vital for seed germination under salt stress.
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Affiliation(s)
- Ancy E J Chandran
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Aliza Finkler
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yvonne Kiere
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Sivan David
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Metsada Pasmanik-Chor
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doron Shkolnik
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
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Wang Y, Jiang W, Li C, Wang Z, Lu C, Cheng J, Wei S, Yang J, Yang Q. Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress. BMC PLANT BIOLOGY 2024; 24:132. [PMID: 38383312 PMCID: PMC10880279 DOI: 10.1186/s12870-024-04804-3] [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: 01/10/2024] [Accepted: 02/06/2024] [Indexed: 02/23/2024]
Abstract
Seed propagation is the main method of mulberry expansion in China, an important economic forest species. However, seed germination is the most sensitive stage to various abiotic stresses, especially salinity stress. To reveal the molecular regulatory mechanism of mulberry seed germination under salt stress, flavonoid metabolomics and transcriptomics analyses were performed on mulberry seeds germinated under 50 and 100 mmol/L NaCl stress. Analysis of the flavonoid metabolome revealed that a total of 145 differential flavonoid metabolites (DFMs) were classified into 9 groups, 40 flavonols, 32 flavones, 16 chalcones and 14 flavanones. Among them, 61.4% (89) of the DFMs accumulated continuously with increasing salt concentration, reaching the highest level at a 100 mmol/L salt concentration; these DFMs included quercetin-3-O-glucoside (isoquercitrin), kaempferol (3,5,7,4'-tetrahydroxyflavone), quercetin-7-O-glucoside, taxifolin (dihydroquercetin) and apigenin (4',5,7-trihydroxyflavone), indicating that these flavonoids may be key metabolites involved in the response to salt stress. Transcriptional analysis identified a total of 3055 differentially expressed genes (DEGs), most of which were enriched in flavonoid biosynthesis (ko00941), phenylpropanoid biosynthesis (ko00940) and biosynthesis of secondary metabolites (ko01110). Combined analysis of flavonoid metabolomic and transcriptomic data indicated that phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), flavonol synthase (FLS), bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) and anthocyanidin reductase (ANR) were the key genes involved in flavonoid accumulation during mulberry seed germination under 50 and 100 mmol/L NaCl stress. In addition, three transcription factors, MYB, bHLH and NAC, were involved in the regulation of flavonoid accumulation under salt stress. The results of quantitative real-time PCR (qRT‒PCR) validation showed that the expression levels of 11 DEGs, including 7 genes involved in flavonoid biosynthesis, under different salt concentrations were consistent with the transcriptomic data, and parallel reaction monitoring (PRM) results showed that the expression levels of 6 key enzymes (proteins) involved in flavonoid synthesis were consistent with the accumulation of flavonoids. This study provides a new perspective for investigating the regulatory role of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress at different concentrations.
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Affiliation(s)
- Yi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
| | - Wei Jiang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Chenlei Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Zhenjiang Wang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, 510610, China
| | - Can Lu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Junsen Cheng
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Shanglin Wei
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Jiasong Yang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Qiang Yang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
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Yang Y, He T, Ravindran P, Wen F, Krishnamurthy P, Wang L, Zhang Z, Kumar PP, Chae E, Lee C. All-organic transparent plant e-skin for noninvasive phenotyping. SCIENCE ADVANCES 2024; 10:eadk7488. [PMID: 38363835 PMCID: PMC10871535 DOI: 10.1126/sciadv.adk7488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Real-time in situ monitoring of plant physiology is essential for establishing a phenotyping platform for precision agriculture. A key enabler for this monitoring is a device that can be noninvasively attached to plants and transduce their physiological status into digital data. Here, we report an all-organic transparent plant e-skin by micropatterning poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) on polydimethylsiloxane (PDMS) substrate. This plant e-skin is optically and mechanically invisible to plants with no observable adverse effects to plant health. We demonstrate the capabilities of our plant e-skins as strain and temperature sensors, with the application to Brassica rapa leaves for collecting corresponding parameters under normal and abiotic stress conditions. Strains imposed on the leaf surface during growth as well as diurnal fluctuation of surface temperature were captured. We further present a digital-twin interface to visualize real-time plant surface environment, providing an intuitive and vivid platform for plant phenotyping.
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Affiliation(s)
- Yanqin Yang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Tianyiyi He
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Pratibha Ravindran
- Department of Biological Sciences and Research Center for Sustainable Urban Farming, National University of Singapore, Singapore 117558, Singapore
| | - Feng Wen
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Pannaga Krishnamurthy
- Department of Biological Sciences and Research Center for Sustainable Urban Farming, National University of Singapore, Singapore 117558, Singapore
| | - Luwei Wang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Zixuan Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences and Research Center for Sustainable Urban Farming, National University of Singapore, Singapore 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences and Research Center for Sustainable Urban Farming, National University of Singapore, Singapore 117558, Singapore
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117608, Singapore
- National University of Singapore Suzhou Research Institute (NUSRI), Suzhou Industrial Park, Suzhou 215123, China
- NUS Graduate School-Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore 119077, Singapore
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32
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Cheng Y, Lawrence DM, Pan M, Zhang B, Graham NT, Lawrence PJ, Liu Z, He X. A bioenergy-focused versus a reforestation-focused mitigation pathway yields disparate carbon storage and climate responses. Proc Natl Acad Sci U S A 2024; 121:e2306775121. [PMID: 38315850 PMCID: PMC10873610 DOI: 10.1073/pnas.2306775121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 12/04/2023] [Indexed: 02/07/2024] Open
Abstract
Limiting global warming to 2 °C requires urgent action on land-based mitigation. This study evaluates the biogeochemical and biogeophysical implications of two alternative land-based mitigation scenarios that aim to achieve the same radiative forcing. One scenario is primarily driven by bioenergy expansion (SSP226Lu-BIOCROP), while the other involves re/afforestation (SSP126Lu-REFOREST). We find that overall, SSP126Lu-REFOREST is a more efficient strategy for removing CO2 from the atmosphere by 2100, resulting in a net carbon sink of 242 ~ 483 PgC with smaller uncertainties compared to SSP226Lu-BIOCROP, which exhibits a wider range of -78 ~ 621 PgC. However, SSP126Lu-REFOREST leads to a relatively warmer planetary climate than SSP226Lu-BIOCROP, and this relative warming can be intensified in certain re/afforested regions where local climates are not favorable for tree growth. Despite the cooling effect on a global scale, SSP226Lu-BIOCROP reshuffles regional warming hotspots, amplifying summer temperatures in vulnerable tropical regions such as Central Africa and Southeast Asia. Our findings highlight the need for strategic land use planning to identify suitable regions for re/afforestation and bioenergy expansion, thereby improving the likelihood of achieving the intended climate mitigation outcomes.
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Affiliation(s)
- Yanyan Cheng
- Department of Industrial Systems Engineering and Management, National University of Singapore, 117576, Singapore
| | - David M. Lawrence
- Climate and Global Dynamics Laboratory, National Science Foundation National Center for Atmospheric Research, Boulder, CO80305
| | - Ming Pan
- Center for Western Weather and Water Extremes, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Baoqing Zhang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu730000, China
| | - Neal T. Graham
- Joint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD20740
| | - Peter J. Lawrence
- Climate and Global Dynamics Laboratory, National Science Foundation National Center for Atmospheric Research, Boulder, CO80305
| | - Zhongfang Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai200092, China
| | - Xiaogang He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
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Wu C, Luo J, Xiao Y. Multi-omics assists genomic prediction of maize yield with machine learning approaches. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:14. [PMID: 38343399 PMCID: PMC10853138 DOI: 10.1007/s11032-024-01454-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
With the improvement of high-throughput technologies in recent years, large multi-dimensional plant omics data have been produced, and big-data-driven yield prediction research has received increasing attention. Machine learning offers promising computational and analytical solutions to interpret the biological meaning of large amounts of data in crops. In this study, we utilized multi-omics datasets from 156 maize recombinant inbred lines, containing 2496 single nucleotide polymorphisms (SNPs), 46 image traits (i-traits) from 16 developmental stages obtained through an automatic phenotyping platform, and 133 primary metabolites. Based on benchmark tests with different types of prediction models, some machine learning methods, such as Partial Least Squares (PLS), Random Forest (RF), and Gaussian process with Radial basis function kernel (GaussprRadial), achieved better prediction for maize yield, albeit slight difference for method preferences among i-traits, genomic, and metabolic data. We found that better yield prediction may be caused by various capabilities in ranking and filtering data features, which is found to be linked with biological meaning such as photosynthesis-related or kernel development-related regulations. Finally, by integrating multiple omics data with the RF machine learning approach, we can further improve the prediction accuracy of grain yield from 0.32 to 0.43. Our research provides new ideas for the application of plant omics data and artificial intelligence approaches to facilitate crop genetic improvements. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01454-z.
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Affiliation(s)
- Chengxiu Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Wan Y, Xiao Q, Xiao X, Huang Y, Liu S, Feng W, Liu T, Ren Z, Ren W, Luo X, Luo S. Response of tomatoes to inactivated endophyte LSE01 under combined stress of high-temperature and drought. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108321. [PMID: 38181639 DOI: 10.1016/j.plaphy.2023.108321] [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: 09/19/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
Endophytes can assist crops in adapting to high temperatures and drought conditions, thereby reducing agricultural losses. However, the mechanism through which endophytes regulate crop resistance to high temperatures and drought stress remains unclear, and concerns regarding safety and stability exist with active endophytes. Thus, heat-treated endophytic bacteria LSE01 (HTB) were employed as a novel microbial fertilizer to investigate their effects on plant adaptation to high temperatures and drought conditions. The results indicated that the diameter and weight of tomatoes treated with HTB under stress conditions increased by 23.04% and 71.15%, respectively, compared to the control. Tomato yield did not significantly decrease compared to non-stress conditions. Additionally, the contents of vitamin C, soluble sugars, and proteins treated with HTB increased by 18.81%, 11.54%, and 99.75%, respectively. Mechanistic research revealed that HTB treatment enhances tomato's stress resistance by elevating photosynthetic pigment and proline contents, enhancing antioxidant enzyme activities, and reducing the accumulation of MDA. Molecular biology research demonstrates that HTB treatment upregulates the expression of drought-resistant genes (GA2ox7, USP1, SlNAC3, SlNAC4), leading to modifications in stomatal conductance, plant morphology, photosynthetic intensity, and antioxidant enzyme synthesis to facilitate adaptation to dry conditions. Furthermore, the upregulation of the heat-resistant gene (SlCathB2-2) can increases the thickness of tomato cell walls, rendering them less vulnerable to heat stress. In summary, HTB endows tomatoes with the ability to adapt to high temperatures and drought conditions, providing new opportunities for sustainable agriculture.
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Affiliation(s)
- Yuke Wan
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Qicheng Xiao
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Xiao Xiao
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China.
| | - Yutian Huang
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Shiqi Liu
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Weiran Feng
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Ting Liu
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Zhong Ren
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Wei Ren
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
| | - Xubiao Luo
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China; Key Laboratory of Jiangxi Province for Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region, School of Life Sciences, Jinggangshan University, Ji'an, 343009, PR China
| | - Shenglian Luo
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, PR China; National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resources Utilization, Nanchang Hangkong University, Nanchang, 330063, PR China
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Chaudhary M, Singh P, Singh GP, Rathi B. Structural Features of Carbon Dots and Their Agricultural Potential. ACS OMEGA 2024; 9:4166-4185. [PMID: 38313515 PMCID: PMC10831853 DOI: 10.1021/acsomega.3c04638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 02/06/2024]
Abstract
Carbon dots (CDs) have drawn attention due to their enticing physical, chemical, and surface properties. Besides, good conductivity, low toxicity, environmental friendliness, simple synthetic routes, and comparable optical properties are advantageous features of CDs. Further, recently, CDs have been explored for biological systems, including plants. Among biological systems, only plants form the basis for sustainability and life on Earth. In this Review, we reviewed suitable properties and applications of CDs, such as promoting the growth of agricultural plants, disease resistance, stress tolerance, and target transportation. Summing up the available studies, we believe that the applications of CDs are yet to be explored significantly for innovation and technology-based agriculture.
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Affiliation(s)
- Monika Chaudhary
- Department
of Chemistry, Hansraj College, University
of Delhi, Delhi 110007, India
| | - Priyamvada Singh
- Department
of Chemistry, Miranda House, University
of Delhi, Delhi 110007, India
| | - Gajendra Pratap Singh
- Disruptive
and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology
(SMART), 138602 Singapore
| | - Brijesh Rathi
- Department
of Chemistry, Hansraj College, University
of Delhi, Delhi 110007, India
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Ikram M, Rauf A, Rao MJ, Maqsood MFK, Bakhsh MZM, Ullah M, Batool M, Mehran M, Tahira M. CRISPR-Cas9 based molecular breeding in crop plants: a review. Mol Biol Rep 2024; 51:227. [PMID: 38281301 DOI: 10.1007/s11033-023-09086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024]
Abstract
Traditional crop breeding techniques are not quickly boosting yields to fulfill the expanding population needs. Long crop lifespans hinder the ability of plant breeding to develop superior crop varieties. Due to the arduous crossing, selecting, and challenging processes, it can take decades to establish new varieties with desired agronomic traits. Develop new plant varieties instantly to reduce hunger and improve food security. As a result of the adoption of conventional agricultural techniques, crop genetic diversity has decreased over time. Several traditional and molecular techniques, such as genetic selection, mutant breeding, somaclonal variation, genome-wide association studies, and others, have improved agronomic traits associated with agricultural plant productivity, quality, and resistance to biotic and abiotic stresses. In addition, modern genome editing approaches based on programmable nucleases, CRISPR, and Cas9 proteins have escorted an exciting new era of plant breeding. Plant breeders and scientists worldwide rely on cutting-edge techniques like quick breeding, genome editing tools, and high-throughput phenotyping to boost crop breeding output. This review compiles discoveries in numerous areas of crop breeding, such as using genome editing tools to accelerate the breeding process and create yearly crop generations with the desired features, to describe the shift from conventional to modern plant breeding techniques.
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Affiliation(s)
- Muhammad Ikram
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Abdul Rauf
- National Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei, China
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | | | | | - Maaz Ullah
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maria Batool
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Mehran
- Key Laboratory of Arable Land Conservation, Huazhong Agricultural University, Ministry of Agriculture, Wuhan, 430070, China
| | - Maryam Tahira
- National Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei, China
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Guo Z, Wang S, Zhang F, Xiang D, Yang J, Li D, Bai B, Dai M, Luo J, Xiong L. Common and specific genetic basis of metabolite-mediated drought responses in rice. STRESS BIOLOGY 2024; 4:6. [PMID: 38253937 PMCID: PMC10803723 DOI: 10.1007/s44154-024-00150-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Plants orchestrate drought responses at metabolic level but the genetic basis remains elusive in rice. In this study, 233 drought-responsive metabolites (DRMs) were quantified in a large rice population comprised of 510 diverse accessions at the reproductive stage. Large metabolic variations in drought responses were detected, and little correlation of metabolic levels between drought and normal conditions were observed. Interestingly, most of these DRMs could predict drought resistance in high accuracy. Genome-wide association study revealed 2522 significant association signals for 233 DRMs, and 98% (2471/2522) of the signals were co-localized with the association loci for drought-related phenotypic traits in the same population or the linkage-mapped QTLs for drought resistance in other populations. Totally, 10 candidate genes were efficiently identified for nine DRMs, seven of which harbored cis-eQTLs under drought condition. Based on comparative GWAS of common DRMs in rice and maize, representing irrigated and upland crops, we have identified three pairs of homologous genes associated with three DRMs between the two crops. Among the homologous genes, a transferase gene responsible for metabolic variation of N-feruloylputrescine was confirmed to confer enhanced drought resistance in rice. Our study provides not only genetic architecture of metabolic responses to drought stress in rice but also metabolic data resources to reveal the common and specific metabolite-mediated drought responses in different crops.
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Affiliation(s)
- Zilong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Feng Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Dong Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baowei Bai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Sanchez D, Allier A, Ben Sadoun S, Mary-Huard T, Bauland C, Palaffre C, Lagardère B, Madur D, Combes V, Melkior S, Bettinger L, Murigneux A, Moreau L, Charcosset A. Assessing the potential of genetic resource introduction into elite germplasm: a collaborative multiparental population for flint maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:19. [PMID: 38214870 PMCID: PMC10786986 DOI: 10.1007/s00122-023-04509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/18/2023] [Indexed: 01/13/2024]
Abstract
KEY MESSAGE Implementing a collaborative pre-breeding multi-parental population efficiently identifies promising donor x elite pairs to enrich the flint maize elite germplasm. Genetic diversity is crucial for maintaining genetic gains and ensuring breeding programs' long-term success. In a closed breeding program, selection inevitably leads to a loss of genetic diversity. While managing diversity can delay this loss, introducing external sources of diversity is necessary to bring back favorable genetic variation. Genetic resources exhibit greater diversity than elite materials, but their lower performance levels hinder their use. This is the case for European flint maize, for which elite germplasm has incorporated only a limited portion of the diversity available in landraces. To enrich the diversity of this elite genetic pool, we established an original cooperative maize bridging population that involves crosses between private elite materials and diversity donors to create improved genotypes that will facilitate the incorporation of original favorable variations. Twenty donor × elite BC1S2 families were created and phenotyped for hybrid value for yield related traits. Crosses showed contrasted means and variances and therefore contrasted potential in terms of selection as measured by their usefulness criterion (UC). Average expected mean performance gain over the initial elite material was 5%. The most promising donor for each elite line was identified. Results also suggest that one more generation, i.e., 3 in total, of crossing to the elite is required to fully exploit the potential of a donor. Altogether, our results support the usefulness of incorporating genetic resources into elite flint maize. They call for further effort to create fixed diversity donors and identify those most suitable for each elite program.
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Affiliation(s)
- Dimitri Sanchez
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Antoine Allier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Syngenta, 12 Chemin de L'Hobit, 31790, Saint-Sauveur, France
| | - Sarah Ben Sadoun
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris Saclay, 91120, Palaiseau, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Bernard Lagardère
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | | | | | - Alain Murigneux
- Limagrain Europe, 28 Route d'Ennezat, 63720, Chappes, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France.
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Claussen J, Wittenberg T, Uhlmann N, Gerth S. "Chamber #8" - a holistic approach of high-throughput non-destructive assessment of plant roots. FRONTIERS IN PLANT SCIENCE 2024; 14:1269005. [PMID: 38239230 PMCID: PMC10794641 DOI: 10.3389/fpls.2023.1269005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/01/2023] [Indexed: 01/22/2024]
Abstract
Introduction In the past years, it has been observed that the breeding of plants has become more challenging, as the visible difference in phenotypic data is much smaller than decades ago. With the ongoing climate change, it is necessary to breed crops that can cope with shifting climatic conditions. To select good breeding candidates for the future, phenotypic experiments can be conducted under climate-controlled conditions. Above-ground traits can be assessed with different optical sensors, but for the root growth, access to non-destructively measured traits is much more challenging. Even though MRI or CT imaging techniques have been established in the past years, they rely on an adequate infrastructure for the automatic handling of the pots as well as the controlled climate. Methods To address both challenges simultaneously, the non-destructive imaging of plant roots combined with a highly automated and standardized mid-throughput approach, we developed a workflow and an integrated scanning facility to study root growth. Our "chamber #8" contains a climate chamber, a material flow control, an irrigation system, an X-ray system, a database for automatic data collection, and post-processing. The goals of this approach are to reduce the human interaction with the various components of the facility to a minimum on one hand, and to automate and standardize the complete process from plant care via measurements to root trait calculation on the other. The user receives standardized phenotypic traits and properties that were collected objectively. Results The proposed holistic approach allows us to study root growth of plants in a field-like substrate non-destructively over a defined period and to calculate phenotypic traits of root architecture. For different crops, genotypic differences can be observed in response to climatic conditions which have already been applied to a wide variety of root structures, such as potatoes, cassava, or corn. Discussion It enables breeders and scientists non-destructive access to root traits. Additionally, due to the non-destructive nature of X-ray computed tomography, the analysis of time series for root growing experiments is possible and enables the observation of kinetic traits. Furthermore, using this automation scheme for simultaneously controlled plant breeding and non-destructive testing reduces the involvement of human resources.
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Affiliation(s)
- Joelle Claussen
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
| | - Thomas Wittenberg
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department for Visual Computing, Erlangen, Germany
| | - Norman Uhlmann
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
| | - Stefan Gerth
- Fraunhofer Institute for Integrated Circuits (IIS), Department Development Center X-ray Technology, Fuerth, Germany
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Pal G, Ingole KD, Yavvari PS, Verma P, Kumari A, Chauhan C, Chaudhary D, Srivastava A, Bajaj A, Vemanna RS. Exogenous application of nanocarrier-mediated double-stranded RNA manipulates physiological traits and defence response against bacterial diseases. MOLECULAR PLANT PATHOLOGY 2024; 25:e13417. [PMID: 38279851 PMCID: PMC10799200 DOI: 10.1111/mpp.13417] [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: 08/01/2023] [Revised: 12/09/2023] [Accepted: 12/17/2023] [Indexed: 01/29/2024]
Abstract
Stability and delivery are major challenges associated with exogenous double-stranded RNA (dsRNA) application into plants. We report the encapsulation and delivery of dsRNA in cationic poly-aspartic acid-derived polymer (CPP6) into plant cells. CPP6 stabilizes the dsRNAs during long exposure at varied temperatures and pH, and protects against RNase A degradation. CPP6 helps dsRNA uptake through roots or foliar spray and facilitates systemic movement to induce endogenous gene silencing. The fluorescence of Arabidopsis GFP-overexpressing transgenic plants was significantly reduced after infiltration with gfp-dsRNA-CPP6 by silencing of the transgene compared to plants treated only with gfp-dsRNA. The plant endogenous genes flowering locus T (FT) and phytochrome interacting factor 4 (PIF4) were downregulated by a foliar spray of ft-dsRNA-CPP6 and pif4-dsRNA-CPP6 in Arabidopsis, with delayed flowering and enhanced biomass. The rice PDS gene targeted by pds-dsRNA-CPP6 through root uptake was effectively silenced and plants showed a dwarf and albino phenotype. The NaCl-induced OsbZIP23 was targeted through root uptake of bzip23-dsRNA-CPP6 and showed reduced transcripts and seedling growth compared to treatment with naked dsRNA. The negative regulators of plant defence SDIR1 and SWEET14 were targeted through foliar spray to provide durable resistance against bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Overall, the study demonstrates that transient silencing of plant endogenous genes using polymer-encapsulated dsRNA provides prolonged and durable resistance against Xoo, which could be a promising tool for crop protection and for sustaining productivity.
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Affiliation(s)
- Garima Pal
- Laboratory of Plant Functional GenomicsRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
| | - Kishor D. Ingole
- Laboratory of Plant Functional GenomicsRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
| | | | - Priyanka Verma
- Laboratory of Nanotechnology and Chemical BiologyRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
| | - Ankit Kumari
- Plant Genetic Engineering LabCentre for Biotechnology, Maharshi Dayananda UniversityRohtakIndia
| | - Chetan Chauhan
- Laboratory of Plant Functional GenomicsRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
| | - Darshna Chaudhary
- Plant Genetic Engineering LabCentre for Biotechnology, Maharshi Dayananda UniversityRohtakIndia
| | - Aasheesh Srivastava
- Department of ChemistryIndian Institute of Science Education and ResearchBhopalIndia
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical BiologyRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
| | - Ramu S. Vemanna
- Laboratory of Plant Functional GenomicsRegional Centre for Biotechnology, NCR Biotech Science ClusterFaridabadIndia
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Chen X, Gao J, Chen L, Khanna M, Gong B, Auffhammer M. The spatiotemporal pattern of surface ozone and its impact on agricultural productivity in China. PNAS NEXUS 2024; 3:pgad435. [PMID: 38152458 PMCID: PMC10752353 DOI: 10.1093/pnasnexus/pgad435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
The slowing of agricultural productivity growth globally over the past two decades has brought a new urgency to detect its drivers and potential solutions. We show that air pollution, particularly surface ozone (O3), is strongly associated with declining agricultural total factor productivity (TFP) in China. We employ machine learning algorithms to generate estimates of high-resolution surface O3 concentrations from 2002 to 2019. Results indicate that China's O3 pollution has intensified over this 18-year period. We coupled these O3 estimates with a statistical model to show that rising O3 pollution during nonwinter seasons has reduced agricultural TFP by 18% over the 2002-2015 period. Agricultural TFP is projected to increase by 60% if surface O3 concentrations were reduced to meet the WHO air quality standards. This productivity gain has the potential to counter expected productivity losses from 2°C warming.
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Affiliation(s)
- Xiaoguang Chen
- Research Institute of Economics and Management, Southwestern University of Finance and Economics, 610074 Chengdu, China
| | - Jing Gao
- Research Institute of Economics and Management, Southwestern University of Finance and Economics, 610074 Chengdu, China
| | - Luoye Chen
- Carbon Neutrality and Climate Change Thrust, Society Hub, Hong Kong University of Science and Technology (Guangzhou), 511453 Guangzhou, China
| | - Madhu Khanna
- Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Binlei Gong
- China Academy for Rural Development (CARD) and School of Public Affairs, Zhejiang University, 310025 Hangzhou, China
| | - Maximilian Auffhammer
- Department of Agricultural and Resource Economics, University of California, Berkeley, CA 94720, USA
- National Bureau of Economic Research, Cambridge, MA 02138, USA
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Zhao S, Luo J, Tang M, Zhang C, Song M, Wu G, Yan X. Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line. Int J Mol Sci 2023; 25:174. [PMID: 38203344 PMCID: PMC10778984 DOI: 10.3390/ijms25010174] [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: 10/23/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.
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Affiliation(s)
- Shengbo Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Min Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Miaoying Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohong Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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Deng K, Zhang H, Wu J, Zhao Z, Wang D, Xu G, Yu J, Ling Y, Zhao F. Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783. Int J Mol Sci 2023; 24:17305. [PMID: 38139135 PMCID: PMC10744095 DOI: 10.3390/ijms242417305] [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: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China; (K.D.); (H.Z.); (J.W.); (Z.Z.); (D.W.); (G.X.); (J.Y.); (Y.L.)
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47
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Strelin MM, Diggle PK, Aizen MA. Flower heterochrony and crop yield. TRENDS IN PLANT SCIENCE 2023; 28:1360-1369. [PMID: 37612211 DOI: 10.1016/j.tplants.2023.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/17/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Crop improvement has focused on enhancing yield, nutrient content, harvestability, and stress resistance using a trait-centered reductionist approach. This has downplayed the fact that plants are developmentally integrated and respond coordinately and predictably to genetic and environmental variation, with potential consequences for food production. Crop yield, including both fruit/seed production and the possibility of generating hybrid crop varieties, is highly dependent on flower morphology and sex, which, in turn, can be profoundly affected by slight shifts in the timing and rate of flower organ development (i.e., flower heterochrony). We argue that understanding the genetic and environmental bases of flower heterochrony and their effect on flower morphology and sex in cultivated plants and in their wild relatives can facilitate crop improvement.
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Affiliation(s)
- Marina M Strelin
- Grupo de Investigación en Ecología de la Polinización, Laboratorio Ecotono, INIBIOMA (CONICET - Universidad Nacional del Comahue), San Carlos de Bariloche, Río Negro, Argentina.
| | - Pamela K Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Marcelo A Aizen
- Grupo de Investigación en Ecología de la Polinización, Laboratorio Ecotono, INIBIOMA (CONICET - Universidad Nacional del Comahue), San Carlos de Bariloche, Río Negro, Argentina
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48
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Jin Y, Xiao L, Zheng J, Su F, Yu Z, Mu Y, Zhang W, Li L, Han G, Ma P. Genetic Analysis and Molecular Identification of the Powdery Mildew Resistance in 116 Elite Wheat Cultivars/Lines. PLANT DISEASE 2023; 107:3801-3809. [PMID: 37272049 DOI: 10.1094/pdis-04-23-0792-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease worldwide. Host resistance is the preferred method for limiting the disease epidemic, protecting the environment, and minimizing economic losses. In the present study, the reactions to powdery mildew for a collection of 600 wheat cultivars and breeding lines from different wheat-growing regions were tested using the Bgt isolate E09. Next, 116 resistant genotypes were identified and then crossed with susceptible wheat cultivars/lines to produce segregating populations for genetic analysis. Among them, 87, 19, and 10 genotypes displayed single, dual, and multiple genic inheritance, respectively. To identify the Pm gene(s) in those resistant genotypes, 16 molecular markers for 13 documented Pm genes were used to test the resistant and susceptible parents and their segregating populations. Of the 87 wheat genotypes that fitted the monogenic inheritance, 75 carried the Pm2a allele. Three, two, one, and two genotypes carried Pm21, Pm6, Pm4, and the recessive genes pm6 and pm42, respectively. Four genotypes did not carry any of the tested genes, suggesting that they might have other uncharacterized or new genes. The other 29 wheat cultivars/lines carried two or more of the tested Pm genes and/or other untested genes, including Pm2, Pm5, Pm6, and/or pm42. It was obvious that Pm2 was widely used in wheat production, whereas Pm1, Pm24, Pm33, Pm34, Pm35, Pm45, and Pm47 were not detected in any of these resistant wheat genotypes. This study clarified the genetic basis of the powdery mildew resistance of these wheat cultivars/lines to provide information for their rational utilization in different wheat-growing regions. Moreover, some wheat genotypes which may have novel Pm gene(s) were mined to enrich the diversity of resistance source.
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Affiliation(s)
- Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Luning Xiao
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Jianpeng Zheng
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Fuyu Su
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Ziyang Yu
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Yanjun Mu
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Wenjing Zhang
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
| | - Linzhi Li
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China
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Sobiech A, Tomkowiak A, Bocianowski J, Szymańska G, Nowak B, Lenort M. Identification and Analysis of Candidate Genes Associated with Maize Fusarium Cob Resistance Using Next-Generation Sequencing Technology. Int J Mol Sci 2023; 24:16712. [PMID: 38069033 PMCID: PMC10705949 DOI: 10.3390/ijms242316712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The pressure to reduce mineral fertilization and the amount of pesticides used has become a factor limiting production growth, as has the elimination of many crop protection chemicals from the market. A key condition for this to be an effective form of protection is the use of varieties with higher levels of resistance. The most effective and fastest way to assist in the selection and control of pathogens is the conducting of genome-wide association studies. These are useful tools for identifying candidate genes, especially when combined with QTL mapping to map and validate loci for quantitative traits. The aim of this study was to identify new markers coupled to genes that determine maize plant resistance to fusarium head blight through the use of next-generation sequencing, association and physical mapping, and to optimize diagnostic procedures to identify selected molecular markers coupled to plant resistance to this fungal disease. As a result of field experiments and molecular analyses, molecular markers coupled to potential genes for resistance to maize ear fusariosis were selected. The newly selected markers were tested against reference genotypes. As a result of the analyses, it was found that two markers (11801 and 20607) out of the ten that were tested differentiated between susceptible and resistant genotypes. Marker number 11801 proved to be the most effective, with a specious product of 237 bp appearing for genotypes 1, 3, 5, 9 and 10. These genotypes were characterized by a field resistance of 4-6 on the 9° scale (1 being susceptible, 9 being resistant) and for all genotypes except 16 and 20, which were characterized by a field resistance of 9. In the next step, this marker will be tested on a wider population of extreme genotypes in order to use it for the preliminary selection of fusarium-resistant genotypes, and the phosphoenolpyruvate carboxylase kinase 1 gene coupled to it will be subjected to expression analysis.
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Affiliation(s)
- Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (M.L.)
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (M.L.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland;
| | - Grażyna Szymańska
- Department of Agronomy, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Bartosz Nowak
- Smolice Plant Breeding Sp. Z o.o. IHAR Group, Smolice 146, 63-740 Kobylin, Poland;
| | - Maciej Lenort
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (M.L.)
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50
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Fang X, Feng X, Sun X, Yang X, Li Q, Yang X, Xu J, Zhou M, Lin C, Sui Y, Zhao L, Liu B, Kong F, Zhang C, Li M. Natural variation of MS2 confers male fertility and drives hybrid breeding in soybean. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2322-2332. [PMID: 37475199 PMCID: PMC10579707 DOI: 10.1111/pbi.14133] [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: 05/09/2023] [Revised: 06/14/2023] [Accepted: 07/06/2023] [Indexed: 07/22/2023]
Abstract
A complete and genetically stable male sterile line with high outcrossing rate is a prerequisite for the development of commercial hybrid soybean. It was reported in the last century that the soybean male sterile ms2 mutant has the highest record with seed set. Here we report the cloning and characterization of the MS2 gene in soybean, which encodes a protein that is specifically expressed in the anther. MS2 functions in the tapetum and microspore by directly regulating genes involved in the biosynthesis of secondary metabolites and the lipid metabolism, which is essential for the formation of microspore cell wall. Through comparison of the field performance with the widely used male sterile mutants in the same genetic background, we demonstrated that the ms2 mutant conducts the best in outcrossing rate and makes it an ideal tool in building a cost-effective hybrid system for soybean.
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Affiliation(s)
- Xiaolong Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Xiangchi Feng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Xiaoyuan Sun
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Xiangdong Yang
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural AffairsJilin Academy of Agricultural SciencesChangchunChina
| | - Qing Li
- State Key Laboratory of Rice Biology, China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouChina
| | - Xulei Yang
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural AffairsJilin Academy of Agricultural SciencesChangchunChina
| | - Jie Xu
- Core Facility and Technical Service Center for SLSB, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Minghui Zhou
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Chunjing Lin
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural AffairsJilin Academy of Agricultural SciencesChangchunChina
| | - Yi Sui
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Limei Zhao
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural AffairsJilin Academy of Agricultural SciencesChangchunChina
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Chunbao Zhang
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural AffairsJilin Academy of Agricultural SciencesChangchunChina
| | - Meina Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
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