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Zhang Z, Lv Y, Sun Q, Yao X, Yan H. Comparative Phenotypic and Transcriptomic Analyses Provide Novel Insights into the Molecular Mechanism of Seed Germination in Response to Low Temperature Stress in Alfalfa. Int J Mol Sci 2024; 25:7244. [PMID: 39000350 PMCID: PMC11241472 DOI: 10.3390/ijms25137244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Low temperature is the most common abiotic factor that usually occurs during the seed germination of alfalfa (Medicago sativa L.). However, the potential regulatory mechanisms involved in alfalfa seed germination under low temperature stress are still ambiguous. Therefore, to determine the relevant key genes and pathways, the phenotypic and transcriptomic analyses of low-temperature sensitive (Instict) and low-temperature tolerant (Sardi10) alfalfa were conducted at 6 and 15 h of seed germination under normal (20 °C) and low (10 °C) temperature conditions. Germination phenotypic results showed that Sardi10 had the strongest germination ability under low temperatures, which was manifested by the higher germination-related indicators. Further transcriptome analysis indicated that differentially expressed genes were mainly enriched in galactose metabolism and carbon metabolism pathways, which were the most commonly enriched in two alfalfa genotypes. Additionally, fatty acid metabolism and glutathione metabolism pathways were preferably enriched in Sardi10 alfalfa. The Weighted Gene Co-Expression Network Analysis (WGCNA) suggested that genes were closely related to galactose metabolism, fatty acid metabolism, and glutathione metabolism in Sardi10 alfalfa at the module with the highest correlation (6 h of germination under low temperature). Finally, qRT-PCR analysis further validated the related genes involved in the above pathways, which might play crucial roles in regulating seed germination of alfalfa under low temperature conditions. These findings provide new insights into the molecular mechanisms of seed germination underlying the low temperature stress in alfalfa.
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Affiliation(s)
- Zhao Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Yanzhen Lv
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Qingying Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Xingjie Yao
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Huifang Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
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Balech R, Maalouf F, Kaur S, Jighly A, Joukhadar R, Alsamman AM, Hamwieh A, Khater LA, Rubiales D, Kumar S. Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.). Sci Rep 2024; 14:10215. [PMID: 38702403 PMCID: PMC11068770 DOI: 10.1038/s41598-024-59695-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop.
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Affiliation(s)
- Rind Balech
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon.
| | - Fouad Maalouf
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon.
| | - Sukhjiwan Kaur
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Abdulqader Jighly
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Reem Joukhadar
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | | | | | - Lynn Abou Khater
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Das Laha S, Kundu A, Podder S. Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits. PLANTA 2024; 259:97. [PMID: 38520529 DOI: 10.1007/s00425-024-04379-1] [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: 11/09/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.
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Affiliation(s)
- Shayani Das Laha
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Avijit Kundu
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India.
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Zhang L, Liu L, Li H, He J, Chao H, Yan S, Yin Y, Zhao W, Li M. 3D genome structural variations play important roles in regulating seed oil content of Brassica napus. PLANT COMMUNICATIONS 2024; 5:100666. [PMID: 37496273 PMCID: PMC10811347 DOI: 10.1016/j.xplc.2023.100666] [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: 03/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan 430075, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Yontai Yin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China.
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Yi S, Zhu Z, Li F, Zhu L, Wu C, Ge F, Ji X, Tian J. Metagenomic and proteomic insights into the self-adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium-phenanthrene co-pollutant in rice. Environ Microbiol 2024; 26:e16577. [PMID: 38183371 DOI: 10.1111/1462-2920.16577] [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: 09/11/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Cell surface hydrophobicity (CSH) dominates the interactions between rhizobacteria and pollutants at the soil-water interface, which is critical for understanding the dissipation of pollutants in the rhizosphere microzone of rice. Herein, we explored the effects of self-adaptive CSH of Sphingomonas sp. strain PAH02 on the translocation and biotransformation behaviour of cadmium-phenanthrene (Cd-Phe) co-pollutant in rice and rhizosphere microbiome. We evidenced that strain PAH02 reduced the adsorption of Cd-Phe co-pollutant on the rice root surface while enhancing the degradation of Phe and adsorption of Cd via its self-adaptive CSH in the hydroponic experiment. The significant upregulation of key protein expression levels such as MerR, ARHDs and enoyl-CoA hydratase/isomerase, ensures self-adaptive CSH to cope with the stress of Cd-Phe co-pollutant. Consistently, the bioaugmentation of strain PAH02 promoted the formation of core microbiota in the rhizosphere soil of rice (Oryza sativa L.), such as Bradyrhizobium and Streptomyces and induced gene enrichment of CusA and PobA that are strongly associated with pollutant transformation. Consequently, the contents of Cd and Phe in rice grains at maturity decreased by 17.2% ± 0.2% and 65.7% ± 0.3%, respectively, after the bioaugmentation of strain PAH02. These findings present new opportunities for the implementation of rhizosphere bioremediation strategies of co-contaminants in paddy fields.
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Affiliation(s)
- Shengwei Yi
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Zhongnan Zhu
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Feng Li
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chen Wu
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Fei Ge
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Xionghui Ji
- Hunan Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jiang Tian
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
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Peng Z, Yu S, Meng J, Jia KH, Zhang J, Li X, Gao W, Wan S. Alternative polyadenylation regulates acetyl-CoA carboxylase function in peanut. BMC Genomics 2023; 24:637. [PMID: 37875812 PMCID: PMC10594767 DOI: 10.1186/s12864-023-09696-5] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Polyadenylation is a crucial process that terminates mRNA molecules at their 3'-ends. It has been observed that alternative polyadenylation (APA) can generate multiple transcripts from a single gene locus, each with different polyadenylation sites (PASs). This leads to the formation of several 3' untranslated regions (UTRs) that vary in length and composition. APA has a significant impact on approximately 60-70% of eukaryotic genes and has far-reaching implications for cell proliferation, differentiation, and tumorigenesis. RESULTS In this study, we conducted long-read, single-molecule sequencing of mRNA from peanut seeds. Our findings revealed that over half of all peanut genes possess over two PASs, with older developing seeds containing more PASs. This suggesting that the PAS exhibits high tissue specificity and plays a crucial role in peanut seed maturation. For the peanut acetyl-CoA carboxylase A1 (AhACCA1) gene, we discovered four 3' UTRs referred to UTR1-4. RT-PCR analysis showed that UTR1-containing transcripts are predominantly expressed in roots, leaves, and early developing seeds. Transcripts containing UTR2/3 accumulated mainly in roots, flowers, and seeds, while those carrying UTR4 were constitutively expressed. In Nicotiana benthamiana leaves, we transiently expressed all four UTRs, revealing that each UTR impacted protein abundance but not subcellular location. For functional validation, we introduced each UTR into yeast cells and found UTR2 enhanced AhACCA1 expression compared to a yeast transcription terminator, whereas UTR3 did not. Furthermore, we determined ACC gene structures in seven plant species and identified 51 PASs for 15 ACC genes across four plant species, confirming that APA of the ACC gene family is universal phenomenon in plants. CONCLUSION Our data demonstrate that APA is widespread in peanut seeds and plays vital roles in peanut seed maturation. We have identified four 3' UTRs for AhACCA1 gene, each showing distinct tissue-specific expression patterns. Through subcellular location experiment and yeast transformation test, we have determined that UTR2 has a stronger impact on gene expression regulation compared to the other three UTRs.
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Affiliation(s)
- Zhenying Peng
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China.
| | - Shuang Yu
- College of Agricultural, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jingjing Meng
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Jialei Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Xinguo Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Wenwei Gao
- College of Agricultural, Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Shubo Wan
- Shandong Academy of Agricultural Science, Jinan, 250100, China.
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Jin H, Yang X, Zhao H, Song X, Tsvetkov YD, Wu Y, Gao Q, Zhang R, Zhang J. Genetic analysis of protein content and oil content in soybean by genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1182771. [PMID: 37346139 PMCID: PMC10281628 DOI: 10.3389/fpls.2023.1182771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023]
Abstract
Soybean seed protein content (PC) and oil content (OC) have important economic value. Detecting the loci/gene related to PC and OC is important for the marker-assisted selection (MAS) breeding of soybean. To detect the stable and new loci for PC and OC, a total of 320 soybean accessions collected from the major soybean-growing countries were used to conduct a genome-wide association study (GWAS) by resequencing. The PC ranged from 37.8% to 46.5% with an average of 41.1% and the OC ranged from 16.7% to 22.6% with an average of 21.0%. In total, 23 and 29 loci were identified, explaining 3.4%-15.4% and 5.1%-16.3% of the phenotypic variations for PC and OC, respectively. Of these, eight and five loci for PC and OC, respectively, overlapped previously reported loci and the other 15 and 24 loci were newly identified. In addition, nine candidate genes were identified, which are known to be involved in protein and oil biosynthesis/metabolism, including lipid transport and metabolism, signal transduction, and plant development pathway. These results uncover the genetic basis of soybean protein and oil biosynthesis and could be used to accelerate the progress in enhancing soybean PC and OC.
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Affiliation(s)
- Hui Jin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Haibin Zhao
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xizhang Song
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yordan Dimitrov Tsvetkov
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - YuE Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiang Gao
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jumei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Adhikary D, Kisiala A, Sarkar A, Basu U, Rahman H, Emery N, Kav NNV. Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus. Mol Omics 2022; 18:991-1014. [PMID: 36382681 DOI: 10.1039/d2mo00251e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Clubroot, a devastating soil-borne root disease, in Brassicaceae is caused by Plasmodiophora brassicae Woronin (P. brassicae W.), an obligate biotrophic protist. Plant growth and development, as well as seed yield of Brassica crops, are severely affected due to this disease. Several reports described the molecular responses of B. napus to P. brassicae; however, information on the early stages of pathogenesis is limited. In this study, we have used transcriptomics and metabolomics to characterize P. brassicae pathogenesis at 1-, 4-, and 7-days post-inoculation (DPI) in clubroot resistant (CR) and susceptible (CS) doubled-haploid (DH) canola lines. When we compared between inoculated and uninoculated groups, a total of 214 and 324 putative genes exhibited differential expression (q-value < 0.05) at one or more time-points in the CR and CS genotypes, respectively. When the inoculated CR and inoculated CS genotypes were compared, 4765 DEGs were differentially expressed (q-value < 0.05) at one or more time-points. Several metabolites related to organic acids (e.g., citrate, pyruvate), amino acids (e.g., proline, aspartate), sugars, and mannitol, were differentially accumulated in roots in response to pathogen infection when the CR and CS genotypes were compared. Several DEGs also corresponded to differentially accumulated metabolites, including pyrroline-5-carboxylate reductase (BnaC04g11450D), citrate synthase (BnaC02g39080D), and pyruvate kinase (BnaC04g23180D) as detected by transcriptome analysis. Our results suggest important roles for these genes in mediating resistance to clubroot disease. To our knowledge, this is the first report of an integrated transcriptome and metabolome analysis aimed at characterizing the molecular basis of resistance to clubroot in canola.
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Affiliation(s)
- Dinesh Adhikary
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Anna Kisiala
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Ananya Sarkar
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Urmila Basu
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Habibur Rahman
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Neil Emery
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Nat N V Kav
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
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