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Salami M, Heidari B, Alizadeh B, Batley J, Wang J, Tan XL, Dadkhodaie A, Richards C. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1342359. [PMID: 38567131 PMCID: PMC10985355 DOI: 10.3389/fpls.2024.1342359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security. Methods In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season. Results The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation. Discussion The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
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Affiliation(s)
- Maryam Salami
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Alizadeh
- Oil Crops Research Department, Seed and Plant Improvement Institute, Agricultural Research Education and Extension, Organization, (AREEO), Karaj, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Zhou T, He Y, Zeng X, Cai B, Qu S, Wang S. Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection. Int J Mol Sci 2022; 23:ijms232214202. [PMID: 36430679 PMCID: PMC9693243 DOI: 10.3390/ijms232214202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Alternaria blotch disease, caused by the Alternaria alternata apple pathotype (A. alternata AP), is one of the most serious fungal diseases in apples. Alternative splicing (AS), one of the pivotal post-transcriptional regulatory mechanisms, plays essential roles in various disease resistance responses. Here, we performed RNA-Seq for two apple cultivars (resistant cultivar 'Jonathan' (J) and susceptible cultivar 'Starking Delicious' (SD)) infected by A. alternata AP to further investigate their AS divergence. In total, 1454, 1780, 1367 and 1698 specifically regulated differential alternative splicing (DAS) events were detected in J36, J72, SD36 and SD72 groups, respectively. Retained intron (RI) was the dominant AS pattern. Conformably, 642, 764, 585 and 742 uniquely regulated differentially spliced genes (DSGs) were found during A. alternata AP infection. Comparative analysis of AS genes in differential splicing and expression levels suggested that only a small proportion of DSGs overlapped with differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis demonstrated that the DSGs were significantly enriched at multiple levels of gene expression regulation. Briefly, the specific AS was triggered in apple defense against A. alternata AP. Therefore, this study facilitates our understanding on the roles of AS regulation in response to A. alternata AP infection in apples.
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Gao C, Lu S, Zhou R, Ding J, Fan J, Han B, Chen M, Wang B, Cao Y. Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family. BMC Genomics 2022; 23:744. [DOI: 10.1186/s12864-022-08956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
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Yang L, Yang L, Zhao C, Liu J, Tong C, Zhang Y, Cheng X, Jiang H, Shen J, Xie M, Liu S. Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009998. [PMID: 36311064 PMCID: PMC9608124 DOI: 10.3389/fpls.2022.1009998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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Affiliation(s)
- Lingli Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Yang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Liu L, Wu D, Gu Y, Liu F, Liu B, Mao F, Yi X, Tang T, Zhao X. Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:44. [PMID: 37313517 PMCID: PMC10248609 DOI: 10.1007/s11032-022-01314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level, which increases the transcriptomic diversity. Oilseed rape (Brassica napus L.), one of the main oil crops worldwide, is prone to secondary dormancy. However, how alternative splicing landscape of oilseed rape seed changes in response to secondary dormancy is unknown. Here, we analyzed twelve RNA-seq libraries from varieties "Huaiyou-SSD-V1" and "Huaiyou-WSD-H2" which exhibited high (> 95%) and low (< 5%) secondary dormancy potential, respectively, and demonstrated that alternative splicing changes led to a significant increase with the diversity of the transcripts in response to secondary dormancy induction via polyethylene glycol 6000 (PEG6000) treatment. Among the four basic alternative splicing types, intron retention dominates, and exon skipping shows the rarest frequency. A total of 8% of expressed genes had two or more transcripts after PEG treatment. Further analysis revealed that global isoform expression percentage variations in alternative splicing in differently expressed genes (DEGs) is more than three times as much as those in non-DEGs, suggesting alternative splicing change is associated with the transcriptional activity change in response to secondary dormancy induction. Eventually, 342 differently spliced genes (DSGs) associated with secondary dormancy were identified, five of which were validated by RT-PCR. The number of the overlapped genes between DSGs and DEGs associated with secondary dormancy was much less than that of either DSGs or DEGs, suggesting that DSGs and DEGs may independently regulates secondary dormancy. Functional annotation analysis of DSGs revealed that spliceosome components are overrepresented among the DSGs, including small nuclear ribonucleoprotein particles (snRNPs), serine/arginine-rich (SR) proteins, and other splicing factors. Thus, it is proposed that the spliceosome components could be exploited to reduce secondary dormancy potential in oilseed rape. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01314-8.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei 066600 China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
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Arzalluz-Luque A, Salguero P, Tarazona S, Conesa A. acorde unravels functionally interpretable networks of isoform co-usage from single cell data. Nat Commun 2022; 13:1828. [PMID: 35383181 PMCID: PMC8983708 DOI: 10.1038/s41467-022-29497-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms establish co-expression networks that may be relevant in cellular function has not been explored yet. Here, we present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships. To achieve this, we develop and validate percentile correlations, an innovative approach that overcomes data sparsity and yields accurate co-expression estimates from single-cell data. Next, acorde uses correlations to cluster co-expressed isoforms into a network, unraveling cell type-specific alternative isoform usage patterns. By selecting same-gene isoforms between these clusters, we subsequently detect and characterize genes with co-differential isoform usage (coDIU) across cell types. Finally, we predict functional elements from long read-defined isoforms and provide insight into biological processes, motifs, and domains potentially controlled by the coordination of post-transcriptional regulation. The code for acorde is available at https://github.com/ConesaLab/acorde .
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Affiliation(s)
- Angeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain.,Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Pedro Salguero
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain.
| | - Ana Conesa
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain. .,Microbiology and Cell Sciences Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA.
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