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Chen Y, Liu Z, Han D, Yang Q, Li C, Shi X, Zhang M, Yang C, Qiu L, Jia H, Wang S, Lu W, Ma Q, Yan L. Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:178. [PMID: 38976061 DOI: 10.1007/s00122-024-04685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
KEY MESSAGE Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.
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Affiliation(s)
- Yuehan Chen
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Zhi Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Qing Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chenhui Li
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm and Biotechnology (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongchang Jia
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Shu Wang
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China.
| | - Qian Ma
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
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Montúfar-Romero M, Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C. Hypoxia in the Blue Mussel Mytilus chilensis Induces a Transcriptome Shift Associated with Endoplasmic Reticulum Stress, Metabolism, and Immune Response. Genes (Basel) 2024; 15:658. [PMID: 38927594 PMCID: PMC11203016 DOI: 10.3390/genes15060658] [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: 03/28/2024] [Revised: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
The increase in hypoxia events, a result of climate change in coastal and fjord ecosystems, impacts the health and survival of mussels. These organisms deploy physiological and molecular responses as an adaptive mechanism to maintain cellular homeostasis under environmental stress. However, the specific effects of hypoxia on mussels of socioeconomic interest, such as Mytilus chilensis, are unknown. Using RNA-seq, we investigated the transcriptomic profiles of the gills, digestive gland, and adductor muscle of M. chilensis under hypoxia (10 days at 2 mg L-1) and reoxygenation (10 days at 6 mg L-1). There were 15,056 differentially expressed transcripts identified in gills, 11,864 in the digestive gland, and 9862 in the adductor muscle. The response varied among tissues, showing chromosomal changes in Chr1, Chr9, and Chr10 during hypoxia. Hypoxia regulated signaling genes in the Toll-like, mTOR, citrate cycle, and apoptosis pathways in gills, indicating metabolic and immunological alterations. These changes suggest that hypoxia induced a metabolic shift in mussels, reducing reliance on aerobic respiration and increasing reliance on anaerobic metabolism. Furthermore, hypoxia appeared to suppress the immune response, potentially increasing disease susceptibility, with negative implications for the mussel culture industry and natural bed populations. This study provides pivotal insights into metabolic and immunological adaptations to hypoxia in M. chilensis, offering candidate genes for adaptive traits.
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Affiliation(s)
- Milton Montúfar-Romero
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (D.V.-M.)
- Biotecnology Center, Universidad de Concepción, Concepción 4030000, Chile
- Instituto Público de Investigación de Acuicultura y Pesca (IPIAP), Guayaquil 090314, Ecuador
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (D.V.-M.)
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Concepción 4030000, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (D.V.-M.)
- Biotecnology Center, Universidad de Concepción, Concepción 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción 4030000, Chile; (M.M.-R.); (V.V.-M.); (D.V.-M.)
- Biotecnology Center, Universidad de Concepción, Concepción 4030000, Chile
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Zan X, Zhou Z, Wan J, Chen H, Zhu J, Xu H, Zhang J, Li X, Gao X, Chen R, Huang Z, Xu Z, Li L. Overexpression of OsHAD3, a Member of HAD Superfamily, Decreases Drought Tolerance of Rice. RICE (NEW YORK, N.Y.) 2023; 16:31. [PMID: 37468664 DOI: 10.1186/s12284-023-00647-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Haloacid dehalogenase-like hydrolase (HAD) superfamily have been shown to get involved in plant growth and abiotic stress response. Although the various functions and regulatory mechanism of HAD superfamily have been well demonstrated, we know little about the function of this family in conferring abiotic stress tolerance to rice. Here, we report OsHAD3, a HAD superfamily member, could affect drought tolerance of rice. Under drought stress, overexpression of OsHAD3 increases the accumulation of reactive oxygen species and malondialdehyde than wild type. OsHAD3-overexpression lines decreased but antisense-expression lines increased the roots length under drought stress and the transcription levels of many well-known stress-related genes were also changed in plants with different genotypes. Furthermore, overexpression of OsHAD3 also decreases the oxidative tolerance. Our results suggest that overexpression of OsHAD3 could decrease the drought tolerance of rice and provide a new strategy for improving drought tolerance in rice.
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Affiliation(s)
- Xiaofei Zan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Zhanmei Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jiale Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Hao Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jiali Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Haoran Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Jia Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaohong Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaoling Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China.
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, 611130, People's Republic of China.
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Zuo R, Xie M, Gao F, Sumbal W, Cheng X, Liu Y, Bai Z, Liu S. The Characterization of the Phloem Protein 2 Gene Family Associated with Resistance to Sclerotinia sclerotiorum in Brassica napus. Int J Mol Sci 2022; 23:3934. [PMID: 35409295 PMCID: PMC8999561 DOI: 10.3390/ijms23073934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
In plants, phloem is not only a vital structure that is used for nutrient transportation, but it is also the location of a response that defends against various stresses, named phloem-based defense (PBD). Phloem proteins (PP2s) are among the predominant proteins in phloem, indicating their potential functional role in PBD. Sclerotinia disease (SD), which is caused by the necrotrophic fungal pathogen S. sclerotiorum (Sclerotinia sclerotiorum), is a devastating disease that affects oil crops, especially Brassica napus (B. napus), mainly by blocking nutrition and water transportation through xylem and phloem. Presently, the role of PP2s in SD resistance is still largely estimated. Therefore, in this study, we identified 62 members of the PP2 gene family in the B. napus genome with an uneven distribution across the 19 chromosomes. A phylogenetic analysis classified the BnPP2s into four clusters (I-IV), with cluster I containing the most members (28 genes) as a consequence of its frequent genome segmental duplication. A comparison of the gene structures and conserved motifs suggested that BnPP2 genes were well conserved in clusters II to IV, but were variable in cluster I. Interestingly, the motifs in different clusters displayed unique features, such as motif 6 specifically existing in cluster III and motif 1 being excluded from cluster IV. These results indicated the possible functional specification of BnPP2s. A transcriptome data analysis showed that the genes in clusters II to IV exhibited dynamic expression alternation in tissues and the stimulation of S. sclerotiorum, suggesting that they could participate in SD resistance. A GWAS analysis of a rapeseed population comprising 324 accessions identified four BnPP2 genes that were potentially responsible for SD resistance and a transgenic study that was conducted by transiently expressing BnPP2-6 in tobacco (Nicotiana tabacum) leaves validated their positive role in regulating SD resistance in terms of reduced lesion size after inoculation with S. sclerotiorum hyphal plugs. This study provides useful information on PP2 gene functions in B. napus and could aid elaborated functional studies on the PP2 gene family.
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Affiliation(s)
| | | | | | | | | | | | - Zetao Bai
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (R.Z.); (M.X.); (F.G.); (W.S.); (X.C.); (Y.L.); (S.L.)
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