1
|
Long Z, Tu M, Xu Y, Pak H, Zhu Y, Dong J, Lu Y, Jiang L. Genome-wide-association study and transcriptome analysis reveal the genetic basis controlling the formation of leaf wax in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2726-2739. [PMID: 36724105 DOI: 10.1093/jxb/erad047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/01/2023] [Indexed: 06/06/2023]
Abstract
Cuticular wax protects plants from various biotic and abiotic stresses. However, the genetic network of wax biosynthesis and the environmental factors influencing leaf wax production in rapeseed (Brassica napus) remains unclear. Here, we demonstrated the role of leaf wax in the resistance to Sclerotinia infection in rapeseed. We found that leaves grown under high light intensity had higher expression of genes involved in wax biosynthesis, and produced more wax on the leaf surface, compared with those grown under low light conditions. Genome-wide association study (GWAS) identified 89 single nucleotide polymorphisms significantly associated with leaf wax coverage. A cross-analysis between GWAS and differentially expressed genes (DEGs) in the leaf epidermis of the accessions with contrasting differences in wax content revealed 17 candidate genes that control this variation in rapeseed. Selective sweep analysis combined with DEG analysis unveiled 510 candidate genes with significant selective signatures. From the candidate genes, we selected BnaA02.LOX4, a putative lipoxygenase, and BnaCnn.CER1, BnaA02.CER3, BnaC02.CER3, and BnaA01.CER4 (ECERIFERUM1-4) that were putatively responsible for wax biosynthesis, to analyse the allelic forms and haplotypes corresponding to high or low leaf wax coverage. These data enrich our knowledge about wax formation, and provide a gene pool for breeding an ideal leaf wax content in rapeseed.
Collapse
Affiliation(s)
- Zhengbiao Long
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Haksong Pak
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| |
Collapse
|
2
|
Fang S, Zhao P, Tan Z, Peng Y, Xu L, Jin Y, Wei F, Guo L, Yao X. Combining Physio-Biochemical Characterization and Transcriptome Analysis Reveal the Responses to Varying Degrees of Drought Stress in Brassica napus L. Int J Mol Sci 2022; 23:ijms23158555. [PMID: 35955689 PMCID: PMC9368929 DOI: 10.3390/ijms23158555] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
Brassica napus L. has become one of the most important oil-bearing crops, and drought stress severely influences its yield and quality. By combining physio-biochemical characterization and transcriptome analysis, we studied the response of B. napus plants to different degrees of drought stress. Some physio-biochemical traits, such as fresh weight (FW), dry weight (DW), abscisic acid (ABA) content, net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr), were measured, and the total content of the epidermal wax/cutin, as well as their compositions, was determined. The results suggest that both stomatal transpiration and cuticular transpiration are affected when B. napus plants are subjected to varying degrees of drought stress. A total of 795 up-regulated genes and 1050 down-regulated genes were identified under severe drought stress by transcriptome analysis. Gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the up-regulated genes were mainly enriched in the stress response processes, such as response to water deprivation and abscisic acid, while the down-regulated genes were mainly enriched in the chloroplast-related parts affecting photosynthesis. Moreover, overexpression of BnaA01.CIPK6, an up-regulated DEG, was found to confer drought tolerance in B. napus. Our study lays a foundation for a better understanding of the molecular mechanisms underlying drought tolerance in B. napus.
Collapse
Affiliation(s)
- Shuai Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Peimin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yan Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- 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
| | - Lintang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yutong Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Fang Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China;
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, 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
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence:
| |
Collapse
|
3
|
Wang A, Guo J, Wang S, Zhang Y, Lu F, Duan J, Liu Z, Ji W. BoPEP4, a C-Terminally Encoded Plant Elicitor Peptide from Broccoli, Plays a Role in Salinity Stress Tolerance. Int J Mol Sci 2022; 23:ijms23063090. [PMID: 35328511 PMCID: PMC8952307 DOI: 10.3390/ijms23063090] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022] Open
Abstract
Plant peptide hormones play various roles in plant development, pathogen defense and abiotic stress tolerance. Plant elicitor peptides (Peps) are a type of damage-associated molecular pattern (DAMP) derived from precursor protein PROPEPs. In this study, we identified nine PROPEP genes in the broccoli genome. qRT-PCR analysis indicated that the expression levels of BoPROPEPs were induced by NaCl, ABA, heat, SA and P. syringae DC3000 treatments. In order to study the functions of Peps in salinity stress response, we synthesized BoPep4 peptide, the precursor gene of which, BoPROPEP4, was significantly responsive to NaCl treatment, and carried out a salinity stress assay by exogenous application of BoPep4 in broccoli sprouts. The results showed that the application of 100 nM BoPep4 enhanced tolerance to 200 mM NaCl in broccoli by reducing the Na+/K+ ratio and promoting accumulation of wax and cutin in leaves. Further RNA-seq analysis identified 663 differentially expressed genes (DGEs) under combined treatment with BoPep4 and NaCl compared with NaCl treatment, as well as 1776 genes differentially expressed specifically upon BoPep4 and NaCl treatment. GO and KEGG analyses of these DEGs indicated that most genes were enriched in auxin and ABA signal transduction, as well as wax and cutin biosynthesis. Collectively, this study shows that there was crosstalk between peptide hormone BoPep4 signaling and some well-established signaling pathways under salinity stress in broccoli sprouts, which implies an essential function of BoPep4 in salinity stress defense.
Collapse
|
4
|
Hyten DL. Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations. Methods Mol Biol 2022; 2481:29-42. [PMID: 35641757 DOI: 10.1007/978-1-0716-2237-7_3] [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] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) in crops requires genotyping platforms that are capable of producing accurate high density genotyping data on hundreds of plants in a cost-effective manner. Currently there are multiple commercial platforms available that are being effectively used across crops. These platforms include genotyping arrays such as the Illumina Infinium arrays and the Applied Biosystems Axiom Arrays along with a variety of resequencing methods. These methods are being used to genotype tens of thousands of markers up to millions of markers on GWAS panels. They are being used on crops with simple genomes to crops with very complex, large, polyploid genomes. Depending on the crop and the goal of the GWAS, there are several options and practical considerations to take into account when selecting a genotyping technology to ensure that the right coverage, accuracy, and cost for the study is achieved.
Collapse
Affiliation(s)
- David L Hyten
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
| |
Collapse
|
5
|
Zhou C, Pan W, Peng Q, Chen Y, Zhou T, Wu C, Hartley W, Li J, Xu M, Liu C, Li P, Rao L, Wang Q. Characteristics of Metabolites by Seed-Specific Inhibition of FAD2 in Brassica napus L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5452-5462. [PMID: 33969684 DOI: 10.1021/acs.jafc.0c06867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fatty acid desaturase-2 (FAD2) is a key enzyme in the production of polyunsaturated fatty acids in plants. RNAi technology can reduce the expression of FAD2 genes in Brassica napus seeds and acquire transgenic B. napus plants with a high oleic acid content, but the effect of seed-specific inhibition of FAD2 expression on B. napus seed metabolites is not clear. Here we use widely targeted metabolomics to investigate the metabolites of normal-oleic-acid rapeseed (OA) and high-oleic-acid rapeseed (HOA) seeds, resulting in a total of 726 metabolites being detected. Among them, 24 differential metabolites were significantly downregulated and 88 differential metabolites were significantly upregulated in HOA rapeseed. In further lipid profile experiments, more lipids in B. napus seeds were accurately quantified. The contents of glycolipids and phospholipids that contain C18:1 increased significantly and C18:2 decreased because FAD2 expression was inhibited. The changes in the expression of key genes in related pathways were also consistent with the changes in metabolites. The insertion site of the ihpRNA plant expression vector was reconfirmed through genomewide resequencing, and the transgenic event did not change the sequence of FAD2 genes. There was no significant difference in the germination rate and germination potential between OA and HOA rapeseed seeds because the seed-specific ihpRNA plant expression vector did not affect other stages of plant growth. This work provides a theoretical and practical guidance for subsequent molecular breeding of high OA B. napus.
Collapse
Affiliation(s)
- Chi Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Weisong Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yanchao Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Ting Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Chuan Wu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - William Hartley
- Agriculture and Environment Department, Harper Adams University, Newport TF10 8NB, Shropshire, United Kingdom
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Minhui Xu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Chuwei Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Peng Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Liqun Rao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Qiming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|