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Tan Z, Han X, Dai C, Lu S, He H, Yao X, Chen P, Yang C, Zhao L, Yang QY, Zou J, Wen J, Hong D, Liu C, Ge X, Fan C, Yi B, Zhang C, Ma C, Liu K, Shen J, Tu J, Yang G, Fu T, Guo L, Zhao H. Functional genomics of Brassica napus: Progresses, challenges, and perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:484-509. [PMID: 38456625 DOI: 10.1111/jipb.13635] [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: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024]
Abstract
Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.
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Affiliation(s)
- Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Xu Han
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanzi He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Liu W, Wang S, Ye X, Xu F. BnaA4.BOR2 contributes the tolerance of rapeseed to boron deficiency by improving the transport of boron from root to shoot. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108508. [PMID: 38490152 DOI: 10.1016/j.plaphy.2024.108508] [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: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Boron (B) is essential for plant growth. However, the molecular mechanism of B transport in rapeseed (Brassica napus L.) is unknown well. Here, we report that B transporter BnaA4.BOR2 is involved in the transport of B from root to shoot and its distribution in shoot cell wall and flower in rapeseed. The results of GUS staining and in-situ PCR analysis showed that BnaA4.BOR2 is mainly expressed in cortex and endodermis of root tip meristem zone and endodermis of mature zone. BnaA4.BOR2 was mainly localized in plasma membrane and showed B transport activity in yeast. Overexpression of Bna4.BOR2 could rescue the phenotype of Arabidopsis mutant bor2-2 under low-B condition. Furthermore, knockout of BnaA4.BOR2 could significantly enhance the sensitivity of rapeseed mutants to B deficiency, including inhibition of root elongation and biomass decrease of roots and shoots. The B concentration in xylem sap of BnaA4.BOR2 mutants was significantly decreased under B deficiency, which resulted in significantly lower B concentrations in shoot cell wall at seedling stage and flower organ at reproductive stage compared to that of wild-type QY10. The growth of BnaA4.BOR2 mutants were severely inhibited, exhibiting a typical B-deficient phenotype of "flowering without seed setting", leading to a sharp decrease in seed yield in B deficient soil. Taken together, these results indicate that BnaA4.BOR2 is critical for rapeseed growth and seed yield production under low B level, which is mainly expressed in cortex and endodermis, and contributed to the transport of B from roots to shoots and its distribution in shoot.
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Affiliation(s)
- Wei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheliang Wang
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangsheng Ye
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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Zhou T, Wu PJ, Chen JF, Du XQ, Feng YN, Hua YP. Pectin demethylation-mediated cell wall Na + retention positively regulates salt stress tolerance in oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:54. [PMID: 38381205 DOI: 10.1007/s00122-024-04560-w] [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: 01/03/2024] [Accepted: 01/20/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE Integrated phenomics, ionomics, genomics, transcriptomics, and functional analyses present novel insights into the role of pectin demethylation-mediated cell wall Na+ retention in positively regulating salt tolerance in oilseed rape. Genetic variations in salt stress tolerance identified in rapeseed genotypes highlight the complicated regulatory mechanisms. Westar is ubiquitously used as a transgenic receptor cultivar, while ZS11 is widely grown as a high-production and good-quality cultivar. In this study, Westar was found to outperform ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profile characterization, pectin demethylation-mediated cell wall Na+ retention was proposed to be a major regulator responsible for differential salt tolerance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differential expression profiling, and gene co-expression networks identified BnaC9.PME47, encoding a pectin methylesterase, as a positive regulator conferring salt tolerance in rapeseed. BnaC9.PME47, located in two reported QTL regions for salt tolerance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression of BnaC9.PME47 in Westar than in several salt-sensitive rapeseed genotypes. Loss of function of AtPME47 resulted in the hypersensitivity of Arabidopsis plants to salt stress. The integrated multiomics analyses revealed novel insights into pectin demethylation-mediated cell wall Na+ retention in regulating differential salt tolerance in allotetraploid rapeseed genotypes. Furthermore, these analyses have provided key information regarding the rapid dissection of quantitative trait genes responsible for nutrient stress tolerance in plant species with complex genomes.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Xiao-Qian Du
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China.
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Zhou T, Sun SS, Song HL, Chen JF, Yue CP, Huang JY, Feng YN, Hua YP. Morpho-physiological, Genomic, and Transcriptional Diversities in Response to Potassium Deficiency in Rapeseed ( Brassica napus L.) Genotypes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2381-2396. [PMID: 38232380 DOI: 10.1021/acs.jafc.3c06694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Variations in the resistance to potassium (K) deficiency among rapeseed genotypes emphasize complicated regulatory mechanisms. In this study, a low-K-sensitivity accession (L49) responded to K deficiency with smaller biomasses, severe leaf chlorosis, weaker photosynthesis ability, and deformed stomata morphology compared to a low-K resistant accession (H280). H280 accumulated more K+ than L49 under low K. Whole-genome resequencing (WGS) revealed a total of 5,538,622 single nucleotide polymorphisms (SNPs) and 859,184 insertions/deletions (InDels) between H280 and L49. RNA-seq identified more differentially expressed K+ transporter genes with higher expression in H280 than in L49 under K deficiency. Based on the K+ profiles, differential expression profiling, weighted gene coexpression network analysis, and WGS data between H280 and L49, BnaC4.AKT1 was proposed to be mainly responsible for root K absorption-mediated low K resistance. BnaC4.AKT1 was expressed preferentially in the roots and localized on the plasma membrane. An SNP and an InDel found in the promoter region of BnaC4.AKT1 were proposed to be responsible for its differential expression between rapeseed genotypes. This study identified a gene resource for improving low-K resistance. It also facilitates an integrated knowledge of the differential physiological and transcriptional responses to K deficiency in rapeseed genotypes.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Si-Si Sun
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin-Yong Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Verwaaijen B, Alcock TD, Spitzer C, Liu Z, Fiebig A, Bienert MD, Bräutigam A, Bienert GP. The Brassica napus boron deficient inflorescence transcriptome resembles a wounding and infection response. PHYSIOLOGIA PLANTARUM 2023; 175:e14088. [PMID: 38148205 DOI: 10.1111/ppl.14088] [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: 05/17/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/28/2023]
Abstract
Oilseed rape and other crops of Brassica napus have a high demand for boron (B). Boron deficiencies result in the inhibition of root growth, and eventually premature flower abortion. Understanding the genetic mechanisms underlying flower abortion in B-limiting conditions could provide the basis to enhance B-efficiency and prevent B-deficiency-related yield losses. In this study, we assessed transcriptomic responses to B-deficiency in diverse inflorescence tissues at multiple time points of soil-grown plants that were phenotypically unaffected by B-deficiency until early flowering. Whilst transcript levels of known B transporters were higher in B-deficient samples, these remained remarkably stable as the duration of B-deficiency increased. Meanwhile, GO-term enrichment analysis indicated a growing response resembling that of a pathogen or pest attack, escalating to a huge transcriptome response in shoot heads at mid-flowering. Grouping differentially expressed genes within this tissue into MapMan functional bins indicated enrichment of genes related to wounding, jasmonic acid and WRKY transcription factors. Individual candidate genes for controlling the "flowering-without-seed-setting" phenotype from within MapMan biotic stress bins include those of the metacaspase family, which have been implicated in orchestrating programmed cell death. Overall temporal expression patterns observed here imply a dynamic response to B-deficiency, first increasing expression of B transporters before recruiting various biotic stress-related pathways to coordinate targeted cell death, likely in response to as yet unidentified B-deficiency induced damage-associated molecular patterns (DAMPs). This response indicates new pathways to target and dissect to control B-deficiency-induced flower abortion and to develop more B-efficient crops.
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Affiliation(s)
- Bart Verwaaijen
- Computational Biology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
- Center of Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Genetics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas David Alcock
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
| | - Christoph Spitzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Zhaojun Liu
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Manuela Désirée Bienert
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
| | - Andrea Bräutigam
- Computational Biology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
- Center of Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Gerd Patrick Bienert
- Crop Physiology, School of Life Sciences, Technical University of Munich, Freising, Germany
- HEF World Agricultural Systems Center, Technical University of Munich, Freising, Germany
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Ibrahim S, Ahmad N, Kuang L, Li K, Tian Z, Sadau SB, Tajo SM, Wang X, Wang H, Dun X. Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1194914. [PMID: 37546248 PMCID: PMC10400329 DOI: 10.3389/fpls.2023.1194914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.
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Affiliation(s)
- Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Department of Plant Biology, Faculty of Life Sciences, College of Natural and Pharmaceutical Sciences, Bayero University, Kano, Nigeria
| | - Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Keqi Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Salisu Bello Sadau
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (Institute of Cotton Research (ICR), CAAS), Anyang, China
| | - Sani Muhammad Tajo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (Institute of Cotton Research (ICR), CAAS), Anyang, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Wang W, Liu H, Xie Y, King GJ, White PJ, Zou J, Xu F, Shi L. Rapid identification of a major locus qPRL-C06 affecting primary root length in Brassica napus by QTL-seq. ANNALS OF BOTANY 2023; 131:569-583. [PMID: 36181516 PMCID: PMC10147330 DOI: 10.1093/aob/mcac123] [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: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brassica napus is one of the most important oilseed crops worldwide. Seed yield of B. napus significantly correlates with the primary root length (PRL). The aims of this study were to identify quantitative trait loci (QTLs) for PRL in B. napus. METHODS QTL-seq and conventional QTL mapping were jointly used to detect QTLs associated with PRL in a B. napus double haploid (DH) population derived from a cross between 'Tapidor' and 'Ningyou 7'. The identified major locus was confirmed and resolved by an association panel of B. napus and an advanced backcross population. RNA-seq analysis of two long-PRL lines (Tapidor and TN20) and two short-PRL lines (Ningyou 7 and TN77) was performed to identify differentially expressed genes in the primary root underlying the target QTLs. KEY RESULTS A total of 20 QTLs impacting PRL in B. napus grown at a low phosphorus (P) supply were found by QTL-seq. Eight out of ten QTLs affecting PRL at a low P supply discovered by conventional QTL mapping could be detected by QTL-seq. The locus qPRL-C06 identified by QTL-seq was repeatedly detected at both an optimal P supply and a low P supply by conventional QTL mapping. This major constitutive QTL was further confirmed by regional association mapping. qPRL-C06 was delimited to a 0.77 Mb genomic region on chromosome C06 using an advanced backcross population. A total of 36 candidate genes within qPRL-C06 were identified that showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in primary root between the long-PRL and short-PRL lines, including five genes involved in phytohormone biosynthesis and signaling. CONCLUSIONS These results both demonstrate the power of the QTL-seq in rapid QTL detection for root traits and will contribute to marker-assisted selective breeding of B. napus cultivars with increased PRL.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Graham John King
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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8
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Wang X, Song B, Wu Z, Zhao X, Song X, Adil MF, Riaz M, Lal MK, Huang W. Insights into physiological and molecular mechanisms underlying efficient utilization of boron in different boron efficient Beta vulgaris L. varieties. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107619. [PMID: 36931121 DOI: 10.1016/j.plaphy.2023.02.049] [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: 12/26/2022] [Revised: 02/10/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Boron (B) deficiency and consequent limitation of plant yield and quality, particularly of sugar beet (Beta vulgaris L.) has emerged as a maior problem,which is exacerbating due to cultivar dependent variability in B deficiency tolerance. Pertinently, the current study was designed to elucidate the physiological and molecular mechanisms of B deficiency tolerance of sugar beet varieties KWS1197 (B-efficient variety) and KWS0143 (B-inefficient variety). A hydroponic experiment was conducted employing two B levels B0.1 (0.1 μM L-1 H3BO3, deficiency) and B50 (50 μM L-1 H3BO3, adequacy). Boron deficiency greatly inhibited root elongation and dry matter accumulation; however, formation of lateral roots stimulated and average root diameter was increased. Results exhibited that by up-regulating the expression of NIP5-1, NIP6-1, and BOR2, and suppressing the expression of BOR4, cultivar KWS1197, in contrast to KWS0143, managed to transfer sufficient amount of B to the aboveground plant parts, facilitating its effective absorption and utilization. Accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) was also mellowed in KWS1197, as well as the oxidative damage to root cells via preservation of the antioxidant enzyme system. Additionally, the expression of essential enzymes for biosynthesis of phytohormone (PYR/PYL) and lignin (COMT, POX, and CCoAOMT) were found to be highly up-regulated in KWS1197. Deductively, through effective B absorption and transportation, balanced nutrient accumulation, and an activated antioxidant enzyme system, B-efficient cultivars may cope with B deficiency while retaining a superior cellular structure to enable root development.
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Affiliation(s)
- Xiangling Wang
- Sugar Beet Engineering Research Center of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
| | - Baiquan Song
- Sugar Beet Engineering Research Center of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China.
| | - Zhenzhen Wu
- Sugar Beet Engineering Research Center of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
| | - Xiaoyu Zhao
- Sugar Beet Engineering Research Center of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
| | - Xin Song
- Sugar Beet Engineering Research Center of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China
| | - Muhammad Faheem Adil
- Zhejiang Key Laboratory of Crop Germplasm Resources, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Riaz
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Wengong Huang
- Heilongjiang Academy of Agricultural Sciences, Safety and Quality Institute of Agricultural Products, Harbin, 150086, China
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9
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Interaction between Boron and Other Elements in Plants. Genes (Basel) 2023; 14:genes14010130. [PMID: 36672871 PMCID: PMC9858995 DOI: 10.3390/genes14010130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Boron (B) is an essential mineral nutrient for growth of plants, and B deficiency is now a worldwide problem that limits production of B deficiency-sensitive crops, such as rape and cotton. Agronomic practice has told that balanced B and other mineral nutrient fertilizer applications is helpful to promote crop yield. In recent years, much research has reported that applying B can also reduce the accumulation of toxic elements such as cadmium and aluminum in plants and alleviate their toxicity symptoms. Therefore, the relation between B and other elements has become an interesting issue for plant nutritionists. Here we summarize the research progress of the interaction between B and macronutrients such as nitrogen, phosphorus, calcium, potassium, magnesium, and sulfur, essential micronutrients such as iron, manganese, zinc, copper, and molybdenum, and beneficial elements such as sodium, selenium, and silicon. Moreover, the interaction between B and toxic elements such as cadmium and aluminum, which pose a serious threat to agriculture, is also discussed in this paper. Finally, the possible physiological mechanisms of the interaction between B and other elements in plants is reviewed. We propose that the cell wall is an important intermediary between interaction of B and other elements, and competitive inhibition of elements and related signal transduction pathways also play a role. Currently, research on the physiological role of B in plants mainly focuses on its involvement in the structure and function of cell walls, and our understanding of the details for interactions between B and other elements also tend to relate to the cell wall. However, we know little about the metabolic process of B inside cells, including its interactions with other elements. More research is needed to address the aforementioned research questions in future.
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10
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Xu F, Chen S, Zhou S, Yue C, Yang X, Zhang X, Zhan K, He D. Genome-wide association, RNA-seq and iTRAQ analyses identify candidate genes controlling radicle length of wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:939544. [PMID: 36247556 PMCID: PMC9554269 DOI: 10.3389/fpls.2022.939544] [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: 05/09/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
The radicle, present in the embryo of a seed, is the first root to emerge at germination, and its rapid growth is essential for establishment and survival of the seedling. However, there are few studies on the critical mechanisms underlying radicle and then radicle length in wheat seedlings, despite its importance as a food crop throughout the world. In the present study, 196 wheat accessions from the Huanghuai Wheat Region were screened to measure radicle length under 4 hydroponic culture environments over 3 years. Different expression genes and proteins (DEGs/DEPs) between accessions with extremely long [Yunong 949 (WRL1), Zhongyu 9,302 (WRL2)] and short roots [Yunong 201 (WRS1), Beijing 841 (WRS2)] were identified in 12 sets of root tissue samples by RNA-seq and iTRAQ (Isobaric tags for relative and absolute quantification). Phenotypic results showed that the elongation zone was significantly longer in root accessions with long roots compared to the short-rooted accessions. A genome-wide association study (GWAS) identified four stable chromosomal regions significantly associated with radicle length, among which 1A, 4A, and 7A chromosomes regions explained 7.17% to12.93% of the phenotypic variation. The omics studies identified the expression patterns of 24 DEGs/DEPs changed at both the transcriptional and protein levels. These DEGs/DEPs were mainly involved in carbon fixation in photosynthetic organisms, photosynthesis and phenylpropanoid biosynthesis pathways. TraesCS1A02G104100 and TraesCS2B02G519100 were involved in the biosynthesis of tricin-lignins in cell walls and may affect the extension of cell walls in the radicle elongation zone. A combination of GWAS and RNA-seq analyses revealed 19 DEGs with expression changes in the four accessions, among which, TraesCS1A02G422700 (a cysteine-rich receptor-like protein kinase 6, CRK6) also showed upregulation in the comparison group by RNA-seq, iTRAQ, and qRT-PCR. BSMV-mediated gene silencing also showed that TaCRK6 improves root development in wheat. Our data suggest that TaCRK6 is a candidate gene regulating radicle length in wheat.
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Affiliation(s)
- Fengdan Xu
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Research Institute of Plant Nutrition and Resources and Environments, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shulin Chen
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Sumei Zhou
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Chao Yue
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Xiwen Yang
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Xiang Zhang
- Research Institute of Plant Nutrition and Resources and Environments, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Kehui Zhan
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Dexian He
- College of Agronomy of Henan Agricultural University/National Engineering Research Center for Wheat/Co-construction State Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
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11
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Wang Y, Zhao Z, Wang S, Shi L, Xu F. Genotypic differences in the synergistic effect of nitrogen and boron on the seed yield and nitrogen use efficiency of Brassica napus. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3563-3571. [PMID: 34854085 DOI: 10.1002/jsfa.11700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus) is highly sensitive to nitrogen (N) and boron (B) deficiency; however, the synergistic effects of these elements on rapeseed production are poorly understood. The aim of this study was to investigate the effects of co-application of N and B on seed yield, N uptake and N use efficiency (NUE) of rapeseed. Three rapeseed cultivars (W10, ZS11 and HG) were treated with different N and B application rates, and the seed yield, N uptake and NUE were examined in 2-year field experiments. RESULTS The application of B fertilizer (4.5, 9 kg borax ha-1 ) improved N uptake, NUE and seed yield. However, the magnitude of increase in seed yield by B fertilization was dependent upon the rate of N supply and genotype. The benefit of B was much greater at 180 kg N ha-1 than at 0 or 60 kg N ha-1 . The combination of N and B also improved N remobilization from sources (stems and husks) to sinks (seeds) and increased N recovery efficiency (NRE). Compared with the B-inefficient cultivar W10, the B-efficient cultivars ZS11 and HG were superior in growth, seed yield, N uptake and NUE on B deficient soils. Furthermore, B-efficient cultivars showed great potential in saving N input, and the yield increased by more than 40% under B deficiency conditions. CONCLUSION This study highlights a markedly synergistic effect of N and B nutrition on rapeseed NUE and yield production and shows that B-efficient genotypes can increase yield and reduce N inputs under B-deficient conditions. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Youqiang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Zhe Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, China
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12
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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13
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Onuh AF, Miwa K. Regulation, Diversity and Evolution of Boron Transporters in Plants. PLANT & CELL PHYSIOLOGY 2021; 62:590-599. [PMID: 33570563 DOI: 10.1093/pcp/pcab025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Boron (B) is an essential trace element in plants, and borate cross-linking of pectic polysaccharide rhamnogalacturonan-II (RG-II) in cell walls is required for normal cell growth. High concentrations of B are toxic to cells. Therefore, plants need to control B transport to respond to B conditions in the environment. Over the past two decades, genetic analyses of Arabidopsis thaliana have revealed that B transport is governed by two types of membrane transport molecules: NIPs (nodulin-26-like intrinsic proteins), which facilitate boric acid permeation, and BORs, which export borate from cells. In this article, we review recent findings on the (i) regulation at the cell level, (ii) diversity among plant species and (iii) evolution of these B transporters in plants. We first describe the systems regulating these B transporters at the cell level, focusing on the molecular mechanisms underlying the polar localization of proteins and B-dependent expression, as well as their physiological significance in A. thaliana. Then, we examine the presence of homologous genes and characterize the functions of NIPs and BORs in B homeostasis, in a wide range of plant species, including Brassica napus, Oryza sativa and Zea mays. Finally, we discuss the evolutionary aspects of NIPs and BORs as B transporters, and the possible relationship between the diversification of B transport and the occurrence of RG-II in plants. This review considers the sophisticated systems of B transport that are conserved among various plant species, which were established to meet mineral nutrient requirements.
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Affiliation(s)
- Amarachukwu Faith Onuh
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, North-10, West-5, Kita-ku, Sapporo, 060-0810 Japan
| | - Kyoko Miwa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, North-10, West-5, Kita-ku, Sapporo, 060-0810 Japan
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14
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Li K, Wang J, Kuang L, Tian Z, Wang X, Dun X, Tu J, Wang H. Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:178. [PMID: 34507599 PMCID: PMC8431925 DOI: 10.1186/s13068-021-02032-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/30/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In terms of global demand, rapeseed is the third-largest oilseed crop after soybeans and palm, which produces vegetable oil for human consumption and biofuel for industrial production. Roots are vital organs for plant to absorb water and attain mineral nutrients, thus they are of great importance to plant productivity. However, the genetic mechanisms regulating root development in rapeseed remain unclear. In the present study, seven root-related traits and shoot biomass traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. RESULTS The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout the investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. A total of 367 differentially expressed genes (DEGs) with persistent differential expressions throughout root development were identified, and these DEGs were significantly enriched in GO terms, such as energy metabolism and response to biotic or abiotic stress. Totally, 485 stage-specific DEGs with different expressions at specific stage were identified, and these DEGs were enriched in GO terms, such as nitrogen metabolism. Four candidate genes were identified as key persistent genetic factors and eight as stage-specific ones by integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. These candidate genes were speculated to regulate root system development, and they were less than 100 kb away from peak SNPs of QTL clusters. The homologs of three genes (BnaA03g52990D, BnaA06g37280D, and BnaA09g07580D) out of 12 candidate genes have been reported to regulate root development in previous studies. CONCLUSIONS Sixteen QTL clusters and four candidate genes controlling persistently root development, and 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed were detected in this study. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.
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Affiliation(s)
- Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Jie Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Ze Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
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15
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He M, Zhang C, Chu L, Wang S, Shi L, Xu F. Specific and multiple-target gene silencing reveals function diversity of BnaA2.NIP5;1 and BnaA3.NIP5;1 in Brassica napus. PLANT, CELL & ENVIRONMENT 2021; 44:3184-3194. [PMID: 33937996 DOI: 10.1111/pce.14077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Rapeseed (Brassica napus) is an economically important oilseed crop in the world, but its production is strongly dependent on boron (B) supplies. Major intrinsic protein NIP5;1 is essential for B uptake and plant development under B limitation. In this study, phylogenetic and expression analyses identified two NIP5;1 orthologue genes, BnaA2.NIP5;1 and BnaA3.NIP5;1, which are mainly expressed in roots of B. napus. Specific and multiple-target RNAi was used to suppress BnaA3.NIP5;1 or both BnaA2.NIP5;1 and BnaA3.NIP5;1 expression in B-efficient rapeseed Qingyou 10 (QY10), respectively, for revealing the roles of BnaA2.NIP5;1 and BnaA3.NIP5;1 in low-B tolerance in B. napus. We found that both BnaA2.NIP5;1 and BnaA3.NIP5;1 are important for B. napus normal growth under low-B conditions, while these two genes have distinct roles. BnaA2.NIP5;1 is mainly expressed in the epidermis cells, which is required for efficient B uptake into roots, hence for B translocation to the shoots. BnaA3.NIP5;1 is specifically localized in the distal part of lateral root cap cells to promoter root elongation under low-B conditions, which is important for seed production in the maturity stage of B. napus. Taken together, our specific and multiple-target RNAi strategy provides novel insights into the gene function diversification between BnaA2.NIP5;1 and BnaA3.NIP5;1, such an approach can be potentially applicable to other polyploid crops.
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Affiliation(s)
- Mingliang He
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zhang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Liuyang Chu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
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16
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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17
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Zhou T, Yue CP, Zhang TY, Liu Y, Huang JY, Hua YP. Integrated ionomic and transcriptomic dissection reveals the core transporter genes responsive to varying cadmium abundances in allotetraploid rapeseed. BMC PLANT BIOLOGY 2021; 21:372. [PMID: 34388971 PMCID: PMC8362225 DOI: 10.1186/s12870-021-03136-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Oilseed rape (B. napus L.) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Soil properties and the presence of other soluble compounds or ions, cause a heterogeneous distribution of Cd. RESULTS The aim of our study was to reveal the differential responses of B. napus to different Cd abundances. Herein, we found that high Cd (50 μM) severely inhibited the growth of B. napus, which was not repressed by low Cd (0.50 μM) under hydroponic culture system. ICP-MS assays showed that the Cd2+ concentrations in both shoots and roots under 50 μM Cd were over 10 times higher than those under 0.50 μM Cd. Under low Cd, the concentrations of only shoot Ca2+/Mn2+ and root Mn2+ were obviously changed (both reduced); under high Cd, the concentrations of most cations assayed were significantly altered in both shoots and roots except root Ca2+ and Mg2+. High-throughput transcriptomic profiling revealed a total of 18,021 and 1408 differentially expressed genes under high Cd and low Cd conditions, respectively. The biological categories related to the biosynthesis of plant cell wall components and response to external stimulus were over-accumulated under low Cd, whereas the terms involving photosynthesis, nitrogen transport and response, and cellular metal ion homeostasis were highly enriched under high Cd. Differential expression of the transporters responsible for Cd uptake (NRAMPs), transport (IRTs and ZIPs), sequestration (HMAs, ABCs, and CAXs), and detoxification (MTPs, PCR, MTs, and PCSs), and some other essential nutrient transporters were investigated, and gene co-expression network analysis revealed the core members of these Cd transporters. Some Cd transporter genes, especially NRAMPs and IRTs, showed opposite responsive patterns between high Cd and low Cd conditions. CONCLUSIONS Our findings would enrich our understanding of the interaction between essential nutrients and Cd, and might also provide suitable gene resources and important implications for the genetic improvement of plant Cd accumulation and resistance through molecular engineering of these core genes under varying Cd abundances in soils.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Cai-peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Tian-yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Ying Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Jin-yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Ying-peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 China
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18
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He M, Wang S, Zhang C, Liu L, Zhang J, Qiu S, Wang H, Yang G, Xue S, Shi L, Xu F. Genetic variation of BnaA3.NIP5;1 expressing in the lateral root cap contributes to boron deficiency tolerance in Brassica napus. PLoS Genet 2021; 17:e1009661. [PMID: 34197459 PMCID: PMC8279314 DOI: 10.1371/journal.pgen.1009661] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/14/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022] Open
Abstract
Boron (B) is essential for vascular plants. Rapeseed (Brassica napus) is the second leading crop source for vegetable oil worldwide, but its production is critically dependent on B supplies. BnaA3.NIP5;1 was identified as a B-efficient candidate gene in B. napus in our previous QTL fine mapping. However, the molecular mechanism through which this gene improves low-B tolerance remains elusive. Here, we report genetic variation in BnaA3.NIP5;1 gene, which encodes a boric acid channel, is a key determinant of low-B tolerance in B. napus. Transgenic lines with increased BnaA3.NIP5;1 expression exhibited improved low-B tolerance in both the seedling and maturity stages. BnaA3.NIP5;1 is preferentially polar-localized in the distal plasma membrane of lateral root cap (LRC) cells and transports B into the root tips to promote root growth under B-deficiency conditions. Further analysis revealed that a CTTTC tandem repeat in the 5'UTR of BnaA3.NIP5;1 altered the expression level of the gene, which is tightly associated with plant growth and seed yield. Field tests with natural populations and near-isogenic lines (NILs) confirmed that the varieties carried BnaA3.NIP5;1Q allele significantly improved seed yield. Taken together, our results provide novel insights into the low-B tolerance of B. napus, and the elite allele of BnaA3.NIP5;1 could serve as a direct target for breeding low-B-tolerant cultivars.
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Affiliation(s)
- Mingliang He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Sheliang Wang
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Liu Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinyao Zhang
- Institute of Agricultural Resource and Regional Planning, CAAS, Beijing, China
| | - Shou Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hong Wang
- Institute of Agricultural Resource and Regional Planning, CAAS, Beijing, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shaowu Xue
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, China
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19
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Dong Z, Alam MK, Xie M, Yang L, Liu J, Helal MMU, Huang J, Cheng X, Liu Y, Tong C, Zhao C, Liu S. Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus. G3-GENES GENOMES GENETICS 2021; 11:6219302. [PMID: 33836054 PMCID: PMC8495924 DOI: 10.1093/g3journal/jkab118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022]
Abstract
Plant height is a crucial element related to plant architecture that influences the seed yield of oilseed rape (Brassica napus L.). In this study, we isolated a natural B. napus mutant, namely a semi-dwarf mutant (sdw-e), which exhibits a 30% reduction in plant height compared with Zhongshuang 11-HP (ZS11-HP). Quantitative trait locus sequencing (QTL-seq) was conducted using two extreme DNA bulks in F2 populations in Wuchang-2017 derived from ZS11-HP × sdw-e to identify QTLs associated with plant height. The result suggested that two QTL intervals were located on chromosome A10. The F2 population consisting of 200 individuals in Yangluo-2018 derived from ZS11-HP × sdw-e was used to construct a high-density linkage map using whole-genome resequencing. The high-density linkage map harbored 4323 bin markers and covered a total distance of 2026.52 cM with an average marker interval of 0.47 cM. The major QTL for plant height named qPHA10 was identified on linkage group A10 by interval mapping and composite interval mapping methods. The major QTL qPHA10 was highly consistent with the QTL-seq results. And then, we integrated the variation sites and expression levels of genes in the major QTL interval to predict the candidate genes. Thus, the identified QTL and candidate genes could be used in marker-assisted selection for B. napus breeding in the future.
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Affiliation(s)
- Zhixue Dong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Muhammad Khorshed Alam
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Meili Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Li Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Jie Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - M M U Helal
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Junyan Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Xiaohui Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Yueying Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chuanji Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Shengyi Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
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20
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Jia Z, Bienert MD, von Wirén N, Bienert GP. Genome-wide association mapping identifies HvNIP2;2/HvLsi6 accounting for efficient boron transport in barley. PHYSIOLOGIA PLANTARUM 2021; 171:809-822. [PMID: 33481273 DOI: 10.1111/ppl.13340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/18/2020] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Boron (B) is an essential mineral element for plant growth, and the seed B pool of crops can be crucial when seedlings need to establish on low-B soils. To date, it is poorly understood how B accumulation in grain crops is genetically controlled. Here, we assessed the genotypic variation of the B concentration in grains of a spring barley (Hordeum vulgare L.) association panel that represents broad genetic diversity. We found a large genetic variation of the grain B concentration and detected in total 23 quantitative trait loci (QTLs) using genome-wide association mapping. HvNIP2;2/HvLsi6, encoding a potential B-transporting membrane protein, mapped closely to a major-effect QTL accounting for the largest proportion of grain B variation. Based on transport studies using heterologous expression systems and gene expression analysis, we demonstrate that HvNIP2;2/HvLsi6 represents a functional B channel and that expression variation in its transcript level associates with root and shoot B concentrations as well as with root dry mass formation under B-deficient conditions.
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Affiliation(s)
- Zhongtao Jia
- Department of Physiology and Cell Biology, Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Manuela Désirée Bienert
- Department of Physiology and Cell Biology, Metalloid Transport, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Crop Physiology, Department of Molecular Life Sciences, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Gerd Patrick Bienert
- Department of Physiology and Cell Biology, Metalloid Transport, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Crop Physiology, Department of Molecular Life Sciences, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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21
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Song G, Li X, Munir R, Khan AR, Azhar W, Khan S, Gan Y. BnaA02.NIP6;1a encodes a boron transporter required for plant development under boron deficiency in Brassica napus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:36-45. [PMID: 33561659 DOI: 10.1016/j.plaphy.2021.01.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Boron (B) is an essential micronutrient for the plant normal growth. In Arabidopsis, NIP6;1 is a boric acid channel required for the proper distribution of boric acid, especially in the nodal regions of shoots. BnaA02.NIP6;1a, a homologous gene of AtNIP6;1 in Brassica napus, was reported to play a key role in B transport activity. However, little is known about the other functions of BnaA02.NIP6;1a in Brassica napus. In this study, we found that BnaA02.NIP6; 1a was localized in both plasma membrane and cytoplasm, which was different from that in Arabidopsis. The transgenic Arabidopsis plant containing a BnaA02.NIP6;1a promoter driven GUS reporter gene displayed strong GUS activity in roots, stems, leaves, especially in buds and open flowers, which are different from the expression pattern from its homologous gene in Arabidopsis. Silencing BnaA02.NIP6;1a repressed vegetative growth under B-deficient condition in Brassica napus. More importantly, knockdown of BnaA02.NIP6;1a in rapeseed resulted in the reduction of boron accumulation in the flower under boron deficiency and lead to severe sterility, which has not yet been reported before. Furthermore, nip6;1 mutant in Arabidopsis only showed the loss of apical dominance phenotype under boron deficiency at reproductive stage, whereas BnaA02.NIP6;1 RNAi lines exhibited large amounts of abnormal development of the inflorescence as compared with the wild type under boron limitation. Taken together, our results demonstrate that BnaA02.NIP6;1a encodes a boron transporter required for plant development under boron deficiency in Brassica napus, which shows its novel and diverse function in rapeseed compared with model plant Arabidopsis.
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Affiliation(s)
- Ge Song
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xueping Li
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Raheel Munir
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wardah Azhar
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Sulaiman Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China; Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province, 572025, China.
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22
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Zhao Z, Wang Y, Shi J, Wang S, White PJ, Shi L, Xu F. Effect of balanced application of boron and phosphorus fertilizers on soil bacterial community, seed yield and phosphorus use efficiency of Brassica napus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141644. [PMID: 32866830 DOI: 10.1016/j.scitotenv.2020.141644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/09/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
Rapeseed (Brassica napus L.) is extremely sensitive to both boron (B) and phosphorus (P) deficiencies. Application of chemical fertilizers is generally considered to be an effective agronomic practice to improve crop productivity, and it also affects soil bacterial community. However, there are few studies of the effects of balanced B and P fertilizer applications on crop yield and bacterial communities. In the present study, field experiments with five P application rates (0, 45, 90, 135 and 180 kg P2O5 ha-1) and four B application rates (0, 4.5, 9 and 18 kg Na2B4O7·5H2O ha-1) were conducted in 2016-2017 and 2017-2018 to investigate their effects on seed yield and P use efficiency (PUE) of B. napus. The smallest seed yields were obtained when B or P fertilizers were not applied (P90B0 or P0B9). Balanced B and P applications benefitted yields. The P45B4.5 treatment produced greater seed yield and PUE than the P45B18 treatment, and the P180B18 treatment produced greater seed yield and PUE than the P180B4.5 treatment. Sequencing of 16S rRNA genes revealed that the P90B9 treatment had greater soil bacterial diversity, and a different bacterial community composition, compared with the P90B0 or P0B9 treatments. Overall, our results underline the importance of balanced B and P nutrition for maximal seed yield of B. napus and the effects of B and P fertilizers on the soil bacterial community of B. napus.
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Affiliation(s)
- Zhe Zhao
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
| | - Youqiang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jianqi Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China; The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
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23
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Zhao Z, Wang S, White PJ, Wang Y, Shi L, Xu F. Boron and Phosphorus Act Synergistically to Modulate Absorption and Distribution of Phosphorus and Growth of Brassica napus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7830-7838. [PMID: 32614576 DOI: 10.1021/acs.jafc.0c02522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Rapeseed (Brassica napus L.) is highly susceptible to boron (B) and phosphorus (P) deficiencies, yet knowledge of how these two essential elements interact to contribute to plant growth and crop yield is limited. To this end, a pot experiment with three P application rates (5, 75, and 150 mg P2O5 kg-1 dry soil) and two B application rates (0.25 and 1 mg B kg-1 dry soil) was conducted. The results showed that high P combined with high B optimized plant growth and facilitated P distribution forward to seeds compared with high P and low B combination at the maturity stage. Under low P conditions, low B supply was more beneficial for P absorption at seedling and bolting stages and increased P distribution ratio in seeds at the maturity stage, resulting in higher photosynthetic efficiency and growth parameters than low P and high B combination. Interestingly, high B supply could upregulate the expression of the P-starvation-induced gene BnaC3.SPX3 and P transport genes in roots under low P conditions, so low B-facilitated P absorption appears to be a BnaPHT1s-independent process. Significant differences of B and P interaction on the seed yield, net photosynthetic rate, and total P absorption and distribution at the maturity stage between two cultivars might reflect the distinct genotypic properties. Overall, our findings highlight the importance of balanced B and P nutrition which acts synergistically to modulate growth and yield formation of B. napus either in nutrition deficiency or sufficiency.
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Affiliation(s)
- Zhe Zhao
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Youqiang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
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24
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Wimmer MA, Abreu I, Bell RW, Bienert MD, Brown PH, Dell B, Fujiwara T, Goldbach HE, Lehto T, Mock HP, von Wirén N, Bassil E, Bienert GP. Boron: an essential element for vascular plants: A comment on Lewis (2019) 'Boron: the essential element for vascular plants that never was'. THE NEW PHYTOLOGIST 2020; 226:1232-1237. [PMID: 31674046 DOI: 10.1111/nph.16127] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Monika A Wimmer
- Department Quality of Plant Products, Institute of Crop Science, University of Hohenheim, 70599, Stuttgart, Germany
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Richard W Bell
- Agriculture Discipline, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Manuela D Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Patrick H Brown
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Bernard Dell
- Agriculture Discipline, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Heiner E Goldbach
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Tarja Lehto
- School of Forest Sciences, University of Eastern Finland, 80110, Joensuu, Finland
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Elias Bassil
- Horticultural Sciences Department and Tropical Research and Education Center, University of Florida, Homestead, FL, 33031, USA
| | - Gerd P Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
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25
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Feng Y, Cui R, Wang S, He M, Hua Y, Shi L, Ye X, Xu F. Transcription factor BnaA9.WRKY47 contributes to the adaptation of Brassica napus to low boron stress by up-regulating the boric acid channel gene BnaA3.NIP5;1. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1241-1254. [PMID: 31705705 PMCID: PMC7152615 DOI: 10.1111/pbi.13288] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/17/2019] [Accepted: 11/01/2019] [Indexed: 05/08/2023]
Abstract
Boron (B) deficiency is one of the major causes of growth inhibition and yield reduction in Brassica napus (B. napus). However, the molecular mechanisms of low B adaptation in B. napus are largely unknown. Here, fifty-one BnaWRKY transcription factors were identified as responsive to B deficiency in B. napus, in which BnaAn.WRKY26, BnaA9.WRKY47, BnaA1.WKRY53 and BnaCn.WRKY57 were tested in yeast one-hybrid assays and showed strong binding activity with conserved sequences containing a W box in the promoters of the B transport-related genes BnaNIP5;1s and BnaBOR1s. Green fluorescent protein fused to the target protein demonstrated the nuclear localization of BnaA9.WRKY47. CRISPR/Cas9-mediated knockout lines of BnaA9.WRKY47 in B. napus had increased sensitivity to low B and lower contents of B than wild-type plants. In contrast, overexpression of BnaA9.WRKY47 enhanced the adaptation to low B with higher B contents in tissues than in wild-type plants. Consistent with the phenotypic response and B accumulation in these transgenic lines, the transcription activity of BnaA3.NIP5;1, a B efficiency candidate gene, was decreased in the knockout lines but was significantly increased in the overexpressing lines under low B conditions. Electrophoretic mobility shift assays, transient expression experiments in tobacco and in situ hybridizations showed that BnaA9.WRKY47 directly activated BnaA3.NIP5;1 expression through binding to the specific cis-element. Taken together, our findings support BnaWRKYs as new participants in response to low B, and BnaA9.WRKY47 contributes to the adaptation of B. napus to B deficiency through up-regulating BnaA3.NIP5;1 expression to facilitate efficient B uptake.
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Affiliation(s)
- Yingna Feng
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Rui Cui
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Mingliang He
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Yingpeng Hua
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Lei Shi
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Xiangsheng Ye
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic ImprovementMicroelement Research CentreHuazhong Agricultural UniversityWuhanChina
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26
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Zhou T, Yue CP, Huang JY, Cui JQ, Liu Y, Wang WM, Tian C, Hua YP. Genome-wide identification of the amino acid permease genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed. BMC PLANT BIOLOGY 2020; 20:151. [PMID: 32268885 PMCID: PMC7140331 DOI: 10.1186/s12870-020-02367-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 03/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Nitrogen (N), referred to as a "life element", is a macronutrient essential for optimal plant growth and yield production. Amino acid (AA) permease (AAP) genes play pivotal roles in root import, long-distance translocation, remobilization of organic amide-N from source organs to sinks, and other environmental stress responses. However, few systematic analyses of AAPs have been reported in Brassica napus so far. RESULTS In this study, we identified a total of 34 full-length AAP genes representing eight subgroups (AAP1-8) from the allotetraploid rapeseed genome (AnAnCnCn, 2n = 4x = 38). Great differences in the homolog number among the BnaAAP subgroups might indicate their significant differential roles in the growth and development of rapeseed plants. The BnaAAPs were phylogenetically divided into three evolutionary clades, and the members in the same subgroups had similar physiochemical characteristics, gene/protein structures, and conserved AA transport motifs. Darwin's evolutionary analysis suggested that BnaAAPs were subjected to strong purifying selection pressure. Cis-element analysis showed potential differential transcriptional regulation of AAPs between the model Arabidopsis and B. napus. Differential expression of BnaAAPs under nitrate limitation, ammonium excess, phosphate shortage, boron deficiency, cadmium toxicity, and salt stress conditions indicated their potential involvement in diverse nutrient stress responses. CONCLUSIONS The genome-wide identification of BnaAAPs will provide a comprehensive insight into their family evolution and AAP-mediated AA transport under diverse abiotic stresses. The molecular characterization of core AAPs can provide elite gene resources and contribute to the genetic improvement of crop stress resistance through the modulation of AA transport.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Cai-peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Jin-yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Jia-qian Cui
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Ying Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Wen-ming Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
| | - Chuang Tian
- Sinochem Modern Agricultural Platform, Changchun, 130000 China
| | - Ying-peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000 China
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Luo H, Pandey MK, Khan AW, Wu B, Guo J, Ren X, Zhou X, Chen Y, Chen W, Huang L, Liu N, Lei Y, Liao B, Varshney RK, Jiang H. Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2356-2369. [PMID: 31087470 PMCID: PMC6835129 DOI: 10.1111/pbi.13153] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/01/2019] [Accepted: 05/12/2019] [Indexed: 05/24/2023]
Abstract
Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350 plant species. A few peanut cultivars were found to possess stable and durable bacterial wilt resistance (BWR). Genomics-assisted breeding can accelerate the process of developing resistant cultivars by using diagnostic markers. Here, we deployed sequencing-based trait mapping approach, QTL-seq, to discover genomic regions, candidate genes and diagnostic markers for BWR in a recombination inbred line population (195 progenies) of peanut. The QTL-seq analysis identified one candidate genomic region on chromosome B02 significantly associated with BWR. Mapping of newly developed single nucleotide polymorphism (SNP) markers narrowed down the region to 2.07 Mb and confirmed its major effects and stable expressions across three environments. This candidate genomic region had 49 nonsynonymous SNPs affecting 19 putative candidate genes including seven putative resistance genes (R-genes). Two diagnostic markers were successfully validated in diverse breeding lines and cultivars and could be deployed in genomics-assisted breeding of varieties with enhanced BWR.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
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28
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Zhang ZH, Zhou T, Tang TJ, Song HX, Guan CY, Huang JY, Hua YP. A multiomics approach reveals the pivotal role of subcellular reallocation in determining rapeseed resistance to cadmium toxicity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5437-5455. [PMID: 31232451 PMCID: PMC6793439 DOI: 10.1093/jxb/erz295] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/13/2019] [Indexed: 05/04/2023]
Abstract
Oilseed rape (Brassica napus) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Enhanced plant Cd resistance (PCR) is a crucial prerequisite for phytoremediation through hyper-accumulation of excess Cd. However, the complexity of the allotetraploid genome of rapeseed hinders our understanding of PCR. To explore rapeseed Cd-resistance mechanisms, we examined two genotypes, 'ZS11' (Cd-resistant) and 'W10' (Cd-sensitive), that exhibit contrasting PCR while having similar tissue Cd concentrations, and characterized their different fingerprints in terms of plant morphophysiology (electron microscopy), ion abundance (inductively coupled plasma mass spectrometry), DNA variation (whole-genome resequencing), transcriptomics (high-throughput mRNA sequencing), and metabolomics (ultra-high performance liquid chromatography-mass spectrometry). Fine isolation of cell components combined with ionomics revealed that more Cd accumulated in the shoot vacuoles and root pectins of the resistant genotype than in the sensitive one. Genome and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in pectin modification, ion binding, and compartmentalization. Transcriptomics-assisted gene co-expression networks characterized BnaCn.ABCC3 and BnaA8.PME3 as the central members involved in the determination of rapeseed PCR. High-resolution metabolic profiles revealed greater accumulation of shoot Cd chelates, and stronger biosynthesis and higher demethylation of root pectins in the resistant genotype than in the sensitive one. Our comprehensive examination using a multiomics approach has greatly improved our understanding of the role of subcellular reallocation of Cd in the determination of PCR.
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Affiliation(s)
- Zhen-Hua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Ting Zhou
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Tian-Jiao Tang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Hai-Xing Song
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Chun-Yun Guan
- National Center of Oilseed Crop Improvement, Hunan Branch, Changsha, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Peng Hua
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Correspondence:
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29
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Diehn TA, Bienert MD, Pommerrenig B, Liu Z, Spitzer C, Bernhardt N, Fuge J, Bieber A, Richet N, Chaumont F, Bienert GP. Boron demanding tissues of Brassica napus express specific sets of functional Nodulin26-like Intrinsic Proteins and BOR1 transporters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:68-82. [PMID: 31148338 PMCID: PMC6852077 DOI: 10.1111/tpj.14428] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/01/2019] [Accepted: 05/28/2019] [Indexed: 05/22/2023]
Abstract
The sophisticated uptake and translocation regulation of the essential element boron (B) in plants is ensured by two transmembrane transporter families: the Nodulin26-like Intrinsic Protein (NIP) and BOR transporter family. Though the agriculturally important crop Brassica napus is highly sensitive to B deficiency, and NIPs and BORs have been suggested to be responsible for B efficiency in this species, functional information of these transporter subfamilies is extremely rare. Here, we molecularly characterized the NIP and BOR1 transporter family in the European winter-type cv. Darmor-PBY018. Our transport assays in the heterologous oocyte and yeast expression systems as well as in growth complementation assays in planta demonstrated B transport activity of NIP5, NIP6, NIP7 and BOR1 isoforms. Moreover, we provided functional and quantitative evidence that also members of the NIP2, NIP3 and NIP4 groups facilitate the transport of B. A detailed B- and tissue-dependent B-transporter expression map was generated by quantitative polymerase chain reaction. We showed that NIP5 isoforms are highly upregulated under B-deficient conditions in roots, but also in shoot tissues. Moreover, we detected transcripts of several B-permeable NIPs from various groups in floral tissues that contribute to the B distribution within the highly B deficiency-sensitive flowers.
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Affiliation(s)
- Till Arvid Diehn
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Manuela Désirée Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Benjamin Pommerrenig
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
- Division of Plant PhysiologyUniversity KaiserslauternKaiserslautern67663Germany
| | - Zhaojun Liu
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Christoph Spitzer
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nadine Bernhardt
- Experimental Taxonomy, Genebank DepartmentLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Jacqueline Fuge
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Annett Bieber
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nicolas Richet
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - François Chaumont
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Gerd Patrick Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
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30
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Luo H, Pandey MK, Khan AW, Guo J, Wu B, Cai Y, Huang L, Zhou X, Chen Y, Chen W, Liu N, Lei Y, Liao B, Varshney RK, Jiang H. Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1248-1260. [PMID: 30549165 PMCID: PMC6576108 DOI: 10.1111/pbi.13050] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 05/12/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high-quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics-assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL-seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68-4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89-790.32 million reads and achieving 91.85%-93.18% genome coverage and 14.04-21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68-4/two bulks) using the QTL-seq pipeline resulted in discovery of two overlapped genomic regions (2.75 Mb on A09 and 1.1 Mb on B02). Nine candidate genes affected by 10 SNPs with non-synonymous effects or in UTRs were identified in these regions for SP. Cost-effective KASP (Kompetitive Allele-Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yan Cai
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
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31
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Gu J, Li W, Wang S, Zhang X, Coules A, Ding G, Xu F, Ren J, Lu C, Shi L. Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes (Basel) 2019; 10:genes10030224. [PMID: 30889858 PMCID: PMC6471828 DOI: 10.3390/genes10030224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/07/2019] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) can increase transcriptome diversity, protein diversity and protein yield, and is an important mechanism to regulate plant responses to stress. Oilseed rape (Brassica napus L.), one of the main oil crops in China, shows higher sensitivity to boron (B) deficiency than other species. Here, we demonstrated AS changes that largely increased the diversity of the mRNA expressed in response to B deficiency in B. napus. Each gene had two or more transcripts on average. A total of 33.3% genes in both Qingyou10 (QY10, B-efficient cultivar) and Westar10 (W10, B-inefficient cultivar) showed AS in both B conditions. The types of AS events were mainly intron retention, 3′ alternative splice site, 5′ alternative splice site and exon skipping. The tolerance ability of QY10 was higher than that of W10, possibly because there were far more differential alternative splicing (DAS) genes identified in QY10 at low B conditions than in W10. The number of genes with both DAS and differentially expressed (DE) was far lower than that of the genes that were either with DAS or DE in QY10 and W10, suggesting that the DAS and DE genes were independent. Four Serine/Arginine-rich (SR) splicing factors, BnaC06g14780D, BnaA01g14750D, BnaA06g15930D and BnaC01g41640D, underwent differentially alternative splicing in both cultivars. There existed gene–gene interactions between BnaC06g14780D and the genes associated with the function of B in oilseed rape at low B supply. This suggests that oilseed rape could regulate the alterative pre-mRNA splicing of SR protein related genes to increase the plant tolerance to B deficiency.
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Affiliation(s)
- Jin Gu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoyan Zhang
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Anne Coules
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
| | - Chungui Lu
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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32
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Zhang ZH, Zhou T, Liao Q, Yao JY, Liang GH, Song HX, Guan CY, Hua YP. Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation. BMC PLANT BIOLOGY 2018; 18:322. [PMID: 30509163 PMCID: PMC6278020 DOI: 10.1186/s12870-018-1507-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/26/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (AnAnCnCn, 2n = 4x = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes. RESULTS In this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO3-) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance. CONCLUSIONS We identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.
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Affiliation(s)
- Zhen-hua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Ting Zhou
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Qiong Liao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Jun-yue Yao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Gui-hong Liang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Hai-xing Song
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Chun-yun Guan
- National Center of Oilseed Crop Improvement, Hunan Branch, Changsha, China
| | - Ying-peng Hua
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
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33
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Chen H, Zhang Q, He M, Wang S, Shi L, Xu F. Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of BnaC04.BOR1;1c in Brassica napus. BMC PLANT BIOLOGY 2018; 18:193. [PMID: 30217178 PMCID: PMC6137915 DOI: 10.1186/s12870-018-1407-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/30/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Boron (B) deficiency is an agricultural problem that causes significant losses of crop yield in many areas of the world. However, systematic analysis of BOR family genes for B transport in rapeseed is still lacking. We aimed to identify and characterize BOR transporters in Brassica napus and the potential role of these transporters in B homeostasis in response to B deficiency. RESULTS Here, we identified 20 BOR transporters from the Brassica napus genome, which were classified into six distinct groups that represent clear orthologous relationships to their family members in Arabidopsis. qRT-PCR revealed distinct expression profiles for BnBORs in different tissues and in response to external B levels. The B-efficient cultivar QY10 accumulated more B in shoots than the B-inefficient cultivar W10, and overexpression of BnaBOR1;1c could alleviate shoot B-deficiency symptoms in W10 by distributing more B from roots to shoots. Additionally, BnBOR1;1c expression was up-regulated by B deficiency, and the induction of BnBOR1;1c was more intense in QY10. Moreover, two conserved InDels were found in the promoter regions of BnBOR1;1c within different B-efficient genotypes. CONCLUSIONS Overall, the molecular characterization of the BnBOR genes of two B-efficient cultivars and their responses to B deficiency highlights the diversity of the family members in B. napus, and BnaC4.BOR1;1c has potential as a candidate gene for improving B nutrition.
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Affiliation(s)
- Haifei Chen
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Quan Zhang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Mingliang He
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070 China
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34
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Pommerrenig B, Junker A, Abreu I, Bieber A, Fuge J, Willner E, Bienert MD, Altmann T, Bienert GP. Identification of Rapeseed ( Brassica napus) Cultivars With a High Tolerance to Boron-Deficient Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1142. [PMID: 30131820 PMCID: PMC6091279 DOI: 10.3389/fpls.2018.01142] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 05/22/2023]
Abstract
Boron (B) is an essential micronutrient for seed plants. Information on B-efficiency mechanisms and B-efficient crop and model plant genotypes is very scarce. Studies evaluating the basis and consequences of B-deficiency and B-efficiency are limited by the facts that B occurs as a trace contaminant essentially everywhere, its bioavailability is difficult to control and soil-based B-deficiency growth systems allowing a high-throughput screening of plant populations have hitherto been lacking. The crop plant Brassica napus shows a very high sensitivity toward B-deficient conditions. To reduce B-deficiency-caused yield losses in a sustainable manner, the identification of B-efficient B. napus genotypes is indispensable. We developed a soil substrate-based cultivation system which is suitable to study plant growth in automated high-throughput phenotyping facilities under defined and repeatable soil B conditions. In a comprehensive screening, using this system with soil B concentrations below 0.1 mg B (kg soil)-1, we identified three highly B-deficiency tolerant B. napus cultivars (CR2267, CR2280, and CR2285) among a genetically diverse collection comprising 590 accessions from all over the world. The B-efficiency classification of cultivars was based on a detailed assessment of various physical and high-throughput imaging-based shoot and root growth parameters in soil substrate or in in vitro conditions, respectively. We identified cultivar-specific patterns of B-deficiency-responsive growth dynamics. Elemental analysis revealed striking differences only in B contents between contrasting genotypes when grown under B-deficient but not under standard conditions. Results indicate that B-deficiency tolerant cultivars can grow with a very limited amount of B which is clearly below previously described critical B-tissue concentration values. These results suggest a higher B utilization efficiency of CR2267, CR2280, and CR2285 which would represent a unique trait among so far identified B-efficient B. napus cultivars which are characterized by a higher B-uptake capacity. Testing various other nutrient deficiency treatments, we demonstrated that the tolerance is specific for B-deficient conditions and is not conferred by a general growth vigor at the seedling stage. The identified B-deficiency tolerant cultivars will serve as genetic and physiological "tools" to further understand the mechanisms regulating the B nutritional status in rapeseed and to develop B-efficient elite genotypes.
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Affiliation(s)
- Benjamin Pommerrenig
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Isidro Abreu
- Department of Biology, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Annett Bieber
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jacqueline Fuge
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Evelin Willner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Manuela D. Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Gerd P. Bienert
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes. G3-GENES GENOMES GENETICS 2018; 8:2757-2771. [PMID: 29967053 PMCID: PMC6071586 DOI: 10.1534/g3.118.200481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (AnAnCnCn, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype “XY15” and an N-inefficient (lower NUE) genotype “814” of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50× depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the An and Cn subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.
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Zhou T, Hua Y, Zhang B, Zhang X, Zhou Y, Shi L, Xu F. Low-Boron Tolerance Strategies Involving Pectin-Mediated Cell Wall Mechanical Properties in Brassica napus. PLANT & CELL PHYSIOLOGY 2017; 58:1991-2005. [PMID: 29016959 DOI: 10.1093/pcp/pcx130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/22/2017] [Indexed: 05/18/2023]
Abstract
Boron (B) is an essential micronutrient for the growth and development of plants. Oilseed rape (Brassica napus L.) is a staple oleaginous crop, which is greatly susceptible to B deficiency. Significant differences in tolerance of low-B stresses are observed in rapeseed genotypes, but the underlying mechanism remains unclear, particularly at the single-cell level. Here we provide novel insights into pectin-mediated cell wall (CW) mechanical properties implicated in the differential tolerance of low B in rapeseed genotypes. Under B deficiency, suspension cells of the low-B-sensitive genotype 'W10' showed more severely deformed morphology, lower viabilities and a more easily ruptured CW than those of the low-B-tolerant genotype 'QY10'. Cell rupture was attributed to the weakened CW mechanical strength detected by atomic force microscopy; the CW mechanical strength of 'QY10' was reduced by 13.6 and 17.4%, whereas that of 'W10' was reduced by 29.0 and 30.4% under 0.25 and 0.10 μM B conditions, respectively. The mechanical strength differences between 'QY10' and 'W10' were diminished after the removal of pectin. Further, 'W10' exhibited significantly higher pectin concentrations with much more rhamnogalacturonan II (RG-II) monomer, and also presented obviously higher mRNA abundances of pectin biosynthesis-related genes than 'QY10' under B deficiency. CW regeneration was more difficult for protoplasts of 'W10' than for those of 'QY10'. Taking the results together, we conclude that the variations in pectin-endowed CW mechanical properties play key roles in modulating the differential genotypic tolerance of rapeseed to low-B stresses at both the single-cell and the plant level, and this can potentially be used as a selection trait for low-B-tolerant rapeseed breeding.
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Affiliation(s)
- Ting Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingpeng Hua
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiuqing Zhang
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
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Zhang Q, Chen H, He M, Zhao Z, Cai H, Ding G, Shi L, Xu F. The boron transporter BnaC4.BOR1;1c is critical for inflorescence development and fertility under boron limitation in Brassica napus. PLANT, CELL & ENVIRONMENT 2017; 40:1819-1833. [PMID: 28545156 DOI: 10.1111/pce.12987] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/01/2017] [Indexed: 05/05/2023]
Abstract
Boron (B) is an essential micronutrient for plants, but the molecular mechanisms underlying the uptake and distribution of B in allotetraploid rapeseed (Brassica napus) are unclear. Here, we identified a B transporter of rapeseed, BnaC4.BOR1;1c, which is expressed in shoot nodes and involved in distributing B to the reproductive organs. Transgenic Arabidopsis plants containing a BnaC4.BOR1;1c promoter-driven GUS reporter gene showed strong GUS activity in roots, nodal regions of the shoots and immature floral buds. Overexpressing BnaC4.BOR1;1c in Arabidopsis wild type or in bor1-1 mutants promoted wild-type growth and rescued the bor1-1 mutant phenotype. Conversely, knockdown of BnaC4.BOR1;1c in a B-efficient rapeseed line reduced B accumulation in flower organs, eventually resulting in severe sterility and seed yield loss. BnaC4.BOR1;1c RNAi plants exhibited large amounts of disintegrated stigma papilla cells with thickened cell walls accompanied by abnormal proliferation of lignification under low-B conditions, indicating that the sterility may be a result of altered cell wall properties in flower organs. Taken together, our results demonstrate that BnaC4.BOR1;1c is a AtBOR1-homologous B transporter gene expressing in both roots and shoot nodes that is essential for the developing inflorescence tissues, which highlights its diverse functions in allotetraploid rapeseed compared with diploid model plant Arabidopsis.
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Affiliation(s)
- Quan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingliang He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuqing Zhao
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
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Chao H, Wang H, Wang X, Guo L, Gu J, Zhao W, Li B, Chen D, Raboanatahiry N, Li M. Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus. Sci Rep 2017; 7:46295. [PMID: 28393910 PMCID: PMC5385559 DOI: 10.1038/srep46295] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/15/2017] [Indexed: 02/07/2023] Open
Abstract
High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.
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Affiliation(s)
- Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Xiaodong Wang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Dengyan Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
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Lu K, Peng L, Zhang C, Lu J, Yang B, Xiao Z, Liang Y, Xu X, Qu C, Zhang K, Liu L, Zhu Q, Fu M, Yuan X, Li J. Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:206. [PMID: 28261256 PMCID: PMC5309214 DOI: 10.3389/fpls.2017.00206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/03/2017] [Indexed: 05/19/2023]
Abstract
Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Liu Peng
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- School of Management, Xihua UniversityChengdu, China
| | - Chao Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural SciencesGuiyang, China
| | - Junhua Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Bo Yang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Zhongchun Xiao
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Xingfu Xu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Qinlong Zhu
- College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Minglian Fu
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Xiaoyan Yuan
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Jiana Li
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Yuan D, Li W, Hua Y, King GJ, Xu F, Shi L. Genome-Wide Identification and Characterization of the Aquaporin Gene Family and Transcriptional Responses to Boron Deficiency in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1336. [PMID: 28824672 PMCID: PMC5539139 DOI: 10.3389/fpls.2017.01336] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/17/2017] [Indexed: 05/18/2023]
Abstract
Aquaporins (AQPs) are an abundant protein family and play important roles to facilitate small neutral molecule transport across membranes. Oilseed rape (Brassica napus L.) is an important oil crop in China and elsewhere in the world, and is very sensitive to low boron (B) stress. Several AQP family genes have been reported to be involved in B transport across plasma membranes in plants. In this study, a total of 121 full-length AQPs were identified and characterized in B. napus (AC genome), and could be classified into four sub-families, including 43 PIPs (plasma membrane intrinsic proteins), 35 TIPs (tonoplast intrinsic proteins), 32 NIPs (NOD26-like intrinsic proteins), and 11 SIPs (small basic intrinsic proteins). The gene characteristics of BnaAQPs were similar to those of BraAQPs (A genome) and BolAQPs (C genome) including the composition of each sub-family, gene structure, and substrate selectivity filters. The BnaNIP was the most complex AQP sub-family, reflecting the composition of substrate selectivity filter structures which affect the permeation of solution molecules. In this study, the seedlings of both B-efficient (QY10) and B-inefficient (W10) cultivars were treated with two boron (B) levels: deficient (0.25 μM B) and sufficient (25 μM B). The transcription of AQP genes in root (R), juvenile leaf (JL), and old leaf (OL) tissues of both cultivars was investigated under B deficient and sufficient conditions. Transcription of most BnaPIPs and BnaTIPs was significantly increased compared with other BnaAQPs in all the three tissues, especially in the roots, of both B-efficient and B-inefficient cultivars under both B conditions. With B deprivation, the expression of the majority of the BnaPIPs and BnaTIPs was down-regulated in the roots. However, the BnaNIPs were up-regulated. In addition, the BnaCnn_random.PIP1;4b, BnaPIP2;4s, BnaC04.TIP4;1a, BnaAnn_random.TIP1;1b, and BnaNIP5;1s (except for BnaA07.NIP5;1c and BnaC06.NIP5;1c) exhibited obvious differences at low B between B-efficient and B-inefficient cultivars. These results will help us to understand boron homeostasis in B. napus.
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Affiliation(s)
- Dan Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Wei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yingpeng Hua
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Graham J. King
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Lei Shi
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Teng C, Du D, Xiao L, Yu Q, Shang G, Zhao Z. Mapping and Identifying a Candidate Gene ( Bnmfs) for Female-Male Sterility through Whole-Genome Resequencing and RNA-Seq in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2086. [PMID: 29326731 PMCID: PMC5733364 DOI: 10.3389/fpls.2017.02086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/22/2017] [Indexed: 05/03/2023]
Abstract
In oilseed crops, carpel and stamen development play vital roles in pollination and rapeseed yield, but the genetic mechanisms underlying carpel and stamen development remain unclear. Herein, a male- and female-sterile mutant was obtained in offspring of a (Brassica napus cv. Qingyou 14) × (Qingyou 14 × B. rapa landrace Dahuang) cross. Subsequently, F2-F9 populations were generated through selfing of the heterozygote plants among the progeny of each generation. The male- and female-sterility exhibited stable inheritance in successive generations and was controlled by a recessive gene. The mutant kept the same chromosome number (2n = 38) as B. napus parent but showed abnormal meiosis for male and female. One candidate gene for the sterility was identified by simple sequence repeat (SSR) and insertion deletion length polymorphism (InDel) markers in F7-F9 plants, and whole-genome resequencing with F8 pools and RNA sequencing with F9 pools. Whole-genome resequencing found three candidate intervals (35.40-35.68, 35.74-35.75, and 45.34-46.45 Mb) on chromosome C3 in B. napus and candidate region for Bnmfs was narrowed to approximately 1.11-Mb (45.34-46.45 M) by combining SSR and InDel marker analyses with whole-genome resequencing. From transcriptome profiling in 0-2 mm buds, all of the genes in the candidate interval were detected, and only two genes with significant differences (BnaC03g56670D and BnaC03g56870D) were revealed. BnaC03g56870D was a candidate gene that shared homology with the CYP86C4 gene of Arabidopsis thaliana. Quantitative reverse transcription (qRT)-PCR analysis showed that Bnmfs primarily functioned in flower buds. Thus, sequencing and expression analyses provided evidence that BnaC03g56870D was the candidate gene for male and female sterility in the B. napus mutant.
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A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Sci Rep 2016; 6:36452. [PMID: 27811979 PMCID: PMC5095561 DOI: 10.1038/srep36452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
Harvest index (HI), the ratio of seed mass to total biomass of the aboveground plant parts, is an important trait for harvestable yield of crops. Unfortunately, HI of Brassica napus is lower than that of other economically important crops. To identify candidate genes associated with high HI, a genome-wide association study of HI and four HI-related traits was conducted with 520 B. napus accessions cultivated in both Yunnan and Chongqing. We detected 294 single nucleotide polymorphisms significantly associated with the abovementioned traits, including 79 SNPs that affected two or more traits. Differentially expressed genes between extremely high- and low-HI accessions were identified in 8 tissues at two cultivated regions. Combination of linkage disequilibrium and transcriptome analyses revealed 33 functional candidate genes located within the confidence intervals of significant SNPs associated with more than one trait, such as SHOOT GRAVITROPISM 5 (Bna.SGR5), ATP-CITRATE LYASE A-3 (Bna.ACLA-3) and CAROTENOID CLEAVAGE DIOXYGENASE 1 (Bna.CCD1), their orthologs in the Arabidopsis thaliana have been shown to play key roles in photosynthesis, inflorescence, and silique development. Our results provide insight into the molecular mechanisms underlying establishment of high-HI B. napus and lay a foundation for characterization of candidate genes aimed at developing high-HI B. napus varieties.
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Hua Y, Zhou T, Ding G, Yang Q, Shi L, Xu F. Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5769-5784. [PMID: 27639094 PMCID: PMC5066495 DOI: 10.1093/jxb/erw342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Allotetraploid rapeseed (Brassica napus L. AnAnCnCn, 2n=4x=38) is highly susceptible to boron (B) deficiency, a widespread limiting factor that causes severe losses in seed yield. The genetic variation in the sensitivity to B deficiency found in rapeseed genotypes emphasizes the complex response architecture. In this research, a B-inefficient genotype, 'Westar 10' ('W10'), responded to B deficiencies during vegetative and reproductive development with an over-accumulation of reactive oxygen species, severe lipid peroxidation, evident plasmolysis, abnormal floral organogenesis, and widespread sterility compared to a B-efficient genotype, 'Qingyou 10' ('QY10'). Whole-genome re-sequencing (WGS) of 'QY10' and 'W10' revealed a total of 1 605 747 single nucleotide polymorphisms and 218 755 insertions/deletions unevenly distributed across the allotetraploid rapeseed genome (~1130Mb). Digital gene expression (DGE) profiling identified more genes related to B transporters, antioxidant enzymes, and the maintenance of cell walls and membranes with higher transcript levels in the roots of 'QY10' than in 'W10' under B deficiency. Furthermore, based on WGS and bulked segregant analysis of the doubled haploid (DH) line pools derived from 'QY10' and 'W10', two significant quantitative trait loci (QTLs) for B efficiency were characterized on chromosome C2, and DGE-assisted QTL-seq analyses then identified a nodulin 26-like intrinsic protein gene and an ATP-binding cassette (ABC) transporter gene as the corresponding candidates regulating B efficiency. This research facilitates a more comprehensive understanding of the differential physiological and transcriptional responses to B deficiency and abundant genetic diversity in rapeseed genotypes, and the DGE-assisted QTL-seq analyses provide novel insights regarding the rapid dissection of quantitative trait genes in plant species with complex genomes.
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Affiliation(s)
- Yingpeng Hua
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Ting Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyong Yang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
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