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Khuman A, Kumar V, Chaudhary B. Evolutionary expansion and expression dynamics of cytokinin-catabolizing CKX gene family in the modern amphidiploid mustard ( Brassica sp.). 3 Biotech 2022; 12:233. [PMID: 35996674 PMCID: PMC9391556 DOI: 10.1007/s13205-022-03294-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/02/2022] [Indexed: 11/01/2022] Open
Abstract
Plant cytokinins (CKs) promote development and physiological processes, drought tolerance, root architecture, and ultimately crop productivity. Biologically active CKs (iP, tZ, and cZ) are precisely maintained in the vegetative and floral tissues through their irreversible degradation by developmentally regulated CK-catabolizing cytokinin oxidase/dehydrogenase (CKX) enzyme. A meta-analysis of CKX proteins was performed through an exhaustive exploration of multiple genome databases of cyanobacteria, bryophyte, monocot and eudicot plants to reveal the intricate evolutionary profiles of CKX enzymes specific to the family Brassicaceae. At least 175 unique paralogous/orthologous CKX sequences were successfully retrieved and phylogenetically clustered into distinct groups. Observations of structural divergences among paralogous sequences compared to their orthologs indicated that the progenitor CKX sequence had been subjected to massive structural modifications, possibly as a result of the evolutionary split between monocots and eudicots. An analysis of dN/dS comparisons of orthologous genes revealed that segmental CKX gene duplications have evolved primarily under purifying selection. Further, 24 CKX genes with conserved signature domain were identified in the amphidiploid Brassica juncea genome (AABB; 2n = 36). Genetic evolution of paralogous and orthologous genes was largely responsible for the expansion of CKX homoeologs in the amphidiploid Brassica genomes. Also, comparative analyses of 1.5 kb-long upstream regulatory regions of BjCKX genes identified various development- and stress-responsive elements. Spatial and temporal expression profiles of CKX genes were primarily attributed to their structural diversity observed in the 5'-regulatory regions along with species evolution. This data suggested that CKX duplicate genes had partitioned their spatial expression (= function) during evolution. These findings illustrated the evolutionary importance of CKX genes during plant development, and also suggested their deployment for future crop improvement programs. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03294-0.
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Affiliation(s)
| | - Vijay Kumar
- Department of Botany, Shivaji College, University of Delhi, New Delhi, 110027 India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312 India
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2
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Genome-Wide Identification and Expression Analysis of SNARE Genes in Brassica napus. PLANTS 2022; 11:plants11050711. [PMID: 35270180 PMCID: PMC8912762 DOI: 10.3390/plants11050711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/17/2022]
Abstract
SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are central components that drive membrane fusion events during exocytosis and endocytosis and play important roles in different biological processes of plants. In this study, we identified 237 genes encoding SNARE family proteins in B. napus in silico at the whole-genome level. Phylogenetic analysis showed that BnaSNAREs could be classified into five groups (Q (a-, b-, c-, bc-) and R) like other plant SNAREs and clustered into twenty-five subclades. The gene structure and protein domain of each subclade were found to be highly conserved. In many subclades, BnaSNAREs are significantly expanded compared with the orthologous genes in Arabidopsis thaliana. BnaSNARE genes are expressed differentially in the leaves and roots of B. napus. RNA-seq data and RT-qPCR proved that some of the BnaSNAREs are involved in the plant response to S. sclerotiorum infection as well as treatments with toxin oxalic acid (OA) (a virulence factor often secreted by S. sclerotiorum) or abscisic acid (ABA), methyl jasmonate (MeJA), and salicylic acid (SA), which individually promote resistance to S. sclerotiorum. Moreover, the interacted proteins of BnaSNAREs contain some defense response-related proteins, which increases the evidence that BnaSNAREs are involved in plant immunity. We also found the co-expression of BnaSYP121/2s, BnaSNAPs, and BnaVAMP722/3s in B. napus due to S. sclerotiorum infection as well as the probable interaction among them.
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3
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Huang L, Min Y, Schiessl S, Xiong X, Jan HU, He X, Qian W, Guan C, Snowdon RJ, Hua W, Guan M, Qian L. Integrative analysis of GWAS and transcriptome to reveal novel loci regulation flowering time in semi-winter rapeseed. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110980. [PMID: 34315596 DOI: 10.1016/j.plantsci.2021.110980] [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: 04/02/2021] [Revised: 05/15/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Flowering is an important turning point from vegetative growth to reproductive growth, and vernalization is an essential condition for the flowering of annual winter plants. To investigate the genetic architecture of flowering time in rapeseed, we used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with flowering time in 203 Chinese semi-winter rapeseed inbred lines. Twenty-one haplotype regions carrying one or more candidate genes showed a significant association with flowering time. Interestingly, we detected a SNP (Bn-scaff_22728_1-p285715) located in exon 3 of the BnVIN3-C03 gene that showed a significant association with flowering time on chromosome C03. Based on the SNP alleles A and G, two groups of accessions with early and late flowering time phenotypes were selected, respectively, and PCR amplification and gene expression analysis were combined to reveal the structural variation of the BnVIN3-C03 gene that affected flowering time. Moreover, we found that BnVIN3-C03 inhibited the expression of BnFLC-A02, BnFLC-A03.1, BnFLC-A10 and BnFLC-C03.1, thus modulating the flowering time of Brassica napus. This result provides insight into the genetic improvement of flowering time in B. napus.
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Affiliation(s)
- Luyao Huang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Yao Min
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Xinghua Xiong
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Habib U Jan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Qian
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Wei Hua
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China; 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
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.
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4
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Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae. Genomics 2021; 113:3185-3197. [PMID: 34182082 DOI: 10.1016/j.ygeno.2021.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/26/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022]
Abstract
Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.
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Larkan NJ, Ma L, Haddadi P, Buchwaldt M, Parkin IA, Djavaheri M, Borhan MH. The Brassica napus wall-associated kinase-like (WAKL) gene Rlm9 provides race-specific blackleg resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:892-900. [PMID: 32794614 PMCID: PMC7756564 DOI: 10.1111/tpj.14966] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 05/12/2023]
Abstract
In plants, race-specific defence against microbial pathogens is facilitated by resistance (R) genes which correspond to specific pathogen avirulence genes. This study reports the cloning of a blackleg R gene from Brassica napus (canola), Rlm9, which encodes a wall-associated kinase-like (WAKL) protein, a newly discovered class of race-specific plant RLK resistance genes. Rlm9 provides race-specific resistance against isolates of Leptosphaeria maculans carrying the corresponding avirulence gene AvrLm5-9, representing only the second WAKL-type R gene described to date. The Rlm9 protein is predicted to be cell membrane-bound and while not conclusive, our work did not indicate direct interaction with AvrLm5-9. Rlm9 forms part of a distinct evolutionary family of RLK proteins in B. napus, and while little is yet known about WAKL function, the Brassica-Leptosphaeria pathosystem may prove to be a model system by which the mechanism of fungal avirulence protein recognition by WAKL-type R genes can be determined.
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Affiliation(s)
- Nicholas J. Larkan
- Armatus Genetics IncSaskatoonSKCanada
- Agriculture & Agri‐Food CanadaSaskatoonSKCanada
| | - Lisong Ma
- Agriculture & Agri‐Food CanadaSaskatoonSKCanada
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6
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Matuszczak M, Spasibionek S, Gacek K, Bartkowiak-Broda I. Cleaved amplified polymorphic sequences (CAPS) marker for identification of two mutant alleles of the rapeseed BnaA.FAD2 gene. Mol Biol Rep 2020; 47:7607-7621. [PMID: 32979163 PMCID: PMC7588397 DOI: 10.1007/s11033-020-05828-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/07/2020] [Indexed: 11/30/2022]
Abstract
Two mutants of winter rapeseed (Brassica napus L. var. oleifera) with an increased amount of oleic acid in seeds were created by chemical mutagenesis (HOR3-M10453 and HOR4-M10464). The overall performance of the mutated plants was much lower than that of wild-type cultivars. Multiple rounds of crossing with high-yielding double-low ("00") cultivars and breeding lines having valuable agronomic traits, followed by selection of high oleic acid genotypes is then needed to obtain new "00" varieties of rapeseed having high oleic acid content in seeds. To perform such selection, the specific codominant cleaved amplified polymorphic sequences (CAPS) marker was used. This marker was designed to detect the presence of two relevant point mutations in the desaturase gene BnaA.FAD2, and it was previously described and patented. The specific polymerase chain reaction product (732 bp) was digested using FspBI restriction enzyme that recognizes the 5'-C↓TAG-3' sequence which is common to both mutated alleles, thereby yielding band patterns specific for those alleles. The method proposed in the patent was redesigned, adjusted to specific laboratory conditions, and thoroughly tested. Different DNA extraction protocols were tested to optimize the procedure. Two variants of the CAPS method (with and without purification of amplified product) were considered to choose the best option. In addition, the ability of the studied marker to detect heterozygosity in the BnaA.FAD2 locus was also tested. Finally, we also presented some examples for the use of the new CAPS marker in the marker-assisted selection (MAS) during our breeding programs. The standard CTAB method of DNA extraction and the simplified, two-step (amplification/digestion) procedure for the CAPS marker are recommended. The marker was found to be useful for the detection of two mutated alleles of the studied BnaA.FAD2 desaturase gene and can potentially assure the breeders of the purity of their HOLL lines. However, it was also shown that it could not detect any other alleles or genes that were revealed to play a role in the regulation of oleic acid level.
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Affiliation(s)
- Marcin Matuszczak
- Research Division in Poznań, Plant Breeding and Acclimatization Institute, National Research Institute, Strzeszyńska 36, Poznań, Poland.
| | - Stanisław Spasibionek
- Research Division in Poznań, Plant Breeding and Acclimatization Institute, National Research Institute, Strzeszyńska 36, Poznań, Poland
| | - Katarzyna Gacek
- Research Division in Poznań, Plant Breeding and Acclimatization Institute, National Research Institute, Strzeszyńska 36, Poznań, Poland
| | - Iwona Bartkowiak-Broda
- Research Division in Poznań, Plant Breeding and Acclimatization Institute, National Research Institute, Strzeszyńska 36, Poznań, Poland
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7
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Liu Y, Wang X, Wei Y, Liu Z, Lu Q, Liu F, Zhang T, Peng R. Chromosome Painting Based on Bulked Oligonucleotides in Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:802. [PMID: 32695125 PMCID: PMC7338755 DOI: 10.3389/fpls.2020.00802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 05/06/2023]
Abstract
Chromosome painting is one of the key technologies in cytogenetic research, which can accurately identify chromosomes or chromosome regions. Oligonucleotide (oligo) probes designed based on genome sequences have both flexibility and specificity, which would be ideal probes for fluorescence in situ hybridization (FISH) analysis of genome structure. In this study, the bulked oligos of the two arms of chromosome seven of cotton were developed based on the genome sequence of Gossypium raimondii (DD, 2n = 2× = 26), and each arm contains 12,544 oligos. Chromosome seven was easily identified in both D genome and AD genome cotton species using the bulked chromosome-specific painting probes. Together with 45S ribosomal DNA (rDNA) probe, the chromosome-specific painting probe was also successfully used to correct the chromosomal localization of 45S rDNA in G. raimondii. The study reveals that bulked oligos specific to a chromosome is a useful tool for chromosome painting in cotton.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, China
| | | | | | - Zhen Liu
- Anyang Institute of Technology, Anyang, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang,
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, China
- Renhai Peng,
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Lohani N, Golicz AA, Singh MB, Bhalla PL. Genome-wide analysis of the Hsf gene family in Brassica oleracea and a comparative analysis of the Hsf gene family in B. oleracea, B. rapa and B. napus. Funct Integr Genomics 2019; 19:515-531. [DOI: 10.1007/s10142-018-0649-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 02/05/2023]
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9
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Shivaraj SM, Jain A, Singh A. Highly preserved roles of Brassica MIR172 in polyploid Brassicas: ectopic expression of variants of Brassica MIR172 accelerates floral transition. Mol Genet Genomics 2018; 293:1121-1138. [PMID: 29752548 DOI: 10.1007/s00438-018-1444-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/03/2018] [Indexed: 12/21/2022]
Abstract
Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes. Copy number analysis revealed higher retention of MIR172 loci relative to AP2 in diploid and amphi-diploid Brassica species. Dendrogram of 87 MIR172 sequences from Brassicaceae showed five major clusters corresponding to MIR172a-MIR172e which further separated into sub-genome and progenitor genome specific clades. Similar groupings were observed in the phylogeny of 11 Brassica AP2 and AP2-like genes. Over-expression of a pair of natural variants for each of MIR172b, MIR172d and MIR172e representing sub-genomes, progenitor genomes and species of Brassicas displayed floral acceleration in all transgenic lines indicating a strong selection pressure on MIR172. All gain-of-function lines, except 35S::MIR172e and 35S::MIR172e' displayed floral organ defects implying altered target spectrum of MIR172e relative to MIR172b and MIR172d. Expression of MIR172e caused marginal earliness in flowering time in B. juncea. In conclusion, this study demonstrates tightly preserved role of homeologs and natural variants of MIR172 family in mediating flowering in Brassicas and suggests their deployment for introgression of early flowering trait.
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Affiliation(s)
- S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
- Département de Phytologie-Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, QC, Canada
| | - Aditi Jain
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India.
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10
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Miao L, Lv Y, Kong L, Chen Q, Chen C, Li J, Zeng F, Wang S, Li J, Huang L, Cao J, Yu X. Genome-wide identification, phylogeny, evolution, and expression patterns of MtN3/saliva/SWEET genes and functional analysis of BcNS in Brassica rapa. BMC Genomics 2018; 19:174. [PMID: 29499648 PMCID: PMC5834901 DOI: 10.1186/s12864-018-4554-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 02/19/2018] [Indexed: 11/23/2022] Open
Abstract
Background Members of the MtN3/saliva/SWEET gene family are present in various organisms and are highly conserved. Their precise biochemical functions remain unclear, especially in Chinese cabbage. Based on the whole genome sequence, this study aims to identify the MtN3/saliva/SWEETs family members in Chinese cabbage and to analyze their classification, gene structure, chromosome distribution, phylogenetic relationship, expression pattern, and biological functions. Results We identified 34 SWEET genes in Chinese cabbage and analyzed their localization on chromosomes and transmembrane regions of their corresponding proteins. Analysis of a phylogenetic tree indicated that there were at least 17 supposed ancestor genes before the separation in Brassica rapa and Arabidopsis. The expression patterns of these genes in different tissues and flower developmental stages of Chinese cabbage showed that they are mainly involved in reproductive development. The Ka/Ks ratio between paralogous SWEET gene pairs of B. rapa were far less than 1. In our previous study, At2g39060 homologous gene Bra000116 (BraSWEET9, also named BcNS, Brassica Nectary and Stamen) played an important role during flower development in Chinese cabbage. Instantaneous expression experiments in onion epidermal cells showed that the gene encoding this protein is localized to the plasma membrane. A basal nectary split is the phenotype of transgenic plants transformed with the antisense expression vector. Conclusion This study is the first to perform a sequence analysis, structures analysis, physiological and biochemical characteristics analysis of the MtN3/saliva/SWEETs gene in Chinese cabbage and to verify the function of BcNS. A total of 34 SWEET genes were identified and they are distributed among ten chromosomes and one scaffold. The Ka/Ks ratio implies that the duplication genes suffered strong purifying selection for retention. These genes were differentially expressed in different floral organs. The phenotypes of the transgenic plants indicated that BcNs participates in the development of the floral nectary. This study provides a basis for further functional analysis of the MtN3/saliva/SWEETs gene family. Electronic supplementary material The online version of this article (10.1186/s12864-018-4554-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liming Miao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Yanxia Lv
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Qizhen Chen
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Chaoquan Chen
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Jia Li
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Fanhuan Zeng
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Shenyun Wang
- Institute of Vegetable Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P. R. China.,Jiangsu Key Laboratory for Horticulture Crop Genetic Improvement, Nanjing, 210014, P. R. China
| | - Jianbin Li
- Institute of Vegetable Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P. R. China.,Jiangsu Key Laboratory for Horticulture Crop Genetic Improvement, Nanjing, 210014, P. R. China
| | - Li Huang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China.,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China.,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang Province, Hangzhou, 310058, P. R. China. .,Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Zhejiang Province, Hangzhou, 310058, P. R. China. .,Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang Province, Hangzhou, 310058, P. R. China.
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11
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Zhou Q, Han D, Mason AS, Zhou C, Zheng W, Li Y, Wu C, Fu D, Huang Y. Earliness traits in rapeseed (Brassica napus): SNP loci and candidate genes identified by genome-wide association analysis. DNA Res 2017; 25:229-244. [PMID: 29236947 PMCID: PMC6014513 DOI: 10.1093/dnares/dsx052] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/14/2017] [Indexed: 11/29/2022] Open
Abstract
Life cycle timing is critical for yield and productivity of Brassica napus (rapeseed) cultivars grown in different environments. To facilitate breeding for earliness traits in rapeseed, SNP loci and underlying candidate genes associated with the timing of initial flowering, maturity and final flowering, as well as flowering period (FP) were investigated in two environments in a diversity panel comprising 300 B. napus inbred lines. Genome-wide association studies (GWAS) using 201,817 SNP markers previously developed from SLAF-seq (specific locus amplified fragment sequencing) revealed a total of 131 SNPs strongly linked (P < 4.96E-07) to the investigated traits. Of these 131 SNPs, 40 fell into confidence intervals or were physically adjacent to previously published flowering time QTL or SNPs. Phenotypic effect analysis detected 35 elite allelic variants for early maturing, and 90 for long FP. Candidate genes present in the same linkage disequilibrium blocks (r2>0.6) or in 100 kb regions around significant trait-associated SNPs were screened, revealing 57 B. napus genes (33 SNPs) orthologous to 39 Arabidopsis thaliana flowering time genes. These results support the practical and scientific value of novel large-scale SNP data generation in uncovering the genetic control of agronomic traits in B. napus, and also provide a theoretical basis for molecular marker-assisted selection of earliness breeding in rapeseed.
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Affiliation(s)
- Qinghong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Depeng Han
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen 35392, Germany
| | - Can Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wei Zheng
- Jiangxi Institute of Red Soil, Jinxian, 331717, China
| | - Yazhen Li
- Jiangxi Institute of Red Soil, Jinxian, 331717, China
| | - Caijun Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
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12
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Owji H, Hajiebrahimi A, Seradj H, Hemmati S. Identification and functional prediction of stress responsive AP2/ERF transcription factors in Brassica napus by genome-wide analysis. Comput Biol Chem 2017; 71:32-56. [PMID: 28961511 DOI: 10.1016/j.compbiolchem.2017.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
Abstract
Using homology and domain authentication, 321 putative AP2/ERF transcription factors were identified in Brassica napus, called BnAP2/ERF TFs. BnAP2/ERF TFs were classified into five major subfamilies, including DREB, ERF, AP2, RAV, and BnSoloist. This classification is based on phylogenetic analysis, motif identification, gene structure analysis, and physiochemical characterization. These TFs were annotated based on phylogenetic relationship with Brassica rapa. BnAP2/ERF TFs were located on 19 chromosomes of B. napus. Orthologs and paralogs were identified using synteny-based methods Ks calculation within B. napus genome and between B. napus with other species such as B. rapa, Brassica oleracea, and Arabidopsis thaliana indicated that BnAP2/ERF TFs were formed through duplication events occurred before B. napus formation. Kn/Ks values were between 0 and 1, suggesting the purifying selection among BnAP2/ERF TFs. Gene ontology annotation, cis-regulatory elements and functional interaction networks suggested that BnAP2/ERF TFs participate in response to stressors, including drought, high salinity, heat and cold as well as developmental processes particularly organ specification and embryogenesis. The identified cis-regulatory elements in the upstream of BnAP2/ERF TFs were responsive to abscisic acid. Analysis of the expression data derived from Illumina Hiseq 2000 RNA sequencing revealed that BnAP2/ERF genes were highly expressed in the roots comparing to flower buds, leaves, and stems. Also, the ERF subfamily was over-expressed under salt and fungal treatments. BnERF039 and BnERF245 are candidates for salt-tolerant B. napus. BnERF253-256 and BnERF260-277 are potential cytokinin response factors. BnERF227, BnERF228, BnERF234, BnERF134, BnERF132, BnERF176, and BnERF235 were suggested for resistance against Leptosphaeria maculan and Leptosphaeria biglobosa.
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Affiliation(s)
- Hajar Owji
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Seradj
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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13
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Zhao BY, Hu YF, Li JJ, Yao X, Liu KD. BnaABF2, a bZIP transcription factor from rapeseed (Brassica napus L.), enhances drought and salt tolerance in transgenic Arabidopsis. BOTANICAL STUDIES 2016; 57:12. [PMID: 28597422 PMCID: PMC5432893 DOI: 10.1186/s40529-016-0127-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/27/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Abiotic stresses such as drought and salt stresses have a negative effect on the growth and productivity of plants. Improvement of stress tolerance through genetic engineering in plants has been reported in intense studies. Transcription factors play vital roles in plant adaptation to stresses by regulating expression of a great deal of target genes. A family of Arabidopsis basic region leucine zipper (bZIP) transcription factors that can recognize and bind to the abscisic acid (ABA)-responsive elements (ABREs) in promoter is named as ABRE binding factors (ABFs)/ABRE binding proteins (AREBs). They play a key role in the regulation of expression of downstream stress-responsive genes in ABA signalling. Genetic transformation of ABF/ABRE transcription factors has been suggested to be an effective approach for engineering stress-tolerant plants. However, whether the ABF/ABRE transcription factors are able to be used for generating stress-tolerant rapeseed plants has not yet been studied. RESULTS BnaABF2, encoding a bZIP transcription factor, was cloned from rapeseed in this study. Subcellular localization and transactivation analyses showed that BnaABF2 was localized to the nucleus with transactivation activity in plant cells. BnaABF2 gene expression was induced by drought and salt stresses and BnaABF2 positively functions in ABA signalling during the vegetative stage. Overexpression of BnaABF2 was found to render drought and salt tolerance to Arabidopsis plants. The resistance of the BnaABF2-expressing transgenic plants to drought and salt stresses is due to reduced water-loss rate and expression of stress-responsive genes such as RD29B, RAB18 and KIN2. The expression of RD29B, RAB18 and KIN2 regulated by BnaABF2 is involved in an ABA-dependent stress signalling. CONCLUSIONS Identification of the positive role of rapeseed BnaABF2 in plant tolerance to drought and salt provides evidence for ability of engineering stress-tolerant rapeseed plants by genetic transformation of BnaABF2.
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Affiliation(s)
- Bi-Yan Zhao
- College of plant science and technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yu-Feng Hu
- College of plant science and technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Juan-juan Li
- College of plant science and technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuan Yao
- College of plant science and technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ke-de Liu
- College of plant science and technology, Huazhong Agricultural University, Wuhan, 430070 China
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Glutathione Transferases Superfamily: Cold-Inducible Expression of Distinct GST Genes in Brassica oleracea. Int J Mol Sci 2016; 17:ijms17081211. [PMID: 27472324 PMCID: PMC5000609 DOI: 10.3390/ijms17081211] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 02/08/2023] Open
Abstract
Plants, as sessile organisms, can suffer serious growth and developmental consequences under cold stress conditions. Glutathione transferases (GSTs, EC 2.5.1.18) are ubiquitous and multifunctional conjugating proteins, which play a major role in stress responses by preventing oxidative damage by reactive oxygen species (ROS). Currently, understanding of their function(s) during different biochemical and signaling pathways under cold stress condition remain unclear. In this study, using combined computational strategy, we identified 65 Brassica oleracea glutathione transferases (BoGST) and characterized them based on evolutionary analysis into 11 classes. Inter-species and intra-species duplication was evident between BoGSTs and Arabidopsis GSTs. Based on localization analyses, we propose possible pathways in which GST genes are involved during cold stress. Further, expression analysis of the predicted putative functions for GST genes were investigated in two cold contrasting genotypes (cold tolerance and susceptible) under cold condition, most of these genes were highly expressed at 6 h and 1 h in the cold tolerant (CT) and cold susceptible (CS) lines, respectively. Overall, BoGSTU19, BoGSTU24, BoGSTF10 are candidate genes highly expressed in B. oleracea. Further investigation of GST superfamily in B. oleracea will aid in understanding complex mechanism underlying cold tolerance in plants.
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Greer MS, Pan X, Weselake RJ. Two Clades of Type-1 Brassica napus Diacylglycerol Acyltransferase Exhibit Differences in Acyl-CoA Preference. Lipids 2016; 51:781-6. [PMID: 27138895 DOI: 10.1007/s11745-016-4158-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
Diacylglycerol acyltransferase (DGAT) catalyzes the acyl-CoA-dependent acylation of sn-1, 2-diacylglycerol to produce triacylglycerol, which is the main component of the seed oil of Brassica oilseed species. Phylogenetic analysis of the amino acid sequences encoded by four transcriptionally active DGAT1 genes from Brassica napus suggests that the gene forms diverged over time into two clades (I and II), with representative members in each genome (A and C). The majority of the amino acid sequence differences in these forms of DGAT1, however, reside outside of motifs suggested to be involved in catalysis. Despite this, the clade II enzymes displayed a significantly enhanced preference for linoleoyl-CoA when assessed using in-vitro enzyme assays with yeast microsomes containing recombinant enzyme forms. These findings contribute to our understanding of triacylglycerol biosynthesis in B. napus, and may advance our ability to engineer DGAT1s with desired substrate selectivity properties.
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Affiliation(s)
- Michael S Greer
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Xue Pan
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Randall J Weselake
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Liu J, Wang W, Mei D, Wang H, Fu L, Liu D, Li Y, Hu Q. Characterizing Variation of Branch Angle and Genome-Wide Association Mapping in Rapeseed (Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:21. [PMID: 26870051 PMCID: PMC4740498 DOI: 10.3389/fpls.2016.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/08/2016] [Indexed: 05/20/2023]
Abstract
Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Li Fu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Daoming Liu
- Agricultural Sciences Institute of Lu'an MunicipalLu'an, China
| | - Yunchang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Qiong Hu
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17
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Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Res 2015; 23:43-52. [PMID: 26659471 PMCID: PMC4755526 DOI: 10.1093/dnares/dsv035] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/04/2015] [Indexed: 01/06/2023] Open
Abstract
Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.
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Affiliation(s)
- Liping Xu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenqian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Song Chen
- Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Wei Hua
- The Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
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18
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Rosato M, Moreno-Saiz JC, Galián JA, Rosselló JA. Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events. AOB PLANTS 2015; 7:plv135. [PMID: 26578742 PMCID: PMC4683978 DOI: 10.1093/aobpla/plv135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/07/2015] [Indexed: 05/20/2023]
Abstract
Several genome duplications have been identified in the evolution of seed plants, providing unique systems for studying karyological processes promoting diversification and speciation. Knowledge about the number of ribosomal DNA (rDNA) loci, together with their chromosomal distribution and structure, provides clues about organismal and molecular evolution at various phylogenetic levels. In this work, we aim to elucidate the evolutionary dynamics of karyological and rDNA site-number variation in all known taxa of subtribe Vellinae, showing a complex scenario of ancestral and more recent polyploid events. Specifically, we aim to infer the ancestral chromosome numbers and patterns of chromosome number variation, assess patterns of variation of both 45S and 5S rDNA families, trends in site-number change of rDNA loci within homoploid and polyploid series, and reconstruct the evolutionary history of rDNA site number using a phylogenetic hypothesis as a framework. The best-fitting model of chromosome number evolution with a high likelihood score suggests that the Vellinae core showing x = 17 chromosomes arose by duplication events from a recent x = 8 ancestor. Our survey suggests more complex patterns of polyploid evolution than previously noted for Vellinae. High polyploidization events (6x, 8x) arose independently in the basal clade Vella castrilensis-V. lucentina, where extant diploid species are unknown. Reconstruction of ancestral rDNA states in Vellinae supports the inference that the ancestral number of loci in the subtribe was two for each multigene family, suggesting that an overall tendency towards a net loss of 5S rDNA loci occurred during the splitting of Vellinae ancestors from the remaining Brassiceae lineages. A contrasting pattern for rDNA site change in both paleopolyploid and neopolyploid species was linked to diversification of Vellinae lineages. This suggests dynamic and independent changes in rDNA site number during speciation processes and a significant lack of correlation between 45S and 5S rDNA evolutionary pathways.
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Affiliation(s)
- Marcela Rosato
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain
| | - Juan C Moreno-Saiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - José A Galián
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain
| | - Josep A Rosselló
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain Carl Faust Fdn., PO Box 112, E-17300 Blanes, Spain
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19
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Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas. Dev Genes Evol 2015; 225:287-303. [DOI: 10.1007/s00427-015-0513-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022]
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20
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Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress. Int J Mol Sci 2015; 16:18752-77. [PMID: 26270661 PMCID: PMC4581270 DOI: 10.3390/ijms160818752] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 02/03/2023] Open
Abstract
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in “stimulus” “stress” biological process, and activated genes in leaf mainly functioned in “cell” “cell part” components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.
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Kirov IV, Van Laere K, Khrustaleva LI. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa. BMC Genet 2015; 16:74. [PMID: 26134672 PMCID: PMC4488978 DOI: 10.1186/s12863-015-0233-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. RESULTS Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. CONCLUSIONS High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.
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Affiliation(s)
- Ilya V Kirov
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Ludmila I Khrustaleva
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia.
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Babula-Skowrońska D, Ludwików A, Cieśla A, Olejnik A, Cegielska-Taras T, Bartkowiak-Broda I, Sadowski J. Involvement of genes encoding ABI1 protein phosphatases in the response of Brassica napus L. to drought stress. PLANT MOLECULAR BIOLOGY 2015; 88:445-57. [PMID: 26059040 PMCID: PMC4486095 DOI: 10.1007/s11103-015-0334-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/22/2015] [Indexed: 05/21/2023]
Abstract
In this report we characterized the Arabidopsis ABI1 gene orthologue and Brassica napus gene paralogues encoding protein phosphatase 2C (PP2C, group A), which is known to be a negative regulator of the ABA signaling pathway. Six homologous B. napus sequences were identified and characterized as putative PP2C group A members. To gain insight into the conservation of ABI1 function in Brassicaceae, and understand better its regulatory effects in the drought stress response, we generated transgenic B. napus plants overexpressing A. thaliana ABI1. Transgenic plants subjected to drought showed a decrease in relative water content, photosynthetic pigments content and expression level of RAB18- and RD19A-drought-responsive marker genes relative to WT plants. We present the characterization of the drought response of B. napus with the participation of ABI1-like paralogues. The expression pattern of two evolutionarily distant paralogues, BnaA01.ABI1.a and BnaC07.ABI1.b in B. napus and their promoter activity in A. thaliana showed differences in the induction of the paralogues under dehydration stress. Comparative sequence analysis of both BnaABI1 promoters showed variation in positions of cis-acting elements that are especially important for ABA- and stress-inducible expression. Together, these data reveal that subfunctionalization following gene duplication may be important in the maintenance and functional divergence of the BnaABI1 paralogues. Our results provide a framework for a better understanding of (1) the role of ABI1 as a hub protein regulator of the drought response, and (2) the differential involvement of the duplicated BnaABI1 genes in the response of B. napus to dehydration-related stresses.
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Affiliation(s)
- Danuta Babula-Skowrońska
- />Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Agnieszka Ludwików
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Agata Cieśla
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Anna Olejnik
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Teresa Cegielska-Taras
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Iwona Bartkowiak-Broda
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Jan Sadowski
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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23
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Dun X, Shen W, Hu K, Zhou Z, Xia S, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T, Lagercrantz U. Neofunctionalization of duplicated Tic40 genes caused a gain-of-function variation related to male fertility in Brassica oleracea lineages. PLANT PHYSIOLOGY 2014; 166:1403-19. [PMID: 25185122 PMCID: PMC4226349 DOI: 10.1104/pp.114.246470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.
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Affiliation(s)
- Xiaoling Dun
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Wenhao Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Zhengfu Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Shengqian Xia
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
| | - Ulf Lagercrantz
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China (X.D., W.S., K.H., Z.Z., S.X., J.W., B.Y., J.S., C.M., J.T., T.F.); andDepartment of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala SE-75236, Sweden (U.L.)
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Liu Z, Zhang M, Kong L, Lv Y, Zou M, Lu G, Cao J, Yu X. Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis). DNA Res 2014; 21:379-96. [PMID: 24585003 PMCID: PMC4131832 DOI: 10.1093/dnares/dsu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/20/2014] [Indexed: 12/27/2022] Open
Abstract
In plants, a two component system (TCS) composed of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs) has been employed in cytokinin signal transduction. A TCS exhibits important functions in diverse biological processes, including plant growth, development, and response to environmental stimuli. Conducting an exhaustive search of the Chinese cabbage genome, a total of 20 HK(L) (11 HKs and 9 HKLs), 8 HP (7 authentic and 1 pseudo), and 57 RR (21 Type-A, 17 Type-B, 4 Type-C, and 15 pseudo) proteins were identified. The structures, conserved domains, and phylogenetic relationships of these protein-coding genes were analysed in detail. The duplications, evolutionary patterns, and divergence of the TCS genes were investigated. The transcription levels of TCS genes in various tissues, organs, and developmental stages were further analysed to obtain information of the functions of these genes. Cytokinin-related binding elements were found in the putative promoter regions of Type-A BrRR genes. Furthermore, gene expression patterns to adverse environmental stresses (drought and high salinity) and exogenous phytohormones (tZ and ABA) were investigated. Numerous stress-responsive candidate genes were obtained. Our systematic analyses provided insights into the characterization of the TCS genes in Chinese cabbage and basis for further functional studies of such genes.
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Affiliation(s)
- Zhenning Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Mei Zhang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Yanxia Lv
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Minghua Zou
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Gang Lu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
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25
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Zou J, Raman H, Guo S, Hu D, Wei Z, Luo Z, Long Y, Shi W, Fu Z, Du D, Meng J. Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1593-605. [PMID: 24824567 DOI: 10.1007/s00122-014-2321-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/25/2014] [Indexed: 05/10/2023]
Abstract
An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time. An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq(TM) markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
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26
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Kagale S, Robinson SJ, Nixon J, Xiao R, Huebert T, Condie J, Kessler D, Clarke WE, Edger PP, Links MG, Sharpe AG, Parkin IAP. Polyploid evolution of the Brassicaceae during the Cenozoic era. THE PLANT CELL 2014; 26:2777-91. [PMID: 25035408 PMCID: PMC4145113 DOI: 10.1105/tpc.114.126391] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/07/2014] [Accepted: 06/19/2014] [Indexed: 05/18/2023]
Abstract
The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (∼7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.
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Affiliation(s)
- Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | | | - John Nixon
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Rong Xiao
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | - Dallas Kessler
- Plant Gene Resources of Canada, Saskatoon SK S7N 0X2, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
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27
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Guo Y, Hans H, Christian J, Molina C. Mutations in single FT- and TFL1-paralogs of rapeseed (Brassica napus L.) and their impact on flowering time and yield components. FRONTIERS IN PLANT SCIENCE 2014; 5:282. [PMID: 24987398 PMCID: PMC4060206 DOI: 10.3389/fpls.2014.00282] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/30/2014] [Indexed: 05/05/2023]
Abstract
Rapeseed (Brassica napus L.) is grown in different geographical regions of the world. It is adapted to different environments by modification of flowering time and requirement for cold. A broad variation exists from very early-flowering spring-type to late-flowering winter cultivars which only flower after exposure to an extended cold period. B. napus is an allopolyploid species which resulted from the hybridization between B. rapa and B. oleracea. In Arabidopsis thaliana, the PEBP-domain genes FLOWERING LOCUS-T (FT) and TERMINAL FLOWER-1 (TFL1) are important integrators of different flowering pathways. Six FT and four TFL1 paralogs have been identified in B. napus. However, their role in flowering time control is unknown. We identified EMS mutants of the B. napus winter-type inbreed line Express 617. In total, 103 mutant alleles have been determined for BnC6FTb, BnC6FTa, and BnTFL1-2 paralogs. We chose three non-sense and 15 missense mutant lines (M3) which were grown in the greenhouse. Although only two out of 6 FT paralogs were mutated, 6 out of 8 BnC6FTb mutant lines flowered later as the control, whereas all five BnC6FTa mutant lines started flowering as the non-mutated parent. Mutations within the BnTFL1-2 paralog had no large effects on flowering time but on yield components. F1 hybrids between BnTFL1-2 mutants and non-mutated parents had increased seed number per pod and total seeds per plant suggesting that heterozygous mutations in a TFL1 paralog may impact heterosis in rapeseed. We demonstrate that single point-mutations in BnFT and BnTFL1 paralogs have effects on flowering time despite the redundancy of the rapeseed genome. Moreover, our results suggest pleiotropic effects of BnTFL1 paralogs beyond the regulation of flowering time.
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Affiliation(s)
| | | | | | - Carlos Molina
- *Correspondence: Carlos Molina, Plant Breeding Institute, University of Kiel, Olshausenstrasse 40, D-24098, Kiel, Germany e-mail:
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28
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Liu Z, Kong L, Zhang M, Lv Y, Liu Y, Zou M, Lu G, Cao J, Yu X. Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF genes and cytokinin response factors in Brassica rapa ssp. pekinensis. PLoS One 2013; 8:e83444. [PMID: 24386201 PMCID: PMC3875448 DOI: 10.1371/journal.pone.0083444] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 11/05/2013] [Indexed: 11/18/2022] Open
Abstract
The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I- XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage.
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Affiliation(s)
- Zhenning Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Lijun Kong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Mei Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Yanxia Lv
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Yapei Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Minghau Zou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Gang Lu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Xiaolin Yu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, People’s Republic of China
- Laboratory of Horticultural Plant Growth & Quality Regulation, Ministry of Agriculture, Hangzhou, People’s Republic of China
- * E-mail:
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29
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Liu Z, Lv Y, Zhang M, Liu Y, Kong L, Zou M, Lu G, Cao J, Yu X. Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 2013; 14:594. [PMID: 24001366 PMCID: PMC3766048 DOI: 10.1186/1471-2164-14-594] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/22/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families. RESULTS In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated. CONCLUSIONS The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous hormones, such as 6-BA and ABA, suggesting their potential roles in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. The appropriate modulation of endogenous CKs levels by IPT and CKX genes is a promising approach for developing economically important high-yielding and high-quality stress-tolerant crops in agriculture.
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Affiliation(s)
- Zhenning Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P,R,China.
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Cheng F, Mandáková T, Wu J, Xie Q, Lysak MA, Wang X. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. THE PLANT CELL 2013; 25:1541-54. [PMID: 23653472 PMCID: PMC3694691 DOI: 10.1105/tpc.113.110486] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/23/2013] [Accepted: 04/17/2013] [Indexed: 05/18/2023]
Abstract
The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Terezie Mandáková
- Plant Cytogenomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Martin A. Lysak
- Plant Cytogenomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Address correspondence to
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Larkan NJ, Lydiate DJ, Parkin IAP, Nelson MN, Epp DJ, Cowling WA, Rimmer SR, Borhan MH. The Brassica napus blackleg resistance gene LepR3 encodes a receptor-like protein triggered by the Leptosphaeria maculans effector AVRLM1. THE NEW PHYTOLOGIST 2013; 197:595-605. [PMID: 23206118 DOI: 10.1111/nph.12043] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/05/2012] [Indexed: 05/18/2023]
Abstract
LepR3, found in the Brassica napus cv 'Surpass 400', provides race-specific resistance to the fungal pathogen Leptosphaeria maculans, which was overcome after great devastation in Australia in 2004. We investigated the LepR3 locus to identify the genetic basis of this resistance interaction. We employed a map-based cloning strategy, exploiting collinearity with the Arabidopsis thaliana and Brassica rapa genomes to enrich the map and locate a candidate gene. We also investigated the interaction of LepR3 with the L. maculans avirulence gene AvrLm1 using transgenics. LepR3 was found to encode a receptor-like protein (RLP). We also demonstrated that avirulence towards LepR3 is conferred by AvrLm1, which is responsible for both the Rlm1 and LepR3-dependent resistance responses in B. napus. LepR3 is the first functional B. napus disease resistance gene to be cloned. AvrLm1's interaction with two independent resistance loci, Rlm1 and LepR3, highlights the need to consider redundant phenotypes in 'gene-for-gene' interactions and offers an explanation as to why LepR3 was overcome so rapidly in parts of Australia.
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Affiliation(s)
- N J Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D J Lydiate
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - I A P Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - M N Nelson
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D J Epp
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - W A Cowling
- The UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S R Rimmer
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - M H Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
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Abstract
Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome arms, or entire chromosomes via fluorescence in situ hybridization (FISH). For CP in plants, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the target species or from a closely related species (comparative chromosome painting, CCP) are typically applied as painting probes. Extended pachytene chromosomes provide the highest resolution of CP in plants. CP enables identification and tracing of particular chromosome regions and/or entire chromosomes throughout all meiotic stages as well as corresponding chromosome territories in premeiotic interphase nuclei. Meiotic pairing and structural chromosome rearrangements (typically inversions and translocations) can be identified by CP. Here, we describe step-by-step protocols of CP and CCP in plant species including chromosome preparation, BAC DNA labeling, and multicolor FISH.
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Li ZG, Yin WB, Song LY, Chen YH, Guan RZ, Wang JQ, Wang RRC, Hu ZM. Genes encoding the biotin carboxylase subunit of acetyl-CoA carboxylase from Brassica napus and parental species: cloning, expression patterns, and evolution. Genome 2011; 54:202-11. [PMID: 21423283 DOI: 10.1139/g10-110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Comparative genomics is a useful tool to investigate gene and genome evolution. Biotin carboxylase (BC), an important subunit of heteromeric acetyl-CoA carboxylase (ACCase) that is a rate-limiting enzyme in fatty acid biosynthesis in dicots, catalyzes ATP, biotin carboxyl carrier protein, and CO2 to form carboxybiotin carboxyl carrier protein. In this study, we cloned four genes encoding BC from Brassica napus L. (namely BnaC.BC.a, BnaC.BC.b, BnaA.BC.a, and BnaA.BC.b), and two were cloned from each of the two parental species Brassica rapa L. (BraA.BC.a and BraA.BC.b) and Brassica oleracea L. (BolC.BC.a and BolC.BC.b). Sequence analyses revealed that in B. napus the genes BnaC.BC.a and BnaC.BC.b were from the C genome of B. oleracea, whereas BnaA.BC.a and BnaA.BC.b were from the A genome of B. rapa. Comparative and cluster analysis indicated that these genes were divided into two major groups, BnaC.BC.a, BnaA.BC.a, BraA.BC.a, and BolC.BC.a in group-1 and BnaC.BC.b, BnaA.BC.b, BraA.BC.b, and BolC.BC.b in group-2. The divergence of group-1 and group-2 genes occurred in their common ancestor 13-17 million years ago (MYA), soon after the divergence of Arabidopsis and Brassica (15-20 MYA). This time of divergence is identical to the previously reported triplicated time of paralogous subgenomes of diploid Brassica species and the divergence date of group-1 and group-2 genes of α-carboxyltransferase, another subunit of heteromeric ACCase, in Brassica. Reverse transcription PCR revealed that the expression level of group-1 and group-2 genes varied in different organs, and the expression patterns of the two groups of genes were similar in different organs, except in flower. However, two paralogs of group-2 BC genes from B. napus could express differently in mature plants tested by generating BnaA.BC.b and BnaC.BC.b promoter-β-glucuronidase (GUS) fusions. The amino acid sequences of proteins encoded by these genes were highly conserved, except the sequence encoding predicted plastid transit peptides. The plastid transit peptides on the BC precursors of Brassica (71-72 amino acid residues) were predicted based on AtBC protein, compared, and confirmed by fusion with green fluorescent protein. Our results will be helpful in elucidating the evolution and the regulation of ACCase in the genus Brassica.
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Affiliation(s)
- Zhi-Guo Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Han F, Zhu B. Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean. Gene 2011; 473:23-35. [PMID: 21056641 DOI: 10.1016/j.gene.2010.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/19/2010] [Accepted: 10/25/2010] [Indexed: 02/06/2023]
Abstract
GAs are plant hormones that play fundamental roles in plant growth and development. GA2ox, GA3ox, and GA20ox are three key enzymes in GA biosynthesis. These enzymes belong to the 2OG-Fe (II) oxygenase superfamily and are independently encoded by different gene families. To date, genome-wide comparative analyses of GA oxidases in plant species have not been thoroughly carried out. In the present work, 61 GA oxidase family genes from rice (Oryza sativa), Arabidopsis, and soybean (Glycine max) were identified and a full study of these genes including phylogenetic tree construction, gene structure, gene family expansion and analysis of functional motifs was performed. Based on phylogeny, most of the GA oxidases were divided into four subgroups that reflected functional classifications. Intron/intron average length of GA oxidase genes in rice analysis revealed that GA oxidase genes in rice experienced substantial evolutionary divergence. Segmental duplication events were mainly found in soybean genome. However, in rice and Arabidopsis, no single expansion pattern exhibited dominance, indicating that GA oxidase genes from these species might have been subjected to a more complex evolutionary mechanism. In addition, special functional motifs were discovered in GA20ox, GA3ox, and GA2ox, which suggested that different functional motifs are associated with differences in protein function. Taken together our results suggest that GA oxidase family genes have undergone divergent evolutionary routes, especially at the monocot-dicot split, with dynamic evolution occurring in Arabidopsis thaliana and soybean.
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Affiliation(s)
- Fengming Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Nelson MN, Parkin IA, Lydiate DJ. The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome. Genome 2011; 54:33-41. [DOI: 10.1139/g10-097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.
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Affiliation(s)
- Matthew N. Nelson
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Isobel A.P. Parkin
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Derek J. Lydiate
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A 2010; 107:18724-8. [PMID: 20921408 DOI: 10.1073/pnas.0909766107] [Citation(s) in RCA: 307] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two- to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2- to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous-Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil-producing plants.
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Chester M, Leitch AR, Soltis PS, Soltis DE. Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation). Genes (Basel) 2010; 1. [PMID: 24710040 PMCID: PMC3954085 DOI: 10.3390/genes1010166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
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Affiliation(s)
- Michael Chester
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary, University of London, UK.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
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38
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Chester M, Leitch AR, Soltis PS, Soltis DE. Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation). Genes (Basel) 2010; 1:166-92. [PMID: 24710040 PMCID: PMC3954085 DOI: 10.3390/genes1020166] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 11/16/2022] Open
Abstract
The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
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Affiliation(s)
- Michael Chester
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary, University of London, UK.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
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Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA. Fast diploidization in close mesopolyploid relatives of Arabidopsis. THE PLANT CELL 2010; 22:2277-90. [PMID: 20639445 PMCID: PMC2929090 DOI: 10.1105/tpc.110.074526] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Revised: 06/09/2010] [Accepted: 06/22/2010] [Indexed: 05/18/2023]
Abstract
Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred approximately 6 to 9 million years ago. The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.
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Affiliation(s)
- Terezie Mandáková
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Simon Joly
- Institut de Recherche en Biologie Végétale, Université de Montréal and Montreal Botanical Garden, 4101 Sherbrooke East, Montreal, Quebec, Canada H1X 2B2
| | - Martin Krzywinski
- Canada’s Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada V5Z 4S6
| | - Klaus Mummenhoff
- FB Biologie/Chemie, Botanik, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - Martin A. Lysak
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
- Address correspondence to
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40
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Whittle CA, Malik MR, Li R, Krochko JE. Comparative transcript analyses of the ovule, microspore, and mature pollen in Brassica napus. PLANT MOLECULAR BIOLOGY 2010; 72:279-99. [PMID: 19949835 DOI: 10.1007/s11103-009-9567-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Accepted: 10/26/2009] [Indexed: 05/20/2023]
Abstract
Transcriptome data for plant reproductive organs/cells currently is very limited as compared to sporophytic tissues. Here, we constructed cDNA libraries and obtained ESTs for Brassica napus pollen (4,864 ESTs), microspores (i.e., early stage pollen development; 6,539 ESTs) and ovules (10,468 ESTs). Clustering and assembly of the 21,871 ESTs yielded a total of 10,782 unigenes, with 3,362 contigs and 7,420 singletons. The pollen transcriptome contained high levels of polygalacturonases and pectinesterases, which are involved in cell wall synthesis and expansion, and very few transcription factors or transcripts related to protein synthesis. The set of genes expressed in mature pollen showed little overlap with genes expressed in ovules or in microspores, suggesting in the latter case that a marked differentiation had occurred from the early microspore stages through to pollen development. Remarkably, the microspores and ovules exhibited a high number of co-expressed genes (N = 1,283) and very similar EST functional profiles, including high transcript numbers for transcriptional and translational processing genes, protein modification genes and unannotated genes. In addition, examination of expression values for genes co-expressed among microspores and ovules revealed a highly statistically significant correlation among these two tissues (R = 0.360, P = 1.2 x 10(-40)) as well as a lack of differentially expressed genes. Overall, the results provide new insights into the transcriptional profile of rarely studied ovules, the transcript changes during pollen development, transcriptional regulation of pollen tube growth and germination, and describe the parallels in the transcript populations of microspore and ovules which could have implications for understanding the molecular foundation of microspore totipotency in B. napus.
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Affiliation(s)
- Carrie A Whittle
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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Kaczmarek M, Koczyk G, Ziolkowski PA, Babula-Skowronska D, Sadowski J. Comparative analysis of the Brassica oleracea genetic map and the Arabidopsis thaliana genome. Genome 2010; 52:620-33. [PMID: 19767893 DOI: 10.1139/g09-035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We further investigated genome macrosynteny for Brassica species and Arabidopsis thaliana. This work aimed at comparative map construction for B. oleracea and A. thaliana chromosomes based on 160 known A. thaliana probes: 147 expressed sequence tags (ESTs) and 13 full-length cDNA clones. Based on an in silico study of the A. thaliana genome, most of the selected ESTs (83%) represented unique or low-copy genes. We identified conserved segments by the visual inspection of comparative data with a priori assumptions, and established their significance with the LineUp algorithm. Evaluation of the number of B. oleracea gene copies per A. thaliana EST revealed a fixed upward trend. We established a segregation distortion pattern for all genetic loci, with particular consideration of the type of selection (gametic or zygotic), and discuss its possible impact on genetic map construction. Consistent with previous reports, we found evidence for numerous chromosome rearrangements and the genome fragment replication of B. oleracea that have taken place since the divergence of the two species. Also, we found that over 54% of the B. oleracea genome is covered by 24 segments conserved with the A. thaliana genome. The average conserved segment is composed of 5 loci covering 19.3 cM in the B. oleracea genetic map and 2.42 Mb in the A. thaliana physical map. We have also attempted to use a unified system of conserved blocks (previously described) to verify our results and perform a comprehensive comparison with other Brassica species.
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Affiliation(s)
- Malgorzata Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland
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Wang J, Long Y, Wu B, Liu J, Jiang C, Shi L, Zhao J, King GJ, Meng J. The evolution of Brassica napus FLOWERING LOCUS T paralogues in the context of inverted chromosomal duplication blocks. BMC Evol Biol 2009; 9:271. [PMID: 19939256 PMCID: PMC2794288 DOI: 10.1186/1471-2148-9-271] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 11/25/2009] [Indexed: 12/22/2022] Open
Abstract
Background The gene FLOWERING LOCUS T (FT) and its orthologues play a central role in the integration of flowering signals within Arabidopsis and other diverse species. Multiple copies of FT, with different cis-intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as Brassica napus (AACC), a member of the same plant family as Arabidopsis. Results We have identified six BnFT paralogues from the genome of B. napus and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of Arabidopsis chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of BnFT paralogues showed 92-99% identities to each other and 85-87% identity with that of Arabidopsis. However, two of the paralogues on chromosomes A2 and C2, BnA2.FT and BnC2.FT, were found to lack the distinctive CArG box that is located within intron 1 that has been shown in Arabidopsis to be the binding site for theFLC protein. Three BnFT paralogues (BnA2.FT, BnC6.FT.a and BnC6.FT.b) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two BnFT paralogues (BnC6.FT.a and BnC6.FT.b) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three BnFT paralogues across 55 cultivars of B. napus showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral FT homologues in Brassica evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the divergence of B. rapa (AA) and B. oleracea (CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole B. napus genome. Conclusion Six orthologues of Arabidopsis FT were identified and mapped in the genome of B. napus which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of BnFT paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed Brassica. The prevalent inverted duplicated blocks, two of which were located by four of the six BnFT paralogues, contributed to gene duplications and might represent predominant pathway of evolution in Brassica.
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Affiliation(s)
- Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China.
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Nelson MN, Mason AS, Castello MC, Thomson L, Yan G, Cowling WA. Microspore culture preferentially selects unreduced (2n) gametes from an interspecific hybrid of Brassica napus L. x Brassica carinata Braun. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:497-505. [PMID: 19436985 DOI: 10.1007/s00122-009-1056-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/24/2009] [Indexed: 05/24/2023]
Abstract
We analysed the products of male meiosis in microspore-derived progeny from a Brassica napus (AAC(n)C(n)) x Brassica carinata (BBC(c)C(c)) interspecific hybrid (ABC(n)C(c)). Genotyping at 102 microsatellite marker loci and nuclear DNA contents provided strong evidence that 26 of the 28 progeny (93%) were derived from unreduced (2n) gametes. The high level of C(n)C(c) marker heterozygosity, and parallel spindles at Anaphase II in the ABC(n)C(c) hybrid, indicated that unreduced gametes were formed by first division restitution. The frequency of dyads at the tetrad stage of pollen development (2.6%) suggested that unreduced gametes were preferentially selected in microspore culture. Segregation of marker alleles in the microspore-derived progeny was consistent with homologous recombination between C(n) and C(c) chromosomes and homoeologous recombination involving A-, B- and C-genome chromosomes during meiosis in the ABC(n)C(c) hybrid. We discuss the potential for using microspore culture of unreduced gametes in interspecific hybrids to map Brassica centromeres through half-tetrad analysis.
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Affiliation(s)
- Matthew N Nelson
- Faculty of Natural and Agricultural Sciences, School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia.
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Qiu D, Gao M, Li G, Quiros C. Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana. PLANT CELL REPORTS 2009; 28:649-661. [PMID: 19112567 DOI: 10.1007/s00299-008-0661-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 10/14/2008] [Accepted: 12/09/2008] [Indexed: 05/27/2023]
Abstract
We sequenced five BAC clones of Brassica oleracea doubled haploid 'Early Big' broccoli containing major genes in the aliphatic glucosinolate pathway, and comparatively analyzed them with similar sequences in A. thaliana and B. rapa. Additionally, we included in the analysis published sequences from three other B. oleracea BAC clones and a contig of this species corresponding to segments in A. thaliana chromosomes IV and V. A total of 2,946 kb of B. oleracea, 1,069 kb of B. rapa sequence and 2,607 kb of A. thaliana sequence were compared and analyzed. We found conserved collinearity for gene order and content restricted to specific chromosomal segments, but breaks in collinearity were frequent resulting in gene absence likely not due to gene loss but rearrangements. B. oleracea has the lowest gene density of the three species, followed by B. rapa. The genome expansion of the Brassica species, B. oleracea in particular, is due to larger introns and gene spacers resulting from frequent insertion of DNA transposons and retrotransposons. These findings are discussed in relation to the possible origin and evolution of the Brassica genomes.
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Affiliation(s)
- Dan Qiu
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Ziolkowski PA, Koczyk G, Galganski L, Sadowski J. Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res 2009; 37:3189-201. [PMID: 19305000 PMCID: PMC2691826 DOI: 10.1093/nar/gkp183] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are ∼8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.
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Affiliation(s)
- Piotr A Ziolkowski
- Department of Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species. Genetics 2008; 179:581-92. [PMID: 18493073 DOI: 10.1534/genetics.107.085761] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
It has been hypothesized that polyploidy permits the proliferation of transposable elements, due to both the masking of deleterious recessive mutations and the breakdown of host silencing mechanisms. We investigated the patterns of insertion polymorphism of an Ac-like transposable element and nucleotide diversity at 18 gene fragments in the allotetraploid Arabidopsis suecica and the autotetraploid A. arenosa. All identified insertions were fixed in A. suecica, and many were clearly inherited from the parental species A. thaliana or A. arenosa. These results are inconsistent with a rapid increase in transposition associated with hybrid breakdown but support the evidence from nucleotide polymorphism patterns of a recent single origin of this species leading to genomewide fixations of transposable elements. In contrast, most insertions were segregating at very low frequencies in A. arenosa samples, showing a significant departure from neutrality in favor of purifying selection, even when we account for population subdivision inferred from sequence variation. Patterns of nucleotide variation at reference genes are consistent with the TE results, showing evidence for higher effective population sizes in A. arenosa than in related diploid taxa but a near complete population bottleneck associated with the origins of A. suecica.
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Hong CP, Kwon SJ, Kim JS, Yang TJ, Park BS, Lim YP. Progress in understanding and sequencing the genome of Brassica rapa. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:582837. [PMID: 18288250 PMCID: PMC2233773 DOI: 10.1155/2008/582837] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 11/21/2007] [Indexed: 05/24/2023]
Abstract
Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day "diploid" Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization.
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Affiliation(s)
- Chang Pyo Hong
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
| | - Soo-Jin Kwon
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Jung Sun Kim
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Tae-Jin Yang
- Department of Plant Science,
College of Agriculture and Life Sciences,
Seoul National University,
Seoul 151921,
South Korea
| | - Beom-Seok Park
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Yong Pyo Lim
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
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Armstead I, Huang L, King J, Ougham H, Thomas H, King I. Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation. BMC Genomics 2007; 8:283. [PMID: 17708759 PMCID: PMC2041955 DOI: 10.1186/1471-2164-8-283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Accepted: 08/20/2007] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. RESULTS A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. CONCLUSION Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.
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Affiliation(s)
- Ian Armstead
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Lin Huang
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Julie King
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Helen Ougham
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Howard Thomas
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Ian King
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
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Jenkins G, Hasterok R. BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment. Nat Protoc 2007; 2:88-98. [PMID: 17401342 DOI: 10.1038/nprot.2006.490] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) with large genomic DNA inserts as probes (BAC 'landing') is a powerful means by which eukaryotic genomes can be physically mapped and compared. Here we report a BAC landing protocol that has been developed specifically for the weedy grass species Brachypodium distachyon, which has been adopted recently by the scientific community as an alternative model for the temperate cereals and grasses. The protocol describes the preparation of somatic and meiotic chromosome substrates for FISH, the labeling of BACs, a chromosome mapping strategy, empirical conditions for optimal in situ hybridization and stringency washing, the detection of probes and the capturing and processing of images. The expected outcome of the protocol is the specific assignment of BACs containing single-copy inserts to one of the five linkage groups of the genome of this species. Once somatic or meiotic material is available, the entire protocol can be completed in about 3 d. The protocol has been customized empirically for B. distachyon and its near relatives, but it can be adapted with minor modifications to diverse plant species.
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Affiliation(s)
- Glyn Jenkins
- Institute of Biological Sciences, University of Wales Aberystwyth, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK.
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Abstract
The genus Brassica contains a wide range of diploid and amphipolyploid species including some of the most important vegetable, condiment and oilseed crops worldwide. As members of the Brassicaceae family the brassicas are the closest crop relatives to the model plant Arabidopsis thaliana, and hence are major beneficiaries from the vast array of Arabidopsis molecular genetic and genomic tools and the increasingly good annotation to major Brassica crop genomes. In this review examples are shown from recent studies that demonstrate the potential for intergenome navigation from model to crop plant and for comparisons among genetic and cytogenetic maps between the model and crop species and among different crop brassicas. The use of interspecific and intergeneric hybridization for introgression of novel traits into Brassica genomes from the secondary and tertiary crucifer genepools is described. In this context the use of the Brassica triangle of three diploid species and their corresponding amphiploids as an excellent model system for studying the mechanisms and control of homeologous recombination and polyploidization is discussed from a crop breeding perspective.
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Affiliation(s)
- Rod J Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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