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Shuang LS, Cuevas H, Lemke C, Kim C, Shehzad T, Paterson AH. Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line. G3 (BETHESDA, MD.) 2023; 13:jkad163. [PMID: 37506262 PMCID: PMC10627287 DOI: 10.1093/g3journal/jkad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 08/10/2022] [Accepted: 03/14/2023] [Indexed: 07/30/2023]
Abstract
To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering 78.56% of the cauliflower genome, were selected from an advanced backcross population using cauliflower [Brassica oleracea var. botrytis L., mutant for Orange gene (ORG)] as the donor parent and a rapid cycling line (TO1434) as recurrent parent. Subsets of the advanced backcross population and NIILs were planted in the field for 8 seasons, finding 141 marker-trait associations for 15 leaf-, stem-, and flower-traits. Exemplifying the usefulness of these lines, we delineated the previously known flower color gene to a 4.5 MB interval on C3; a gene for small plant size to a 3.4 MB region on C8; and a gene for large plant size and flowering time to a 6.1 MB region on C9. This approach unmasked closely linked QTL alleles with opposing effects (on chr. 8) and revealed both alleles with expected phenotypic effects and effects opposite the parental phenotypes. Selected B. oleracea NIILs with short generation time add new value to widely used research and teaching materials.
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Affiliation(s)
- Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Hugo Cuevas
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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Khadivi A, Mirheidari F, Moradi Y. Selection of superior accessions of turnip ( Brassica rapa var. rapa L.) based on tuber quality-related characters. Food Sci Nutr 2022; 10:2667-2680. [PMID: 35959251 PMCID: PMC9361458 DOI: 10.1002/fsn3.2871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/07/2022] Open
Abstract
Turnip (Brassica rapa var. rapa L.) (syn. B. campestris L. ssp. rapifera Sinsk) is an important crop species belonging to the Brassicaceae family. The 185 accessions belonging to this crop were collected from several areas of Toodshak region in Isfahan province, Iran, and their tubers were cultivated under homogeneous conditions in loamy clay soil. The morphological traits of different organs of those accessions were evaluated. Significant variations were detected among the accessions studied based on the traits recorded. Tuber shape showed high variation and included globose, oblong, ovate, obovate, and fusiform. Also, tuber skin color was highly variable, including white, bicolor white-violet, light violet, and dark violet. Tuber weight ranged from 1.56 to 35.70 g, while total soluble solids (TSS) of tuber flesh ranged from 7.00 to 11.80%. Principal component analysis (PCA) showed that 18 components were extracted by explaining 74.88% of total variance. The dendrogram obtained based on all the characters measured clustered the accessions into two major clusters. Sixteen accessions were placed into the first cluster, while the remaining accessions were placed into the second cluster which was divided into six subclusters. High level of morphological variabilities was observed among the accessions, which is applicable and useful for B. rapa var. rapa breeding programs. Based on the commercial and quality traits, 17 accessions could be selected for direct cultivation. Also, the promising accessions identified here can be utilized directly in breeding programs for genetic enhancement of this crop.
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Affiliation(s)
- Ali Khadivi
- Department of Horticultural SciencesFaculty of Agriculture and Natural ResourcesArak UniversityArakIran
| | - Farhad Mirheidari
- Department of Horticultural SciencesFaculty of Agriculture and Natural ResourcesArak UniversityArakIran
| | - Younes Moradi
- Department of Horticultural SciencesFaculty of Agriculture and Natural ResourcesArak UniversityArakIran
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Akhatar J, Goyal A, Kaur N, Atri C, Mittal M, Singh MP, Kaur R, Rialch I, Banga SS. Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss. Sci Rep 2021; 11:4278. [PMID: 33608616 PMCID: PMC7896068 DOI: 10.1038/s41598-021-83689-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
Timely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.
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Affiliation(s)
- Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mohini Prabha Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Indu Rialch
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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Stansell Z, Farnham M, Björkman T. Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population. FRONTIERS IN PLANT SCIENCE 2019; 10:1104. [PMID: 31620146 PMCID: PMC6759917 DOI: 10.3389/fpls.2019.01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 05/19/2023]
Abstract
Improving horticultural quality in regionally adapted broccoli (Brassica oleracea var. italica) and other B. oleracea crops is challenging due to complex genetic control of traits affecting morphology, development, and yield. Mapping horticultural quality traits to genomic loci is an essential step in these improvement efforts. Understanding the mechanisms underlying horticultural quality enables multi-trait marker-assisted selection for improved, resilient, and regionally adapted B. oleracea germplasm. The publicly-available biparental double-haploid BolTBDH mapping population (Chinese kale × broccoli; N = 175) was evaluated for 25 horticultural traits in six trait classes (architecture, biomass, phenology, leaf morphology, floral morphology, and head quality) by multiple quantitative trait loci mapping using 1,881 genotype-by-sequencing derived single nucleotide polymorphisms. The physical locations of 56 single and 41 epistatic quantitative trait locus (QTL) were identified. Four head quality QTL (OQ_C03@57.0, OQ_C04@33.3, OQ_CC08@25.5, and OQ_C09@49.7) explain a cumulative 81.9% of phenotypic variance in the broccoli heading phenotype, contain the FLOWERING LOCUS C (FLC) homologs Bo9g173400 and Bo9g173370, and exhibit epistatic effects. Three key genomic hotspots associated with pleiotropic control of the broccoli heading phenotype were identified. One phenology hotspot reduces days to flowering by 7.0 days and includes an additional FLC homolog Bo3g024250 that does not exhibit epistatic effects with the three horticultural quality hotspots. Strong candidates for other horticultural traits were identified: BoLMI1 (Bo3g002560) associated with serrated leaf margins and leaf apex shape, BoCCD4 (Bo3g158650) implicated in flower color, and BoAP2 (Bo1g004960) implicated in the hooked sepal horticultural trait. The BolTBDH population provides a framework for B. oleracea improvement by targeting key genomic loci contributing to high horticultural quality broccoli and enabling de novo mapping of currently unexplored traits.
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Affiliation(s)
- Zachary Stansell
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
- *Correspondence: Zachary Stansell,
| | - Mark Farnham
- USDA-ARS Vegetable Laboratory, Department of Horticulture, Charleston, SC, United States
| | - Thomas Björkman
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
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Subtropical adaptation of a temperate plant (Brassica oleracea var. italica) utilizes non-vernalization-responsive QTLs. Sci Rep 2018; 8:13609. [PMID: 30206285 PMCID: PMC6134136 DOI: 10.1038/s41598-018-31987-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/28/2018] [Indexed: 11/08/2022] Open
Abstract
While many tropical plants have been adapted to temperate cultivation, few temperate plants have been adapted to the tropics. Originating in Western Europe, Brassica oleracea vernalization requires a period of low temperature and BoFLC2 regulates the transition to floral development. In B. oleracea germplasm selected in Taiwan, a non-vernalization pathway involving BoFLC3 rather than BoFLC2 regulates curd induction. In 112 subtropical breeding lines, specific haplotype combinations of BoFLC3 and PAN (involved in floral organ identity and a positional candidate for additional curd induction variation) adapt B. oleracea to high ambient temperature and short daylength. Duplicated genes permitted evolution of alternative pathways for control of flowering in temperate and tropical environments, a principle that might be utilized via natural or engineered approaches in other plants. New insight into regulation of Brassica flowering exemplifies translational agriculture, tapping knowledge of botanical models to improve food security under projected climate change scenarios.
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Yi L, Chen C, Yin S, Li H, Li Z, Wang B, King GJ, Wang J, Liu K. Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus. BMC PLANT BIOLOGY 2018; 18:32. [PMID: 29433434 PMCID: PMC5810009 DOI: 10.1186/s12870-018-1253-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 02/06/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Allelic variation at the FRIGIDA (FRI) locus is a major contributor to natural variation of flowering time and vernalization requirement in Arabidopsis thaliana. Dominant FRI inhibits flowering by activating the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC), which represses flowering prior to vernalization. Four FRI orthologues had been identified in the domesticated amphidiploid Brassica napus. Linkage and association studies had revealed that one of the FRI orthologues, BnaA3.FRI, contributes to flowering time variation and crop type differentiation. RESULTS Sequence analyses indicated that three out of the four BnaFRI paralogues, BnaA3.FRI, BnaA10.FRI and BnaC3.FRI, contained a large number of polymorphic sites. Haplotype analysis in a panel of 174 B. napus accessions using PCR markers showed that all the three paralogues had a biased distribution of haplotypes in winter type oilseed rape (P < 0.01). Association analysis indicated that only BnaA3.FRI contributes to flowering time variation in B. napus. In addition, transgenic functional complementation demonstrated that mutations in the coding sequence of BnaA3.FRI lead to weak alleles, and subsequently to flowering time variation. CONCLUSION This study for the first time provides a molecular basis for flowering time control by BnaA3.FRI in B. napus, and will facilitate predictive oilseed rape breeding to select varieties with favorable flowering time and better adaption to latitude and seasonal shifts due to changing climate.
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Affiliation(s)
- Licong Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Chunhong Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Shuai Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhaohong Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480 Australia
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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Rosen A, Hasan Y, Briggs W, Uptmoor R. Genome-Based Prediction of Time to Curd Induction in Cauliflower. FRONTIERS IN PLANT SCIENCE 2018; 9:78. [PMID: 29467774 PMCID: PMC5807883 DOI: 10.3389/fpls.2018.00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
The development of cauliflower (Brassica oleracea var. botrytis) is highly dependent on temperature due to vernalization requirements, which often causes delay and unevenness in maturity during months with warm temperatures. Integrating quantitative genetic analyses with phenology modeling was suggested to accelerate breeding strategies toward wide-adaptation cauliflower. The present study aims at establishing a genome-based model simulating the development of doubled haploid (DH) cauliflower lines to predict time to curd induction of DH lines not used for model parameterization and test hybrids derived from the bi-parental cross. Leaf appearance rate and the relation between temperature and thermal time to curd induction were examined in greenhouse trials on 180 DH lines at seven temperatures. Quantitative trait loci (QTL) analyses carried out on model parameters revealed ten QTL for leaf appearance rate (LAR), five for the slope and two for the intercept of linear temperature-response functions. Results of the QTL-based phenology model were compared to a genomic selection (GS) model. Model validation was carried out on data comprising four field trials with 72 independent DH lines, 160 hybrids derived from the parameterization set, and 34 hybrids derived from independent lines of the population. The QTL model resulted in a moderately accurate prediction of time to curd induction (R2 = 0.42-0.51) while the GS model generated slightly better results (R2 = 0.52-0.61). Predictions of time to curd induction of test hybrids from independent DH lines were less precise with R2 = 0.40 for the QTL and R2 = 0.48 for the GS model. Implementation of juvenile-to-adult phase transition is proposed for model improvement.
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Affiliation(s)
- Arne Rosen
- Faculty of Agriculture and Environmental Science, University of Rostock, Rostock, Germany
| | - Yaser Hasan
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | | | - Ralf Uptmoor
- Faculty of Agriculture and Environmental Science, University of Rostock, Rostock, Germany
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Rahman H, Bennett RA, Kebede B. Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus. PLoS One 2018; 13:e0189723. [PMID: 29320498 PMCID: PMC5761838 DOI: 10.1371/journal.pone.0189723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/30/2017] [Indexed: 12/29/2022] Open
Abstract
Earliness of flowering and maturity are important traits in spring Brassica napus canola–whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Rick A. Bennett
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
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Matschegewski C, Zetzsche H, Hasan Y, Leibeguth L, Briggs W, Ordon F, Uptmoor R. Genetic variation of temperature-regulated curd induction in cauliflower: elucidation of floral transition by genome-wide association mapping and gene expression analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:720. [PMID: 26442034 PMCID: PMC4564693 DOI: 10.3389/fpls.2015.00720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/27/2015] [Indexed: 05/09/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis) is a vernalization-responsive crop. High ambient temperatures delay harvest time. The elucidation of the genetic regulation of floral transition is highly interesting for a precise harvest scheduling and to ensure stable market supply. This study aims at genetic dissection of temperature-dependent curd induction in cauliflower by genome-wide association studies and gene expression analysis. To assess temperature-dependent curd induction, two greenhouse trials under distinct temperature regimes were conducted on a diversity panel consisting of 111 cauliflower commercial parent lines, genotyped with 14,385 SNPs. Broad phenotypic variation and high heritability (0.93) were observed for temperature-related curd induction within the cauliflower population. GWA mapping identified a total of 18 QTL localized on chromosomes O1, O2, O3, O4, O6, O8, and O9 for curding time under two distinct temperature regimes. Among those, several QTL are localized within regions of promising candidate flowering genes. Inferring population structure and genetic relatedness among the diversity set assigned three main genetic clusters. Linkage disequilibrium (LD) patterns estimated global LD extent of r(2) = 0.06 and a maximum physical distance of 400 kb for genetic linkage. Transcriptional profiling of flowering genes FLOWERING LOCUS C (BoFLC) and VERNALIZATION 2 (BoVRN2) was performed, showing increased expression levels of BoVRN2 in genotypes with faster curding. However, functional relevance of BoVRN2 and BoFLC2 could not consistently be supported, which probably suggests to act facultative and/or might evidence for BoVRN2/BoFLC-independent mechanisms in temperature-regulated floral transition in cauliflower. Genetic insights in temperature-regulated curd induction can underpin genetically informed phenology models and benefit molecular breeding strategies toward the development of thermo-tolerant cultivars.
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Affiliation(s)
- Claudia Matschegewski
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
- *Correspondence: Claudia Matschegewski, Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, D-18059 Rostock, Germany,
| | - Holger Zetzsche
- Institute of Resistance Research and Stress Tolerance, Julius-Kuehn InstituteQuedlinburg, Germany
| | - Yaser Hasan
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Lena Leibeguth
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
| | | | - Frank Ordon
- Institute of Resistance Research and Stress Tolerance, Julius-Kuehn InstituteQuedlinburg, Germany
| | - Ralf Uptmoor
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
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Dechaine JM, Brock MT, Iniguez-Luy FL, Weinig C. Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa. THE NEW PHYTOLOGIST 2014; 201:657-669. [PMID: 26012723 DOI: 10.1111/nph.12520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/15/2013] [Indexed: 05/16/2023]
Abstract
Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environment × ontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTL × environment × ontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing.
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Affiliation(s)
- Jennifer M Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, WA, 98926, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Federico L Iniguez-Luy
- Agri-Aquaculture Nutritional Genomic Center, Genetic and Bioinformatics Unit, Instituto de Investigaciones Agropecuarias-Carillanca, Codigo Postal, 4780000, Temuco, Chile
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
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Huang Y, Jiang L, Ruan Y, Shen W, Liu C. An allotetraploid Brassica napus early-flowering mutant has BnaFLC2-regulated flowering. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:3763-3768. [PMID: 23749702 DOI: 10.1002/jsfa.6254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/28/2013] [Accepted: 06/07/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Flowering time is an important agronomic trait, and wide variation in flowering time exists among Brassica napus accessions. GX50 early-flowering mutant, induced from Brassica napus by Ethyl Methane Sulfonate (EMS), exhibits a remarkable early transition from vegetative to reproductive growth. RESULTS GX50 plants flowered about 60 days earlier than the control wild-type plant B. napus XY15 under greenhouse conditions. Cytological examination revealed that the GX50 plants form inflorescences as early as from 5 weeks old, flower primordium from 6 weeks old, and siliques from 10 weeks old, whereas 10-week-old XY15 plants are still at vegetative growth stage. To unravel the molecular mechanisms underlying the GX50 flowering phenotype, we analyzed the expression of several key regulatory genes. Expressions of all five BnaFLCs (BnaFLC1 to BnaFLC5), BnaFT and BnaSOC1 were detected. Interestingly, BnaFLCs expression levels were lower in GX50 than those in XY15. Among the five BnaFLCs, only the expression pattern of BnaFLC2 corresponded to the timing of floral organ differentiation in GX50. In agreement with previous knowledge that BnaFLCs repress expression of BnaFT and BnaSOC1, increased levels of BnaFT and BnaSOC1 were observed in GX50 compared with XY15. CONCLUSION BnaFLC2, but not the other BnaFLC genes, plays an important role in B. napus GX50 floral transition.
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Affiliation(s)
- Yong Huang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, Hunan, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
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12
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Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella. Genetics 2012; 192:729-39. [PMID: 22865739 PMCID: PMC3454893 DOI: 10.1534/genetics.112.143958] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species’ range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago.
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Cho K, O'Neill CM, Kwon SJ, Yang TJ, Smooker AM, Fraser F, Bancroft I. Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:591-9. [PMID: 19929877 DOI: 10.1111/j.1365-313x.2009.04084.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We conducted a sequence-level comparative analyses, at the scale of complete bacterial artificial chromosome (BAC) clones, between the genome of the most economically important Brassica species, Brassica napus (oilseed rape), and those of Brassica rapa, the genome of which is currently being sequenced, and Arabidopsis thaliana. We constructed a new B. napus BAC library and identified and sequenced clones that contain homoeologous regions of the genome including stearoyl-ACP desaturase-encoding genes. We sequenced the orthologous region of the genome of B. rapa and conducted comparative analyses between the Brassica sequences and those of the orthologous region of the genome of A. thaliana. The proportion of genes conserved (approximately 56%) is lower than has been reported previously between A. thaliana and Brassica (approximately 66%). The gene models for sets of conserved genes were used to determine the extent of nucleotide conservation of coding regions. This was found to be 84.2 +/- 3.9% and 85.8 +/- 3.7% between the B. napus A and C genomes, respectively, and that of A. thaliana, which is consistent with previous results for other Brassica species, and 97.5 +/- 3.1% between the B. napus A genome and B. rapa, and 93.1 +/- 4.9% between the B. napus C genome and B. rapa. The divergence of the B. napus genes from the A genome and the B. rapa genes was greater than anticipated and indicates that the A genome ancestor of the B. napus cultivar studied was relatively distantly related to the cultivar of B. rapa selected for genome sequencing.
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Affiliation(s)
- Kwangsoo Cho
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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Kim KD, Shin JH, Van K, Kim DH, Lee SH. Dynamic rearrangements determine genome organization and useful traits in soybean. PLANT PHYSIOLOGY 2009; 151:1066-76. [PMID: 19684227 PMCID: PMC2773080 DOI: 10.1104/pp.109.141739] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 08/10/2009] [Indexed: 05/08/2023]
Abstract
Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the changes in genome structure produced by the relatively recent polyploidy event, but little is known about the ancient polyploidy due to the high frequency of gene loss after duplication. Our previous study, regarding a region responsible for bacterial leaf pustule, reported two homeologous Rxp regions produced by the recent whole-genome duplication event. In this study, we identified the full set of four homeologous Rxp regions (ranging from 1.96 to 4.60 Mb) derived from both the recent and ancient polyploidy events, and this supports the quadruplicated structure of the soybean genome. Among the predicted genes on chromosome 17 (linkage group D2), 71% of them were conserved in a recently duplicated region, while 21% and 24% of duplicated genes were retained in two homeologous regions formed by the ancient polyploidy. Furthermore, comparative analysis showed a 2:1 relationship between soybean and Medicago truncatula, since M. truncatula did not undergo the recent polyploidy event that soybean did. Unlike soybean, M. truncatula homeologous regions were highly fractionated and their synteny did not exist, revealing different rates of diploidization process between the two species. Our data show that extensive synteny remained in the four homeologous regions in soybean, even though the soybean genome experienced dynamic genome rearrangements following paleopolyploidy events. Moreover, multiple Rxp quantitative trait loci on different soybean chromosomes actually comprise homeologous regions produced by two rounds of polyploidy events.
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Affiliation(s)
| | | | | | | | - Suk-Ha Lee
- Department of Plant Science (K.D.K., J.H.S., K.V., D.H.K., S.-H.L.), Research Institute for Agriculture and Life Sciences (K.D.K., J.H.S., K.V., D.H.K., S.-H.L.), and Plant Genomics and Breeding Institute (S.-H.L.), Seoul National University, Seoul 151–921, Korea
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Razi H, Howell EC, Newbury HJ, Kearsey MJ. Does sequence polymorphism of FLC paralogues underlie flowering time QTL in Brassica oleracea? TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:179-92. [PMID: 17938878 DOI: 10.1007/s00122-007-0657-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 09/21/2007] [Indexed: 05/09/2023]
Abstract
Previous locations of flowering time (FT) QTL in several Brassica species, coupled with Arabidopsis synteny, suggest that orthologues of the genes FLC, FY or CONSTANS might be the candidates. We focused on FLC, and cloned paralogous copies in Brassica oleracea, obtained their genomic DNA sequences, and confirmed their locations relative to those of known FT-QTL by genetical mapping. They varied in total length mainly due to the variable size of the first and last introns. A high level of identity was observed among Brassica FLC genes at the amino acid level but non-synonymous differences were present. Comparative analysis of the promoter and intragenic regions of BoFLC paralogues with Arabidopsis FLC revealed extensive differences in overall structure and organisation but showed high conservation within those segments known to be essential in regulating FLC expression. Four B. oleracea FLC copies (BoFLC1, BoFLC3, BoFLC4 and BoFLC5) were located to their respective linkage groups based on allelic sequence variation in lines from a doubled haploid population. All except BoFLC4 were within the confidence intervals of known FT-QTL. Sequence data indicated that relevant non-synonymous polymorphisms were present between parents A12DHd and GDDH33 for BoFLC genes. However, BoFLC alleles segregated independently of FT in backcrosses while the study provided evidence that BoFLC4 and BoFLC5 contain premature stop codons and so could not contribute to flowering time variation. Therefore, there is strong evidence against any of the 4 BoFLC being FT-QTL candidates in this population.
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Affiliation(s)
- H Razi
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK.
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Okazaki K, Sakamoto K, Kikuchi R, Saito A, Togashi E, Kuginuki Y, Matsumoto S, Hirai M. Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:595-608. [PMID: 17136371 DOI: 10.1007/s00122-006-0460-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 11/06/2006] [Indexed: 05/12/2023]
Abstract
The FLC gene product is an inhibitor of flowering in Arabidopsis. FLC homologs in Brassica species are thought to control vernalization. We cloned four FLC homologs (BoFLCs) from Brassica oleracea. Three of these, BoFLC1, BoFLC3 and BoFLC5, have been previously characterized. The fourth novel sequence displayed 98% sequence homology to the previously identified gene BoFLC4, but also showed 91% homology to BrFLC2 from Brassica rapa. Phylogenetic analysis showed that this clone belongs to the FLC2 clade. Therefore, we designated this gene BoFLC2. Based on the segregation of RFLP, SRAP, CAPS, SSR and AFLP loci, a detailed linkage map of B. oleracea was constructed in the F(2) progeny obtained from a cross of B. oleracea cv. Green Comet (broccoli; non-vernalization type) and B. oleracea cv. Reiho (cabbage; vernalization type), which covered 540 cM, 9 major linkage groups. Six quantitative trait loci (QTL) controlling flowering time were detected. BoFLC1, BoFLC3 and BoFLC5 were not linked to the QTLs controlling flowering time. However, the largest QTL effect was located in the region where BoFLC2 was mapped. Genotyping of F(2 )plants at the BoFLC2 locus showed that most of the early flowering plants were homozygotes of BoFLC-GC, whereas most of the late- and non-flowering plants were homozygotes of BoFLC-Rei. The BoFLC2 homologs present in plants of the non-vernalization type were non-functional, due to a frameshift in exon 4. Moreover, duplications and deletions of BoFLC2 were detected in broccoli and a rapid cycling line, respectively. These results suggest that BoFLC2 contributes to the control of flowering time in B. oleracea.
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Affiliation(s)
- K Okazaki
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
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Saito M, Kubo N, Matsumoto S, Suwabe K, Tsukada M, Hirai M. Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 114:81-91. [PMID: 17039346 DOI: 10.1007/s00122-006-0412-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 09/08/2006] [Indexed: 05/12/2023]
Abstract
A linkage map of Chinese cabbage (Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F(3) population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences in the top arm of Arabidopsis chromosome 3, suggesting a synteny between the two species. For fine mapping of Crr3, a number of STS markers were developed based on genomic information from Arabidopsis. We obtained polymorphisms in 23 Arabidopsis-derived STS markers, 11 of which were closely linked to Crr3. The precise position of Crr3 was determined using a population of 888 F(2) plants. Eighty plants showing recombination around Crr3 locus were selected and used for the mapping. A fine map of 4.74 cM was obtained, in which two markers (BrSTS-41 and BrSTS-44) and three markers (OPC11-2S, BrSTS-54 and BrSTS-61) were cosegregated. Marker genotypes of the 21 selected F(2) families and CR tests of their progenies strongly suggested that the Crr3 gene is located in a 0.35 cM segment between the two markers, BrSTS-33 and BrSTS-78.
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Affiliation(s)
- M Saito
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan
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Delourme R, Falentin C, Huteau V, Clouet V, Horvais R, Gandon B, Specel S, Hanneton L, Dheu JE, Deschamps M, Margale E, Vincourt P, Renard M. Genetic control of oil content in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1331-45. [PMID: 16960716 DOI: 10.1007/s00122-006-0386-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 07/31/2006] [Indexed: 05/11/2023]
Abstract
In oilseed rape (Brassica napus L.) like in most oleaginous crops, seed oil content is the main qualitative determinant that confers its economic value to the harvest. Increasing seed oil content is then still an important objective in oilseed rape breeding. In the objective to get better knowledge on the genetic determinism of seed oil content, a genetic study was undertaken in two genetic backgrounds. Two populations of 445 and a 242 doubled haploids (DH) derived from the crosses "Darmor-bzh" x "Yudal" (DY) and "Rapid" x "NSL96/25" (RNSL), respectively, were genotyped and evaluated for oil content in different trials. QTL mapping in the two populations indicate that additive effects are the main factors contributing to variation in oil content. A total of 14 and 10 genomic regions were involved in seed oil content in DY and RNSL populations, respectively, of which five and two were consistently revealed across the three trials performed for each population. Most of the QTL detected were not colocalised to QTL involved in flowering time. Few epistatic QTL involved regions that carry additive QTL in one or the other population. Only one QTL located on linkage group N3 was potentially common to the two populations. The comparisons of the QTL location in this study and in the literature showed that: (i) some of the QTL were more consistently revealed across different genetic backgrounds. The QTL on N3 was revealed in all the studies and the QTL on N1, N8 and N13 were revealed in three studies out of five, (ii) some of the QTL were specific to one genetic background with potentially some original alleles, (iii) some QTL were located in homeologous regions, and (iv) some of the regions carrying QTL for oil content in oilseed rape and in Arabidopsis could be collinear. These results show the possibility to combine favourable alleles at different QTL to increase seed oil content and to use Arabidopsis genomic data to derive markers for oilseed rape QTL and identify candidate genes, as well as the interest to combine information from different segregating populations in order to build a consolidated map of QTL involved in a specific trait.
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Affiliation(s)
- R Delourme
- UMR INRA Agrocampus Rennes, Amélioration des Plantes et Biotechnologies Végétales, BP 35327, 35653, Le Rheu Cedex, France.
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Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S. Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 2006; 173:309-19. [PMID: 16723420 PMCID: PMC1461432 DOI: 10.1534/genetics.104.038968] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.
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Affiliation(s)
- Keita Suwabe
- Department of Quality Science, National Institute of Vegetable and Tea Science, Ano, Mie, Japan
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20
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Zhao J, Becker HC, Zhang D, Zhang Y, Ecke W. Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:33-8. [PMID: 16614833 DOI: 10.1007/s00122-006-0267-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 03/17/2006] [Indexed: 05/08/2023]
Abstract
Oil content in rapeseed (Brassica napus L.) is generally regarded as a character with high heritability that is negatively correlated with protein content and influenced by plant developmental and yield related traits. To evaluate possible genetic interrelationships between these traits and oil content, QTL for oil content were mapped using data on oil content and on oil content conditioned on the putatively interrelated traits. Phenotypic data were evaluated in a segregating doubled haploid population of 282 lines derived from the F(1) of a cross between the old German cultivar Sollux and the Chinese cultivar Gaoyou. The material was tested at four locations, two each in Germany and in China. QTLMapper version 1.0 was used for mapping unconditional and conditional QTL with additive (a) and locus pairs with additive x additive epistatic (aa) effects. Clear evidence was found for a strong genetic relationship between oil and protein content. Six QTL and nine epistatic locus pairs were found, which had pleiotropic effects on both traits. Nevertheless, two QTL were also identified, which control oil content independent from protein content and which could be used in practical breeding programs to increase oil content without affecting seed protein content. In addition, six additional QTL with small effects were only identified in the conditional mapping. Some evidence was apparent for a genetic interrelationship between oil content and the number of seeds per silique but no evidence was found for a genetic relationship between oil content and flowering time, grain filling period or single seed weight. The results indicate that for closely correlated traits conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the level of individual QTL. Furthermore, conditional QTL mapping can reveal additional QTL with small effects that are undetectable in unconditional mapping.
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Affiliation(s)
- Jianyi Zhao
- Crop Research Institute, Zhejiang Academy of Agricultural Sciences, 310021 Hangzhou, People's Republic of China
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21
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Somorjai IML, Danzmann RG, Ferguson MM. Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss). Genetics 2004; 165:1443-56. [PMID: 14668393 PMCID: PMC1462839 DOI: 10.1093/genetics/165.3.1443] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We searched for quantitative trait loci (QTL) affecting upper temperature tolerance (UTT) in crosses between the Nauyuk Lake and Fraser River strains of Arctic charr (Salvelinus alpinus) using survival analysis. Two QTL were detected by using two microsatellite markers after correcting for experiment-wide error. A comparative mapping approach localized these two QTL to homologous linkage groups containing UTT QTL in rainbow trout (Oncorhynchus mykiss). Additional marginal associations were detected in several families in regions homologous to those with QTL in rainbow trout. Thus, the genes underlying UTT QTL may antedate the divergence of these two species, which occurred by approximately 16 MYA. The data also indicate that one pair of homeologs (ancestrally duplicated chromosomal segments) have contained QTL in Arctic charr since the evolution of salmonids from a tetraploid ancestor 25-100 MYA. This study represents one of the first examples of comparative QTL mapping in an animal polyploid group and illustrates the fate of QTL after genome duplication and reorganization.
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Affiliation(s)
- Ildiko M L Somorjai
- Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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LUKENS LEWISN, QUIJADA PABLOA, UDALL JOSHUA, PIRES JCHRIS, SCHRANZ MERIC, OSBORN THOMASC. Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00352.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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PIRES JCHRIS, ZHAO JIANWEI, SCHRANZ MERIC, LEON ENRIQUEJ, QUIJADA PABLOA, LUKENS LEWISN, OSBORN THOMASC. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00350.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lionneton E, Aubert G, Ochatt S, Merah O. Genetic analysis of agronomic and quality traits in mustard (Brassica juncea). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:792-799. [PMID: 15340689 DOI: 10.1007/s00122-004-1682-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 03/28/2004] [Indexed: 05/24/2023]
Abstract
To develop an efficient mustard (Brassica juncea) breeding programme, a better knowledge of the genetic control and relationships of the main selected characters is needed. Thus, doubled haploid (DH) lines were evaluated over 2 years in the field. Days to flowering, plant height, thousand-seed weight, fatty acid composition, seed oil content, sinigrin, gluconapin and total glucosinolate contents were determined in the DH population. The influence of seed coat colour was estimated. Results showed significant differences between yellow and brown seeds only for oil and fatty acid contents. Molecular analysis revealed that seed coat colour is associated with two Mendelian trait loci: Bjc1 [on linkage group (LG) 3] and Bjc2 (on LG6). The quantitative trait loci associated with characters-detected by composite interval mapping-were not co-localised and revealed a genetic independence. The results obtained in this study show that the most important agronomic and quality traits of brown mustard could be bred independently. Correlation between the studied traits is also discussed.
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Affiliation(s)
- E Lionneton
- INRA, URLEG, BP 86510, 21065 Dijon Cedex, France
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Schranz ME, Osborn TC. De novo variation in life-history traits and responses to growth conditions of resynthesized polyploid Brassica napus (Brassicaceae). AMERICAN JOURNAL OF BOTANY 2004; 91:174-83. [PMID: 21653373 DOI: 10.3732/ajb.91.2.174] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Variation that arises in generations immediately following polyploidization may be important for the establishment, adaptation, and persistence of new polyploid species. We previously showed divergence for flowering time among lines from a resynthesized Brassica napus allopolyploid lineage derived from a cross of diploid B. rapa and B. oleracea. In this study, we more fully assess phenotypic differentiation of lines from the previously studied lineage and of lines derived from an additional resynthesized B. napus lineage. Nine polyploid lines and their diploid parents were grown under four growth conditions and measured for eight life-history traits. Polyploid lines within a lineage were expected to be genetically identical because they were derived from individual, chromosome-doubled amphihaploid plants. However, significant differences were found among lines within lineages for every phenotypic trait measured and in response to different growth conditions (genotype by environment interactions). When phenotypes of each polyploid line for each trait in each environment were compared with their diploid progenitors, approximately 30% were like one or the other parent, 50% were intermediate, and 20% were transgressive. Our results demonstrate extensive de novo variation in new polyploid lineages. Such changes could contribute to the evolutionary potential in naturally occurring polyploids.
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Affiliation(s)
- M Eric Schranz
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53711 USA
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Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC. Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 2002; 162:1457-68. [PMID: 12454088 PMCID: PMC1462321 DOI: 10.1093/genetics/162.3.1457] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time.
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Affiliation(s)
- M Eric Schranz
- Department of Agronomy, University of Wisconsin, Madison, 53706, USA
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