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Corlouer E, Sauvage C, Leveugle M, Nesi N, Laperche A. Envirotyping within a multi-environment trial allowed identifying genetic determinants of winter oilseed rape yield stability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:164. [PMID: 38898332 PMCID: PMC11186914 DOI: 10.1007/s00122-024-04664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
KEY MESSAGE A comprehensive environmental characterization allowed identifying stable and interactive QTL for seed yield: QA09 and QC09a were detected across environments; whereas QA07a was specifically detected on the most stressed environments. A main challenge for rapeseed consists in maintaining seed yield while adapting to climate changes and contributing to environmental-friendly cropping systems. Breeding for cultivar adaptation is one of the keys to meet this challenge. Therefore, we propose to identify the genetic determinant of seed yield stability for winter oilseed rape using GWAS coupled with a multi-environmental trial and to interpret them in the light of environmental characteristics. Due to a comprehensive characterization of a multi-environmental trial using 79 indicators, four contrasting envirotypes were defined and used to identify interactive and stable seed yield QTL. A total of four QTLs were detected, among which, QA09 and QC09a, were stable (detected at the multi-environmental trial scale or for different envirotypes and environments); and one, QA07a, was specifically detected into the most stressed envirotype. The analysis of the molecular diversity at QA07a showed a lack of genetic diversity within modern lines compared to older cultivars bred before the selection for low glucosinolate content. The results were discussed in comparison with other studies and methods as well as in the context of breeding programs.
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Affiliation(s)
- Erwan Corlouer
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650, Le Rheu, France
| | | | | | - Nathalie Nesi
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650, Le Rheu, France
| | - Anne Laperche
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650, Le Rheu, France.
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Guo J, Zeng L, Chen H, Ma C, Tu J, Shen J, Wen J, Fu T, Yi B. CRISPR/Cas9-Mediated Targeted Mutagenesis of BnaCOL9 Advances the Flowering Time of Brassica napus L. Int J Mol Sci 2022; 23:ijms232314944. [PMID: 36499273 PMCID: PMC9740695 DOI: 10.3390/ijms232314944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. The planting area and output of rapeseed are affected by the flowering time, which is a critical agronomic feature. COL9 controls growth and development in many different plant species as a member of the zinc finger transcription factor family. However, BnaCOL9 in rapeseed has not been documented. The aim of this study was to apply CRISPR/Cas9 technology to create an early-flowering germplasm resource to provide useful material for improving the early-maturing breeding of rapeseed. We identified four COL9 homologs in rapeseed that were distributed on chromosomes A05, C05, A03, and C03. We successfully created quadruple BnaCOL9 mutations in rapeseed using the CRISPR/Cas9 platform. The quadruple mutants of BnaCOL9 flowered earlier than the wild-type. On the other hand, the flowering time of the BnaCOL9 overexpression lines was delayed. An analysis of the expression patterns revealed that these genes were substantially expressed in the leaves and flowers. A subcellular localization experiment demonstrated that BnaCOL9 was in the nucleus. Furthermore, we discovered that two key flowering-related genes, BnaCO and BnaFT, were highly elevated in the BnaCOL9 mutants, but dramatically downregulated in the BnaCOL9 overexpression lines. Our findings demonstrate that BnaCOL9 is a significant flowering inhibitor in rapeseed and may be employed as a crucial gene for early-maturing breeding.
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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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4
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Tudor EH, Jones DM, He Z, Bancroft I, Trick M, Wells R, Irwin JA, Dean C. QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2466-2481. [PMID: 32452611 PMCID: PMC7680531 DOI: 10.1111/pbi.13421] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 05/05/2023]
Abstract
Winter, spring and biennial varieties of Brassica napus that vary in vernalization requirement are grown for vegetable and oil production. Here, we show that the obligate or facultative nature of the vernalization requirement in European winter oilseed rape is determined by allelic variation at a 10 Mbp region on chromosome A02. This region includes orthologues of the key floral regulators FLOWERING LOCUS C (BnaFLC.A02) and FLOWERING LOCUS T (BnaFT.A02). Polymorphism at BnaFLC.A02 and BnaFT.A02, mostly in cis-regulatory regions, results in distinct gene expression dynamics in response to vernalization treatment. Our data suggest allelic variation at BnaFT.A02 is associated with flowering time in the absence of vernalization, while variation at BnaFLC.A02 is associated with flowering time under vernalizing conditions. We hypothesize selection for BnaFLC.A02 and BnaFT.A02 gene expression variation has facilitated the generation of European winter oilseed rape varieties that are adapted to different winter climates. This knowledge will allow for the selection of alleles of flowering time regulators that alter the vernalization requirement of oilseed rape, informing the generation of new varieties with adapted flowering times and improved yields.
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Affiliation(s)
| | | | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
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5
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Fikere M, Barbulescu DM, Malmberg MM, Spangenberg GC, Cogan NOI, Daetwyler HD. Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence. Sci Rep 2020; 10:14300. [PMID: 32868838 PMCID: PMC7459325 DOI: 10.1038/s41598-020-71274-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022] Open
Abstract
Blackleg disease causes yield losses in canola (Brassica napus L.). To identify resistance genes and genomic regions, genome-wide association studies (GWAS) of 585 diverse winter and spring canola accessions were performed using imputed whole-genome sequence (WGS) and transcriptome genotype-by-sequencing (GBSt). Blackleg disease phenotypes were collected across three years in six trials. GWAS were performed in several ways and their respective power was judged by the number of significant single nucleotide polymorphisms (SNP), the false discovery rate (FDR), and the percentage of SNP that validated in additional field trials in two subsequent years. WGS GWAS with 1,234,708 million SNP detected a larger number of significant SNP, achieved a lower FDR and a higher validation rate than GBSt with 64,072 SNP. A meta-analysis combining survival and average internal infection resulted in lower FDR but also lower validation rates. The meta-analysis GWAS identified 79 genomic regions (674 SNP) conferring potential resistance to L. maculans. While several GWAS signals localised in regions of known Rlm genes, fifty-three new potential resistance regions were detected. Seventeen regions had underlying genes with putative functions related to disease defence or stress response in Arabidopsis thaliana. This study provides insight into the genetic architecture and potential molecular mechanisms underlying canola L. maculans resistance.
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Affiliation(s)
- M Fikere
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.,Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - D M Barbulescu
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3401, Australia
| | - M M Malmberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - G C Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - N O I Cogan
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - H D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia. .,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.
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6
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Yin S, Wan M, Guo C, Wang B, Li H, Li G, Tian Y, Ge X, King GJ, Liu K, Li Z, Wang J. Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4729-4741. [PMID: 32417916 DOI: 10.1093/jxb/eraa237] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/10/2020] [Indexed: 05/08/2023]
Abstract
In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.
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Affiliation(s)
- Shuai Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming Wan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ge Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanyong Tian
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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7
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Raman H, Raman R, Qiu Y, Yadav AS, Sureshkumar S, Borg L, Rohan M, Wheeler D, Owen O, Menz I, Balasubramanian S. GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola. BMC Genomics 2019; 20:636. [PMID: 31387521 PMCID: PMC6685183 DOI: 10.1186/s12864-019-5964-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited. Results We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T (FT) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield. Conclusions Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola. Electronic supplementary material The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Lauren Borg
- Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Oliver Owen
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Ian Menz
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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Arifuzzaman M, Oladzadabbasabadi A, McClean P, Rahman M. Shovelomics for phenotyping root architectural traits of rapeseed/canola (Brassica napus L.) and genome-wide association mapping. Mol Genet Genomics 2019; 294:985-1000. [PMID: 30968249 DOI: 10.1007/s00438-019-01563-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 04/03/2019] [Indexed: 01/22/2023]
Abstract
Root system in plants plays an important role in mining moisture and nutrients from the soil and is positively correlated to yield in many crops including rapeseed/canola (Brassica napus L.). Substantial phenotypic diversity in root architectural traits among the B. napus growth types leads to a scope of root system improvement in breeding populations. In this study, 216 diverse genotypes were phenotyped for five different root architectural traits following shovelomics approach in the field condition during 2015 and 2016. A single nucleotide polymorphism (SNP) marker panel consisting of 30,262 SNPs was used to conduct genome-wide association study to detect marker/trait association. A total of 31 significant marker loci were identified at 0.01 percentile tail P value cutoff for different root traits. Six marker loci for soil-level taproot diameter (R1Dia), six loci for belowground taproot diameter (R2Dia), seven loci for number of primary root branches (PRB), eight loci for root angle, and eight loci for root score (RS) were detected in this study. Several markers associated with root diameters R1Dia and R2Dia were also associated with PRB and RS. Significant phenotypic correlation between these traits was observed in both environments. Therefore, taproot diameter appears to be a major determinant of the canola root system architecture and can be used as proxy for other root traits. Fifteen candidate genes related to root traits and root development were detected within 100 kbp upstream and downstream of different significant markers. The identified markers associated with different root architectural traits can be considered for marker-assisted selection for root traits in canola in future.
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Affiliation(s)
| | | | - Phillip McClean
- Departemnt of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Mukhlesur Rahman
- Departemnt of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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9
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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: 24] [Impact Index Per Article: 3.4] [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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10
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Wang N, Chen B, Xu K, Gao G, Li F, Qiao J, Yan G, Li J, Li H, Wu X. Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits. FRONTIERS IN PLANT SCIENCE 2016; 7:338. [PMID: 27047517 PMCID: PMC4805649 DOI: 10.3389/fpls.2016.00338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/04/2016] [Indexed: 05/02/2023]
Abstract
Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10(-4); the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Xiaoming Wu
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Wang N, Chen B, Xu K, Gao G, Li F, Qiao J, Yan G, Li J, Li H, Wu X. Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits. FRONTIERS IN PLANT SCIENCE 2016; 7:338. [PMID: 27047517 DOI: 10.3359/fpls.2016.00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/04/2016] [Indexed: 05/18/2023]
Abstract
Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10(-4); the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China; College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
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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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Kumar M, Choi JY, Kumari N, Pareek A, Kim SR. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica. FRONTIERS IN PLANT SCIENCE 2015; 6:688. [PMID: 26388887 PMCID: PMC4559640 DOI: 10.3389/fpls.2015.00688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/20/2015] [Indexed: 05/19/2023]
Abstract
Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.
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Affiliation(s)
- Manu Kumar
- Plant Molecular Biology Laboratory, Department of Life Science, Sogang University, SeoulSouth Korea
| | - Ju-Young Choi
- Plant Molecular Biology Laboratory, Department of Life Science, Sogang University, SeoulSouth Korea
| | - Nisha Kumari
- College of Medicine, Seoul National University, SeoulSouth Korea
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Science, Jawaharlal Nehru University, New DelhiIndia
| | - Seong-Ryong Kim
- Plant Molecular Biology Laboratory, Department of Life Science, Sogang University, SeoulSouth Korea
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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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15
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Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D, Batley J. SNP markers-based map construction and genome-wide linkage analysis in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:851-60. [PMID: 24698362 DOI: 10.1111/pbi.12186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/29/2014] [Accepted: 02/21/2014] [Indexed: 05/19/2023]
Abstract
An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.
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Affiliation(s)
- Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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16
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Asghari A, Mohammadi SA, Moghaddam M, Mohammaddoost H. Identification of QTLS Controlling Winter Survival inBrassica Napususing Rapd Markers. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2007.10817485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Liu L, Qu C, Wittkop B, Yi B, Xiao Y, He Y, Snowdon RJ, Li J. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L. PLoS One 2013; 8:e83052. [PMID: 24386142 PMCID: PMC3873396 DOI: 10.1371/journal.pone.0083052] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.
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Affiliation(s)
- Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Benjamin Wittkop
- Department of Plant Breeding, Interdisciplinary Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Subcenter of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Yang Xiao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Rod J. Snowdon
- Department of Plant Breeding, Interdisciplinary Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- * E-mail: (RJS); (JL)
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- * E-mail: (RJS); (JL)
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18
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Ma Y, Wang Y. Estimating disease onset distribution functions in mutation carriers with censored mixture data. J R Stat Soc Ser C Appl Stat 2013. [DOI: 10.1111/rssc.12025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yanyuan Ma
- Texas A&M University; College Station USA
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19
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Alessandro MS, Galmarini CR, Iorizzo M, Simon PW. Molecular mapping of vernalization requirement and fertility restoration genes in carrot. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:415-23. [PMID: 23015218 DOI: 10.1007/s00122-012-1989-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/15/2012] [Indexed: 05/20/2023]
Abstract
Carrot (Daucus carota L.) is a cool-season vegetable normally classified as a biennial species, requiring vernalization to induce flowering. Nevertheless, some cultivars adapted to warmer climates require less vernalization and can be classified as annual. Most modern carrot cultivars are hybrids which rely upon cytoplasmic male-sterility for commercial production. One major gene controlling floral initiation and several genes restoring male fertility have been reported but none have been mapped. The objective of the present work was to develop the first linkage map of carrot locating the genomic regions that control vernalization response and fertility restoration. Using an F(2) progeny, derived from the intercross between the annual cultivar 'Criolla INTA' and a petaloid male sterile biennial carrot evaluated over 2 years, both early flowering habit, which we name Vrn1, and restoration of petaloid cytoplasmic male sterility, which we name Rf1, were found to be dominant traits conditioned by single genes. On a map of 355 markers covering all 9 chromosomes with a total map length of 669 cM and an average marker-to-marker distance of 1.88 cM, Vrn1 mapped to chromosome 2 with flanking markers at 0.70 and 0.46 cM, and Rf1 mapped to chromosome 9 with flanking markers at 4.38 and 1.12 cM. These are the first two reproductive traits mapped in the carrot genome, and their map location and flanking markers provide valuable tools for studying traits important for carrot domestication and reproductive biology, as well as facilitating carrot breeding.
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Affiliation(s)
- María S Alessandro
- Estación Experimental Agropecuaria La Consulta, Instituto Nacional de Tecnología Agropecuaria (INTA), Ex Ruta 40, km 96, La Consulta, Mendoza, PC. 5567. CC 8, Argentina
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Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:119-32. [PMID: 22955939 DOI: 10.1007/s00122-012-1966-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 08/10/2012] [Indexed: 05/18/2023]
Abstract
We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga, Australia.
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21
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Raman H, Raman R, Nelson MN, Aslam MN, Rajasekaran R, Wratten N, Cowling WA, Kilian A, Sharpe AG, Schondelmaier J. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 2011; 19:51-65. [PMID: 22193366 PMCID: PMC3276259 DOI: 10.1093/dnares/dsr041] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia.
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22
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Cai CC, Tu JX, Fu TD, Chen BY. The genetic basis of flowering time and photoperiod sensitivity in rapeseed Brassica napus L. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795408030137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Flowering time quantitative trait Loci analysis of oilseed brassica in multiple environments and genomewide alignment with Arabidopsis. Genetics 2008; 177:2433-44. [PMID: 18073439 DOI: 10.1534/genetics.107.080705] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F(2) population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.
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24
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Chen W, Zhang Y, Liu X, Chen B, Tu J, Tingdong F. Detection of QTL for six yield-related traits in oilseed rape (Brassica napus) using DH and immortalized F(2) populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:849-58. [PMID: 17665168 DOI: 10.1007/s00122-007-0613-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2007] [Accepted: 07/08/2007] [Indexed: 05/16/2023]
Abstract
The inheritance of yield-related traits in rapeseed (Brassica napus) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for such traits are only few. QTL related to six traits were mapped which include plant height (PH), height of lowest primary effective branch (HPB), length of main inflorescence (LMI), silique length (SL), number of primary branches (FB) and silique density (SD). A set of 258 doubled haploid (DH) lines derivatives of a cross between a canola variety Quantum and a resynthesized B. napus line No.2127-17, and a fixed immortalized F(2) (designated as IF(2)) population generated by randomly permutated intermating of these DHs were investigated. A genetic linkage map was constructed using 208 SSR and 189 SRAP markers for the DH population. Phenotypic data were collected from three environments for the two populations. Using composite interval mapping analyses, 30 and 22 significant QTL were repeatedly detected across environments for the six traits in the DH and IF(2) populations, respectively. Twenty-nine QTL were common between the two populations. The directions of parental contribution for all common QTL were the same, showing a great potential for marker-assisted selection in improving these traits. Some chromosomal regions harbor QTL for multiple traits, which were consistent with significant phenotypic correlations observed among traits. The results provided a better understanding of the genetic factors controlling yield-related traits in rapeseed.
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Affiliation(s)
- Wei Chen
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
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Quijada PA, Udall JA, Lambert B, Osborn TC. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:549-61. [PMID: 16767447 DOI: 10.1007/s00122-006-0323-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 05/13/2006] [Indexed: 05/10/2023]
Abstract
The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids.
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Affiliation(s)
- Pablo A Quijada
- Plant Breeding and Plant Genetics Program, and Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
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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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Zhao J, Udall JA, Quijada PA, Grau CR, Meng J, Osborn TC. Quantitative trait loci for resistance to Sclerotinia sclerotiorum and its association with a homeologous non-reciprocal transposition in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:509-16. [PMID: 16333614 DOI: 10.1007/s00122-005-0154-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 11/13/2005] [Indexed: 05/05/2023]
Abstract
Sclerotinia stem rot, caused by fungus Sclerotinia sclerotiorum, is one of the most devastating diseases in rapeseed (Brassica napus L.). We report the identification of Quantitative trait loci (QTL) involved in the resistance to S. sclerotiorum in two segregating populations of DH lines: the HUA population, derived from a cross between a partially resistant Chinese winter line (Hua dbl2) and a susceptible European spring line (P1804); and the MS population, derived from a partially resistant French winter cultivar (Major) and a susceptible Canadian spring cultivar (Stellar). A petiole inoculation technique and two scoring methods, days to wilt (DW) and stem lesion length (SLL), were used for the resistance assessment. A total of eight genomic regions affecting resistance were detected in the HUA population, with four of these regions affecting both measures of resistance. Only one region, which affected both measurements, was detected in the MS population. Individual QTL explained 6-22% of the variance. At five of the QTL from both populations, alleles from the resistant parent contributed to the resistance. QTL on N2 from the HUA population had the highest LOD score and R (2) value and was detected for SLL in the first evaluation. The N12 resistance allele in Hua dbl2 was detected in a region containing a homeologous non-reciprocal transposition (HNRT) from the resistance-containing portion of N2. This result suggests that QTL in the N12.N2 HNRT enhanced the resistance of Hua dbl2 by increasing the dosage of resistance genes. The relationship of QTL from different genetic backgrounds and their associations with other agronomic traits are discussed.
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Affiliation(s)
- Jianwei Zhao
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA.
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Abstract
The existing statistical methods for mapping quantitative trait loci (QTL) assume that the phenotype follows a normal distribution and is fully observed. These assumptions may not be satisfied when the phenotype pertains to the survival time or failure time, which has a skewed distribution and is usually subject to censoring due to random loss of follow-up or limited duration of the experiment. In this article, we propose an interval-mapping approach for censored failure time phenotypes. We formulate the effects of QTL on the failure time through parametric proportional hazards models and develop efficient likelihood-based inference procedures. In addition, we show how to assess genome-wide statistical significance. The performance of the proposed methods is evaluated through extensive simulation studies. An application to a mouse cross is provided.
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Affiliation(s)
- Guoqing Diao
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599-7420, USA
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Abstract
Statistical methods for the detection of genes influencing quantitative traits with the aid of genetic markers are well developed for normally distributed, fully observed phenotypes. Many experiments are concerned with failure-time phenotypes, which have skewed distributions and which are usually subject to censoring because of random loss to follow-up, failures from competing causes, or limited duration of the experiment. In this article, we develop semiparametric statistical methods for mapping quantitative trait loci (QTLs) based on censored failure-time phenotypes. We formulate the effects of the QTL genotype on the failure time through the Cox (1972, Journal of the Royal Statistical Society, Series B 34, 187-220) proportional hazards model and derive efficient likelihood-based inference procedures. In addition, we show how to assess statistical significance when searching several regions or the entire genome for QTLs. Extensive simulation studies demonstrate that the proposed methods perform well in practical situations. Applications to two animal studies are provided.
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Affiliation(s)
- Guoqing Diao
- Department of Biostatistics, CB No. 7420, University of North Carolina, Chapel Hill, North Carolina 27599-7420, USA
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Matsumoto E, Hayashida N, Sakamoto K, Ohi M. Behavior of DNA Markers Linked to a Clubroot Resistance Gene in Segregating Populations of Chinese Cabbage (Brassica rapa ssp. pekinensis). ACTA ACUST UNITED AC 2005. [DOI: 10.2503/jjshs.74.367] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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Axelsson T, Shavorskaya O, Lagercrantz U. Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene. Genome 2001. [DOI: 10.1139/g01-082] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantitative trait locus (QTL) analysis was used to study the evolution of genes controlling the timing of flowering in four Brassica genomes that are all extensively replicated. Comparative mapping showed that a chromosomal region from the top of Arabidopsis thaliana chromosome 5 corresponded to three homoeologous copies in each of the diploid species Brassica nigra, B. oleracea, and B. rapa and six copies in the amphidiploid B. juncea. QTLs were detected in two of the three replicated segments in each diploid genome and in three of the six replicated segments in B. juncea. These results indicate that, for the studied trait, multiple QTLs resulting from genome duplication is the rule rather than the exception. Brassica homologues to two candidate genes (CO and FLC) identified from the corresponding A. thaliana region were mapped. CO homologues mapped close to the QTL peaks in eight of nine QTLs, while FLC homologues mapped farther away in those cases where the mapping resolution allowed a comparison. Thus, our data are consistent with the hypothesis that all the major QTLs we detected in the different species of Brassica could be the result of duplicated copies of the same ancestral gene, possibly the ancestor of CO.Key words: Brassica, Arabidopsis, comparative mapping, genome duplication, flowering time.
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Butruille DV, Guries RP, Osborn TC. Linkage analysis of molecular markers and quantitative trait loci in populations of inbred backcross lines of Brassica napus L. Genetics 1999; 153:949-64. [PMID: 10511570 PMCID: PMC1460775 DOI: 10.1093/genetics/153.2.949] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Backcross populations are often used to study quantitative trait loci (QTL) after they are initially discovered in balanced populations, such as F(2), BC(1), or recombinant inbreds. While the latter are more powerful for mapping marker loci, the former have the reduced background genetic variation necessary for more precise estimation of QTL effects. Many populations of inbred backcross lines (IBLs) have been developed in plant and animal systems to permit simultaneous study and dissection of quantitative genetic variation introgressed from one source to another. Such populations have a genetic structure that can be used for linkage estimation and discovery of QTL. In this study, four populations of IBLs of oilseed Brassica napus were developed and analyzed to map genomic regions from the donor parent (a winter-type cultivar) that affect agronomic traits in spring-type inbreds and hybrids. Restriction fragment length polymorphisms (RFLPs) identified among the IBLs were used to calculate two-point recombination fractions and LOD scores through grid searches. This information allowed the enrichment of a composite genetic map of B. napus with 72 new RFLP loci. The selfed and hybrid progenies of the IBLs were evaluated during two growing seasons for several agronomic traits. Both pedigree structure and map information were incorporated into the QTL analysis by using a regression approach. The number of QTL detected for each trait and the number of effective factors calculated by using biometrical methods were of similar magnitude. Populations of IBLs were shown to be valuable for both marker mapping and QTL analysis.
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Affiliation(s)
- D V Butruille
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
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Bohuon EJ, Ramsay LD, Craft JA, Arthur AE, Marshall DF, Lydiate DJ, Kearsey MJ. The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea. Genetics 1998; 150:393-401. [PMID: 9725855 PMCID: PMC1460304 DOI: 10.1093/genetics/150.1.393] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A population of 150 doubled haploid lines of rapid cycling Brassica oleracea, derived from an F1 from a var. alboglabra x var. italica cross, was scored for flowering time in two trials. Using information on 82 mapped molecular markers, spread evenly across the nine linkage groups, QTL were identified at six locations; one each on linkage groups O2 and O3 and two each on linkage groups O5 and O9. In total, these QTL explained 58 and 93% of the genetical variation in the two trials. Three of these QTL, on linkage groups O2, O3, and O9, were situated in regions showing considerable homology both with each other and with chromosome regions of B. nigra that have been shown to affect flowering time. These same regions are all homologous to a single tract of Arabidopsis chromosome 5, which contains a number of the flowering-related genes, one or more of which may be candidates for the QTL found in Brassica.
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Affiliation(s)
- E J Bohuon
- Plant Genetics Group, School of Biological Sciences, The University of Birmingham, Birmingham B15 2TT, United Kingdom
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Teutonico RA, Osborn TC. Mapping loci controlling vernalization requirement in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:1279-83. [PMID: 24170058 DOI: 10.1007/bf00220941] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/1995] [Accepted: 03/17/1995] [Indexed: 05/21/2023]
Abstract
Brassica cultivars are classified as biennial or annual based on their requirement for a period of cold treatment (vernalization) to induce flowering. Genes controlling the vernalization requirement were identified in a Brassica rapa F2 population derived from a cross between an annual and a biennial oilseed cultivar by using an RFLP linkage map and quantitative trait locus (QTL) analysis of flowering time in F3 lines. Two genomic regions were strongly associated with variation for flowering time of unvernalized plants and alleles from the biennial parent in these regions delayed flowering. These QTLs had no significant effect on flowering time after plants were vernalized for 6 weeks, suggesting that they control flowering time through the requirement for vernalization. The two B. rapa linkage groups containing these QTLs had RFLP loci in common with two B. napus linkage groups that were shown previously to contain QTLs for flowering time. An RFLP locus detected by the cold-induced gene COR6.6 cloned from Arabidopsis thaliana mapped very near to one of the B. rapa QTLs for flowering time.
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Affiliation(s)
- R A Teutonico
- Department of Agronomy, University of Wisconsin, 53706, Madison, WI, USA
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