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Ding T, Cai L, He Y, Li Y, Tian E, Zhou Q, Zhou X, Wang X, Yu K, Shen X. BnPLP1 Positively Regulates Flowering Time, Plant Height, and Main Inflorescence Length in Brassica napus. Genes (Basel) 2023; 14:2206. [PMID: 38137028 PMCID: PMC10743044 DOI: 10.3390/genes14122206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein prenylation mediated by the Arabidopsis thaliana PLURIPETALA (AtPLP) gene plays a crucial role in plant growth, development, and environmental response by adding a 15-carbon farnesyl group or one to two 20-carbon geranylgeranyl groups onto one to two cysteine residues at the C-terminus of the target protein. However, the homologous genes and their functions of AtPLP in rapeseed are unclear. In this study, bioinformatics analysis and gene cloning demonstrated the existence of two homologous genes of AtPLP in the Brassica napus L. genome, namely, BnPLP1 and BnPLP2. Evolutionary analysis revealed that BnPLP1 originated from the B. rapa L. genome, while BnPLP2 originated from the B. oleracea L. genome. Genetic transformation analysis revealed that the overexpression of BnPLP1 in Arabidopsis plants exhibited earlier flowering initiation, a prolonged flowering period, increased plant height, and longer main inflorescence length compared to the wild type. Contrarily, the downregulation of BnPLP1 expression in B. napus plants led to delayed flowering initiation, shortened flowering period, decreased plant height, and reduced main inflorescence length compared to the wild type. These findings indicate that the BnPLP1 gene positively regulates flowering time, plant height, and main inflorescence length. This provides a new gene for the genetic improvement of flowering time and plant architecture in rapeseed.
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Affiliation(s)
- Ting Ding
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Lei Cai
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Yuqi He
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Yuanhong Li
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Entang Tian
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Qianhui Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xufan Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China;
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Xinjie Shen
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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Starosta E, Szwarc J, Niemann J, Szewczyk K, Weigt D. Brassica napus Haploid and Double Haploid Production and Its Latest Applications. Curr Issues Mol Biol 2023; 45:4431-4450. [PMID: 37232751 DOI: 10.3390/cimb45050282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.
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Affiliation(s)
- Ewa Starosta
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Justyna Szwarc
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Katarzyna Szewczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
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Raman H, Shamaya N, Pirathiban R, McVittie B, Raman R, Cullis B, Easton A. Quantitative Trait Loci for Genotype and Genotype by Environment Interaction Effects for Seed Yield Plasticity to Terminal Water-Deficit Conditions in Canola ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040720. [PMID: 36840067 PMCID: PMC9964187 DOI: 10.3390/plants12040720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/12/2023]
Abstract
Canola plants suffer severe crop yield and oil content reductions when exposed to water-deficit conditions, especially during the reproductive stages of plant development. There is a pressing need to develop canola cultivars that can perform better under increased water-deficit conditions with changing weather patterns. In this study, we analysed genetic determinants for the main effects of quantitative trait loci (QTL), (Q), and the interaction effects of QTL and Environment (QE) underlying seed yield and related traits utilising 223 doubled haploid (DH) lines of canola in well-watered and water-deficit conditions under a rainout shelter. Moderate water-deficit at the pre-flowering stage reduced the seed yield to 40.8%. Multi-environmental QTL analysis revealed 23 genomic regions associated with days to flower (DTF), plant height (PH) and seed yield (SY) under well-watered and water-deficit conditions. Three seed yield QTL for main effects were identified on chromosomes A09, C03, and C09, while two were related to QE interactions on A02 and C09. Two QTL regions were co-localised to similar genomic regions for flowering time and seed yield (A09) and the second for plant height and chlorophyll content. The A09 QTL was co-located with a previously mapped QTL for carbon isotope discrimination (Δ13C) that showed a positive relationship with seed yield in the same population. Opposite allelic effects for plasticity in seed yield were identified due to QE interactions in response to water stress on chromosomes A02 and C09. Our results showed that QTL's allelic effects for DTF, PH, and SY and their correlation with Δ13C are stable across environments (field conditions, previous study) and contrasting water regimes (this study). The QTL and DH lines that showed high yield under well-watered and water-deficit conditions could be used to manipulate water-use efficiency for breeding improved canola cultivars.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Nawar Shamaya
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Ramethaa Pirathiban
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Brett McVittie
- 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
| | - Brian Cullis
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Andrew Easton
- Advanta Seeds Pty Ltd., 268 Anzac Avenue, Toowoomba, QLD 4350, Australia
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Ren R, Liu W, Yao M, Jia Y, Huang L, Li W, He X, Guan M, Liu Z, Guan C, Hua W, Xiong X, Qian L. Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:69. [PMID: 37313473 PMCID: PMC10248621 DOI: 10.1007/s11032-022-01337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/07/2022] [Indexed: 06/15/2023]
Abstract
Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01337-1.
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Affiliation(s)
- Rui Ren
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Yuan Jia
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Luyao Huang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wenqian Li
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Zhongsong Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinghua Xiong
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
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Fu Y, Zhao H, Huang J, Zhu H, Luan X, Bu S, Liu Z, Wang X, Peng Z, Meng L, Liu G, Zhang G, Wang S. Dynamic analysis of QTLs on plant height with single segment substitution lines in rice. Sci Rep 2022; 12:5465. [PMID: 35361859 PMCID: PMC8971505 DOI: 10.1038/s41598-022-09536-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/24/2022] [Indexed: 01/22/2023] Open
Abstract
Dynamic regulation of QTLs remains mysterious. Single segment substitution lines (SSSLs) and conditional QTL mapping and functional QTL mappings are ideal materials and methods to explore dynamics of QTLs for complex traits. This paper analyzed the dynamics of QTLs on plant height with SSSLs in rice. Five SSSLs were verified with plant height QTLs first. All five QTLs had significant positive effects at one or more developmental stages except QTL1. They interacted each other, with negative effects before 49 d after transplanting and positive effects since then. The five QTLs selectively expressed in specific periods, mainly in the periods from 35 to 42 d and from 49 to 56 d after transplanting. Expressions of epistasis were dispersedly in various periods, negative effects appearing mainly before 35 d. The five QTLs brought the inflexion point ahead of schedule, accelerated growth and degradation, and changed the peak plant height, while their interactions had the opposite effects. The information will be helpful to understand the genetic mechanism for developmental traits.
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Affiliation(s)
- Yu Fu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Hongyuan Zhao
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jiongkai Huang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Haitao Zhu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xin Luan
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Suhong Bu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Zupei Liu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xiaoling Wang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330299, People's Republic of China
| | - Zhiqin Peng
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330299, People's Republic of China
| | - Lijun Meng
- Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 440307, People's Republic of China.
| | - Guifu Liu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Guiquan Zhang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Shaokui Wang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Cui Y, Fan B, Xu X, Sheng S, Xu Y, Wang X. A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. Front Genet 2022; 12:802738. [PMID: 35132310 PMCID: PMC8817757 DOI: 10.3389/fgene.2021.802738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.
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Affiliation(s)
- Yang Cui
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Baolian Fan
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Xu Xu
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Shasha Sheng
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Xiaoyun Wang
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
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Li K, Wang J, Kuang L, Tian Z, Wang X, Dun X, Tu J, Wang H. Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:178. [PMID: 34507599 PMCID: PMC8431925 DOI: 10.1186/s13068-021-02032-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/30/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In terms of global demand, rapeseed is the third-largest oilseed crop after soybeans and palm, which produces vegetable oil for human consumption and biofuel for industrial production. Roots are vital organs for plant to absorb water and attain mineral nutrients, thus they are of great importance to plant productivity. However, the genetic mechanisms regulating root development in rapeseed remain unclear. In the present study, seven root-related traits and shoot biomass traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. RESULTS The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout the investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. A total of 367 differentially expressed genes (DEGs) with persistent differential expressions throughout root development were identified, and these DEGs were significantly enriched in GO terms, such as energy metabolism and response to biotic or abiotic stress. Totally, 485 stage-specific DEGs with different expressions at specific stage were identified, and these DEGs were enriched in GO terms, such as nitrogen metabolism. Four candidate genes were identified as key persistent genetic factors and eight as stage-specific ones by integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. These candidate genes were speculated to regulate root system development, and they were less than 100 kb away from peak SNPs of QTL clusters. The homologs of three genes (BnaA03g52990D, BnaA06g37280D, and BnaA09g07580D) out of 12 candidate genes have been reported to regulate root development in previous studies. CONCLUSIONS Sixteen QTL clusters and four candidate genes controlling persistently root development, and 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed were detected in this study. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.
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Affiliation(s)
- Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Jie Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Ze Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
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Meyer RC, Weigelt-Fischer K, Knoch D, Heuermann M, Zhao Y, Altmann T. Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:476-490. [PMID: 33080013 DOI: 10.1093/jxb/eraa490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2-9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Marc Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, Research Group Quantitative Genetics, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
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10
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Huang C, Yang M, Shao D, Wang Y, Wan S, He J, Meng Z, Guan R. Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus. BMC Genomics 2020; 21:530. [PMID: 32736518 PMCID: PMC7430850 DOI: 10.1186/s12864-020-06947-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 07/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus. Results Here, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC5F3 family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D, encoding Aux/IAA2 proteins) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a segregated population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. The determination of the photosynthetic efficiency showed that the BnUC2 locus was beneficial to improve the photosynthetic efficiency. Our findings may provide an effective foundation for plant type breeding in B. napus. Conclusions Using SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05.IAA2 is inferred to be the candidate gene responsible for the BnUC2 locus.
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Affiliation(s)
- Chengwei Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mao Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danlei Shao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuqing Meng
- Tibet Agriculture and Animal Husbandry College, Linzhi, 860000, Tibet Autonomous Region, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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11
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Wang X, Zheng M, Liu H, Zhang L, Chen F, Zhang W, Fan S, Peng M, Hu M, Wang H, Zhang J, Hua W. Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:42. [PMID: 32175009 PMCID: PMC7063735 DOI: 10.1186/s13068-020-01687-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 02/22/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Brassica napus provides approximately 13-16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood. RESULTS A dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus 'Darmor-bzh' genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in "Darmor-bzh", "Ningyou 7" and "Zhongshuang 11" reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf.C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D. CONCLUSIONS The combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.
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Affiliation(s)
- Xiaodong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Feng Chen
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Shihang Fan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Menlu Peng
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Maolong Hu
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jiefu Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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12
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Knoch D, Abbadi A, Grandke F, Meyer RC, Samans B, Werner CR, Snowdon RJ, Altmann T. Strong temporal dynamics of QTL action on plant growth progression revealed through high-throughput phenotyping in canola. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:68-82. [PMID: 31125482 PMCID: PMC6920335 DOI: 10.1111/pbi.13171] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 05/08/2023]
Abstract
A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases.
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Affiliation(s)
- Dominic Knoch
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Amine Abbadi
- Norddeutsche Pflanzenzucht Innovation GmbH (NPZi)HoltseeGermany
| | - Fabian Grandke
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Rhonda C. Meyer
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Birgit Samans
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
Technische Hochschule Mittelhessen (THM), University of Applied SciencesFachbereich Gesundheit35390GiessenGermany
| | - Christian R. Werner
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
The Roslin InstituteUniversity of EdinburghEaster Bush CampusMidlothianEH25 9RGUK
| | - Rod J. Snowdon
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Thomas Altmann
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
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13
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Mapping dynamic QTL dissects the genetic architecture of grain size and grain filling rate at different grain-filling stages in barley. Sci Rep 2019; 9:18823. [PMID: 31827117 PMCID: PMC6906516 DOI: 10.1038/s41598-019-53620-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/31/2019] [Indexed: 02/07/2023] Open
Abstract
Grain filling is an important growth process in formation of yield and quality for barley final yield determination. To explore the grain development behavior during grain filling period in barley, a high-density genetic map with 1962 markers deriving from a doubled haploid (DH) population of 122 lines was used to identify dynamic quantitative trait locus (QTL) for grain filling rate (GFR) and five grain size traits: grain area (GA), grain perimeter (GP), grain length (GL), grain width (GW) and grain diameter (GD). Unconditional QTL mapping is to detect the cumulative effect of genetic factors on a phenotype from development to a certain stage. Conditional QTL mapping is to detect a net effect of genetic factors on the phenotype at adjacent time intervals. Using unconditional, conditional and covariate QTL mapping methods, we successfully detected 34 major consensus QTLs. Moreover, certain candidate genes related to grain size, plant height, yield, and starch synthesis were identified in six QTL clusters, and individual gene was specifically expressed in different grain filling stages. These findings provide useful information for understanding the genetic basis of the grain filling dynamic process and will be useful for molecular marker-assisted selection in barley breeding.
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14
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Wang J, Kuang L, Wang X, Liu G, Dun X, Wang H. Temporal genetic patterns of root growth in Brassica napus L. revealed by a low-cost, high-efficiency hydroponic system. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2309-2323. [PMID: 31101925 DOI: 10.1007/s00122-019-03356-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Application of a low-cost and high-efficiency hydroponic system in a rapeseed population verified two types of genetic factors ("persistent" and "stage-specific") that control root development. The root system is a vital plant component for nutrient and water acquisition and is targeted to enhance plant productivity. Genetic dissection of the root system generally focuses on a single stage, but roots grow continuously during plant development. To reveal the temporal genetic patterns of root development, we measured nine root-related traits in a rapeseed recombinant inbred line population at six continuous stages during vegetative growth, using a modified hydroponic system with low-cost and high-efficiency features that could synchronize plant growth under controlled conditions. Phenotypic correlation and growth dynamic analysis suggested the existence of two types of genetic factors ("persistent" and "stage-specific") that control root development. Dynamic (unconditional and conditional) quantitative trait loci (QTL) mapping detected 28 stage-specific and 23 persistent QTLs related to root growth. Among them, 13 early stage-specific, 19 persistent and 8 later stage-specific QTLs were detected at 7 DAS (days after sowing), 16 DAS and 5 EL (expanding leaf stage), respectively, providing efficient and adaptable stages for QTL identification. The effective prediction of biomass accumulation using root morphological traits (up to 96.6% or 92.64% at a specific stage or the final stage, respectively) verified that root growth allocation with maximum root uptake area facilitated biomass accumulation. Furthermore, marker-assistant selection, which combined the "persistent" and "stage-specific" QTLs, proved their effectiveness for root improvement with an excellent uptake area. Our results highlight the potential of high-throughput and precise phenotyping to assess the dynamic genetics of root growth and provide new insights into ideotype root system-based biomass breeding.
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Affiliation(s)
- Jie Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China.
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China.
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15
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Han L, Yang G, Dai H, Yang H, Xu B, Feng H, Li Z, Yang X. Fuzzy Clustering of Maize Plant-Height Patterns Using Time Series of UAV Remote-Sensing Images and Variety Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:926. [PMID: 31379905 PMCID: PMC6652214 DOI: 10.3389/fpls.2019.00926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
The application of high-throughput phenotyping (HTP) techniques based on unmanned aerial vehicle (UAV) remote-sensing platforms to study large-scale population breeding opens the way to more efficient acquisition of dynamic phenotypic traits and provides new tools that should help close the gap between genotyping and traditional field-phenotyping methods. Toward this end we used a field UAV-HTP platform to deploy a RGB high-resolution camera to acquire time-series images. By using three-dimensional reconstructed point cloud models, we developed a repeatable processing workflow to extract plant height from time-series images. The plant height determined by the UAV-HTP platform correlated strongly with that measured manually. The plant heights estimated at various growth stages form temporal profiles that give insights into changes and trends in genotyping. Based on fuzzy c-means clustering analysis, we extract the typical dynamic patterns in phenotypic traits (i.e., plant height, average rate of growth of plant height, and rate of contribution of plant height) hidden in the temporal profiles. The fuzzy c-means clustering and set-intersection operation were first applied to analyze the temporal profile to identify how plant-height patterns change and to detect differences in phenotypic variability among the genotypes. The results revealed the capacity of UAV remote sensing to easily evaluate field traits on multiple timescales, for a few breeding plots or for 1000s of breeding plots.
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Affiliation(s)
- Liang Han
- College of Architecture and Geomatics Engineering, Shanxi Datong University, Datong, China
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, China
- College of Geoscience and Surveying Engineering, China University of Mining and Technology-Beijing, Beijing, China
| | - Guijun Yang
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Huayang Dai
- College of Geoscience and Surveying Engineering, China University of Mining and Technology-Beijing, Beijing, China
| | - Hao Yang
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Bo Xu
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Haikuan Feng
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Zhenhai Li
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Xiaodong Yang
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
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16
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Quantitative trait loci analysis of hormone levels in Arabidopsis roots. PLoS One 2019; 14:e0219008. [PMID: 31251768 PMCID: PMC6599112 DOI: 10.1371/journal.pone.0219008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/14/2019] [Indexed: 11/30/2022] Open
Abstract
Quantitative trait loci (QTL) analyses for five groups of hormones, including cytokinins in Arabidopsis roots were performed using recombinant inbred lines (Ler×Cvi). Significant QTLs were detected for cytokinins, jasmonic acid and salicylic acid. Separate analysis of two sub-populations, viz., vegetative and flowering plants revealed that many of the QTLs were development-specific. Using near-isogenic lines, several significant QTLs were confirmed; three co-localized QTL regions were responsible for determining several cytokinin metabolites. Using a knock-out plant, a functional role of zeatin N-glucosyltransferase gene (UGT76C2) underlying a large-effect QTL for levels of tZ-N-glucosides and tZRMP was evaluated in the metabolism of cytokinins. Pleotropic effects of this gene were found for cytokinin levels in both roots and leaves, but significant changes of morphological traits were observed only in roots. Hormone QTL analysis reveals development-specific and organ-dependent aspects of the regulation of plant hormone content and metabolism.
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17
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Miao L, Chao H, Chen L, Wang H, Zhao W, Li B, Zhang L, Li H, Wang B, Li M. Stable and novel QTL identification and new insights into the genetic networks affecting seed fiber traits in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1761-1775. [PMID: 30830267 DOI: 10.1007/s00122-019-03313-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/15/2019] [Indexed: 05/14/2023]
Abstract
QTL mapping for fiber-related traits and elucidation of a stable and novel QTL affecting seed lignin content, cellulose content and seed oil content. Dissection of the genetic networks for fiber biosynthesis is important for improving the seed oil content and meal value of Brassica napus. In this study, the genetic basis of seed fiber biosynthesis in B. napus was investigated via quantitative trait locus (QTL) analysis using a doubled haploid population derived from 'KenC-8' crossed with 'N53-2.' Seed lignin content (LC), cellulose content (CC) and hemicellulose content (HC) were significantly negatively correlated with seed oil content (OC). Co-localization QTLs among LC, CC, HC and OC on A09 were found with contributions ranging from 9.87 to 48.50%. Seven co-localization QTLs involved in the fiber component and OC were further verified by bulked segregant analysis (BSA). The unique QTL uqA9-12 might be a real and new QTL that was commonly identified by QTL mapping and BSA and simultaneously affected LC, CC and OC with opposite additive effects. A potential regulatory network controlling seed fiber biosynthesis was constructed to dissect the complex mechanism of seed fiber and oil accumulation, and numerous candidate genes were identified in the fiber-related QTL regions. These results provided an enrichment of QTLs and potential candidates for fiber biosynthesis, as well as useful new information for understanding the complex genetic mechanism underlying rapeseed seed fiber accumulation.
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Affiliation(s)
- Liyun Miao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- College of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Li Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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18
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Wang H, Zaman QU, Huang W, Mei D, Liu J, Wang W, Ding B, Hao M, Fu L, Cheng H, Hu Q. QTL and Candidate Gene Identification for Silique Length Based on High-Dense Genetic Map in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2019; 10:1579. [PMID: 31850044 PMCID: PMC6895753 DOI: 10.3389/fpls.2019.01579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 05/13/2023]
Abstract
Silique length (SL) is an important yield trait and positively correlates with seeds per silique and seed weight. In the present study, two double haploid (DH) populations, established from crosses Zhongshuang11 × R11 (ZR) and R1 × R2 (RR), containing 280 and 95 DH lines, respectively, were used to map quantitative trait loci (QTL) for SL. A high-dense genetic map from ZR population was constructed comprising 14,658 bins on 19 linkage groups, with map length of 2,198.85 cM and an average marker distance of 0.15 cM. Genetic linkage map from RR population was constructed by using 2,046 mapped markers anchored to 19 chromosomes with 2,217-cM map length and an average marker distance of 1.08 cM. Major QTL qSL_ZR_A09 and qSL_RR_A09b on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL qSL_RR_A09b and qSL_ZR_A09 were located on 68.5-70.8 cM and 91.33-91.94 cM interval with R2 values of 14.99-39.07% and 15.00-20.36% in RR and ZR populations, respectively. Based on the physical positions of single nucleotide polymorphism (SNP) markers flanking qSL_ZR_A09 and gene annotation in Arabidopsis, 26 genes were identified with SNP/Indel variation between parents and two genes (BnaA09g41180D and BnaA09g41380D) were selected as the candidate genes. Expression analysis further revealed BnaA09g41180D, encoding homologs of Arabidopsis fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for qSL_ZR_A09. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in Brassica napus as well as candidate genes underlying the QTL.
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Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qamar U. Zaman
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Graduate School of the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenhui Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Desheng Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenxiang Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Bingli Ding
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Mengyu Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Li Fu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
| | - Qiong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Hongtao Cheng ; Qiong Hu
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Li B, Zhao W, Li D, Chao H, Zhao X, Ta N, Li Y, Guan Z, Guo L, Zhang L, Li S, Wang H, Li M. Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:296-310. [PMID: 30466595 DOI: 10.1016/j.plantsci.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 05/02/2023]
Abstract
Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.
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Affiliation(s)
- Baojun Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiguo Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Na Ta
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Zhoubo Guan
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Lina Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
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20
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Wei C, Zhu L, Wen J, Yi B, Ma C, Tu J, Shen J, Fu T. Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:97-113. [PMID: 29576090 DOI: 10.1016/j.plantsci.2018.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log2Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.
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Affiliation(s)
- Chao Wei
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lixia Zhu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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21
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Su J, Yang X, Zhang F, Wu S, Xiong S, Shi L, Guan Z, Fang W, Chen F. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. PLANTA 2018; 247:899-924. [PMID: 29273861 DOI: 10.1007/s00425-017-2833-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h B2 for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81-18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90-24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.
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Affiliation(s)
- Jiangshuo Su
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xincheng Yang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shaofang Wu
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Siyi Xiong
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liming Shi
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China.
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Shen Y, Xiang Y, Xu E, Ge X, Li Z. Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population. FRONTIERS IN PLANT SCIENCE 2018; 9:390. [PMID: 29643859 PMCID: PMC5883169 DOI: 10.3389/fpls.2018.00390] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/12/2018] [Indexed: 05/18/2023]
Abstract
Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression) and Westar (B. napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage) of the co-localized QTL. In addition, QTL by environment interactions (QEI) mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.
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Affiliation(s)
- Yusen Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Yusen Shen
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ensheng Xu
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Zaiyun Li
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23
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Zhang N, Fan X, Cui F, Zhao C, Zhang W, Zhao X, Yang L, Pan R, Chen M, Han J, Ji J, Liu D, Zhao Z, Tong Y, Zhang A, Wang T, Li J. Characterization of the temporal and spatial expression of wheat (Triticum aestivum L.) plant height at the QTL level and their influence on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1235-1252. [PMID: 28349175 DOI: 10.1007/s00122-017-2884-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/21/2017] [Indexed: 05/05/2023]
Abstract
The temporal and spatial expression patterns of stable QTL for plant height and their influences on yield were characterized. Plant height (PH) is a complex trait in wheat (Triticum aestivum L.) that includes the spike length (SL) and the internode lengths from the first to the fifth internode, which are counted from the top and abbreviated as FIRITL, SECITL, THIITL, FOUITL, and FIFITL, respectively. This study identified eight putative additive quantitative trait loci (QTL) for PH. In addition, unconditional and conditional QTL mapping were used to analyze the temporal and spatial expression patterns of five stable QTL for PH. qPh-3A mainly regulated SL, FIRITL, and FIFITL to affect PH during the booting-heading stage (BS-HS); qPh-3D regulated all internode lengths to affect PH, especially during the BS-HS; before HS, qPh-4B mainly affected FIRITL, SECITL, THIITL, and FOUITL and qPh-5A.1 mainly affected SECITL, THIITL, and FOUITL to regulate PH; and qPh-6B mainly regulated FIRITL to affect the PH after the booting stage (BS). qPhdv-4B, a QTL for the response of PH to nitrogen stress, was stable and co-localized with qPh-4B. All five stable QTL, except for qPh-3A, were related to the 1000 kernel weight and yield per plant. Regions of qPh-3A, qPh-3D, qPh-4B, qPh-5A.1, and qPh-6B showed synteny to parts of rice chromosomes 1, 1, 3, 9, and 2, respectively. Based on comparative genomics analysis, Rht-B1b was cloned and mapped in the CI of qPh-4B. This report provides useful information for fine mapping of the stable QTL for PH and the genetic improvement of wheat plant type.
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Affiliation(s)
- Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong University, Yantai, 264025, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chunhua Zhao
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xueqiang Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lijuan Yang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Ruiqing Pan
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zongwu Zhao
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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Bazakos C, Hanemian M, Trontin C, Jiménez-Gómez JM, Loudet O. New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:435-455. [PMID: 28226236 DOI: 10.1146/annurev-arplant-042916-040820] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies. These strategies are complementary in most instances, and indeed, one is often used to confirm the results of the other. Despite significant advances, an emerging trend is that the outcome and efficiency of the different approaches depend greatly on the genetic architecture of the trait in the genetic material under study.
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Affiliation(s)
- Christos Bazakos
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Mathieu Hanemian
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Charlotte Trontin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
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26
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Shang L, Wang Y, Cai S, Ma L, Liu F, Chen Z, Su Y, Wang K, Hua J. Genetic analysis of Upland cotton dynamic heterosis for boll number per plant at multiple developmental stages. Sci Rep 2016; 6:35515. [PMID: 27748451 PMCID: PMC5066282 DOI: 10.1038/srep35515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/06/2016] [Indexed: 01/28/2023] Open
Abstract
Yield is an important breeding target. As important yield components, boll number per plant (BNP) shows dynamic character and strong heterosis in Upland cotton. However, the genetic basis underlying the dynamic heterosis is poorly understood. In this study, we conducted dynamic quantitative trait loci (QTL) analysis for BNP and heterosis at multiple developmental stages and environments using two recombinant inbred lines (RILs) and two corresponding backcross populations. By the single-locus analysis, 23 QTLs were identified at final maturity, while 99 QTLs were identified across other three developmental stages. A total of 48 conditional QTLs for BNP were identified for the adjacent stages. QTLs detected at later stage mainly existed in the partial dominance to dominance range and QTLs identified at early stage mostly showed effects with the dominance to overdominance range during plant development. By two-locus analysis, we observe that epistasis played an important role not only in the variation of the performance of the RIL population but also in the expression of heterosis in backcross population. Taken together, the present study reveals that the genetic basis of heterosis is dynamic and complicated, and it is involved in dynamic dominance effect, epistasis and QTL by environmental interactions.
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Affiliation(s)
- Lianguang Shang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Shihu Cai
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingling Ma
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Zhiwen Chen
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ying Su
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Jinping Hua
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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27
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Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton. G3-GENES GENOMES GENETICS 2016; 6:3373-3379. [PMID: 27565885 PMCID: PMC5068956 DOI: 10.1534/g3.116.034355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.
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Genome-Wide Association Study Dissecting the Genetic Architecture Underlying the Branch Angle Trait in Rapeseed (Brassica napus L.). Sci Rep 2016; 6:33673. [PMID: 27646167 PMCID: PMC5028734 DOI: 10.1038/srep33673] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 08/31/2016] [Indexed: 12/04/2022] Open
Abstract
The rapeseed branch angle is an important morphological trait because an adequate branch angle enables more efficient light capture under high planting densities. Here, we report that the average angle of the five top branches provides a reliable representation of the average angle of all branches. Statistical analyses revealed a significantly positive correlation between the branch angle and multiple plant-type and yield-related traits. The 60 K Brassica Infinium® single nucleotide polymorphism (SNP) array was utilized to genotype an association panel with 520 diverse accessions. A genome-wide association study was performed to determine the genetic architecture of branch angle, and 56 loci were identified as being significantly associated with the branch angle trait via three models, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Moreover, these loci explained 51.1% of the phenotypic variation when a simple additive model was applied. Within the linkage disequilibrium (LD) decay ranges of 53 loci, we observed plausible candidates orthologous to documented Arabidopsis genes, such as LAZY1, SGR2, SGR4, SGR8, SGR9, PIN3, PIN7, CRK5, TIR1, and APD7. These results provide insight into the genetic basis of the branch angle trait in rapeseed and might facilitate marker-based breeding for improvements in plant architecture.
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Wang Y, He J, Yang L, Wang Y, Chen W, Wan S, Chu P, Guan R. Fine mapping of a major locus controlling plant height using a high-density single-nucleotide polymorphism map in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1479-91. [PMID: 27147069 DOI: 10.1007/s00122-016-2718-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/19/2016] [Indexed: 05/08/2023]
Abstract
A saturated map was constructed using SNP markers to fine-map a Brassica napus dominant locus for dwarf mutant onto a 152-kb interval of chromosome A09 containing 14 genes. Major dwarf loci in crops may play important roles in crop improvement and developmental genetics. The present study investigated and fine-mapped a Brassica napus dwarf-dominant locus BnDWF1. Plants carrying the BnDWF1 locus in populations derived from 'zhongshuang11' and Bndwf1 have deep-green leaves and dwarf architecture that differ sharply from tall plants with normal green leaves. BnDWF1, as a major locus controlling plant height, showed a very high heritability (0.91-0.95). To map this locus, a high-density single-nucleotide polymorphism map was constructed, and the BnDWF1 locus was mapped at an interval between single-nucleotide polymorphism markers, M19704 and M19695, on linkage group A09 of B. napus, with five co-segregating single-nucleotide polymorphism markers. Furthermore, fine mapping narrowed the interval harboring BnDWF1 to 152 kb in length in B. napus. This interval contains 14 annotated or predicted genes, seven of which are candidates responsible for the dwarf trait. This study provides an effective foundation for the study of plant height regulation and plant type breeding in B. napus.
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Affiliation(s)
- Yankun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Jianbo He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Li Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Yu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China.
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Wang X, Chen L, Wang A, Wang H, Tian J, Zhao X, Chao H, Zhao Y, Zhao W, Xiang J, Gan J, Li M. Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus. BMC PLANT BIOLOGY 2016; 16:71. [PMID: 27000872 PMCID: PMC4802616 DOI: 10.1186/s12870-016-0759-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Yield of rapeseed is determined by three components: silique number, seed number per silique and thousand seed weight. Seed number per silique and thousand seed weight are influenced by silique length, seed density, silique breadth, silique thickness and silique volume. Some QTLs for silique traits have been reported in B. napus, however, no studies have focused on the six agronomic traits (seed number per silique, silique length, silique breadth, silique thickness, seed density and silique volume) simultaneously, and the genetic determinism of such complex traits have not been fully elucidated. RESULTS In this study, the six silique traits were evaluated using 348 lines of a doubled haploid population, the KN population. The results showed that 2, 4, 1, 1 and 2 QTLs explaining > 10 % of phenotypic variation were obtained for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively. Notably, three major effect QTLs (cqSB-C6-1, cqSB-C6-2 and cqSV-C6-3) were identified in at least three environments, and 17 unique QTLs controlling at least two traits were obtained. A high-density consensus map containing 1225 markers was constructed for QTL comparison by combining the KN map with other five published maps. The comparative results revealed that 14, 13 and 11 QTLs for silique breadth, silique thickness and silique volume might be the potential new QTLs because few QTLs for these traits were reported in B. napus. In addition, potential new QTLs for silique length (11), seed number per silique (6) and seed density (5) were also identified. Twenty-five candidate genes underlying 27 QTLs for silique related traits were obtained. CONCLUSIONS This study constructed QTL analysis in B. napus, and obtained 60 consensus QTLs for six silique related traits. The potential new QTLs will enhance our understanding of the genetic control of silique traits, and the stable QTLs provided the targets for improving seed yield in future. These findings provided comprehensive insights into the genetic network affecting silique traits at QTL level in B. napus.
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Affiliation(s)
- Xiaodong Wang
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Provincial Key Laboratory of Agrobiology, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Li Chen
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Aina Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hao Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jianhua Tian
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Xiaoping Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hongbo Chao
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Yajun Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Weiguo Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jun Xiang
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Jianping Gan
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Maoteng Li
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
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Zhao W, Wang X, Wang H, Tian J, Li B, Chen L, Chao H, Long Y, Xiang J, Gan J, Liang W, Li M. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:17. [PMID: 26858737 PMCID: PMC4729939 DOI: 10.3389/fpls.2016.00017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments.
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Affiliation(s)
- Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- *Correspondence: Hao Wang
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Li Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Wusheng Liang
- Department of Applied Biological Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- Maoteng Li
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Sun C, Wang B, Yan L, Hu K, Liu S, Zhou Y, Guan C, Zhang Z, Li J, Zhang J, Chen S, Wen J, Ma C, Tu J, Shen J, Fu T, Yi B. Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1102. [PMID: 27512396 PMCID: PMC4961929 DOI: 10.3389/fpls.2016.01102] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/12/2016] [Indexed: 05/18/2023]
Abstract
Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.
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Affiliation(s)
- Chengming Sun
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Lei Yan
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, College of Agronomy, Hunan Agricultural UniversityChangsha, China
| | - Zhenqian Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, College of Agronomy, Hunan Agricultural UniversityChangsha, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Technology Research Center, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Jiangsu Academy of Agricultural ScienceNanjing, China
| | - Song Chen
- Key Laboratory of Cotton and Rapeseed, Jiangsu Academy of Agricultural ScienceNanjing, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Bin Yi
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Wang X, Yu K, Li H, Peng Q, Chen F, Zhang W, Chen S, Hu M, Zhang J. High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2015; 6:1164. [PMID: 26779193 PMCID: PMC4688392 DOI: 10.3389/fpls.2015.01164] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/07/2015] [Indexed: 05/09/2023]
Abstract
The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line 'APL01' and a normally petalled variety 'Holly'. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.
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Affiliation(s)
- Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing, China
| | - Kunjiang Yu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Hongge Li
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Feng Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Wei Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Song Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural SciencesNanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing, China
- *Correspondence: Jiefu Zhang,
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