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Zhang L, Yang B, Li X, Chen S, Zhang C, Xiang S, Sun T, Yang Z, Kong X, Qu C, Lu K, Li J. Integrating GWAS, RNA-Seq and functional analysis revealed that BnaA02.SE mediates silique elongation by affecting cell proliferation and expansion in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38899717 DOI: 10.1111/pbi.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/08/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Rapeseed (Brassica napus) silique is the major carbohydrate source for seed development, and the final silique length has attracted great attention from breeders. However, no studies had focused on the dynamic character of silique elongation length (SEL). Here, the dynamic SEL investigation in a natural population including 588 lines over two years indicate that dynamic SEL during 0-20 days after flowering was the most essential stage associated with seed number per silique (SPS) and thousand seed weight (TSW). Then, nine loci were identified to be associated with SEL based on GWAS analysis, among which five SNPs (over 50%) distributed on the A02 chromosome within 6.08 to 6.48 Mb. Subsequently, we screened 5078 differentially expressed genes between two extreme materials. An unknown protein, BnaA02.SE, was identified combining with GWAS and RNA-Seq analysis. Subcellular localization and expression profiles analysis demonstrated that BnaA02.SE is a chloroplast- and nucleus-localized protein mainly expressed in pericarps and leaves. Furthermore, transgenic verification and dynamic cytological observation reveal that overexpressed BnaA02.SE can promote silique elongation by regulating JA and IAA contents, affecting cell proliferation and expansion, respectively, and finally enhance seed yield by influencing SPS and TSW. Haplotype analysis reveal that the homologs of BnaA02.SE may also be involved in silique elongation regulation. Our findings provided comprehensive insights into a newly SEL trait, and cloned the first gene (BnaA02.SE) controlling silique elongation in B. napus. The identified BnaA02.SE and its homologs can offer a valuable target for improving B. napus yield.
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Affiliation(s)
- Liyuan Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Bo Yang
- Industrial Crops Research Institute, Yunnan Acedemy of Agricultural Sciences, Kunming, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Si Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chao Zhang
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Sirou Xiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Tingting Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ziyan Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xizeng Kong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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2
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Chen L, He W, Yu Y, Wang Y, Zhai X, Ling X, Lu P, Cheng X, Lei W, Fan Z. Molecular mapping and candidate gene identification of two major quantitative trait loci associated with silique length in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:26. [PMID: 38516204 PMCID: PMC10951173 DOI: 10.1007/s11032-024-01464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Rapeseed is a significant global source of plant oil. Silique size, particularly silique length (SL), impacts rapeseed yield. SL is a typical quantitative trait controlled by multiple genes. In our previous study, we constructed a DH population of 178 families known as the 158A-SGDH population. In this study, through SL QTL mapping, we identified twenty-six QTL for SL across five replicates in two environments. A QTL meta-analysis revealed eight consensus QTL, including two major QTL: cqSL.A02-1 (11.32-16.44% of PVE for SL), and cqSL.C06-1 (10.90-11.95% of PVE for SL). Based on biparental resequencing data and microcollinearity analysis of target regions in Brassica napus and Arabidopsis, we identified 11 candidate genes at cqSL.A02-1 and 6 candidate genes at cqSL.C06-1, which are potentially associated with silique development. Furthermore, transcriptome analysis of silique valves from both parents on the 14th, 21st, and 28th days after pollination (DAP) combined with gene function annotation revealed three significantly differentially expressed genes at cqSL.A02-1, BnaA02G0058500ZS, BnaA02G0060100ZS, and BnaA02G0060900ZS. Only the gene BnaC06G0283800ZS showed significant differences in parental transcription at cqSL.C06-1. Two tightly linked insertion-deletion markers for the cqSL.A02-1 and cqSL.C06-1 loci were developed. Using these two QTL, we generated four combinations: A02SGDH284C06158A, A02SGDH284C06SGDH284, A02158AC06158A, and A02158AC06SGDH284. Subsequent analysis identified an ideal QTL combination, A02158AC06SGDH284, which exhibited the longest SL of this type, reaching 6.06 ± 0.10 cm, significantly surpassing the other three combinations. The results will provide the basis for the cloning of SL-related genes of rapeseed, along with the development of functional markers of target genes and the breeding of rapeseed varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01464-x.
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Affiliation(s)
- Lei Chen
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Wangfei He
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Yulin Yu
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Yifan Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xueyang Zhai
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xinxiang Ling
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Pan Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Xinxin Cheng
- College of Agriculture, Anhui Science and Technology University, Fengyang, 233100 China
| | - Weixia Lei
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
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3
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Knoch D, Meyer RC, Heuermann MC, Riewe D, Peleke FF, Szymański J, Abbadi A, Snowdon RJ, Altmann T. Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:713-728. [PMID: 37964699 DOI: 10.1111/tpj.16524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring-type lines which was previously analysed by high-throughput phenotyping of growth-related traits and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly. Genome-wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, 14195, Berlin, Germany
| | - Fritz F Peleke
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Jędrzej Szymański
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Institute of Bio- and Geosciences IBG-4: Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363, Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition (iFZ), Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
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Wang C, Niu J, Wei L, Li C, Li G, Tian Q, Ju M, Ma Q, Cao H, Duan Y, Guo H, Zhang H, Miao H. A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:221. [PMID: 37819543 DOI: 10.1007/s00122-023-04465-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait. Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0 cm) were dominant over normal length (average CL = 3.0 cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830-730,961 bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E-19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756 bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25-39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.
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Affiliation(s)
- Cuiying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Jiaojiao Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hui Guo
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Haiyang Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
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5
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Calderwood A, Siles L, Eastmond PJ, Kurup S, Morris RJ. A causal inference and Bayesian optimisation framework for modelling multi-trait relationships-Proof-of-concept using Brassica napus seed yield under controlled conditions. PLoS One 2023; 18:e0290429. [PMID: 37656702 PMCID: PMC10473526 DOI: 10.1371/journal.pone.0290429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023] Open
Abstract
The improvement of crop yield is a major breeding target and there is a long history of research that has focussed on unravelling the mechanisms and processes that contribute to yield. Quantitative prediction of the interplay between morphological traits, and the effects of these trait-trait relationships on seed production remains, however, a challenge. Consequently, the extent to which crop varieties optimise their morphology for a given environment is largely unknown. This work presents a new combination of existing methodologies by framing crop breeding as an optimisation problem and evaluates the extent to which existing varieties exhibit optimal morphologies under the test conditions. In this proof-of-concept study using spring and winter oilseed rape plants grown under greenhouse conditions, we employ causal inference to model the hierarchically structured effects of 27 morphological yield traits on each other. We perform Bayesian optimisation of seed yield, to identify and quantify the morphologies of ideotype plants, which are expected to be higher yielding than the varieties in the studied panels. Under the tested growth conditions, we find that existing spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant winter varieties. The same approach can be used to evaluate trait (morphology) space for any environment.
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Affiliation(s)
- Alexander Calderwood
- Department of Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Laura Siles
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter J. Eastmond
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Smita Kurup
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
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Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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7
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Ma X, Wang J, Gu Y, Fang P, Nie W, Luo R, Liu J, Qian W, Mei J. Genetic analysis and QTL mapping for silique density in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:128. [PMID: 37191718 DOI: 10.1007/s00122-023-04375-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE Genetic models, QTLs and candidate gene for silique density on main inflorescence of rapeseed were identified. Silique density is one of the critical factors to determine seed yield and plant architecture in rapeseed (Brassica napus L.); however, the genetic control of this trait is largely unknown. In this study, the genetic model for silique density on main inflorescence (SDMI) of rapeseed was estimated according to the phenotypic data of P1 (an inbreed line with high SDMI), P2 (an inbreed line with low SDMI), F1, F2, BC1P1 and BC1P2 populations, revealing that SDMI is probably controlled by multi-minor genes with or without major gene. The QTLs for SDMI and its component characters including silique number on main inflorescence (SNMI) and main inflorescence length (MIL) were consequently mapped from a DH population derived from P1 and P2 by using a genetic linkage map constructed by restriction site-associated DNA sequencing (RAD seq) technology. A total of eight, 14 and three QTLs were identified for SDMI, SNMI and MIL under three environments, respectively, with an overlap among SDMI and SNMI in 55.7-75.4 cm on linkage group C06 which corresponding to 11.6-27.3 Mb on chromosome C06. Genomic resequencing was further conducted between a high- and a low-SDMI pool constructed from the DH population, and QTL-seq analysis identified a 0.15 Mb interval (25.98-26.13 Mb) from the C06-QTL region aforementioned. Transcriptome sequencing and qRT-PCR identified one possible candidate gene (BnARGOS) from the 0.15 Mb interval. This study will provide novel insights into the genetic basis of SD in rapeseed.
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Affiliation(s)
- Xingrong Ma
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Jinhua Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Guizhou Oil Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yongfen Gu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Pengpeng Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, 410125, Hunan, China
- Hunan Hybrid Rice Research Center and State Key Laboratory of Hybrid Rice, Changsha, 410125, Hunan, China
| | - Wenjing Nie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Ruirui Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Jin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
- Organization Department of Qingbaijiang District, Chengdu, 610000, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China.
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China.
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Ma Z, Du R, Xie J, Sun D, Fang H, Jiang L, Cen H. Phenotyping of Silique Morphology in Oilseed Rape Using Skeletonization with Hierarchical Segmentation. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0027. [PMID: 36939450 PMCID: PMC10017417 DOI: 10.34133/plantphenomics.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Silique morphology is an important trait that determines the yield output of oilseed rape (Brassica napus L.). Segmenting siliques and quantifying traits are challenging because of the complicated structure of an oilseed rape plant at the reproductive stage. This study aims to develop an accurate method in which a skeletonization algorithm was combined with the hierarchical segmentation (SHS) algorithm to separate siliques from the whole plant using 3-dimensional (3D) point clouds. We combined the L1-median skeleton with the random sample consensus for iteratively extracting skeleton points and optimized the skeleton based on information such as distance, angle, and direction from neighborhood points. Density-based spatial clustering of applications with noise and weighted unidirectional graph were used to achieve hierarchical segmentation of siliques. Using the SHS, we quantified the silique number (SN), silique length (SL), and silique volume (SV) automatically based on the geometric rules. The proposed method was tested with the oilseed rape plants at the mature stage grown in a greenhouse and field. We found that our method showed good performance in silique segmentation and phenotypic extraction with R 2 values of 0.922 and 0.934 for SN and total SL, respectively. Additionally, SN, total SL, and total SV had the statistical significance of correlations with the yield of a plant, with R values of 0.935, 0.916, and 0.897, respectively. Overall, the SHS algorithm is accurate, efficient, and robust for the segmentation of siliques and extraction of silique morphological parameters, which is promising for high-throughput silique phenotyping in oilseed rape breeding.
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Affiliation(s)
- Zhihong Ma
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Ruiming Du
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Jiayang Xie
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Dawei Sun
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Hui Fang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
| | - Lixi Jiang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, P.R. China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, P.R. China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, P.R. China
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9
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Xing X, Liu H, Ye J, Yao Y, Li K, Li Y, Du D. QTL analysis and candidate gene prediction for seed density per silique by QTL-seq and RNA-seq in spring Brassica napus L. PLoS One 2023; 18:e0281875. [PMID: 36877715 PMCID: PMC9987769 DOI: 10.1371/journal.pone.0281875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Seed density per silique (SD) is an important agricultural trait and plays an important role in the yield performance of Brassica napus L. (B. napus). In this study, a genetic linkage map was constructed using a double haploid (DH) population with 213 lines derived from a cross between a low SD line No. 935 and a high SD line No. 3641, and a total of 1,098,259 SNP (single-nucleotide polymorphisms) markers and 2,102 bins were mapped to 19 linkage groups. Twenty-eight QTLs for SD were detected on chromosomes A02, A04, A05, A09, C02, C03, C06, and C09 of B. napus, of which eight QTLs were on chromosome A09 and explained 5.89%-13.24% of the phenotypic variation. Furthermore, a consistent QTL for SD on chromosome A09, cqSD-A9a, was identified in four environments by QTL meta-analysis, explaining 10.68% of the phenotypic variation. In addition, four pairs of epistatic interactions were detected in the DH population via QTL epistasis analysis, indicating that SD is controlled not only by additive effects but also by epistatic effects that play an important role in spring B. napus., but with little environmental effect. Moreover, 18 closely linked SSR markers for cqSD-A9a were developed, as a result, it was mapped to a 1.86Mb (7.80-9.66 Mb) region on chromosome A09. A total of 13 differentially expressed genes (DEGs) were screened in the candidate interval by RNA-seq analysis, which were differentially expressed in buds, leaves and siliques both between and siliques both between two parents and two pools of extremely high-SD and low-SD lines in the DH population. Three of 13 DEGs were possible candidate genes that might control SD: BnaA09g14070D, which encodes a callose synthase that plays an important role in development and stress responses; BnaA09g14800D, a plant synaptic protein that encodes a membrane component; and BnaA09g18250D, which is responsible for DNA binding, transcriptional regulation, and sequence-specific DNA binding and is involved in the response to growth hormone stimulation. Overall, these results lay a foundation for fine mapping and gene cloning for SD in B. napus.
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Affiliation(s)
- Xiaorong Xing
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Haidong Liu
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
- * E-mail: (HL); (DD)
| | - Jingxiu Ye
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Yanmei Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Kaixiang Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Yanling Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Dezhi Du
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
- * E-mail: (HL); (DD)
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Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L. Int J Mol Sci 2022; 23:ijms232415892. [PMID: 36555533 PMCID: PMC9785822 DOI: 10.3390/ijms232415892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.
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11
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Zandberg JD, Fernandez CT, Danilevicz MF, Thomas WJW, Edwards D, Batley J. The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. PLANTS (BASEL, SWITZERLAND) 2022; 11:2740. [PMID: 36297764 PMCID: PMC9610009 DOI: 10.3390/plants11202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.
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Affiliation(s)
- Jaco D. Zandberg
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | - Monica F. Danilevicz
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- Center for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
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12
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Xiong H, Wang R, Jia X, Sun H, Duan R. Transcriptomic analysis of rapeseed ( Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas. FRONTIERS IN PLANT SCIENCE 2022; 13:927418. [PMID: 35982704 PMCID: PMC9379305 DOI: 10.3389/fpls.2022.927418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/01/2022] [Indexed: 06/12/2023]
Abstract
As one of the most important oil crops, rapeseed (Brassica napus) is cultivated worldwide to produce vegetable oil, animal feed, and biodiesel. As the population grows and the need for renewable energy increases, the breeding and cultivation of high-yield rapeseed varieties have become top priorities. The formation of a high rapeseed yield is so complex because it is influenced not only by genetic mechanisms but also by many environmental conditions, such as climatic conditions and different farming practices. Interestingly, many high-yield areas are located in special eco-environments, for example, in the high-altitude Xiangride area of the Qinghai Plateau. However, the molecular mechanisms underlying the formation of high yields in such a special eco-environment area remain largely unknown. Here, we conducted field yield analysis and transcriptome analysis in the Xiangride area. Compared with the yield and environmental factors in the Xinning area (a low-yielding area), we found that the relatively longer daylight length is the key to high rapeseed yield in the Xiangride area, which leads up to a 52.1% increase in rapeseed yield, especially the increase in thousand seed weight and silique number (SN). Combined with transcriptome H-cluster analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses, we can assume that the grain development of rapeseed in the Xiangride area is ahead of schedule and lasts for a long time, leading to the high-yield results in the Xiangride area, confirmed by the expression analysis by quantitative real-time polymerase chain reaction (qRT-PCR) of yield-related genes. Our results provide valuable information for further exploring the molecular mechanism underlying high yield in special ecological environments and provide a helpful reference for studying seed development characteristics in special-producing regions for Brassica napus.
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Affiliation(s)
- Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruisheng Wang
- Academy of Agricultural and Forestry Sciences of Qinghai University, Key Laboratory of Spring Rape Genetic Improvement of Qinghai Province, Rapeseed Research and Development Center of Qinghai Province, Xining, China
| | - Xianqing Jia
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hezhe Sun
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruijun Duan
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
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13
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Dhaka N, Jain R, Yadav A, Yadav P, Kumar N, Sharma MK, Sharma R. Transcriptome analysis reveals cell cycle-related transcripts as key determinants of varietal differences in seed size of Brassica juncea. Sci Rep 2022; 12:11713. [PMID: 35810218 PMCID: PMC9271088 DOI: 10.1038/s41598-022-15938-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/01/2022] [Indexed: 11/22/2022] Open
Abstract
Brassica juncea is an important oilseed crop, widely grown as a source of edible oil. Seed size is a pivotal agricultural trait in oilseed Brassicas. However, the regulatory mechanisms underlying seed size determination are poorly understood. To elucidate the transcriptional dynamics involved in the determination of seed size in B. juncea, we performed a comparative transcriptomic analysis using developing seeds of two varieties, small-seeded Early Heera2 (EH2) and bold-seeded Pusajaikisan (PJK), at three distinct stages (15, 30 and 45 days after pollination). We detected 112,550 transcripts, of which 27,186 and 19,522 were differentially expressed in the intra-variety comparisons and inter-variety comparisons, respectively. Functional analysis using pathway, gene ontology, and transcription factor enrichment revealed that cell cycle- and cell division-related transcripts stay upregulated during later stages of seed development in the bold-seeded variety but are downregulated at the same stage in the small-seeded variety, indicating that an extended period of cell proliferation in the later stages increased seed weight in PJK as compared to EH2. Further, k-means clustering and candidate genes-based analyses unravelled candidates for employing in seed size improvement of B. juncea. In addition, candidates involved in determining seed coat color, oil content, and other seed traits were also identified.
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Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Pinky Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Neeraj Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | | | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
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Zhao C, Xie M, Liang L, Yang L, Han H, Qin X, Zhao J, Hou Y, Dai W, Du C, Xiang Y, Liu S, Huang X. Genome-Wide Association Analysis Combined With Quantitative Trait Loci Mapping and Dynamic Transcriptome Unveil the Genetic Control of Seed Oil Content in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:929197. [PMID: 35845656 PMCID: PMC9283957 DOI: 10.3389/fpls.2022.929197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed, an allotetraploid oil crop, provides vegetable oil for human consumption. The growing demand for oilseeds has necessitated the development of rapeseed varieties with improved quality. Therefore, a clear understanding of the genetic basis underlying the seed oil content (SOC) is required. In this study, a natural population comprising 204 diverse accessions and recombinant inbred lines (RILs) derived from Brassica napus and Sinapis alba via distant hybridization were collected for genome-wide association analysis (GWAS) and quantitative trait loci (QTL) mapping of the SOC trait, respectively. The variable coefficient of the RIL and natural populations ranged from 7.43 to 10.43% and 8.40 to 10.91%. Then, a high-density linkage map was constructed based on whole genome re-sequencing (WGS); the map harbored 2,799 bin markers and covered a total distance of 1,835.21 cM, with an average marker interval of 0.66 cM. The QTLs for SOC on chromosome A07 were stably detected in both single and multiple environments. Finally, a novel locus qA07.SOC was identified as the major QTL for SOC based on the GWAS and RIL populations. In addition, the RNA-seq results showed that photosynthesis, lipid biosynthesis proteins, fatty acid metabolism, and unsaturated fatty acid biosynthesis were significantly different between the developed seeds of the two parents of the RIL population. By comparing the variation information and expression levels of the syntenic genes within qA07.SOC and its syntenic genomic regions, as well as through haplotype analysis via GWAS, BnaA07.STR18, BnaA07.NRT1, and BnaA07g12880D were predicted as candidate genes in the qA07.SOC interval. These stable QTLs containing candidate genes and haplotypes can potentially provide a reliable basis for marker-assisted selection in B. napus breeding for SOC.
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Affiliation(s)
- Chuanji Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Longbing Liang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Hongshi Han
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xinrong Qin
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jixian Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yan Hou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wendong Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Caifu Du
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianqun Huang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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15
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BnKAT2 Positively Regulates the Main Inflorescence Length and Silique Number in Brassica napus by Regulating the Auxin and Cytokinin Signaling Pathways. PLANTS 2022; 11:plants11131679. [PMID: 35807631 PMCID: PMC9269334 DOI: 10.3390/plants11131679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
Brassica napus is the dominant oil crop cultivated in China for its high quality and high yield. The length of the main inflorescence and the number of siliques produced are important traits contributing to rapeseed yield. Therefore, studying genes related to main inflorescence and silique number is beneficial to increase rapeseed yield. Herein, we focused on the effects of BnKAT2 on the main inflorescence length and silique number in B. napus. We explored the mechanism of BnKAT2 increasing the effective length of main inflorescence and the number of siliques through bioinformatics analysis, transgenic technology, and transcriptome sequencing analysis. The full BnKAT2(BnaA01g09060D) sequence is 3674 bp, while its open reading frame is 2055 bp, and the encoded protein comprises 684 amino acids. BnKAT2 is predicted to possess two structural domains, namely KHA and CNMP-binding domains. The overexpression of BnKAT2 effectively increased the length of the main inflorescence and the number of siliques in B. napus, as well as in transgenic Arabidopsis thaliana. The type-A Arabidopsis response regulator (A-ARR), negative regulators of the cytokinin, are downregulated in the BnKAT2-overexpressing lines. The Aux/IAA, key genes in auxin signaling pathways, are downregulated in the BnKAT2-overexpressing lines. These results indicate that BnKAT2 might regulate the effective length of the main inflorescence and the number of siliques through the auxin and cytokinin signaling pathways. Our study provides a new potential function gene responsible for improvement of main inflorescence length and silique number, as well as a candidate gene for developing markers used in MAS (marker-assisted selection) breeding to improve rapeseed yield.
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A Preliminary Study for Identifying Quantitative Trait Loci Associated with Seed Production in Radish Using Genotyping-by-Sequencing. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The high yield of seeds can reduce the cost of seed production for parental lines, as well as F1 cultivars in radish. The number of seeds per silique and silique length are two important traits among traits determining seed yield, but no study has been conducted on their quantitative trait loci (QTLs) in radish. A high-density linkage map was constructed, based on genotyping-by-sequencing (GBS) of the F2 population, derived from two parental lines, significantly differed by the two traits, which were grown in a controlled environment to minimize the environmental effects. Using the map with 848 SNPs, three significant QTLs were identified, two and one of which were associated with the number of seeds per silique and silique length, respectively. Ortholog analysis was conducted with Arabidopsis thaliana genes, related to the number of seeds per silique, and revealed five radish putative candidate genes. These putative candidate genes appear to be related to ovule, embryo sac, embryo, pollen and seed development, as well as a double fertilization process. The method to pollinate the F2 population, as well as preliminary QTLs and SNPs therein, can be helpful for future QTL studies to improve seed production in radish breeding programs.
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17
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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18
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Zhou X, Zhang H, Wang P, Liu Y, Zhang X, Song Y, Wang Z, Ali A, Wan L, Yang G, Hong D. BnaC7.ROT3, the causal gene of cqSL-C7, mediates silique length by affecting cell elongation in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:154-167. [PMID: 34486674 DOI: 10.1093/jxb/erab407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Siliques are a major carbohydrate source of energy for later seed development in rapeseed (Brassica napus). Thus, silique length has received great attention from breeders. We previously detected a novel quantitative trait locus cqSL-C7 that controls silique length in B. napus. Here, we further validated the cqSL-C7 locus and isolated its causal gene (BnaC7.ROT3) by map-based cloning. In 'Zhongshuang11' (parent line with long siliques), BnaC7.ROT3 encodes the potential cytochrome P450 monooxygenase CYP90C1, whereas in 'G120' (parent line with short siliques), a single nucleotide deletion in the fifth exon of BnaC7.ROT3 results in a loss-of-function truncated protein. Sub-cellular localization and expression pattern analysis revealed that BnaC7.ROT3 is a membrane-localized protein mainly expressed in leaves, flowers and siliques. Cytological observations showed that the cells in silique walls of BnaC7.ROT3-transformed positive plants were longer than those of transgene-negative plants in the background of 'G120', suggesting that BnaC7.ROT3 affects cell elongation. Haplotype analysis demonstrated that most alleles of BnaC7.ROT3 are favorable in B. napus germplasms, and its homologs may also be involved in silique length regulation. Our findings provide novel insights into the regulatory mechanisms of natural silique length variations and valuable genetic resources for the improvement of silique length in rapeseed.
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Affiliation(s)
- Xianming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yixian Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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Zhao X, Yu K, Pang C, Wu X, Shi R, Sun C, Zhang W, Chen F, Zhang J, Wang X. QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:766271. [PMID: 34887891 PMCID: PMC8650614 DOI: 10.3389/fpls.2021.766271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/06/2021] [Indexed: 06/12/2023]
Abstract
As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38-13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.
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Affiliation(s)
- Xiaozhen Zhao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Chengke Pang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xu Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chengming Sun
- 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
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China
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20
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Wang J, Fan Y, Mao L, Qu C, Lu K, Li J, Liu L. Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:214. [PMID: 34743746 PMCID: PMC8573943 DOI: 10.1186/s13068-021-02064-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rapeseed is the third-largest oilseed crop after soybeans and palm that produces vegetable oil for human consumption and biofuel for industrial production. Silique length (SL) is an important trait that is strongly related to seed yield in rapeseed. Although many studies related to SL have been reported in rapeseed, only a few candidate genes have been found and cloned, and the genetic mechanisms regulating SL in rapeseed remain unclear. Here, we dissected the genetic basis of SL by genome-wide association studies (GWAS) combined with transcriptome analysis. RESULTS We identified quantitative trait locus (QTL) for SL using a recombinant inbred line (RIL) population and two independent GWAS populations. Major QTLs on chromosomes A07, A09, and C08 were stably detected in all environments from all populations. Several candidate genes related to starch and sucrose metabolism, plant hormone signal transmission and phenylpropanoid biosynthesis were detected in the main QTL intervals, such as BnaA9.CP12-2, BnaA9.NST2, BnaA7.MYB63, and BnaA7.ARF17. In addition, the results of RNA-seq and weighted gene co-expression network analysis (WGCNA) showed that starch and sucrose metabolism, photosynthesis, and secondary cell wall biosynthesis play an important role in the development of siliques. CONCLUSIONS We propose that photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play important roles in the development of rapeseed siliques.
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Affiliation(s)
- Jia Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Yueling Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Lin Mao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, China.
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21
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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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22
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Pal L, Sandhu SK, Bhatia D, Sethi S. Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed ( Brassica napus subsp. napus). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1933-1951. [PMID: 34629771 PMCID: PMC8484396 DOI: 10.1007/s12298-021-01060-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/19/2021] [Accepted: 08/28/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01060-9.
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Affiliation(s)
- Lalit Pal
- Principal Scientist, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Surinder K. Sandhu
- Principal Scientist, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Dharminder Bhatia
- Principal Scientist, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Sorabh Sethi
- Principal Scientist, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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23
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Chai L, Zhang J, Li H, Cui C, Jiang J, Zheng B, Wu L, Jiang L. Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in Brassica napus by Comparative Transcriptome Analysis. Front Genet 2021; 12:678804. [PMID: 34367242 PMCID: PMC8343136 DOI: 10.3389/fgene.2021.678804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/18/2021] [Indexed: 11/25/2022] Open
Abstract
In higher plants, the structure of a flower is precisely controlled by a series of genes. An aberrance flower results in abnormal fruit morphology. Previously, we reported multi-silique rapeseed (Brassica napus) line zws-ms. We identified two associated regions and investigated differentially expressed genes (DEGs); thus, some candidate genes underlying the multi-silique phenotype in warm area Xindu were selected. However, this phenotype was switched off by lower temperature, and the responsive genes, known as thermomorphogenesis-related genes, remained elusive. So, based on that, in this study, we further investigated the transcriptome data from buds of zws-ms and its near-isogenic line zws-217 grown in colder area Ma’erkang, where both lines showed normal siliques only, and the DEGs between them analyzed. We compared the 129 DEGs from Xindu to the 117 ones from Ma’erkang and found that 33 of them represented the same or similar expression trends, whereas the other 96 DEGs showed different expression trends, which were defined as environment-specific. Furthermore, we combined this with the gene annotations and ortholog information and then selected BnaA09g45320D (chaperonin gene CPN10-homologous) and BnaC08g41780D [Seryl-tRNA synthetase gene OVULE ABORTION 7 (OVA7)-homologous] the possible thermomorphogenesis-related genes, which probably switched off the multi-silique under lower temperature. This study paves a way to a new perspective into flower/fruit development in Brassica plants.
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Affiliation(s)
- Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jinfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lintao Wu
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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Song J, Li B, Cui Y, Zhuo C, Gu Y, Hu K, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time. Int J Mol Sci 2021; 22:ijms22147559. [PMID: 34299178 PMCID: PMC8305928 DOI: 10.3390/ijms22147559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/04/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.
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Affiliation(s)
- Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yanke Cui
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Yuanguo Gu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.S.); (B.L.); (Y.C.); (C.Z.); (K.H.); (J.W.); (B.Y.); (J.S.); (C.M.); (T.F.)
- Correspondence:
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25
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Xin S, Dong H, Yang L, Huang D, Zheng F, Cui Y, Wu S, Liao J, He Y, Wan H, Liu Z, Li X, Qian W. Both overlapping and independent loci underlie seed number per pod and seed weight in Brassica napus by comparative quantitative trait loci analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:41. [PMID: 37309442 PMCID: PMC10236046 DOI: 10.1007/s11032-021-01232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/10/2021] [Indexed: 06/14/2023]
Abstract
Seed number per pod (SNPP) and seed weight (SW) are two components of seed yield in rapeseed (Brassica napus). Here, a natural population of rapeseed was employed for genome-wide association analysis for SNPP and SW across multi-years. A total of 101 and 77 SNPs significantly associated with SNPP and SW with the phenotypic variances (R2) ranging from 1.35 to 29.47% and from 0.78 to 34.58%, respectively. And 43 and 33 homologs of known genes from model plants were located in the 65 and 49 haplotype blocks (HBs) for SNPP and SW, respectively. Notably, we found 5 overlapping loci and 3 sets of loci with collinearity for both SNPP and SW, of which 4 overlapping loci harbored the haplotypes with the same direction of genetic effects on SNPP and SW, indicating high possibility to simultaneously improve SNPP and SW in rapeseed. Our findings revealed both overlapping and independent loci controlling seed number per pod and seed weight in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01232-1.
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Affiliation(s)
- Shuangshuang Xin
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Lei Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Dengwen Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Fajing Zheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Shuang Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Jinghang Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaorong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
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Zhou X, Guo J, Pandey MK, Varshney RK, Huang L, Luo H, Liu N, Chen W, Lei Y, Liao B, Jiang H. Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies. FRONTIERS IN PLANT SCIENCE 2021; 12:637284. [PMID: 34093605 PMCID: PMC8174301 DOI: 10.3389/fpls.2021.637284] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/24/2021] [Indexed: 06/09/2023]
Abstract
Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini-core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. We sequenced the Chinese peanut mini-core collection using genotyping-by-sequencing approach and identified 105,814 high-quality single-nucleotide polymorphisms (SNPs). The population structure analysis showed essentially subspecies patterns in groups and obvious geographical distribution patterns in subgroups. A total of 79 significantly associated loci (P < 4.73 × 10-7) were detected for the six yield-related traits through GWAS. Of these, 31 associations were consistently detected in multiple environments, and 15 loci were commonly detected to be associated with multiple traits. Two major loci located on chromosomal pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits, explaining ∼20% phenotypic variations across environments. The two genomic regions were found 46 putative candidate genes based on gene annotation and expression profile. The diagnostic marker for the yield-related traits from non-synonymous SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation between nucleotide polymorphism and phenotypic variation. This study provided insights into the genetic basis of yield-related traits in peanut and verified one diagnostic marker to facilitate marker-assisted selection for developing high-yield peanut varieties.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Wang H, Yan M, Xiong M, Wang P, Liu Y, Xin Q, Wan L, Yang G, Hong D. Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1321-1335. [PMID: 32002584 DOI: 10.1007/s00122-020-03553-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE: cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D. Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46-13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.
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Affiliation(s)
- Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Min Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mei Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Zhu Y, Ye J, Zhan J, Zheng X, Zhang J, Shi J, Wang X, Liu G, Wang H. Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2020; 11:68. [PMID: 32153604 PMCID: PMC7047150 DOI: 10.3389/fpls.2020.00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.
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Affiliation(s)
| | | | | | | | | | - Jiaqin Shi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministryof Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Di F, Wang T, Ding Y, Chen X, Wang H, Li J, Liu L. Genetic Mapping Combined with a Transcriptome Analysis to Screen for Candidate Genes Responsive to Abscisic Acid Treatment in Brassica napus Embryos During Seed Germination. DNA Cell Biol 2020; 39:533-547. [PMID: 32031882 DOI: 10.1089/dna.2019.5169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Brassica napus embryos contain precursor tissues for the leaves, stem, and root, as well as the cotyledons, and these precursor tissues play key roles in seed germination, seedling survival, and subsequent seedling growth. Abscisic acid (ABA) plays a prominent role in the inhibition of seed germination. The underlying molecular mechanisms of the embryo responses to ABA stress followed by inhibited seed germination have not been reported in B. napus to date. In this study, we conducted quantitative trait locus (QTL) analysis of B. napus seed in response to ABA stress using 170 recombinant inbred lines. Furthermore, we performed transcriptome sequencing (RNA-seq) analyses by using B. napus ZS11 embryos under sterile deionized water (control) and 10 mg/L (10A), 20 mg/L (20A), and 30 mg/L (30A) ABA treatment conditions. In total, 10 QTLs were screened for explaining 2.70-6.73% of the phenotypic variation under ABA stress. In addition, 1495, 3332, and 3868 differentially expressed genes (DEGs) were identified in the "control vs 10A," "control vs 20A," and "control vs 30A" comparisons, respectively. Gene Ontology (GO) enrichment analysis indicated that DEG functions are mainly related to response to stimuli, response to oxygen-containing compounds, response to lipids, and the transport and seed dormancy processes. These DEGs mainly participated in the response to plant hormone signal transduction, starch and sucrose metabolism, cutin, suberine, and wax biosynthesis, and phenylpropanoid biosynthesis processes pathways. Our results provide a foundation for further explorations of the molecular regulatory mechanisms of B. napus embryos in response to abiotic stress during the seed germination stage.
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Affiliation(s)
- Feifei Di
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Tengyue Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Yiran Ding
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Xueping Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shanxi Rapeseed Branch of National Center for Oil Crops Genetic Improvement, Yangling, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
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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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31
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Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie WZ, Cheng Y, Zhang Y, Liu K, Yang QY, Chen LL, Guo L. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. NATURE PLANTS 2020; 6:34-45. [PMID: 31932676 PMCID: PMC6965005 DOI: 10.1038/s41477-019-0577-7] [Citation(s) in RCA: 361] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/29/2019] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2-149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianlin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhiquan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuanfang Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
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Shen W, Qin P, Yan M, Li B, Wu Z, Wen J, Yi B, Ma C, Shen J, Fu T, Tu J. Fine mapping of a silique length- and seed weight-related gene in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2985-2996. [PMID: 31321475 DOI: 10.1007/s00122-019-03400-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Using microarray analysis combined with map-based cloning, a major locus positively regulating SL and SW was mapped to a 98.47 kb interval on A09 in rapeseed. In rapeseed, seed yield is closely associated with silique-related traits such as silique length (SL) and seed weight (SW). Previously identified quantitative trait loci (QTLs) revealed that SL and SW are complex traits and many QTLs overlap. However, the genetic characterization of the association between SL and SW is poorly understood. In the present study, a BC3F3 near isogenic line developed from a short silique plant and the long silique cultivar 'ZS11' was analyzed to identify the locus related to SL. Map-based cloning indicated that a major locus acting as a single Mendelian factor was mapped to a 98.47 kb region on chromosome A09. BLAST analysis and DNA sequencing showed SNP variations and a fragment replacement in the upstream region of the candidate gene BnaA09g55530D may alter gene expression and influence SL. The results showed that this SL locus may also positively affect SW as well as in the 186 rapeseed accessions identified by the associated markers. Therefore, selecting plants with appropriate SL and developing functional markers for the associated gene could play important roles in the molecular breeding of high-yield rapeseed varieties.
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Affiliation(s)
- Wenhao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjiao Yan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zengxiang Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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Shi L, Song J, Guo C, Wang B, Guan Z, Yang P, Chen X, Zhang Q, King GJ, Wang J, Liu K. A CACTA-like transposable element in the upstream region of BnaA9.CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:524-539. [PMID: 30664290 DOI: 10.1111/tpj.14236] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/13/2019] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is a model plant for polyploid crop research and the second-leading source of vegetable oil worldwide. Silique length (SL) and seed weight are two important yield-influencing traits in rapeseed. Using map-based cloning, we isolated qSLWA9, which encodes a P450 monooxygenase (BnaA9.CYP78A9) and functions as a positive regulator of SL. The expression level of BnaA9.CYP78A9 in silique valves of the long-silique variety is much higher than that in the regular-silique variety, which results in elongated cells and a prolonged phase of silique elongation. Plants of the long-silique variety and transgenic plants with high expression of BnaA9.CYP78A9 had a higher concentration of auxin in the developing silique; this induced a number of auxin-related genes but no genes in well-known auxin biosynthesis pathways, suggesting that BnaA9.CYP78A9 may influence auxin concentration by affecting auxin metabolism or an unknown auxin biosynthesis pathway. A 3.7-kb CACTA-like transposable element (TE) inserted in the 3.9-kb upstream regulatory sequence of BnaA9.CYP78A9 elevates the expression level, suggesting that the CACTA-like TE acts as an enhancer to stimulate high gene expression and silique elongation. Marker and sequence analysis revealed that the TE in B. napus had recently been introgressed from Brassica rapa by interspecific hybridization. The insertion of the TE is consistently associated with long siliques and large seeds in both B. napus and B. rapa collections. However, the frequency of the CACTA-like TE in rapeseed varieties is still very low, suggesting that this allele has not been widely used in rapeseed breeding programs and would be invaluable for yield improvement in rapeseed breeding.
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Affiliation(s)
- Liuliu Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jurong Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Li N, Song D, Peng W, Zhan J, Shi J, Wang X, Liu G, Wang H. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:736-749. [PMID: 30191657 PMCID: PMC6419582 DOI: 10.1111/pbi.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
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Affiliation(s)
- Na Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural SciencesThe Laboratory of Melon CropsZhengzhouHenan ProvinceChina
| | - Dongji Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Wei Peng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
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Jian H, Zhang A, Ma J, Wang T, Yang B, Shuang LS, Liu M, Li J, Xu X, Paterson AH, Liu L. Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L. BMC Genomics 2019; 20:21. [PMID: 30626329 PMCID: PMC6325782 DOI: 10.1186/s12864-018-5356-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/09/2018] [Indexed: 01/10/2023] Open
Abstract
Background Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. Results We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. Conclusions We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.,Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Min Liu
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.
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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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Yang S, Zhang B, Liu G, Hong B, Xu J, Chen X, Wang B, Wu Z, Hou F, Yue X, Wang J, Zhang Q, King GJ, Liu K. A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2117-2129. [PMID: 29998372 DOI: 10.1007/s00122-018-3140-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits. Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar 'Zhongyou 821' (ZY821) as the recipient and a re-synthesized line 'No.2127' as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC5F4 were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56 × of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.
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Affiliation(s)
- Shanjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baohua Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsong Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fan Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaopeng Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.). J Appl Genet 2018; 59:377-389. [PMID: 30014258 DOI: 10.1007/s13353-018-0455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/02/2018] [Accepted: 06/27/2018] [Indexed: 01/29/2023]
Abstract
Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creation of a stop codon in the motor domain of SRS3, a kinesin 13 family gene, translating into a truncated protein product. However, transcription of this gene remained unaffected in TEMS5032 compared to the wild type, N22. Further, the mutation was found to affect 13 of the 25 cell cycle-related genes as they showed differential expression with respect to N22. Based on rate of grain filling, dry matter accumulation in the endosperm and histological studies, the effect of mutation in TEMS5032 was found to be similar to a known variant, TCM758, but less severe than sar1 mutant. Sequencing of 88 rice germplasm lines in the kinesin motor domain region did not reveal the presence of this mutation, establishing it as a new variant of SRS3 gene.
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Luo X, Cao D, Zhang J, Chen L, Xia X, Li H, Zhao D, Zhang F, Xue H, Chen L, Li Y, Cao S. Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness. Sci Rep 2018; 8:9292. [PMID: 29915181 PMCID: PMC6006261 DOI: 10.1038/s41598-018-27664-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA-mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA-mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA-mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.
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Affiliation(s)
- Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P.R. China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaocong Xia
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Haoxian Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Diguang Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Fuhong Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Hui Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Lina Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Yongzhou Li
- College of Horticultural Science, Henan Agricultural University, Zhengzhou, 450002, P.R. China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China.
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Chen L, Chen L, Zhang X, Liu T, Niu S, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Identification of miRNAs that regulate silique development in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:106-117. [PMID: 29606207 DOI: 10.1016/j.plantsci.2018.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/05/2018] [Accepted: 01/22/2018] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate these roles. Four small RNA libraries from siliques in an early stage of development were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known and 394 novel miRNAs. Expression analyses revealed that 17 miRNAs were differentially expressed in LS and SS lines. Furthermore, through degradome sequencing, we identified 522 cleavage events. Correlation analysis of the differentially expressed miRNAs and their targets suggested that miR159 and miR319 represses cell proliferation and miR160 regulates auxin signal transduction to control silique length. Additionally, the upregulation of miR2111, miR399, miR827, and miR408 reflected restricted silique development due to inorganic phosphate/copper deficiency. More significantly, high expression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length might be regulated via an auxin-response pathway.
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Affiliation(s)
- Li Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lei Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Xiangxiang Zhang
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingting Liu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Sailun Niu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
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Raboanatahiry N, Chao H, Dalin H, Pu S, Yan W, Yu L, Wang B, Li M. QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:1127. [PMID: 30116254 PMCID: PMC6083399 DOI: 10.3389/fpls.2018.01127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/12/2018] [Indexed: 05/17/2023]
Abstract
Worldwide consumption of oil is increasing with the growing population in need for edible oil and the expansion of industry using biofuels. Then, demand for high yielding varieties of oil crops is always increasing. Brassica napus (rapeseed) is one of the most important oil crop in the world, therefore, increasing rapeseed yield through breeding is inevitable in order to cater for the high demand of vegetable oil and high-quality protein for live stocks. Quantitative trait loci (QTL) analysis is a powerful tool to identify important loci and which is also valuable for molecular marker assisted breeding. Seed-yield (SY) is a complex trait that is controlled by multiple loci and is affected directly by seed weight, seeds per silique and silique number. Some yield-related traits, such as plant height, biomass yield, flowering time, and so on, also affect the SY indirectly. This study reports the assembly of QTLs identified for seed-yield and yield-related traits in rapeseed, in one unique map. A total of 972 QTLs for seed-yield and yield-related were aligned into the physical map of B. napus Darmor-bzh and 92 regions where 198 QTLs overlapped, could be discovered on 16 chromosomes. Also, 147 potential candidate genes were discovered in 65 regions where 131 QTLs overlapped, and might affect nine different traits. At the end, interaction network of candidate genes was studied, and showed nine genes that could highly interact with the other genes, and might have more influence on them. The present results would be helpful to develop molecular markers for yield associated traits and could be used for breeding improvement in B. napus.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- 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
| | - Hongbo Chao
- 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
| | - Hou Dalin
- 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
| | - Shi Pu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, 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
- *Correspondence: Maoteng Li,
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Dong H, Tan C, Li Y, He Y, Wei S, Cui Y, Chen Y, Wei D, Fu Y, He Y, Wan H, Liu Z, Xiong Q, Lu K, Li J, Qian W. Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:921. [PMID: 30073005 PMCID: PMC6058094 DOI: 10.3389/fpls.2018.00921] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/11/2018] [Indexed: 05/13/2023]
Abstract
Seed weight (SW) is one of three determinants of seed yield, which positively correlates with silique length (SL) in Brassica napus (rapeseed). However, the genetic mechanism underlying the relationship between seed weight (SW) and silique length (SL) is largely unknown at present. A natural population comprising 157 inbred lines in rapeseed was genotyped by whole-genome re-sequencing and investigated for SW and SL over four years. The genome-wide association study identified 20 SNPs in significant association with SW on A01, A04, A09, C02, and C06 chromosomes and the phenotypic variation explained by a single locus ranged from 11.85% to 34.58% with an average of 25.43%. Meanwhile, 742 SNPs significantly associated with SL on A02, A03, A04, A07, A08, A09, C01, C03, C04, C06, C07, and C08 chromosomes were also detected and the phenotypic variation explained by a single locus ranged from 4.01 to 48.02% with an average of 33.33%, out of which, more than half of the loci had not been reported in the previous studies. There were 320 overlapping or linked SNPs for both SW and SL on A04, A09, and C06 chromosomes. It indicated that both overlapping and independent genetic loci controlled both SW and SL in B. napus. On the haplotype block on A09 chromosome, the allele variants of a known gene BnaA.ARF18.a controlling both SW and SL were identified in the natural population by developing derived cleaved amplified polymorphic sequence (dCAPS) markers. These findings are valuable for understanding the genetic mechanism of SW and SL and also for rapeseed molecular breeding programs.
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Affiliation(s)
- Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chuandong Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yuzhen Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yan He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Shuai Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yangui Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- *Correspondence: Wei Qian
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He Y, Wu D, Wei D, Fu Y, Cui Y, Dong H, Tan C, Qian W. GWAS, QTL mapping and gene expression analyses in Brassica napus reveal genetic control of branching morphogenesis. Sci Rep 2017; 7:15971. [PMID: 29162897 PMCID: PMC5698412 DOI: 10.1038/s41598-017-15976-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/03/2017] [Indexed: 01/04/2023] Open
Abstract
Branch number is an important trait in plant architecture that can influence crop yield and quality in Brassica napus. Here, we detected the QTLs responsible for branch number in a DH population and its reconstructed F2 population over two years. Further, a GWAS research on branch number was performed using a panel of 327 accessions with 33186 genomic SNPs from the 60 K Brassica Illumina® Infinium SNP array. Through combining linkage analysis and association mapping, a new QTL was fine mapped onto C03. Subsequently, we tested the correlations between the SNP polymorphisms and mRNA expression levels of genes in the target interval to identify potential loci or genes that control branch number through expression. The results show that 4 SNP loci are associated with the corresponding gene expression levels, and one locus (BnaC03g63480D) exhibited a significant correlation between the phenotype variation and gene expression levels. Our results provide insights into the genetic basis for branching morphogenesis and may be valuable for optimizing architecture in rapeseed breeding.
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Affiliation(s)
- Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Daoming Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Ying Fu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chuandong Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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Huang KL, Zhang ML, Ma GJ, Wu H, Wu XM, Ren F, Li XB. Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus. PLoS One 2017; 12:e0179027. [PMID: 28594951 PMCID: PMC5464616 DOI: 10.1371/journal.pone.0179027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Seed oil content is an important agronomic trait in oilseed rape. However, the molecular mechanism of oil accumulation in rapeseeds is unclear so far. In this report, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in siliques of two Brassica napus lines (HFA and LFA which contain high and low oil contents in seeds, respectively) at 15 and 25 days after pollination (DAP). The RNA-Seq results showed that 65746 and 66033 genes were detected in siliques of low oil content line at 15 and 25 DAP, and 65236 and 65211 genes were detected in siliques of high oil content line at 15 and 25 DAP, respectively. By comparative analysis, the differentially expressed genes (DEGs) were identified in siliques of these lines. The DEGs were involved in multiple pathways, including metabolic pathways, biosynthesis of secondary metabolic, photosynthesis, pyruvate metabolism, fatty metabolism, glycophospholipid metabolism, and DNA binding. Also, DEGs were related to photosynthesis, starch and sugar metabolism, pyruvate metabolism, and lipid metabolism at different developmental stage, resulting in the differential oil accumulation in seeds. Furthermore, RNA-Seq and qRT-PCR data revealed that some transcription factors positively regulate seed oil content. Thus, our data provide the valuable information for further exploring the molecular mechanism of lipid biosynthesis and oil accumulation in B. nupus.
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Affiliation(s)
- Ke-Lin Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guang-Jing Ma
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Huan Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiao-Ming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
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Dhaka N, Rout K, Yadava SK, Sodhi YS, Gupta V, Pental D, Pradhan AK. Genetic dissection of seed weight by QTL analysis and detection of allelic variation in Indian and east European gene pool lines of Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:293-307. [PMID: 27744489 DOI: 10.1007/s00122-016-2811-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/08/2016] [Indexed: 05/26/2023]
Abstract
Seed weight QTL identified in different populations were synthesized into consensus QTL which were shown to harbor candidate genes by in silico mapping. Allelic variation inferred would be useful in breeding B. juncea lines with high seed weight. Seed weight is an important yield influencing trait in oilseed Brassicas and is a multigenic trait. Among the oilseed Brassicas, Brassica juncea harbors the maximum phenotypic variation wherein thousand seed weight varies from around 2.0 g to more than 7.0 g. In this study, we have undertaken quantitative trait locus/quantitative trait loci (QTL) analysis of seed weight in B. juncea using four bi-parental doubled-haploid populations. These four populations were derived from six lines (three Indian and three east European lines) with parental phenotypic values for thousand seed weight ranging from 2.0 to 7.6 g in different environments. Multi-environment QTL analysis of the four populations identified a total of 65 QTL ranging from 10 to 25 in each population. Meta-analysis of these component QTL of the four populations identified six 'consensus' QTL (C-QTL) in A3, A7, A10 and B3 by merging 33 of the 65 component Tsw QTL from different bi-parental populations. Allelic diversity analysis of these six C-QTL showed that Indian lines, Pusajaikisan and Varuna, hold the most positive allele in all the six C-QTL. In silico mapping of candidate genes with the consensus QTL localized 11 genes known to influence seed weight in Arabidopsis thaliana and also showed conserved crucifer blocks harboring seed weight QTL between the A subgenomes of B. juncea and B. rapa. These findings pave the way for a better understanding of the genetics of seed weight in the oilseed crop B. juncea and reveal the scope available for improvement of seed weight through marker-assisted breeding.
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Affiliation(s)
- Namrata Dhaka
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kadambini Rout
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Satish K Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Yaspal Singh Sodhi
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Akshay K Pradhan
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Yang Y, Shen Y, Li S, Ge X, Li Z. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population. FRONTIERS IN PLANT SCIENCE 2017; 8:1512. [PMID: 28932230 PMCID: PMC5592274 DOI: 10.3389/fpls.2017.01512] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.
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48
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Chen Y, Ren X, Zheng Y, Zhou X, Huang L, Yan L, Jiao Y, Chen W, Huang S, Wan L, Lei Y, Liao B, Huai D, Wei W, Jiang H. Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut ( Arachis hypogaea L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:17. [PMID: 28216998 PMCID: PMC5285419 DOI: 10.1007/s11032-016-0587-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 11/01/2016] [Indexed: 05/04/2023]
Abstract
The genetic architecture determinants of yield traits in peanut (Arachis hypogaea L.) are poorly understood. In the present study, an effort was made to map quantitative trait loci (QTLs) for yield traits using recombinant inbred lines (RIL). A genetic linkage map was constructed containing 609 loci, covering a total of 1557.48 cM with an average distance of 2.56 cM between adjacent markers. The present map exhibited good collinearity with the physical map of diploid species of Arachis. Ninety-two repeatable QTLs were identified for 11 traits including height of main stem, total branching number, and nine pod- and seed-related traits. Of the 92 QTLs, 15 QTLs were expressed across three environments and 65 QTLs were newly identified. Twelve QTLs for the height of main stem and the pod- and seed-related traits explaining more than 10 % of phenotypic variation showed a great potential for marker-assisted selection in improving these traits. The trait-by-trait meta-analysis revealed 33 consensus QTLs. The consensus QTLs and other QTLs were further integrated into 29 pleiotropic unique QTLs with the confidence interval of 1.86 cM on average. The significant co-localization of QTLs was consistent with the significant phenotypic correlations among these traits. The complexity of the genetic architecture of yield traits was demonstrated. The present QTLs for pod- and seed-related traits could be the most fundamental genetic factors contributing to the yield traits in peanut. The results provide a good foundation for fine mapping, cloning and designing molecular breeding of favorable genes in peanut.
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Affiliation(s)
- Yuning Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaoping Ren
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yanli Zheng
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Xiaojing Zhou
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Li Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liying Yan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yongqing Jiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Weigang Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Shunmou Huang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Liyun Wan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Yong Lei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Boshou Liao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Dongxin Huai
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Wenhui Wei
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
| | - Huifang Jiang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural, Wuhan, 430062 People’s Republic of China
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Lu K, Peng L, Zhang C, Lu J, Yang B, Xiao Z, Liang Y, Xu X, Qu C, Zhang K, Liu L, Zhu Q, Fu M, Yuan X, Li J. Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:206. [PMID: 28261256 PMCID: PMC5309214 DOI: 10.3389/fpls.2017.00206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/03/2017] [Indexed: 05/19/2023]
Abstract
Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Liu Peng
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- School of Management, Xihua UniversityChengdu, China
| | - Chao Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural SciencesGuiyang, China
| | - Junhua Lu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Bo Yang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Zhongchun Xiao
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Xingfu Xu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Qinlong Zhu
- College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Minglian Fu
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Xiaoyan Yuan
- Industrial Crops Institute, Yunnan Academy of Agricultural SciencesKunming, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Jiana Li
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He H, Yang R, Li Y, Ma A, Cao L, Wu X, Chen B, Tian H, Gao Y. Genotypic Variation in Nitrogen Utilization Efficiency of Oilseed Rape ( Brassica napus) Under Contrasting N Supply in Pot and Field Experiments. FRONTIERS IN PLANT SCIENCE 2017; 8:1825. [PMID: 29163565 PMCID: PMC5664426 DOI: 10.3389/fpls.2017.01825] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Oilseed rape (Brassica napus) characteristically has high N uptake efficiency and low N utilization efficiency (NUtE, seed yield/shoot N accumulation). Determining the NUtE phenotype of various genotypes in different growth conditions is a way of finding target traits to improve oilseed rape NUtE. The aim of this study was to compare oilseed rape genotypes grown on contrasting N supply rates in pot and field experiments to investigate the genotypic variations of NUtE and to identify indicators of N efficient genotypes. For 50 oilseed rape genotypes, NUtE, dry matter and N partitioning, morphological characteristics, and the yield components were investigated under high and low N supplies in a greenhouse pot experiment and a field trial. Although the genotype rankings of NUtE were different between the pot experiment and the field trial, some genotypes performed consistently in both two environments. N-responder, N-nonresponder, N-efficient and N-inefficient genotypes were identified from these genotypes with consistent NUtE. The correlations between the pot experiment and the field trial in NUtE were only 0.34 at high N supplies and no significant correlations were found at low N supplies. However, Pearson coefficient correlation (r) and principal component analysis showed NUtE had similar genetic correlations with other traits across the pot and field experiment. Among the yield components, only seeds per silique showed strong and positive correlations with NUtE under varying N supply in both experiments (r = 0.47**; 0.49**; 0.47**; 0.54**). At high and low N supply, NUtE was positively correlated with seed yield (r = 0.45**; 0.53**; 0.39**; 0.87**), nitrogen harvest index (NHI, r = 0.68**; 0.82**; 0.99**; 0.89**), and harvest index (HI, r = 0.79**; 0.83**; 0.90**; 0.78**) and negatively correlated with biomass distribution to stem and leaf (r = -0.34**; -0.45**; -0.37**; 0.62**), all aboveground plant section N concentration (r from -0.30* to -0.80**), N distribution to the vegetative parts (silique husk, stem and leaf) (r from -0.40** to -0.83**). N-efficient (N-responder) genotypes produced more seeds per silique and had significantly higher NHI and HI than did N-inefficient (N-nonresponder) genotypes. In conclusion, across the pot and field experiments, the 50 genotypes had similar underlying traits correlated with NUtE and seeds per silique may be a good indicator of NUtE.
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Affiliation(s)
- Huiying He
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Rui Yang
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Yajun Li
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Aisheng Ma
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Lanqin Cao
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Xiaoming Wu
- Institute of Oil Crop Research, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Institute of Oil Crop Research, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hui Tian
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
| | - Yajun Gao
- College of Natural Resource and Environment, Northwest A and F University, Xianyang Shi, China
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, China
- *Correspondence: Yajun Gao
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