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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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Limbalkar OM, Vasisth P, Singh G, Jain P, Sharma M, Singh R, Dhanasekaran G, Kumar M, Meena ML, Iquebal MA, Jaiswal S, Rao M, Watts A, Bhattacharya R, Singh KH, Kumar D, Singh N. Dissection of QTLs conferring drought tolerance in B. carinata derived B. juncea introgression lines. BMC PLANT BIOLOGY 2023; 23:664. [PMID: 38129793 PMCID: PMC10740311 DOI: 10.1186/s12870-023-04614-z] [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: 09/24/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Drought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% of Brassica juncea (Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87 B. carinata-derived B. juncea introgression lines (ILs) was developed with the goal of creating drought-tolerant genotypes. METHOD The experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map. RESULTS The linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed by B. carinata (BC 4), suggesting a greater contribution of B. carinata towards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome of B. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz., SOS2, SOS2 like, NPR1, FAE1-KCS, HOT5, DNAJA1, NIA1, BRI1, RF21, ycf2, WRKY33, PAL, SAMS2, orf147, MAPK3, WRR1 and SUS, were reported in the genomic regions of identified QTLs. CONCLUSIONS The significance of B. carinata in improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
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Affiliation(s)
- Omkar Maharudra Limbalkar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Present Address: ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Prashant Vasisth
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Guman Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Sewar, Bharatpur, Rajasthan, India
| | - Priyanka Jain
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- Present Address: AIMMSCR, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, 201313, India
| | - Mohit Sharma
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajendra Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gokulan Dhanasekaran
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Manish Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Present Address: College of Agriculture, Navgaon, Alwar, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Mohan Lal Meena
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh Rao
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Kunwar Harendra Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Sewar, Bharatpur, Rajasthan, India
- Present Address: ICAR, Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Naveen Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
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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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4
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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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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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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Zhu J, Lei L, Wang W, Jiang J, Zhou X. QTL mapping for seed density per silique in Brassica napus. Sci Rep 2023; 13:772. [PMID: 36641540 PMCID: PMC9840639 DOI: 10.1038/s41598-023-28066-5] [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: 10/15/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Seed density per silique (SDPS) and valid silique length (VSL) are two important yield-influencing traits in rapeseed. SDPS has a direct or indirect effect on rapeseed yield through its effect on seed per silique. In this study, a quantitative trait locus (QTL) for SDPS was detected on chromosome A09 using the QTL-seq approach and confirmed via linkage analysis in the mapping population obtained from 4263 × 3001 cross. Furthermore, one major QTL for SDPS (qSD.A9-1) was mapped to a 401.8 kb genomic interval between SSR markers Nys9A190 and Nys9A531. In the same genomic region, a QTL (qSL.A9) linked to VSL was also detected. The phenotypic variation of qSD.A9-1 and qSL.A9 was 53.1% and 47.6%, respectively. Results of the additive and dominant effects demonstrated that the expression of genes controlling SDPS and VSL were derived from a different parent in this population. Subsequently, we identified 56 genes that included 45 specific genes with exonic (splicing) variants. Further analysis identified specific genes containing mutations that may be related to seed density as well as silique length. These genes could be used for further studies to understand the details of these traits of rapeseed.
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Affiliation(s)
- Jifeng Zhu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Lei Lei
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Weirong Wang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jianxia Jiang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xirong Zhou
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
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8
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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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9
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Liu J, Wu Y, Cui X, Zhang X, Xie M, Liu L, Liu Y, Huang J, Cheng X, Liu S. Genome-wide characterization of ovate family protein gene family associated with number of seeds per silique in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:962592. [PMID: 36186010 PMCID: PMC9515500 DOI: 10.3389/fpls.2022.962592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Ovate family proteins (OFPs) were firstly identified in tomato as proteins controlling the pear shape of the fruit. Subsequent studies have successively proved that OFPs are a class of negative regulators of plant development, and are involved in the regulation of complex traits in different plants. However, there has been no report about the functions of OFPs in rapeseed growth to date. Here, we identified the OFPs in rapeseed at the genomic level. As a result, a total of 67 members were obtained. We then analyzed the evolution from Arabidopsis thaliana to Brassica napus, illustrated their phylogenetic and syntenic relationships, and compared the gene structure and conserved domains between different copies. We also analyzed their expression patterns in rapeseed, and found significant differences in the expression of different members and in different tissues. Additionally, we performed a GWAS for the number of seeds per silique (NSPS) in a rapeseed population consisting of 204 natural accessions, and identified a new gene BnOFP13_2 significantly associated with NSPS, which was identified as a novel function of OFPs. Haplotype analysis revealed that the accessions with haplotype 3 had a higher NSPS than other accessions, suggesting that BnOFP13_2 is associated with NSPS. Transcript profiling during the five stages of silique development demonstrated that BnOFP13_2 negatively regulates NSPS. These findings provide evidence for functional diversity of OFP gene family and important implications for oilseed rape breeding.
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10
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Qadir M, Qin L, Ye J, Ahmad N, Wang X, Shi J, Wang H. Genetic dissection of the natural variation of ovule number per ovary in oilseed rape germplasm ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:999790. [PMID: 36176675 PMCID: PMC9513589 DOI: 10.3389/fpls.2022.999790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Oilseed rape is one of the world's largest oil and industrial crops, providing humans with various products, such as vegetable oil and biofuel. Ovules are the direct precursors of seeds, and ovule number per ovary (ONPO) largely determines seed number per fruit that affects both yield and fitness of seed crops. The ONPO shows wide variation in oilseed rape, whereas the underlying genes and mechanisms are poorly known. The present study performed the genetic, physiological and transcriptomic analyses of ovule number per ovary using an association panel and the extreme lines. The ONPO of 327 accessions planted in four environments showed a large variation from 19.2 to 43.8, indicating a great potential for the further genetic improvement of ovule number. The genome-wide association study (GWAS) identified a total of 43 significant SNP markers. Further, these SNPs were integrated into 18 association loci, which were distributed on chromosomes A01, A03, A06, A07, A09, C01, C03, C06, C07, and C09, explaining 4.3-11.5% of the phenotypic variance. The ONPO decreased as their appearance order on the inflorescence and was associated with the level of several types of endogenous phytohormones but not related to leaf area and photosynthetic rate. Comparative transcriptomic analysis identified a total of 4,449 DEGs enriched in 30 classes, including DNA, RNA, protein, signaling, transport, development, cell wall, lipid metabolism, and secondary metabolism. Nearly half of DEGs were involved in the known pathways in regulating ovule number, of which 12 were homologous to know ovule number regulating genes, indicating a strong link between the identified DEGs and ovule number. A total of 73 DEGs were located within the genomic regions of association loci, of which six were identified as candidates based on functional annotation. These results provide useful information for the further genetic improvement of ovule and seed number in oilseed rape.
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Affiliation(s)
- Muslim Qadir
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Lei Qin
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jiang Ye
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Nazir Ahmad
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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11
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Hahn C, Howard NP, Albach DC. Different Shades of Kale-Approaches to Analyze Kale Variety Interrelations. Genes (Basel) 2022; 13:genes13020232. [PMID: 35205277 PMCID: PMC8872201 DOI: 10.3390/genes13020232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.
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Affiliation(s)
- Christoph Hahn
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany; (N.P.H.); (D.C.A.)
- Correspondence: ; Tel.: +49-441-798-3343
| | - Nicholas P. Howard
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany; (N.P.H.); (D.C.A.)
- Fresh Forward Breeding & Marketing, 4024 BK Eck en Wiel, The Netherlands
| | - Dirk C. Albach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany; (N.P.H.); (D.C.A.)
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12
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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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13
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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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14
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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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15
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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: 14] [Impact Index Per Article: 4.7] [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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16
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Aakanksha, Yadava SK, Yadav BG, Gupta V, Mukhopadhyay A, Pental D, Pradhan AK. Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies. FRONTIERS IN PLANT SCIENCE 2021; 12:721631. [PMID: 34603351 PMCID: PMC8481694 DOI: 10.3389/fpls.2021.721631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/16/2021] [Indexed: 01/07/2024]
Abstract
The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.
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Affiliation(s)
- Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Bal Govind Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Akshay K. Pradhan
- Department of Genetics, University of Delhi South Campus, New Delhi, India
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
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17
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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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18
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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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19
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Wu D, Liang Z, Yan T, Xu Y, Xuan L, Tang J, Zhou G, Lohwasser U, Hua S, Wang H, Chen X, Wang Q, Zhu L, Maodzeka A, Hussain N, Li Z, Li X, Shamsi IH, Jilani G, Wu L, Zheng H, Zhang G, Chalhoub B, Shen L, Yu H, Jiang L. Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence. MOLECULAR PLANT 2019; 12:30-43. [PMID: 30472326 DOI: 10.1016/j.molp.2018.11.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million single-nucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh" and "Tapidor," respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.
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Affiliation(s)
- Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhe Liang
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lijie Xuan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ulrike Lohwasser
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany
| | - Shuijin Hua
- Institute of Crop and Nuclear Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haoyi Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyang Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Qian Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Le Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Antony Maodzeka
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Nazim Hussain
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhilan Li
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | | | - Ghulam Jilani
- Office of Research, Innovation & Commercialization, PMAS-Arid Agricultural University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Linde Wu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Boulos Chalhoub
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China.
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20
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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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21
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Mapping QTL controlling agronomic traits in a doubled haploid population of winter oilseed rape (Brassica napus L.). J Genet 2018. [DOI: 10.1007/s12041-018-1044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Li B, Zhao W, Li D, Chao H, Zhao X, Ta N, Li Y, Guan Z, Guo L, Zhang L, Li S, Wang H, Li M. Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:296-310. [PMID: 30466595 DOI: 10.1016/j.plantsci.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 05/02/2023]
Abstract
Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.
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Affiliation(s)
- Baojun Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiguo Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Na Ta
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Zhoubo Guan
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Lina Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
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23
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Fattahi F, Fakheri BA, Solouki M, Möllers C, Rezaizad A. Mapping QTL controlling agronomic traits in a doubled haploid population of winter oilseed rape ( Brassica napus L.). J Genet 2018; 97:1389-1406. [PMID: 30555087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Identification of superior alleles for agronomic traits in genetic resources of oilseed rape (Brassica napus L.) would be useful for improving the performance of locally adapted cultivars in Iran. The objective of the present work was to analyse the genetic variation and inheritance of important agronomic traits in a doubled haploid population derived from a cross between two German oilseed rape cultivars, Sansibar and Oase. Field experiments were performed in 2016-2017 with 200 doubled haploid lines and the parental genotypes applying an alpha-lattice design with two replicates. Phenological traits were recorded during the cultivation period and at maturity, seed yield, yield components and seed quality traits were determined. Significant genetic variation was found in most of the traits and heritabilities ranged from medium (48.5%) for days to end of flowering to high (92.6%) for oil content. A molecular marker linkage map was used to map 36 QTL for different traits on 17 linkage groups. Between three and four QTL were identified for each seed yield, seed weight, oil and protein content. Some of the plant material and positive QTL alleles identified for agronomic traits may be useful for improving those characters in locally adapted cultivars in Iran.
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Affiliation(s)
- Farshad Fattahi
- Department of Biotechnology and Plant Breeding, University of Zabol, Zabol 538-98615, Iran.
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24
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Detecting de Novo Homoeologous Recombination Events in Cultivated Brassica napus Using a Genome-Wide SNP Array. G3-GENES GENOMES GENETICS 2018; 8:2673-2683. [PMID: 29907649 PMCID: PMC6071606 DOI: 10.1534/g3.118.200118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The heavy selection pressure due to intensive breeding of Brassica napus has created a narrow gene pool, limiting the ability to produce improved varieties through crosses between B. napus cultivars. One mechanism that has contributed to the adaptation of important agronomic traits in the allotetraploid B. napus has been chromosomal rearrangements resulting from homoeologous recombination between the constituent A and C diploid genomes. Determining the rate and distribution of such events in natural B. napus will assist efforts to understand and potentially manipulate this phenomenon. The Brassica high-density 60K SNP array, which provides genome-wide coverage for assessment of recombination events, was used to assay 254 individuals derived from 11 diverse cultivated spring type B. napus. These analyses identified reciprocal allele gain and loss between the A and C genomes and allowed visualization of de novo homoeologous recombination events across the B. napus genome. The events ranged from loss/gain of 0.09 Mb to entire chromosomes, with almost 5% aneuploidy observed across all gametes. There was a bias toward sub-telomeric exchanges leading to genome homogenization at chromosome termini. The A genome replaced the C genome in 66% of events, and also featured more dominantly in gain of whole chromosomes. These analyses indicate de novo homoeologous recombination is a continuous source of variation in established Brassica napus and the rate of observed events appears to vary with genetic background. The Brassica 60K SNP array will be a useful tool in further study and manipulation of this phenomenon.
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