1
|
Chen J, Hu Y, Zhao T, Huang C, Chen J, He L, Dai F, Chen S, Wang L, Jin S, Zhang T. Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops. BMC Biol 2024; 22:110. [PMID: 38735918 PMCID: PMC11089805 DOI: 10.1186/s12915-024-01909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/02/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Plants differ more than threefold in seed oil contents (SOCs). Soybean (Glycine max), cotton (Gossypium hirsutum), rapeseed (Brassica napus), and sesame (Sesamum indicum) are four important oil crops with markedly different SOCs and fatty acid compositions. RESULTS Compared to grain crops like maize and rice, expanded acyl-lipid metabolism genes and relatively higher expression levels of genes involved in seed oil synthesis (SOS) in the oil crops contributed to the oil accumulation in seeds. Here, we conducted comparative transcriptomics on oil crops with two different SOC materials. In common, DIHYDROLIPOAMIDE DEHYDROGENASE, STEAROYL-ACYL CARRIER PROTEIN DESATURASE, PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE, and oil-body protein genes were both differentially expressed between the high- and low-oil materials of each crop. By comparing functional components of SOS networks, we found that the strong correlations between genes in "glycolysis/gluconeogenesis" and "fatty acid synthesis" were conserved in both grain and oil crops, with PYRUVATE KINASE being the common factor affecting starch and lipid accumulation. Network alignment also found a conserved clique among oil crops affecting seed oil accumulation, which has been validated in Arabidopsis. Differently, secondary and protein metabolism affected oil synthesis to different degrees in different crops, and high SOC was due to less competition of the same precursors. The comparison of Arabidopsis mutants and wild type showed that CINNAMYL ALCOHOL DEHYDROGENASE 9, the conserved regulator we identified, was a factor resulting in different relative contents of lignins to oil in seeds. The interconnection of lipids and proteins was common but in different ways among crops, which partly led to differential oil production. CONCLUSIONS This study goes beyond the observations made in studies of individual species to provide new insights into which genes and networks may be fundamental to seed oil accumulation from a multispecies perspective.
Collapse
Affiliation(s)
- Jinwen Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Yan Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Ting Zhao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Chujun Huang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Jiani Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Lu He
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Fan Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Shuqi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Shangkun Jin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Tianzhen Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China.
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China.
| |
Collapse
|
2
|
Pal L, Sandhu SK, Kaur J, Bhatia D. Deciphering variations, identification of marker-trait associations and candidate genes for seed oil content under terminal heat stress in Indian mustard ( Brassica juncea L. Czern & Coss) germplasm stock. 3 Biotech 2024; 14:140. [PMID: 38689736 PMCID: PMC11056352 DOI: 10.1007/s13205-024-03985-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
This research paper investigates the variability in seed oil content (SOC) in Indian mustard (Brassica juncea L.) under terminal heat stress (THS) conditions. A genetic stock of 488 genotypes of B. juncea was evaluated over two years and grouped into five classes based on the reduction in oil content under THS compared to normal sown crop. Based on heat susceptibility index (HSI), a diverse panel of 96 genotypes was selected and evaluated under THS. Twenty-two heat-tolerant donor genotypes were identified, including introgression lines derived from B. tournefortii, B. carinata and Erucastrum cardaminoides. This study is the first to report on marker-trait associations for SOC in B. juncea under THS using a GWAS approach. Furthermore, candidate genes associated with abiotic stress tolerance and lipid metabolism were identified near the significant SNPs, emphasizing their role in SOC regulation under stress. Notable candidate genes include BjuA003240 (encoding for alcohol-forming fatty acyl-CoA reductase), BjuA003242 (involving in lipid biosynthesis), BjuA003244 (associated with mitochondrial functions and stress tolerance), and BjuA003245 (related to MYB transcription factors regulating lipid biosynthesis). This study provides valuable insights into the genetic basis of SOC variation under THS in B. juncea, highlighting potential breeding targets for improved heat stress resilience in Indian mustard cultivation. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03985-w.
Collapse
Affiliation(s)
- Lalit Pal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004 Punjab India
| | - Surinder K. Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004 Punjab India
| | - Jasneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004 Punjab India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004 Punjab India
| |
Collapse
|
3
|
Smith BE, Lu C. Heat stress during reproductive stages reduces camelina seed productivity and changes seed composition. Heliyon 2024; 10:e26678. [PMID: 38434085 PMCID: PMC10907518 DOI: 10.1016/j.heliyon.2024.e26678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/23/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024] Open
Abstract
Camelina (Camelina sativa L. Crantz) is a low-input oilseed crop with great potential in bioenergy and industrial oils. Improving tolerance to high temperatures is essential for camelina agronomic sustainability. Two genotypes, Suneson and Pryzeth, were exposed to a transient 14-day heat stress at 37 °C during the reproductive stages. Four cohorts of pods along the main stem, which were at different stages from fully developed pods (C1), young pods (C2), open flowers (C3) and flowering buds (C4) at the time of heat treatment, were examined for morphological and seed quality traits at maturity. The main stem length was shortened in both genotypes. Pods and seeds in all cohorts were negatively affected by heat, resulting in lower seed yield and reduced oil content. Seed size and seed weight had the greatest reduction in C1, pod size reduction was found the most in C3, and the number of fertile pods that contain at least one seed was reduced in C3 and C4. These results suggest that heat stress effects are developmental stage specific. Heat stress significantly reduced fertility during flowering and inhibited storage product biosynthesis and accumulation during seed filling which resulted in smaller and lighter seeds. Analyzing seed composition indicated that oil content decreased while protein content increased in seeds from heat treated plants. In addition, fatty acid composition was altered with the reduction of omega-3 α-linolenic acid and concomitantly increased omega-6 linoleic acid being the most significantly affected. Our results also revealed the different responses in the two genotypes examined, suggesting genetic variation in camelina germplasm which can be explored to improve heat tolerance. This study provides resources and guidance for future studies to understand genetic and physiological mechanisms of heat stress and to assist in improving the sustainability of camelina production facing climate change.
Collapse
Affiliation(s)
- Brian E Smith
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| |
Collapse
|
4
|
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.
Collapse
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;
| |
Collapse
|
5
|
Akhatar J, Singh MP, Sharma A, Kaur H, Kaur N, Sharma S, Bharti B, Sardana VK, Banga SS. Association Mapping of Seed Quality Traits Under Varying Conditions of Nitrogen Application in Brassica juncea L. Czern & Coss. Front Genet 2020; 11:744. [PMID: 33088279 PMCID: PMC7490339 DOI: 10.3389/fgene.2020.00744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/22/2020] [Indexed: 12/02/2022] Open
Abstract
Indian mustard (Brassica juncea) is a major source of vegetable oil in the Indian subcontinent. The seed cake left after the oil extraction is used as livestock feed. We examined the genetic architecture of oil, protein, and glucosinolates by conducting a genome-wide association study (GWAS), using an association panel comprising 92 diverse genotypes. We conducted trait phenotyping over 2 years at two levels of nitrogen (N) application. Genotyping by sequencing was used to identify 66,835 loci, covering 18 chromosomes. Genetic diversity and phenotypic variations were high for the studied traits. Trait performances were stable when averaged over years and N levels. However, individual performances differed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits. Population structure, principal components (PCs) analysis, and discriminant analysis of principal components (DAPCs) were included as covariates to overcome the bias due to the population stratification. We identified 16, 23, and 27 loci associated with oil, protein, and glucosinolates, respectively. We also established LD patterns and haplotype structures for the candidate genes. The average block sizes were larger on A-genome chromosomes as compared to the B- genome chromosomes. Genetic associations differed over N levels. However, meta-analysis of GWAS datasets not only improved the power to recognize associations but also helped to identify common SNPs for oil and protein contents. Annotation of the genomic region around the identified SNPs led to the prediction of 21 orthologs of the functional candidate genes related to the biosynthesis of oil, protein, and glucosinolates. Notable among these are: LACS5 (A09), FAD6 (B05), ASN1 (A06), GTR2 (A06), CYP81G1 (B06), and MYB44 (B06). The identified loci will be very useful for marker-aided breeding for seed quality modifications in B. juncea.
Collapse
Affiliation(s)
- Javed Akhatar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Mohini Prabha Singh
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anju Sharma
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Harjeevan Kaur
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
6
|
Xie T, Chen X, Guo T, Rong H, Chen Z, Sun Q, Batley J, Jiang J, Wang Y. Targeted Knockout of BnTT2 Homologues for Yellow-Seeded Brassica napus with Reduced Flavonoids and Improved Fatty Acid Composition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5676-5690. [PMID: 32394708 DOI: 10.1021/acs.jafc.0c01126] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Brassica napus is one of the important oil crops grown worldwide, and oil quality improvement is a major goal in rapeseed breeding. Yellow seed is an excellent trait, which has great potential in improving seed quality and economic value. In this study, we created stable yellow seed mutants using a CRISPR/Cas9 system and obtained the yellow seed phenotype only when the four alleles of two BnTT2 homologues were knocked out, indicating that the two BnTT2 homologues had conserved but redundant functions in regulating seed color. Histochemical staining and flavonoid metabolic analysis proved that the BnTT2 mutation hindered the synthesis and accumulation of proanthocyanidins. Transcriptome analysis also showed that the BnTT2 mutation inhibited the expression of genes in the phenylpropanoid and flavonoid biosynthetic pathway, which might be regulated by the complex of BnTT2, BnTT8 and BnTTG1. In addition, the homozygous mutants of BnTT2 homologues increased oil content and improved fatty acid composition with higher linoleic acid (C18:2) and linolenic acid (C18:3), which could be used for the genetic improvement of rapeseed. Overall, this research showed that the BnTT2 mutation can be used for yellow seed breeding and oil improvement, which is of great significance in improving the economic value of rapeseeds.
Collapse
Affiliation(s)
- Tao Xie
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xin Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tuli Guo
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hao Rong
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ziyi Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qinfu Sun
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou, Jiangsu 225009, China
| |
Collapse
|
7
|
Zhu Q, King GJ, Liu X, Shan N, Borpatragohain P, Baten A, Wang P, Luo S, Zhou Q. Identification of SNP loci and candidate genes related to four important fatty acid composition in Brassica napus using genome wide association study. PLoS One 2019; 14:e0221578. [PMID: 31442274 PMCID: PMC6707581 DOI: 10.1371/journal.pone.0221578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/11/2019] [Indexed: 12/16/2022] Open
Abstract
Rapeseed oil (canola, Brassica napus L.) is an important healthy vegetable oil throughout the world, the nutritional and economical value of which largely depends on its seed fatty acid composition. In this study, based on 201,187 SNP markers developed from the SLAF-seq (specific locus amplified fragment sequencing), a genome wide association study of four important fatty acid content traits (erucic acid, oleic acid, linoleic acid and linolenic acid) in a panel of 300 inbred lines of rapeseed in two environments (JXAU and JXRIS) was carried out. A total of 148 SNP loci significantly associated with these traits were detected by MLM model analysis respectively, and 30 SNP loci on A08 and C03 chromosomes were detected in three traits of erucic acid, oleic acid and linoleic acid contents simultaneously. Furthermore, 108 highly favorable alleles for increasing oleic acid and linoleic acid content, also for decreasing erucic acid content simultaneously were observed. By a basic local alignment search tool (BLAST) search with in a distance of 100 Kb around these significantly SNP-trait associations, we identified 20 orthologs of the functional candidate genes related to fatty acid biosynthesis, including the known vital fatty acid biosynthesis genes of BnaA.FAE1 and BnaC. FAE1 on the A08 and C03 chromosomes, and other potential candidate genes involving in the fatty acid biosynthesis pathway, such as the orthologs genes of FAD2, LACS09, KCS17, CER4, TT16 and ACBP5. This study lays a basis for uncovering the genetic variations and the improvement of fatty acid composition in B. napus.
Collapse
Affiliation(s)
- Qianglong Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Xingyue Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Nan Shan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | | | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Putao Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Sha Luo
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Qinghong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
- * E-mail:
| |
Collapse
|
8
|
Jiang J, Zhu S, Yuan Y, Wang Y, Zeng L, Batley J, Wang YP. Transcriptomic comparison between developing seeds of yellow- and black-seeded Brassica napus reveals that genes influence seed quality. BMC PLANT BIOLOGY 2019; 19:203. [PMID: 31096923 PMCID: PMC6524335 DOI: 10.1186/s12870-019-1821-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/07/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Brassica napus is of substantial economic value for vegetable oil, biofuel, and animal fodder production. The breeding of yellow-seeded B. napus to improve seed quality with higher oil content, improved oil and meal quality with fewer antinutrients merits attention. Screening the genes related to this phenotype is valuable for future rapeseed breeding. RESULTS A total of 85,407 genes, including 4317 novel genes, were identified in the developing seeds of yellow- and black-seeded B. napus, and yellow rapeseed was shown to be an introgression line between black-seeded B. napus and yellow-seeded Sinapis alba. A total of 15,251 differentially expressed genes (DEGs) were identified among all the libraries, and 563 and 397 common DEGs were identified throughout black and yellow seed development, including 80 upregulated and 151 downregulated genes related to seed development and fatty acid accumulation. In addition, 11 up-DEGs and 31 down-DEGs were identified in all developmental stages of yellow rapeseed compared with black seed. Enrichment analysis revealed that many DEGs were involved in biosynthetic processes, pigment metabolism, and oxidation-reduction processes, such as flavonoid and phenylpropanoid biosynthesis, phenylalanine metabolism, flavone and flavonol biosynthesis, and fatty acid biosynthesis and metabolism. We found that more than 77 DEGs were related to flavonoid and lignin biosynthesis, including 4CL, C4H, and PAL, which participated in phenylalanine metabolism, and BAN, CHI/TT5, DFR, F3H, FLS, LDOX, PAP, CHS/TT4, TT5, bHLH/TT8, WD40, MYB, TCP, and CYP, which were involved in flavonoid biosynthesis. Most of these DEGs were downregulated in yellow rapeseed and were consistent with the decreased flavonoid and lignin contents. Both up- and down-DEGs related to fatty acid biosynthesis and metabolism were also analyzed, which could help to explain the improved oil content of yellow rapeseed. CONCLUSION This research provided comprehensive transcriptome data for yellow-seeded B. napus with a unique genetic background, and all the DEGs in comparison with the black-seeded counterpart could help to explain seed quality differences, such as lower pigmentation and lignin contents, and higher oil content.
Collapse
Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Shuang Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Yi Yuan
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Yue Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Lei Zeng
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA Australia
| | - You-Ping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| |
Collapse
|
9
|
Abstract
Studying seed oil metabolism. The seeds of higher plants represent valuable factories capable of converting photosynthetically derived sugars into a variety of storage compounds, including oils. Oils are the most energy-dense plant reserves and fatty acids composing these oils represent an excellent nutritional source. They supply humans with much of the calories and essential fatty acids required in their diet. These oils are then increasingly being utilized as renewable alternatives to petroleum for the chemical industry and for biofuels. Plant oils therefore represent a highly valuable agricultural commodity, the demand for which is increasing rapidly. Knowledge regarding seed oil production is extensively exploited in the frame of breeding programs and approaches of metabolic engineering for oilseed crop improvement. Complementary aspects of this research include (1) the study of carbon metabolism responsible for the conversion of photosynthetically derived sugars into precursors for fatty acid biosynthesis, (2) the identification and characterization of the enzymatic actors allowing the production of the wide set of fatty acid structures found in seed oils, and (3) the investigation of the complex biosynthetic pathways leading to the production of storage lipids (waxes, triacylglycerols). In this review, we outline the most recent developments in our understanding of the underlying biochemical and molecular mechanisms of seed oil production, focusing on fatty acids and oils that can have a significant impact on the emerging bioeconomy.
Collapse
Affiliation(s)
- Sébastien Baud
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
| |
Collapse
|
10
|
Tian Y, Lv X, Xie G, Zhang J, Xu Y, Chen F. Seed-specific overexpression of AtFAX1 increases seed oil content in Arabidopsis. Biochem Biophys Res Commun 2018; 500:370-375. [PMID: 29654768 DOI: 10.1016/j.bbrc.2018.04.081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
Biosynthesis of plant seed oil is accomplished through the coordinate action of multiple enzymes in multiple subcellular compartments. Fatty acid (FA) has to be transported from plastid to endoplasmic reticulum (ER) for TAG synthesis. However, the role of plastid FA transportation during seed oil accumulation has not been evaluated. AtFAX1 (Arabidopsis fatty acid export1) mediated the FA export from plastid. In this study, we overexpressed AtFAX1 under the control of a seed specific promoter in Arabidopsis. The resultant overexpression lines (OEs) produced seeds which contained 21-33% more oil and 24-30% more protein per seed than those of the wild type (WT). The increased oil content was probably because of the enhanced FA and TAG synthetic activity. The seed size and weight were both increased accordingly. In addition, the seed number per silique and silique number per plant had no changes in transgenic plants. Taken together, our results demonstrated that seed specific overexpression of AtFAX1 could promote oil accumulation in Arabidopsis seeds and manipulating FA transportation is a feasible strategy for increasing the seed oil content.
Collapse
Affiliation(s)
- Yinshuai Tian
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu 610065, China
| | - Xueyan Lv
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Guilan Xie
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Zhang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ying Xu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Fang Chen
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| |
Collapse
|
11
|
Rout K, Yadav BG, Yadava SK, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK. QTL Landscape for Oil Content in Brassica juncea: Analysis in Multiple Bi-Parental Populations in High and "0" Erucic Background. FRONTIERS IN PLANT SCIENCE 2018; 9:1448. [PMID: 30386353 PMCID: PMC6198181 DOI: 10.3389/fpls.2018.01448] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
Increasing oil content in oilseed mustard (Brassica juncea) is a major breeding objective-more so, in the lines that have "0" erucic acid content (< 2% of the seed oil) as earlier studies have shown negative pleiotropic effect of erucic acid loci on the oil content, both in oilseed mustard and rapeseed. We report here QTL analysis of oil content in eight different mapping populations involving seven different parents-including a high oil content line J8 (~49%). The parental lines of the mapping populations contained wide variation in oil content and erucic acid content. The eight mapping populations were categorized into two sets-five populations with individuals segregating for erucic acid (SE populations) and the remaining three with zero erucic acid segregants (ZE populations). Meta-analysis of QTL mapped in individual SE populations identified nine significant C-QTL, with two of these merging most of the major oil QTL that colocalized with the erucic acid loci on the linkage groups A08 and B07. QTL analysis of oil content in ZE populations revealed a change in the landscape of the oil QTL compared to the SE populations, in terms of altered allelic effects and phenotypic variance explained by ZE QTL at the "common" QTL and observation of "novel" QTL in the ZE background. The important loci contributing to oil content variation, identified in the present study could be used in the breeding programmes for increasing the oil content in high erucic and "0" erucic backgrounds.
Collapse
Affiliation(s)
- Kadambini Rout
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Bal Govind Yadav
- 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
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, 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
| | - 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
- *Correspondence: Akshay K. Pradhan
| |
Collapse
|
12
|
Chao H, Wang H, Wang X, Guo L, Gu J, Zhao W, Li B, Chen D, Raboanatahiry N, Li M. Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus. Sci Rep 2017; 7:46295. [PMID: 28393910 PMCID: PMC5385559 DOI: 10.1038/srep46295] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/15/2017] [Indexed: 02/07/2023] Open
Abstract
High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.
Collapse
Affiliation(s)
- Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Xiaodong Wang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Dengyan Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| |
Collapse
|
13
|
Kanai M, Mano S, Kondo M, Hayashi M, Nishimura M. Extension of oil biosynthesis during the mid-phase of seed development enhances oil content in Arabidopsis seeds. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1241-50. [PMID: 26503031 DOI: 10.1111/pbi.12489] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/03/2015] [Accepted: 09/11/2015] [Indexed: 05/09/2023]
Abstract
Regulation of oil biosynthesis in plant seeds has been extensively studied, and biotechnological approaches have been designed to increase seed oil content. Oil and protein synthesis is negatively correlated in seeds, but the mechanisms controlling interactions between these two pathways are unknown. Here, we identify the molecular mechanism controlling oil and protein content in seeds. We utilized transgenic Arabidopsis thaliana plants overexpressing WRINKLED1 (WRI1), a master transcription factor regulating seed oil biosynthesis, and knockout mutants of major seed storage proteins. Oil and protein biosynthesis in wild-type plants was sequentially activated during early and late seed development, respectively. The negative correlation between oil and protein contents in seeds arises from competition between the pathways. Extension of WRI1 expression during mid-phase of seed development significantly enhanced seed oil content. This study demonstrates that temporal activation of genes involved in oil or storage protein biosynthesis determines the oil/protein ratio in Arabidopsis seeds. These results provide novel insights into potential breeding strategies to generate crops with high oil contents in seeds.
Collapse
Affiliation(s)
- Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Biological Diversity, Department of Evolutionary and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Biological Diversity, Department of Evolutionary and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Maki Kondo
- Spectrography and Bioimaging Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| |
Collapse
|
14
|
Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus. G3-GENES GENOMES GENETICS 2016; 6:1073-81. [PMID: 26896439 PMCID: PMC4825642 DOI: 10.1534/g3.116.027110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Seed coat color is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds such as seed dormancy, longevity, oil content, protein content and fiber content. In Brassica napus, inheritance of seed coat color is related to maternal effects and pollen effects (xenia effects). In this research we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus, which is named Embryonal Control of Yellow seed coat 1 (Ecy1). Microscopy of transverse sections of the mature seed show that pigment is deposited only in the outer layer of the seed coat. Using Illumina Hisequation 2000 sequencing technology, a total of 12 GB clean data, 116× coverage of coding sequences of B. napus, was achieved from seeds 26 d after pollination (DAP). It was assembled into 172,238 independent transcripts, and 55,637 unigenes. A total of 139 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcribed in seeds. However transcription of all orthologs was independent of embryonal control of seed coat color. Only 55 genes were found to be differentially expressed between brown seeds and the yellow mutant. Of these 55, 50 were upregulated and five were downregulated in yellow seeds as compared to their brown counterparts. By KEGG classification, 14 metabolic pathways were significantly enriched. Of these, five pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways, and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were present at higher levels in the embryos of yellow seeds as compared to those of brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the embryo. The pigment substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe, and disappearance of pigment in the yellow seeded mutant, suggests that embryonal control of seed coat color is related with Phe and Ala metabolism in the embryo of B. napus.
Collapse
|
15
|
Wen J, Xu JF, Long Y, Wu JG, Xu HM, Meng JL, Shi CH. QTL mapping based on the embryo and maternal genetic systems for non-essential amino acids in rapeseed (Brassica napus L.) meal. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:465-473. [PMID: 25645377 DOI: 10.1002/jsfa.7112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/25/2015] [Accepted: 01/25/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Non-essential amino acids are a good source of nitrogen and also very important contributors to the metabolic process. Analysis of quantitative trait locus (QTL) simultaneously located on the amphidiploid embryo and maternal plant nuclear genomes for non-essential amino acid contents in rapeseed meal across different environments was conducive to further clarify the genetic mechanism of seed quality traits. RESULTS Twenty-eight QTLs associated with arginine (five QTLs), histidine (four QTLs), glutamic acid (three QTLs), glycine (three QTLs), proline (three QTLs), alanine (four QTLs) and aspartic acid (six QTLs) contents were identified in present study. All of these QTLs had significant additive main effects from embryo and maternal plant nuclear genomes with eight of them showing significant embryo dominance main effects and 12 showing notable QTL × environment interaction effects. Among them, 12 QTLs were major QTLs which could explain 13.27-35.71% of the phenotypic variation. Specially, five QTL clusters associated with several QTLs related to multiple traits were distributed on chromosomes A1, A4, A5, A7 and C2. CONCLUSION Non-essential amino acids in rapeseed meal could be simultaneously controlled by the genetic effects from the QTLs which were located on the chromosomes both in the embryo and maternal plant genetic systems.
Collapse
Affiliation(s)
- Juan Wen
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jian-Feng Xu
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yan Long
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jian-Guo Wu
- College of Agriculture and Food Science, Zhejiang A & F University, Linan, Zhejiang, 311300, China
| | - Hai-Ming Xu
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jin-Ling Meng
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chun-Hai Shi
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| |
Collapse
|
16
|
Dechaine JM, Brock MT, Weinig C. QTL architecture of reproductive fitness characters in Brassica rapa. BMC PLANT BIOLOGY 2014; 14:66. [PMID: 24641198 PMCID: PMC4004417 DOI: 10.1186/1471-2229-14-66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 03/03/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Reproductive output is critical to both agronomists seeking to increase seed yield and to evolutionary biologists interested in understanding natural selection. We examine the genetic architecture of diverse reproductive fitness traits in recombinant inbred lines (RILs) developed from a crop (seed oil) × wild-like (rapid cycling) genotype of Brassica rapa in field and greenhouse environments. RESULTS Several fitness traits showed strong correlations and QTL-colocalization across environments (days to bolting, fruit length and seed color). Total fruit number was uncorrelated across environments and most QTL affecting this trait were correspondingly environment-specific. Most fitness components were positively correlated, consistent with life-history theory that genotypic variation in resource acquisition masks tradeoffs. Finally, we detected evidence of transgenerational pleiotropy, that is, maternal days to bolting was negatively correlated with days to offspring germination. A QTL for this transgenerational correlation was mapped to a genomic region harboring one copy of FLOWERING LOCUS C, a genetic locus known to affect both days to flowering as well as germination phenotypes. CONCLUSIONS This study characterizes the genetic structure of important fitness/yield traits within and between generations in B. rapa. Several identified QTL are suitable candidates for fine-mapping for the improvement of yield in crop Brassicas. Specifically, brFLC1, warrants further investigation as a potential regulator of phenology between generations.
Collapse
Affiliation(s)
- Jennifer M Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, WA 98926, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
| |
Collapse
|
17
|
Wang X, Wang H, Long Y, Li D, Yin Y, Tian J, Chen L, Liu L, Zhao W, Zhao Y, Yu L, Li M. Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus. PLoS One 2013; 8:e80569. [PMID: 24312482 PMCID: PMC3846612 DOI: 10.1371/journal.pone.0080569] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023] Open
Abstract
Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.
Collapse
Affiliation(s)
- Xiaodong Wang
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dianrong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yongtai Yin
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Li Chen
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yajun Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
18
|
Gan L, Zhang CY, Wang XD, Wang H, Long Y, Yin YT, Li DR, Tian JH, Li ZY, Lin ZW, Yu LJ, Li MT. Proteomic and Comparative Genomic Analysis of Two Brassica napus Lines Differing in Oil Content. J Proteome Res 2013; 12:4965-78. [DOI: 10.1021/pr4005635] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Lu Gan
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-yu Zhang
- National
Key Laboratory of Crop Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, China
| | - Xiao-dong Wang
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Dali 715105, China
| | - Yan Long
- National
Key Laboratory of Crop Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, China
| | - Yong-tai Yin
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dian-Rong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Dali 715105, China
| | - Jian-Hua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Dali 715105, China
| | - Zai-yun Li
- National
Key Laboratory of Crop Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, China
| | - Zhi-wei Lin
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Long-Jiang Yu
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mao-Teng Li
- Institute
of Resource Biology and Biotechnology, College of Life Science and
Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
19
|
RAPD, ISSR and SSR Based Integrated Linkage Map From an F2 Hybrid Population of Resynthesized and Natural Brassica carinata. NATIONAL ACADEMY SCIENCE LETTERS 2012. [DOI: 10.1007/s40009-012-0057-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
20
|
Zhu Y, Cao Z, Xu F, Huang Y, Chen M, Guo W, Zhou W, Zhu J, Meng J, Zou J, Jiang L. Analysis of gene expression profiles of two near-isogenic lines differing at a QTL region affecting oil content at high temperatures during seed maturation in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:515-31. [PMID: 22042481 DOI: 10.1007/s00122-011-1725-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 10/07/2011] [Indexed: 05/24/2023]
Abstract
Seed oil production in oilseed rape is greatly affected by the temperature during seed maturation. However, the molecular mechanism of the interaction between genotype and temperature in seed maturation remains largely unknown. We developed two near-isogenic lines (NIL-9 and NIL-1), differing mainly at a QTL region influencing oil content on Brassica napus chromosome C2 (qOC.C2.2) under high temperature during seed maturation. The NILs were treated under different temperatures in a growth chamber after flowering. RNA from developing seeds was extracted on the 25th day after flowering (DAF), and transcriptomes were determined by microarray analysis. Statistical analysis indicated that genotype, temperature, and the interaction between genotype and temperature (G × T) all significantly affected the expression of the genes in the 25 DAF seeds, resulting in 4,982, 19,111, and 839 differentially expressed unisequences, respectively. NIL-9 had higher seed oil content than NIL-1 under all of the temperatures in the experiments, especially at high temperatures. A total of 39 genes, among which six are located at qOC.C2.2, were differentially expressed among the NILs regardless of temperature, indicating the core genetic divergence that was unaffected by temperature. Increasing the temperature caused a reduction in seed oil content that was accompanied by the downregulation of a number of genes associated with red light response, photosynthesis, response to gibberellic acid stimulus, and translational elongation, as well as several genes of importance in the lipid metabolism pathway. These results contribute to our knowledge of the molecular nature of QTLs and the interaction between genotype and temperature.
Collapse
Affiliation(s)
- Yana Zhu
- College of Agriculture and Biotechnology, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Würschum T, Liu W, Maurer HP, Abel S, Reif JC. Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:153-61. [PMID: 21898051 DOI: 10.1007/s00122-011-1694-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 08/18/2011] [Indexed: 05/18/2023]
Abstract
Detection of QTL in multiple segregating populations is of high interest as it includes more alleles than mapping in a single biparental population. In addition, such populations are routinely generated in applied plant breeding programs and can thus be used to identify QTL which are of direct relevance for a marker-assisted improvement of elite germplasm. Multiple-line cross QTL mapping and joint linkage association mapping were used for QTL detection. We empirically compared these two different biometrical approaches with regard to QTL detection for important agronomic traits in nine segregating populations of elite rapeseed lines. The plants were intensively phenotyped in multi-location field trials and genotyped with 253 SNP markers. Both approaches detected several additive QTL for diverse traits, including flowering time, plant height, protein content, oil content, glucosinolate content, and grain yield. In addition, we identified one epistatic QTL for flowering time. Consequently, both approaches appear suited for QTL detection in multiple segregating populations.
Collapse
Affiliation(s)
- Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany.
| | | | | | | | | |
Collapse
|
22
|
Weselake RJ, Taylor DC, Rahman MH, Shah S, Laroche A, McVetty PBE, Harwood JL. Increasing the flow of carbon into seed oil. Biotechnol Adv 2009; 27:866-878. [PMID: 19625012 DOI: 10.1016/j.biotechadv.2009.07.001] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 01/13/2023]
Abstract
The demand for vegetable oils for food, fuel (bio-diesel) and bio-product applications is increasing rapidly. In Canada alone, it is estimated that a 50 to 75% increase in canola oil production will be required to meet the demand for seed oil in the next 7-10years. Plant breeding and genetics have demonstrated that seed oil content is a quantitative trait based on a number of contributing factors including embryo genetic effects, cytoplasmic effects, maternal genetic effects, and genotype-environment interactions. Despite the involvement of numerous quantitative trait loci in determining seed oil content, genetic engineering to over-express/repress specific genes encoding enzymes and other proteins involved in the flow of carbon into seed oil has led to the development of transgenic lines with significant increases in seed oil content. Proteins encoded by these genes include enzymes catalyzing the production of building blocks for oil assembly, enzymes involved in oil assembly, enzymes regulating metabolic carbon partitioning between oil, carbohydrate and secondary metabolite fractions, and transcription factors which orchestrate metabolism at a more general level.
Collapse
Affiliation(s)
- Randall J Weselake
- Agricultural Lipid Biotechnology Program; Department of Agricultural, Food & Nutritional Science; University of Alberta, Edmonton, Alberta, Canada T6G 2P5.
| | - David C Taylor
- Plant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - M Habibur Rahman
- Agricultural Lipid Biotechnology Program; Department of Agricultural, Food & Nutritional Science; University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Saleh Shah
- Plant Biotechnology Unit, Alberta Research Council, Vegreville, Alberta, Canada T9C 1T4
| | - André Laroche
- Agriculture and Agri-food Canada, Lethbridge, Alberta, Canada T1J 4B1
| | - Peter B E McVetty
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - John L Harwood
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| |
Collapse
|
23
|
Ebrahimi A, Maury P, Berger M, Calmon A, Grieu P, Sarrafi A. QTL mapping of protein content and seed characteristics under water-stress conditions in sunflower. Genome 2009; 52:419-30. [PMID: 19448722 DOI: 10.1139/g09-020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The purpose of this study was to identify genomic regions controlling seed protein content, kernel and hull weights, and seed density in water-stress conditions in sunflower (Helianthus annuus L.). The experiments consisted of a split-plot design (water treatment and recombinant inbred lines) with three blocks in two environments (greenhouse and field). High significant variation was observed between genotypes for all traits as well as for water treatment x genotype interaction. Several specific and nonspecific QTLs were detected for all traits under well-watered and water-stress conditions. Two SSR markers, ORS671_2 and HA2714, linked to protein content were identified that have no interaction with water treatments in greenhouse conditions. We also detected the E35M60_4 marker associated with kernel weight that had no interaction with water treatments. A specific QTL for protein content was detected with important phenotypic variance (17%) under water-stress conditions. Overlapping QTLs for protein content and seed density were identified in linkage group 15. This region probably has a peliotropic effect on protein content and seed density. QTLs for protein content colocated with grain weight traits were also identified.
Collapse
Affiliation(s)
- A Ebrahimi
- INP-ENSAT, IFR 40, Laboratoire de Symbiose et Pathologie des Plantes (SP2), F-31326 Castanet Tolosan, France
| | | | | | | | | | | |
Collapse
|
24
|
Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D. Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics 2008; 9:113. [PMID: 18315867 PMCID: PMC2277410 DOI: 10.1186/1471-2164-9-113] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 03/03/2008] [Indexed: 11/25/2022] Open
Abstract
Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP) markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome) and A. thaliana and analyzed the arrangement of 24 (previously described) genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study) with the A and B genomes of B. napus and B. nigra respectively (described earlier), revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements, translocations and fusions pivotal to karyotype diversification between the A, B and C genomes of Brassica species. The inter-relationships established between the Brassica lineages vis-à-vis Arabidopsis would facilitate the identification and isolation of candidate genes contributing to traits of agronomic value in crop Brassicas and the development of unified tools for Brassica genomics.
Collapse
Affiliation(s)
- Priya Panjabi
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Hajduch M, Casteel JE, Tang S, Hearne LB, Knapp S, Thelen JJ. Proteomic Analysis of Near-Isogenic Sunflower Varieties Differing in Seed Oil Traits. J Proteome Res 2007; 6:3232-41. [PMID: 17580850 DOI: 10.1021/pr070149a] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Near-isogenic sunflower lines containing 25% (inbred RHA280) and 48% (RHA801) oil by seed dry mass were comparatively analyzed in biological triplicate at 18 days after flowering using two-dimensional (both pI 3-10 and 4-7) Difference Gel Electrophoresis. Additionally, two inbred lines varying in oleic acid content, HA89 (18% oleic) and HA341 (89% oleic), were also analyzed in the same manner. Statistical analyses of these sunflower lines was performed beginning with fitting a mixed effects linear model to the log-transformed optical volume of each spot to account for gel variation, followed by testing the significance between varieties for mean transformed optical spot volumes. The p-values from the spot analysis procedures were then used to find the cutoff point for differential expression using a 10% false-discovery rate (FDR). Comparison of the oil content and oleic acid composition lines revealed 77 and 42 protein spots below the 10% FDR cutoff, respectively, and were therefore declared differentially expressed. Liquid chromatography-tandem mass spectrometry analysis of each of these protein spots resulted in assignments for 44 and 17 spots, respectively. Fructokinase, plastid phosphoglycerate kinase, and enolase proteins were determined to be up-regulated in the high oil line, while phosphofructokinase, cytosolic phosphoglucomutase, and cytsolic phosphoglycerate kinase were up-regulated in the low oil variety. Additionally, four activities involved in amino acid synthesis were up-regulated in the low oil variety in addition to 12S storage proteins and a protein similar to legumin storage protein. Interestingly, two 2-DE spots identified as 14-3-3 proteins were found to be up-regulated in high oleic acid variety. Alteration of glycolytic and amino acid biosynthetic enzymes, as well as storage protein levels, suggests seed oil content is tightly linked to carbohydrate metabolism and protein synthesis in a complex manner.
Collapse
Affiliation(s)
- Martin Hajduch
- Department of Biochemistry, 109 Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | | | | | | | | | | |
Collapse
|