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Fu Y, Yao M, Qiu P, Song M, Ni X, Niu E, Shi J, Wang T, Zhang Y, Yu H, Qian L. Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:243. [PMID: 39352575 DOI: 10.1007/s00122-024-04733-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/24/2024] [Indexed: 10/03/2024]
Abstract
KEY MESSAGE We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yao
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Ping Qiu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Maolin Song
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Xiyuan Ni
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Erli Niu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianghua Shi
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tanliu Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Cagirici HB, Andorf CM, Sen TZ. Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. BMC PLANT BIOLOGY 2022; 22:595. [PMID: 36529716 PMCID: PMC9762053 DOI: 10.1186/s12870-022-03985-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND With the advances in the high throughput next generation sequencing technologies, genome-wide association studies (GWAS) have identified a large set of variants associated with complex phenotypic traits at a very fine scale. Despite the progress in GWAS, identification of genotype-phenotype relationship remains challenging in maize due to its nature with dozens of variants controlling the same trait. As the causal variations results in the change in expression, gene expression analyses carry a pivotal role in unraveling the transcriptional regulatory mechanisms behind the phenotypes. RESULTS To address these challenges, we incorporated the gene expression and GWAS-driven traits to extend the knowledge of genotype-phenotype relationships and transcriptional regulatory mechanisms behind the phenotypes. We constructed a large collection of gene co-expression networks and identified more than 2 million co-expressing gene pairs in the GWAS-driven pan-network which contains all the gene-pairs in individual genomes of the nested association mapping (NAM) population. We defined four sub-categories for the pan-network: (1) core-network contains the highest represented ~ 1% of the gene-pairs, (2) near-core network contains the next highest represented 1-5% of the gene-pairs, (3) private-network contains ~ 50% of the gene pairs that are unique to individual genomes, and (4) the dispensable-network contains the remaining 50-95% of the gene-pairs in the maize pan-genome. Strikingly, the private-network contained almost all the genes in the pan-network but lacked half of the interactions. We performed gene ontology (GO) enrichment analysis for the pan-, core-, and private- networks and compared the contributions of variants overlapping with genes and promoters to the GWAS-driven pan-network. CONCLUSIONS Gene co-expression networks revealed meaningful information about groups of co-regulated genes that play a central role in regulatory processes. Pan-network approach enabled us to visualize the global view of the gene regulatory network for the studied system that could not be well inferred by the core-network alone.
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Affiliation(s)
- H Busra Cagirici
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA
| | - Carson M Andorf
- US Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, 50011, USA.
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.
| | - Taner Z Sen
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
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Zhou W, Song S, Segla Koffi Dossou S, Zhou R, Wei X, Wang Z, Sheng C, Zhang Y, You J, Wang L. Genome-wide association analysis and transcriptome reveal novel loci and a candidate regulatory gene of fatty acid biosynthesis in sesame (Sesamum indicum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:220-231. [PMID: 35921726 DOI: 10.1016/j.plaphy.2022.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The regulatory mechanisms of fatty acid (FA) biosynthesis and triacylglycerols (TAGs) assembly remain largely misunderstood in sesame. Gas chromatography was used to analyze the natural variation in FA compositions and oil content (OC) in 400 sesame accessions grown in three different environments. The phenotypic data was associated with the newly released SNP data from whole-genome resequencing, and 43 significant loci for FA and OC were identified. Comparative transcriptomics analysis of high-OC and low-OC materials was performed, and 515 differentially expressed genes (DEGs) were identified across three seed developmental stages. By integrating the genome-wide association study (GWAS) and DEGs analysis, twenty candidate genes were identified, of which SiTPS1 (trehalose-6-phosphate synthase 1) has emerged as a key regulatory gene of FAs and TAGs metabolism in sesame. Overexpression of SiTPS1 in transgenic Arabidopsis influenced FA composition and significantly increased OC. Our study provides resources for the markers-based improvement of OC and quality in sesame and other crops.
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Affiliation(s)
- Wangyi Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Bhinder G, Sharma S, Kaur H, Akhatar J, Mittal M, Sandhu S. Genomic Regions Associated With Seed Meal Quality Traits in Brassica napus Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:882766. [PMID: 35909769 PMCID: PMC9333065 DOI: 10.3389/fpls.2022.882766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The defatted Brassica napus (rapeseed) meal can be high-protein feed for livestock as the protein value of rapeseed meal is higher than that of the majority of other vegetable proteins. Extensive work has already been carried out on developing canola rapeseed where the focus was on reducing erucic acid and glucosinolate content, with less consideration to other antinutritional factors such as tannin, phytate, sinapine, crude fiber, etc. The presence of these antinutrients limits the use and marketing of rapeseed meals and a significant amount of it goes unused and ends up as waste. We investigated the genetic architecture of crude protein, methionine, tryptophan, total phenols, β-carotene, glucosinolates (GLSs), phytate, tannins, sinapine, and crude fiber content of defatted seed meal samples by conducting a genome-wide association study (GWAS), using a diversity panel comprising 96 B. napus genotypes. Genotyping by sequencing was used to identify 77,889 SNPs, spread over 19 chromosomes. Genetic diversity and phenotypic variations were generally high for the studied traits. A total of eleven genotypes were identified which showed high-quality protein, high antioxidants, and lower amount of antinutrients. A significant negative correlation between protein and limiting amino acids and a significant positive correlation between GLS and phytic acid were observed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits and quantile-quantile (QQ) plots were generated to allow the best-fit algorithm. Annotation of genomic regions around associated SNPs helped to predict various trait-related candidates such as ASP2 and EMB1027 (amino acid biosynthesis); HEMA2, GLU1, and PGM (tryptophan biosynthesis); MS3, CYSD1, and MTO1 (methionine biosynthesis); LYC (β-carotene biosynthesis); HDR and ISPF (MEP pathway); COS1 (riboflavin synthesis); UGT (phenolics biosynthesis); NAC073 (cellulose and hemicellulose biosynthesis); CYT1 (cellulose biosynthesis); BGLU45 and BGLU46 (lignin biosynthesis); SOT12 and UGT88A1 (flavonoid pathway); and CYP79A2, DIN2, and GSTT2 (GLS metabolism), etc. The functional validation of these candidate genes could confirm key seed meal quality genes for germplasm enhancement programs directed at improving protein quality and reducing the antinutritional components in B. napus.
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Affiliation(s)
| | - Sanjula Sharma
- Oilseeds Section, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Javed Akhatar
- Oilseeds Section, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Gupta OP, Deshmukh R, Kumar A, Singh SK, Sharma P, Ram S, Singh GP. From gene to biomolecular networks: a review of evidences for understanding complex biological function in plants. Curr Opin Biotechnol 2021; 74:66-74. [PMID: 34800849 DOI: 10.1016/j.copbio.2021.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/10/2021] [Accepted: 10/24/2021] [Indexed: 11/28/2022]
Abstract
Although at the infancy stage, biomolecular network biology is a comprehensive approach to understand complex biological function in plants. Recent advancements in the accumulation of multi-omics data coupled with computational approach have accelerated our current understanding of the complexities of gene function at the system level. Biomolecular networks such as protein-protein interaction, co-expression and gene regulatory networks have extensively been used to decipher the intricacies of transcriptional reprogramming of hundreds of genes and their regulatory interaction in response to various environmental perturbations mainly in the model plant Arabidopsis. This review describes recent applications of network-based approaches to understand the biological functions in plants and focuses on the challenges and opportunities to harness the full potential of the approach.
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Affiliation(s)
- Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132 001, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 160 055, India
| | - Awadhesh Kumar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, Odisha, 753 006, India
| | - Sanjay Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132 001, India
| | - Pradeep Sharma
- Division of Crop Improvement, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132 001, India
| | - Sewa Ram
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132 001, India
| | - Gyanendra Pratap Singh
- Division of Crop Improvement, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132 001, India
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Motallaei M, Ramezani-Jolfaie N, Mohammadi M, Shams-Rad S, Jahanlou AS, Salehi-Abargouei A. Effects of orange juice intake on cardiovascular risk factors: A systematic review and meta-analysis of randomized controlled clinical trials. Phytother Res 2021; 35:5427-5439. [PMID: 34060162 DOI: 10.1002/ptr.7173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/16/2021] [Accepted: 05/16/2021] [Indexed: 12/29/2022]
Abstract
Previous investigations exploring the effects of orange juice (OJ) as a nutrient-dense beverage on cardiovascular risk factors were inconsistent. We aimed to conduct a systematic review and meta-analysis of randomized controlled clinical trials to determine the effectiveness of OJ intake on major cardiometabolic markers including anthropometric indices, blood pressure, lipid profile, inflammation, and glycemic control markers. PubMed, Scopus, and ISI Web of Science were searched from inception until January 2021. Fifteen eligible trials with 639 participants were included in the present study. The meta-analysis showed that OJ intake significantly reduces circulating total cholesterol levels (10 trials; weighted mean difference [WMD] = -6.84 mg/dl; 95% CI: -12.38 to -1.29; p = .01) and homeostatic model assessment for insulin resistance (four trials; WMD = -0.39, 95% CI: -0.77 to -0.006; p = .04) compared to control group. The analyses failed to reveal a significant effect of OJ intake on other cardiometabolic risk factors (p > .05). This review suggests that the intake of OJ might be associated with improved serum total cholesterol and insulin sensitivity. Due to low-to-moderate quality of meta-evidence, our results must be interpreted with caution and more well-designed studies are still needed to confirm the current findings.
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Affiliation(s)
- Maryam Motallaei
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Nutrition, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Nahid Ramezani-Jolfaie
- Department of Community Medicine, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Mohammadi
- Department of Community Medicine, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Shamim Shams-Rad
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Nutrition, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Alireza Shahab Jahanlou
- Department of Community Medicine, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amin Salehi-Abargouei
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Nutrition, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed ( Brassica napus L.). PLANTS 2021; 10:plants10030426. [PMID: 33668258 PMCID: PMC7996214 DOI: 10.3390/plants10030426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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