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Zhu L, Li G, Guo D, Li X, Xue M, Jiang H, Yan Q, Xie F, Ning X, Xie L. Genome-wide association study and genomic selection of flax powdery mildew in Xinjiang Province. FRONTIERS IN PLANT SCIENCE 2024; 15:1403276. [PMID: 38863531 PMCID: PMC11165360 DOI: 10.3389/fpls.2024.1403276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024]
Abstract
Flax powdery mildew (PM), caused by Oidium lini, is a globally distributed fungal disease of flax, and seriously impairs its yield and quality. To data, only three resistance genes and a few putative quantitative trait loci (QTL) have been reported for flax PM resistance. To dissect the resistance mechanism against PM and identify resistant genetic regions, based on four years of phenotypic datasets (2017, 2019 to 2021), a genome-wide association study (GWAS) was performed on 200 flax core accessions using 674,074 SNPs and 7 models. A total of 434 unique quantitative trait nucleotides (QTNs) associated with 331 QTL were detected. Sixty-four loci shared in at least two datasets were found to be significant in haplotype analyses, and 20 of these sites were shared by multiple models. Simultaneously, a large-effect locus (qDI 11.2) was detected repeatedly, which was present in the mapping study of flax pasmo resistance loci. Oil flax had more QTL with positive-effect or favorable alleles (PQTL) and showed higher PM resistance than fiber flax, indicating that effects of these QTL were mainly additive. Furthermore, an excellent resistant variety C120 was identified and can be used to promote planting. Based on 331 QTLs identified through GWAS and the statistical model GBLUP, a genomic selection (GS) model related to flax PM resistance was constructed, and the prediction accuracy rate was 0.96. Our results provide valuable insights into the genetic basis of resistance and contribute to the advancement of breeding programs.
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Affiliation(s)
- Leilei Zhu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Basic Medicine, Xinjiang Second Medical College, Karamay, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Fang Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xuefei Ning
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Fofana B, Soto-Cerda B, Zaidi M, Main D, Fillmore S. Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes. Front Genet 2024; 14:1306519. [PMID: 38357658 PMCID: PMC10864671 DOI: 10.3389/fgene.2023.1306519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool-mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%-7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5-1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate-late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.
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Affiliation(s)
- Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Braulio Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Moshin Zaidi
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - David Main
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Sherry Fillmore
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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Soto-Cerda BJ, Larama G, Cloutier S, Fofana B, Inostroza-Blancheteau C, Aravena G. The Genetic Dissection of Nitrogen Use-Related Traits in Flax ( Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection. Int J Mol Sci 2023; 24:17624. [PMID: 38139451 PMCID: PMC10743809 DOI: 10.3390/ijms242417624] [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: 11/03/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile;
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Claudio Inostroza-Blancheteau
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Gabriela Aravena
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
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He L, Sui Y, Che Y, Wang H, Rashid KY, Cloutier S, You FM. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax. FRONTIERS IN PLANT SCIENCE 2023; 14:1229457. [PMID: 37954993 PMCID: PMC10634603 DOI: 10.3389/fpls.2023.1229457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 11/14/2023]
Abstract
Introduction Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola. Methods In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance. Results We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs. Discussion Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Khalid Y. Rashid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Moyse J, Lecomte S, Marcou S, Mongelard G, Gutierrez L, Höfte M. Overview and Management of the Most Common Eukaryotic Diseases of Flax ( Linum usitatissimum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2811. [PMID: 37570965 PMCID: PMC10420651 DOI: 10.3390/plants12152811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.
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Affiliation(s)
- Julie Moyse
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Sylvain Lecomte
- LINEA–Semences, 20 Avenue Saget, 60210 Grandvilliers, France;
| | - Shirley Marcou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
| | - Gaëlle Mongelard
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
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Paliwal S, Tripathi MK, Tiwari S, Tripathi N, Payasi DK, Tiwari PN, Singh K, Yadav RK, Asati R, Chauhan S. Molecular Advances to Combat Different Biotic and Abiotic Stresses in Linseed ( Linum usitatissimum L.): A Comprehensive Review. Genes (Basel) 2023; 14:1461. [PMID: 37510365 PMCID: PMC10379177 DOI: 10.3390/genes14071461] [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: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Flax, or linseed, is considered a "superfood", which means that it is a food with diverse health benefits and potentially useful bioactive ingredients. It is a multi-purpose crop that is prized for its seed oil, fibre, nutraceutical, and probiotic qualities. It is suited to various habitats and agro-ecological conditions. Numerous abiotic and biotic stressors that can either have a direct or indirect impact on plant health are experienced by flax plants as a result of changing environmental circumstances. Research on the impact of various stresses and their possible ameliorators is prompted by such expectations. By inducing the loss of specific alleles and using a limited number of selected varieties, modern breeding techniques have decreased the overall genetic variability required for climate-smart agriculture. However, gene banks have well-managed collectionns of landraces, wild linseed accessions, and auxiliary Linum species that serve as an important source of novel alleles. In the past, flax-breeding techniques were prioritised, preserving high yield with other essential traits. Applications of molecular markers in modern breeding have made it easy to identify quantitative trait loci (QTLs) for various agronomic characteristics. The genetic diversity of linseed species and the evaluation of their tolerance to abiotic stresses, including drought, salinity, heavy metal tolerance, and temperature, as well as resistance to biotic stress factors, viz., rust, wilt, powdery mildew, and alternaria blight, despite addressing various morphotypes and the value of linseed as a supplement, are the primary topics of this review.
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Affiliation(s)
- Shruti Paliwal
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Devendra K Payasi
- All India Coordinated Research Project on Linseed, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Regional Agricultural Research Station, Sagar 470001, India
| | - Prakash N Tiwari
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Kirti Singh
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Ruchi Asati
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Kaur V, Singh M, Wankhede DP, Gupta K, Langyan S, Aravind J, Thangavel B, Yadav SK, Kalia S, Singh K, Kumar A. Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies - a review. Front Nutr 2023; 10:1165580. [PMID: 37324736 PMCID: PMC10267467 DOI: 10.3389/fnut.2023.1165580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/27/2023] [Indexed: 06/17/2023] Open
Abstract
Linseed or flaxseed is a well-recognized nutritional food with nutraceutical properties owing to high omega-3 fatty acid (α-Linolenic acid), dietary fiber, quality protein, and lignan content. Currently, linseed enjoys the status of a 'superfood' and its integration in the food chain as a functional food is evolving continuously as seed constituents are associated with lowering the risk of chronic ailments, such as heart diseases, cancer, diabetes, and rheumatoid arthritis. This crop also receives much attention in the handloom and textile sectors as the world's coolest fabric linen is made up of its stem fibers which are endowed with unique qualities such as luster, tensile strength, density, bio-degradability, and non-hazardous nature. Worldwide, major linseed growing areas are facing erratic rainfall and temperature patterns affecting flax yield, quality, and response to biotic stresses. Amid such changing climatic regimes and associated future threats, diverse linseed genetic resources would be crucial for developing cultivars with a broad genetic base for sustainable production. Furthermore, linseed is grown across the world in varied agro-climatic conditions; therefore it is vital to develop niche-specific cultivars to cater to diverse needs and keep pace with rising demands globally. Linseed genetic diversity conserved in global genebanks in the form of germplasm collection from natural diversity rich areas is expected to harbor genetic variants and thus form crucial resources for breeding tailored crops to specific culinary and industrial uses. Global genebank collections thus potentially play an important role in supporting sustainable agriculture and food security. Currently, approximately 61,000 germplasm accessions of linseed including 1,127 wild accessions are conserved in genebanks/institutes worldwide. This review analyzes the current status of Linum genetic resources in global genebanks, evaluation for agro-morphological traits, stress tolerance, and nutritional profiling to promote their effective use for sustainable production and nutrition enhancement in our modern diets.
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Affiliation(s)
- Vikender Kaur
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mamta Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kavita Gupta
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jayaraman Aravind
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Boopathi Thangavel
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi, India
| | - Kuldeep Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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Povkhova LV, Pushkova EN, Rozhmina TA, Zhuchenko AA, Frykin RI, Novakovskiy RO, Dvorianinova EM, Gryzunov AA, Borkhert EV, Sigova EA, Vladimirov GN, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA, Melnikova NV. Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil. PLANTS (BASEL, SWITZERLAND) 2022; 12:95. [PMID: 36616223 PMCID: PMC9824437 DOI: 10.3390/plants12010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Roman I. Frykin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | | | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Yadav B, Kaur V, Narayan OP, Yadav SK, Kumar A, Wankhede DP. Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:931275. [PMID: 35958216 PMCID: PMC9358615 DOI: 10.3389/fpls.2022.931275] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 05/03/2023]
Abstract
Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.
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Affiliation(s)
- Bindu Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om Prakash Narayan
- College of Arts and Sciences, University of Florida, Gainesville, FL, United States
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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