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Guo D, Jiang H, Xie L. An R2R3-MYB Transcriptional Factor LuMYB314 Associated with the Loss of Petal Pigmentation in Flax ( Linum usitatissimum L.). Genes (Basel) 2024; 15:511. [PMID: 38674445 PMCID: PMC11050253 DOI: 10.3390/genes15040511] [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: 03/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a phylogenetic analysis, and transgenic testing to identify genes responsible for the transition from blue to white petals in flax. This study found no correspondence between the petal color and seed color, refuting the conclusion that a locus controlling the seed coat color is associated with the petal color, as reported in previous studies. The locus controlling the petal color was mapped using a BSA-seq analysis based on the F2 population. However, no significantly associated genomic regions were detected. Our genome-wide association study identified a highly significant QTL (BP4.1) on chromosome 4 associated with flax petal color in the natural population. The combination of a local Manhattan plot and an LD heat map identified LuMYB314, an R2R3-MYB transcription factor, as a potential gene responsible for the natural variations in petal color in flax. The overexpression of LuMYB314 in both Arabidopsis thaliana and Nicotiana tabacum resulted in anthocyanin deposition, indicating that LuMYB314 is a credible candidate gene for controlling the petal color in flax. Additionally, our study highlights the limitations of the BSA-seq method in low-linkage genomic regions, while also demonstrating the powerful detection capabilities of GWAS based on high-density genomic variation mapping. This study enhances our genetic insight into petal color variations and has potential breeding value for engineering LuMYB314 to develop colored petals, bast fibers, and seeds for multifunctional use in flax.
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Affiliation(s)
- Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
| | - Haixia Jiang
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi 830017, China;
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
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2
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Hoque A, Anderson JV, Rahman M. Genomic prediction for agronomic traits in a diverse Flax (Linum usitatissimum L.) germplasm collection. Sci Rep 2024; 14:3196. [PMID: 38326469 PMCID: PMC10850546 DOI: 10.1038/s41598-024-53462-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
Breeding programs require exhaustive phenotyping of germplasms, which is time-demanding and expensive. Genomic prediction helps breeders harness the diversity of any collection to bypass phenotyping. Here, we examined the genomic prediction's potential for seed yield and nine agronomic traits using 26,171 single nucleotide polymorphism (SNP) markers in a set of 337 flax (Linum usitatissimum L.) germplasm, phenotyped in five environments. We evaluated 14 prediction models and several factors affecting predictive ability based on cross-validation schemes. Models yielded significant variation among predictive ability values across traits for the whole marker set. The ridge regression (RR) model covering additive gene action yielded better predictive ability for most of the traits, whereas it was higher for low heritable traits by models capturing epistatic gene action. Marker subsets based on linkage disequilibrium decay distance gave significantly higher predictive abilities to the whole marker set, but for randomly selected markers, it reached a plateau above 3000 markers. Markers having significant association with traits improved predictive abilities compared to the whole marker set when marker selection was made on the whole population instead of the training set indicating a clear overfitting. The correction for population structure did not increase predictive abilities compared to the whole collection. However, stratified sampling by picking representative genotypes from each cluster improved predictive abilities. The indirect predictive ability for a trait was proportionate to its correlation with other traits. These results will help breeders to select the best models, optimum marker set, and suitable genotype set to perform an indirect selection for quantitative traits in this diverse flax germplasm collection.
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Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - James V Anderson
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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3
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Cloutier S, Edwards T, Zheng C, Booker HM, Islam T, Nabetani K, Kutcher HR, Molina O, You FM. Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:27. [PMID: 38245903 PMCID: PMC10800302 DOI: 10.1007/s00122-023-04528-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.
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Affiliation(s)
- S Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - T Edwards
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - C Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - H M Booker
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
| | - T Islam
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - K Nabetani
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - H R Kutcher
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - O Molina
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - F M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, 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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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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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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Dvorianinova EM, Zinovieva OL, Pushkova EN, Zhernova DA, Rozhmina TA, Povkhova LV, Novakovskiy RO, Sigova EA, Turba AA, Borkhert EV, Krasnov GS, Ruan C, Dmitriev AA, Melnikova NV. Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data. Int J Mol Sci 2023; 24:14885. [PMID: 37834335 PMCID: PMC10573214 DOI: 10.3390/ijms241914885] [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: 08/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.
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Affiliation(s)
| | - Olga L. Zinovieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Zhao X, Yi L, Zuo Y, Gao F, Cheng Y, Zhang H, Zhou Y, Jia X, Su S, Zhang D, Zhang X, Ren Y, Mu Y, Jin X, Li Q, Bateer S, Lu Z. High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement. PLANTS (BASEL, SWITZERLAND) 2023; 12:2773. [PMID: 37570928 PMCID: PMC10421198 DOI: 10.3390/plants12152773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023]
Abstract
Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.
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Affiliation(s)
- Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Liuxi Yi
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Yongchun Zuo
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Hohhot 010019, China
| | - Fengyun Gao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Hui Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yu Zhou
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaoyun Jia
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Shaofeng Su
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Dejian Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yongfeng Ren
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yanxin Mu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiaolei Jin
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Qiang Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Siqin Bateer
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
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11
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Chabi M, Goulas E, Galinousky D, Blervacq AS, Lucau-Danila A, Neutelings G, Grec S, Day A, Chabbert B, Haag K, Müssig J, Arribat S, Planchon S, Renaut J, Hawkins S. Identification of new potential molecular actors related to fiber quality in flax through Omics. FRONTIERS IN PLANT SCIENCE 2023; 14:1204016. [PMID: 37528984 PMCID: PMC10390313 DOI: 10.3389/fpls.2023.1204016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 08/03/2023]
Abstract
One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.
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Affiliation(s)
- Malika Chabi
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Dmitry Galinousky
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Anne-Sophie Blervacq
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Anca Lucau-Danila
- Université de Lille, UMRT 1158 BioEcoAgro, Institut Charles Viollette, Lille, France
| | - Godfrey Neutelings
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Arnaud Day
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Fibres Recherche Développement, Technopole de l’Aube en Champagne – Hôtel de Bureaux 2, 2 rue Gustave Eiffel, CS 90601, Troyes, France
| | - Brigitte Chabbert
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France
| | - Katharina Haag
- Fraunhofer-Institute for Manufacturing Technology and Advanced Materials IFAM, Bremen, Germany
| | - Jörg Müssig
- The Biological Materials Group, HSB – City University of Applied Sciences, Bremen, Germany
| | - Sandrine Arribat
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Planchon
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Simon Hawkins
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Saroha A, Gomashe SS, Kaur V, Pal D, Ujjainwal S, Aravind J, Singh M, Rajkumar S, Singh K, Kumar A, Wankhede DP. Genetic dissection of thousand-seed weight in linseed ( Linum usitatissimum L.) using multi-locus genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1166728. [PMID: 37332700 PMCID: PMC10272591 DOI: 10.3389/fpls.2023.1166728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/08/2023] [Indexed: 06/20/2023]
Abstract
Flaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified using multi-locus genome-wide association study (ML-GWAS). Field evaluation was carried out in five environments in multi-year-location trials. SNP genotyping information of the AM panel of 131 accessions comprising 68,925 SNPs was employed for ML-GWAS. From the six ML-GWAS methods employed, five methods helped identify a total of 84 unique significant QTNs for TSW. QTNs identified in ≥ 2 methods/environments were designated as stable QTNs. Accordingly, 30 stable QTNs have been identified for TSW accounting up to 38.65% trait variation. Alleles with positive effect on trait were analyzed for 12 strong QTNs with r 2 ≥ 10.00%, which showed significant association of specific alleles with higher trait value in three or more environments. A total of 23 candidate genes have been identified for TSW, which included B3 domain-containing transcription factor, SUMO-activating enzyme, protein SCARECROW, shaggy-related protein kinase/BIN2, ANTIAUXIN-RESISTANT 3, RING-type E3 ubiquitin transferase E4, auxin response factors, WRKY transcription factor, and CBS domain-containing protein. In silico expression analysis of candidate genes was performed to validate their possible role in different stages of seed development process. The results from this study provide significant insight and elevate our understanding on genetic architecture of TSW trait in linseed.
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Affiliation(s)
- Ankit Saroha
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sunil S. Gomashe
- ICAR-National Bureau of Plant Genetic Resources, Regional Station Akola, Maharashtra, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Deepa Pal
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shraddha Ujjainwal
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - J. Aravind
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mamta Singh
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. Rajkumar
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Singh
- 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
| | - Dhammaprakash Pandhari Wankhede
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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13
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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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15
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The flax genome reveals orbitide diversity. BMC Genomics 2022; 23:534. [PMID: 35870878 PMCID: PMC9308333 DOI: 10.1186/s12864-022-08735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ribosomally-synthesized cyclic peptides are widely found in plants and exhibit useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the growing number of sequenced genomes. While previous research largely focused on the chemical diversity of these peptides across various species, there is little attention to a broader range of potential peptides that are not chemically identified. Results A pioneering study was initiated to explore the genetic diversity of linusorbs, a group of cyclic peptides uniquely occurring in cultivated flax (Linum usitatissimum). Phylogenetic analysis clustered the 5 known linusorb precursor proteins into two clades and one singleton. Preliminary tBLASTn search of the published flax genome using the whole protein sequence as query could only retrieve its homologues within the same clade. This limitation was overcome using a profile-based mining strategy. After genome reannotation, a hidden Markov Model (HMM)-based approach identified 58 repeats homologous to the linusorb-embedded repeats in 8 novel proteins, implying that they share common ancestry with the linusorb-embedded repeats. Subsequently, we developed a customized profile composed of a random linusorb-like domain (LLD) flanked by 5 conserved sites and used it for string search of the proteome, which extracted 281 LLD-containing repeats (LLDRs) in 25 proteins. Comparative analysis of different repeat categories suggested that the 5 conserved flanking sites among the non-homologous repeats have undergone convergent evolution driven by functional selection. Conclusions The profile-based mining approach is suitable for analyzing repetitive sequences. The 25 LLDR proteins identified herein represent the potential diversity of cyclic peptides within the flax genome and lay a foundation for further studies on the functions and evolution of these protein tandem repeats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08735-x.
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16
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Dvorianinova EM, Bolsheva NL, Pushkova EN, Rozhmina TA, Zhuchenko AA, Novakovskiy RO, Povkhova LV, Sigova EA, Zhernova DA, Borkhert EV, Kaluzhny DN, Melnikova NV, Dmitriev AA. Isolating Linum usitatissimum L. Nuclear DNA Enabled Assembling High-Quality Genome. Int J Mol Sci 2022; 23:ijms232113244. [PMID: 36362031 PMCID: PMC9656206 DOI: 10.3390/ijms232113244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
High-quality genome sequences help to elucidate the genetic basis of numerous biological processes and track species evolution. For flax (Linum usitatissimum L.)—a multifunctional crop, high-quality assemblies from Oxford Nanopore Technologies (ONT) data were unavailable, largely due to the difficulty of isolating pure high-molecular-weight DNA. This article proposes a scheme for gaining a contiguous L. usitatissimum assembly using Nanopore data. We developed a protocol for flax nuclei isolation with subsequent DNA extraction, which allows obtaining about 5 μg of pure high-molecular-weight DNA from 0.5 g of leaves. Such an amount of material can be collected even from a single plant and yields more than 30 Gb of ONT data in two MinION runs. We performed a comparative analysis of different genome assemblers and polishers on the gained data and obtained the final 447.1-Mb assembly of L. usitatissimum line 3896 genome using the Canu—Racon (two iterations)—Medaka combination. The genome comprised 1695 contigs and had an N50 of 6.2 Mb and a completeness of 93.8% of BUSCOs from eudicots_odb10. Our study highlights the impact of the chosen genome construction strategy on the resulting assembly parameters and its eligibility for future genomic studies.
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Affiliation(s)
- Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Correspondence: (E.M.D.); (A.A.D.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow 115598, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Correspondence: (E.M.D.); (A.A.D.)
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17
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Adaptive Response and Transcriptomic Analysis of Flax (Linum usitatissimum L.) Seedlings to Salt Stress. Genes (Basel) 2022; 13:genes13101904. [DOI: 10.3390/genes13101904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Soil salinity constrains agricultural development in arid regions. Flax is an economically important crop in many countries, and screening or breeding salinity-resistant flax cultivars is necessary. Based on the previous screening of flaxseed cultivars C71 (salt-sensitive) and C116 (salt-tolerant) as test materials, flax seedlings stressed with different concentrations of NaCl (0, 100, 150, 200, and 250 mmol/L) for 21 days were used to investigate the effects of salt stress on the growth characteristics, osmotic regulators, and antioxidant capacity of these flax seedlings and to reveal the adaptive responses of flax seedlings to salt stress. The results showed that plant height and root length of flax were inhibited, with C116 showing lower growth than C71. The concentrations of osmotic adjustment substances such as soluble sugars, soluble proteins, and proline were higher in the resistant material, C116, than in the sensitive material, C71, under different concentrations of salt stress. Consistently, C116 showed a better rapid scavenging ability for reactive oxygen species (ROS) and maintained higher activities of antioxidant enzymes to balance salt injury stress by inhibiting growth under salt stress. A transcriptome analysis of flax revealed that genes related to defense and senescence were significantly upregulated, and genes related to the growth and development processes were significantly downregulated under salt stress. Our results indicated that one of the important adaptations to tolerance to high salt stress is complex physiological remediation by rapidly promoting transcriptional regulation in flax.
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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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Speck A, Trouvé JP, Enjalbert J, Geffroy V, Joets J, Moreau L. Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:871633. [PMID: 35812909 PMCID: PMC9263915 DOI: 10.3389/fpls.2022.871633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew is one of the most important diseases of flax and is particularly prejudicial to its yield and oil or fiber quality. This disease, caused by the obligate biotrophic ascomycete Oïdium lini, is progressing in France. Genetic resistance of varieties is critical for the control of this disease, but very few resistance genes have been identified so far. It is therefore necessary to identify new resistance genes to powdery mildew suitable to the local context of pathogenicity. For this purpose, we studied a worldwide diversity panel composed of 311 flax genotypes both phenotyped for resistance to powdery mildew resistance over 2 years of field trials in France and resequenced. Sequence reads were mapped on the CDC Bethune reference genome revealing 1,693,910 high-quality SNPs, further used for both population structure analysis and genome-wide association studies (GWASs). A number of four major genetic groups were identified, separating oil flax accessions from America or Europe and those from Asia or Middle-East and fiber flax accessions originating from Eastern Europe and those from Western Europe. A number of eight QTLs were detected at the false discovery rate threshold of 5%, located on chromosomes 1, 2, 4, 13, and 14. Taking advantage of the moderate linkage disequilibrium present in the flax panel, and using the available genome annotation, we identified potential candidate genes. Our study shows the existence of new resistance alleles against powdery mildew in our diversity panel, of high interest for flax breeding program.
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Affiliation(s)
| | | | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Johann Joets
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
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Saroha A, Pal D, Gomashe SS, Akash, Kaur V, Ujjainwal S, Rajkumar S, Aravind J, Radhamani J, Kumar R, Chand D, Sengupta A, Wankhede DP. Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study. Front Genet 2022; 13:811924. [PMID: 35774513 PMCID: PMC9237403 DOI: 10.3389/fgene.2022.811924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed.
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Saha D, Shaw AK, Datta S, Mitra J, Kar G. DNA hypomethylation is the plausible driver of heat stress adaptation in Linum usitatissimum. PHYSIOLOGIA PLANTARUM 2022; 174:e13689. [PMID: 35462427 DOI: 10.1111/ppl.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Heat stress has a significant impact on the climatic adaptation of flax, a cool-season economic crop. Genome-wide DNA methylation patterns are crucial for understanding how flax cultivars respond to heat adversities. It is worth noting that the DNA methylome in flax has yet to be investigated at the nucleotide level. Although heat stress above 40°C caused oxidative damage in flax leaves, 5-azacytidine, a hypomethylating agent, reduced this effect by 15%-24%. Differences in the expression of the LuMET1 (DNA methyltransferase) gene suggested that DNA methylation/demethylation may play a major role in the flax heat stress response. Thus, whole-genome bisulfite sequencing-derived DNA methylation profiles in flax, with or without heat stress and 5-azaC, were developed and analyzed here. In response to heat stress, a high percentage of significant differentially methylated regions (DMRs), particularly hypomethylated DMRs, were identified in the CHH nucleotide sequence context (H = A/T/C). Some of these DMRs overlapped with transposable element insertions. The majority of DMRs were discovered in intergenic regions, but several DMR loci were also found near genes relevant to heat stress response and epigenetic processes. These DMRs, in particular, are linked to CpG islands, implying a possible role in promoter methylation and gene silencing. The DMRs discovered in this study are crucial for understanding and identifying the key players in heat stress response in flax, which will help in developing climate-smart flax varieties.
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Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Arun Kumar Shaw
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Gouranga Kar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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22
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Innes P, Gossweiler A, Jensen S, Tilley D, St. John L, Jones T, Kitchen S, Hulke BS. Assessment of biogeographic variation in traits of Lewis flax ( Linum lewisii) for use in restoration and agriculture. AOB PLANTS 2022; 14:plac005. [PMID: 35273788 PMCID: PMC8906388 DOI: 10.1093/aobpla/plac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Lewis flax (Linum lewisii) is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in de novo domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess biogeographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain West region, the pre-variety germplasm Maple Grove (L. lewisii) and the cultivar 'Appar' (L. perenne) and related this variation to collection site geography and climate. Results from linear mixed models suggest there is extensive phenotypic variation among populations of Lewis flax within the Intermountain West. Using a multivariate approach, we identify a key suite of traits that are related to latitude and climate and may facilitate adaptation, including flowering indeterminacy, seed mass and stem number. These traits should be taken into account when considering the release of new germplasm for restoration efforts. We also find that Lewis flax seed contains desirably high amounts of alpha-linolenic acid and is otherwise mostly indistinguishable in fatty acid composition from oil-type varieties of domesticated flax (L. usitatissimum), making it a strong candidate for domestication. This study provides fundamental knowledge for future research into the ecology and evolution of Lewis flax, which will inform its use in both restoration and agriculture.
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Affiliation(s)
- Peter Innes
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - André Gossweiler
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Scott Jensen
- Rocky Mountain Research Station, United States Department of Agriculture – Forest Service, Provo, UT 84606, USA
| | - Derek Tilley
- Aberdeen Plant Materials Center, United States Department of Agriculture – Natural Resources Conservation Service, Aberdeen, ID 83210, USA
| | - Loren St. John
- Aberdeen Plant Materials Center, United States Department of Agriculture – Natural Resources Conservation Service, Aberdeen, ID 83210, USA
| | - Thomas Jones
- Forage and Range Research Laboratory, United States Department of Agriculture – Agricultural Research Service, Logan, UT 84322, USA
| | - Stanley Kitchen
- Rocky Mountain Research Station, United States Department of Agriculture – Forest Service, Provo, UT 84606, USA
| | - Brent S Hulke
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture – Agricultural Research Service, Fargo, ND 58102, USA
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House MA, Young LW, Robinson SJ, Booker HM. Transcriptomic Analysis of Early Flowering Signals in ‘Royal’ Flax. PLANTS 2022; 11:plants11070860. [PMID: 35406840 PMCID: PMC9002848 DOI: 10.3390/plants11070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.
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Affiliation(s)
- Megan A. House
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Lester W. Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada;
| | - Helen M. Booker
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 56829)
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Young L, Akhov L, Kulkarni M, You F, Booker H. Fine-mapping of a putative glutathione S-transferase (GST) gene responsible for yellow seed colour in flax (Linum usitatissimum). BMC Res Notes 2022; 15:72. [PMID: 35184755 PMCID: PMC8859895 DOI: 10.1186/s13104-022-05964-x] [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: 10/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Objective The brown seed coat colour of flax (Linum ustiatissimum) results from proanthocyanidin synthesis and accumulation. Glutathione S-transferases (GSTs), such as the TT19 protein in Arabidopsis, have been implicated in the transport of anthocyanidins during the synthesis of the brown proanthocyanidins. This study fine mapped the g allele responsible for yellow seed colour in S95407 and identified it as a putative mutated GST. Results We developed a Recombinant Inbred Line population with 320 lines descended from a cross between CDC Bethune (brown seed coat) and S95407 (yellow seed) and used molecular markers to fine map the G gene on Chromosome 6 (Chr 6). We used Next Generation Sequencing (NGS) to identify a putative GST was identified in this region and Sanger sequenced the gene from CDC Bethune, S95407 and other yellow seeded genotypes. The putative GST from S95407 had 13 SNPs encoding, including four non-synonymous amino acid changes, compared to the CDC Bethune reference sequence and the other genotypes. The GST encoded by Lus10019895 is a lambda-GST in contrast to the Arabidopsis TT19 which is a phi-GST. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-05964-x.
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Affiliation(s)
- Lester Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7H 3R2, Canada.
| | - Leonid Akhov
- National Research Council Saskatoon, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Manoj Kulkarni
- National Research Council Saskatoon, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Frank You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Crop Science Building, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
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Pokhrel S, Meyers BC. Heat-responsive microRNAs and phased small interfering RNAs in reproductive development of flax. PLANT DIRECT 2022; 6:e385. [PMID: 35224420 PMCID: PMC8845017 DOI: 10.1002/pld3.385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
Plants will face increased heat stress due to rising global temperatures. Heat stress affects plant reproductive development and decreases productivity; however, the underlying molecular mechanisms of these processes are poorly characterized. Plant small RNAs (sRNAs) have important regulatory roles in plant reproductive development following abiotic stress responses. We generated sRNA transcriptomes of reproductive bud stages at three different time points to identify sRNA-mediated pathways responsive to heat stress in flax (Linum usitatissimum). With added sRNA transcriptomes of vegetative tissues, we comprehensively annotated miRNA and phasiRNA-encoding genes (PHAS) in flax. We identified 173 miRNA genes, of which 42 are newly annotated. Our analysis revealed that 141 miRNA genes were differentially accumulated between tissue types, while 18 miRNA genes were differentially accumulated in reproductive tissues following heat stress, including members of miR482/2118 and miR2275 families, known triggers of reproductive phasiRNAs. Furthermore, we identified 68 21-PHAS flax loci from protein-coding and noncoding regions, four 24-PHAS loci triggered by miR2275, and 658 24-PHAS-like loci with unknown triggers, derived mostly from noncoding regions. The reproductive phasiRNAs are mostly downregulated in response to heat stress. Overall, we found that several previously unreported miRNAs and phasiRNAs are responsive to heat stress in flax reproductive tissues.
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Affiliation(s)
- Suresh Pokhrel
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Blake C. Meyers
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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Meng X, Liu J, Zhao M. Genome-wide identification of RING finger genes in flax ( Linum usitatissimum) and analyses of their evolution. PeerJ 2021; 9:e12491. [PMID: 34820204 PMCID: PMC8601054 DOI: 10.7717/peerj.12491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.
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Affiliation(s)
- Xianwen Meng
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Jing Liu
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Mingde Zhao
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
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29
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Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, Zulkifli MA, Heslop-Harrison JSP. Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species. Chromosome Res 2021; 29:373-390. [PMID: 34657216 DOI: 10.1007/s10577-021-09675-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/26/2022]
Abstract
Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.
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Affiliation(s)
- Noorhariza Mohd Zaki
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | | | - Rajinder Singh
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | | | - Nordiana Hanim Mohd Nor
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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30
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Sa R, Yi L, Siqin B, An M, Bao H, Song X, Wang S, Li Z, Zhang Z, Hazaisi H, Guo J, Su S, Li J, Zhao X, Lu Z. Chromosome-Level Genome Assembly and Annotation of the Fiber Flax ( Linum usitatissimum) Genome. Front Genet 2021; 12:735690. [PMID: 34589116 PMCID: PMC8473814 DOI: 10.3389/fgene.2021.735690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rula Sa
- School of Pharmaceutical Sciences, Baotou Medical College, Baotou, China
| | - Liuxi Yi
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Bateer Siqin
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Biotechnology Research Center, Hohhot, China
| | - Ming An
- School of Pharmaceutical Sciences, Baotou Medical College, Baotou, China
| | - Haizhu Bao
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoling Song
- School of Pharmaceutical Sciences, Baotou Medical College, Baotou, China
| | - Shuyan Wang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiwei Li
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Zheng Zhang
- Yili Institute of Agricultural Science, Xinjiang, China
| | | | - Jingjing Guo
- School of Pharmaceutical Sciences, Baotou Medical College, Baotou, China
| | - Shaofeng Su
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Biotechnology Research Center, Hohhot, China
| | - Jinhuan Li
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Biotechnology Research Center, Hohhot, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Biotechnology Research Center, Hohhot, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Biotechnology Research Center, Hohhot, China
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31
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Tsai H, Kippes N, Firl A, Lieberman M, Comai L, Henry IM. Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture. G3-GENES GENOMES GENETICS 2021; 11:6321234. [PMID: 34544134 PMCID: PMC8496254 DOI: 10.1093/g3journal/jkab232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/25/2021] [Indexed: 11/12/2022]
Abstract
The sustainability of many crops is hindered by the lack of genomic resources and a poor understanding of natural genetic diversity. Particularly, application of modern breeding requires high-density linkage maps that are integrated into a highly contiguous reference genome. Here, we present a rapid method for deriving haplotypes and developing linkage maps, and its application to Mentha suaveolens, one of the diploid progenitors of cultivated mints. Using sequence-capture via DNA hybridization to target single nucleotide polymorphisms (SNPs), we successfully genotyped ∼5000 SNPs within the genome of >400 individuals derived from a self cross. After stringent quality control, and identification of nonredundant SNPs, 1919 informative SNPs were retained for linkage map construction. The resulting linkage map defined a total genetic space of 942.17 cM divided among 12 linkage groups, ranging from 56.32 to 122.61 cM in length. The linkage map is in good agreement with pseudomolecules from our preliminary genome assembly, proving this resource effective for the correction and validation of the reference genome. We discuss the advantages of this method for the rapid creation of linkage maps.
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Affiliation(s)
- Helen Tsai
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Nestor Kippes
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Alana Firl
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Meric Lieberman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
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Dmitriev AA, Pushkova EN, Novakovskiy RO, Beniaminov AD, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Muravenko OV, Povkhova LV, Dvorianinova EM, Kezimana P, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms. Front Genet 2021; 11:590282. [PMID: 33519894 PMCID: PMC7841463 DOI: 10.3389/fgene.2020.590282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/02/2020] [Indexed: 01/11/2023] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Sertse D, You FM, Ravichandran S, Soto-Cerda BJ, Duguid S, Cloutier S. Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:191-212. [PMID: 33047220 DOI: 10.1007/s00122-020-03691-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/18/2020] [Indexed: 05/19/2023]
Abstract
QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today's agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Centre (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Scott Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada.
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada.
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34
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Dmitriev AA, Novakovskiy RO, Pushkova EN, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Beniaminov AD, Mitkevich VA, Povkhova LV, Dvorianinova EM, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Transcriptomes of Different Tissues of Flax ( Linum usitatissimum L.) Cultivars With Diverse Characteristics. Front Genet 2020; 11:565146. [PMID: 33363567 PMCID: PMC7755106 DOI: 10.3389/fgene.2020.565146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Galinousky D, Mokshina N, Padvitski T, Ageeva M, Bogdan V, Kilchevsky A, Gorshkova T. The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality. Front Genet 2020; 11:589881. [PMID: 33281880 PMCID: PMC7690631 DOI: 10.3389/fgene.2020.589881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective manipulation of technical fiber quality. A key step was to identify genes with tissue and stage-specific pattern of expression in the developing fibers. In the current study, we investigated the relationship between gene expression evaluated in bast fibers of developing flax plants and the quality parameters of technical fibers measured after plant harvesting. Based on previously published transcriptomic data, two sets of genes that are upregulated in fibers during intrusive growth and tertiary cell wall deposition were selected. The expression level of the selected genes and fiber quality parameters were measured in fiber flax, linseed (oil flax) cultivars, and wild species that differ in type of yield and fiber quality parameters. Based on gene expression data, linear regression models for technical stem length, fiber tensile strength, and fiber flexibility were constructed, resulting in the identification of genes that have high potential for manipulating fiber quality. Chromosomal localization and single nucleotide polymorphism distribution in the selected genes were characterized for the efficacy of their use in conventional breeding and genome editing programs. Transcriptome-based selection is a highly targeted functional approach that could be used during the development of new cultivars of various crops.
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Affiliation(s)
- Dmitry Galinousky
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Tsimafei Padvitski
- Cellular Network and Systems Biology Group, University of Cologne, CECAD, Cologne, Germany
| | - Marina Ageeva
- Laboratory of Microscopy, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Victor Bogdan
- Laboratory of Fiber Flax Breeding, Institute of Flax, Ustie, Belarus
| | - Alexander Kilchevsky
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
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Khan N, You FM, Datla R, Ravichandran S, Jia B, Cloutier S. Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). BMC Genomics 2020; 21:722. [PMID: 33076828 PMCID: PMC7574471 DOI: 10.1186/s12864-020-07121-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome. Results Here we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains’ composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization. Conclusion Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.
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Affiliation(s)
- Nadeem Khan
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Bosen Jia
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada. .,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
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Dmitriev AA, Kezimana P, Rozhmina TA, Zhuchenko AA, Povkhova LV, Pushkova EN, Novakovskiy RO, Pavelek M, Vladimirov GN, Nikolaev EN, Kovaleva OA, Kostyukevich YI, Chagovets VV, Romanova EV, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines. BMC PLANT BIOLOGY 2020; 20:301. [PMID: 33050879 PMCID: PMC7557025 DOI: 10.1186/s12870-020-02499-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/15/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is grown for fiber and seed in many countries. Flax cultivars differ in the oil composition and, depending on the ratio of fatty acids, are used in pharmaceutical, food, or paint industries. It is known that genes of SAD (stearoyl-ACP desaturase) and FAD (fatty acid desaturase) families play a key role in the synthesis of fatty acids, and some alleles of these genes are associated with a certain composition of flax oil. However, data on genetic polymorphism of these genes are still insufficient. RESULTS On the basis of the collection of the Institute for Flax (Torzhok, Russia), we formed a representative set of 84 cultivars and lines reflecting the diversity of fatty acid composition of flax oil. An approach for the determination of full-length sequences of SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes using the Illumina platform was developed and deep sequencing of the 6 genes in 84 flax samples was performed on MiSeq. The obtained high coverage (about 400x on average) enabled accurate assessment of polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes and evaluation of cultivar/line heterogeneity. The highest level of genetic diversity was observed for FAD3A and FAD3B genes - 91 and 62 polymorphisms respectively. Correlation analysis revealed associations between particular variants in SAD and FAD genes and predominantly those fatty acids whose conversion they catalyze: SAD - stearic and oleic acids, FAD2 - oleic and linoleic acids, FAD3 - linoleic and linolenic acids. All except one low-linolenic flax cultivars/lines contained both the substitution of tryptophan to stop codon in the FAD3A gene and histidine to tyrosine substitution in the FAD3B gene, while samples with only one of these polymorphisms had medium content of linolenic acid and cultivars/lines without them were high-linolenic. CONCLUSIONS Genetic polymorphism of SAD and FAD genes was evaluated in the collection of flax cultivars and lines with diverse oil composition, and associations between particular polymorphisms and the ratio of fatty acids were revealed. The achieved results are the basis for the development of marker-assisted selection and DNA-based certification of flax cultivars.
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Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | | - Vitaliy V Chagovets
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Elena V Romanova
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Hoque A, Fiedler JD, Rahman M. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genomics 2020; 21:557. [PMID: 32795254 PMCID: PMC7430851 DOI: 10.1186/s12864-020-06922-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/17/2020] [Indexed: 11/25/2022] Open
Abstract
Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
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Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Jason D Fiedler
- Cereal Crops Research, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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Akhmetshina AO, Strygina KV, Khlestkina EK, Porokhovinova EA, Brutch NB. High-throughput sequencing techniques to flax genetics and breeding. ECOLOGICAL GENETICS 2020. [PMID: 0 DOI: 10.17816/ecogen16126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatissimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.
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Zou XG, Li J, Sun PL, Fan YW, Yang JY, Deng ZY. Orbitides isolated from flaxseed induce apoptosis against SGC-7901 adenocarcinoma cells. Int J Food Sci Nutr 2020; 71:929-939. [PMID: 32281434 DOI: 10.1080/09637486.2020.1750573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Unique plant-derived cyclic peptides family exhibiting various key biological activities has great possibility for anticancer therapy. In this study, we investigated the effects of orbitides isolated from flax (Linum usitatissimum L.) on the growth of SGC-7901 cancer cells and the potential mechanism. Results showed that flaxseed orbitides killed off cancer cells by inducing apoptosis in a dose-dependent manner, which was confirmed by the appearance of nuclear shrinkage and DNA fragmentation, and the inhibitory effect was stronger than that of pure orbitide [1-9-NαC]-linusorb B2 or [1-9-NαC]-linusorb B3. Besides, the mitochondrial apoptosis pathway-related protein cytochrome C (Cyt C) was released from mitochondria to cytosol, associated with the activation of caspases 9 and 3, and the cleavage of PARP. Taken together, these results indicated that flaxseed orbitides induced apoptosis via the mitochondrial pathway, releasing Cyt C, increasing Bax/Bcl-2 ratio and elevating the expression of cleaved caspase 9 and 3 in SGC-7901 cells.
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Affiliation(s)
- Xian-Guo Zou
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Pei-Long Sun
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Ya-Wei Fan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Jian-Yuan Yang
- College of Pharmaceutical and Life Sciences, Jiujiang University, Jiujiang, Jiangxi, China
| | - Ze-Yuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
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You FM, Cloutier S. Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax. Methods Protoc 2020; 3:mps3020028. [PMID: 32260372 PMCID: PMC7359702 DOI: 10.3390/mps3020028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 01/07/2023] Open
Abstract
Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.
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Zhang J, Qi Y, Wang L, Wang L, Yan X, Dang Z, Li W, Zhao W, Pei X, Li X, Liu M, Tan M, Wang L, Long Y, Wang J, Zhang X, Dang Z, Zheng H, Liu T. Genomic Comparison and Population Diversity Analysis Provide Insights into the Domestication and Improvement of Flax. iScience 2020; 23:100967. [PMID: 32240956 PMCID: PMC7114909 DOI: 10.1016/j.isci.2020.100967] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/17/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023] Open
Abstract
Flax has been cultivated for its oil and fiber for thousands of years. However, it remains unclear how the modifications of agronomic traits occurred on the genetic level during flax cultivation. In this study, we conducted genome-wide variation analyses on multiple accessions of oil-use, fiber-use, landraces, and pale flax to identify the genomic variations during flax cultivation. Our findings indicate that, during flax domestication, genes relevant to flowering, dehiscence, oil production, and plant architecture were preferentially selected. Furthermore, regardless of origins, the improvement of the modern oil-use flax preceded that of the fiber-use flax, although the dual selection on oil-use and fiber-use characteristics might have occurred in the early flax domestication. We also found that the expansion of MYB46/MYB83 genes may have contributed to the unique secondary cell wall biosynthesis in flax and the directional selections on MYB46/MYB83 may have shaped the morphological profile of the current oil-use and fiber-use flax. Assemblies of genomes, including oil-use flax, fiber-use flax and pale flax Comparative genomic analysis between pale flax and cultivated flax Dual-selection mode on oil-use and fiber-use characteristics might be existing Expansion and selection of MYB46/MYB83 may shape the morphological profile of flax
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Affiliation(s)
- Jianping Zhang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China.
| | - Yanni Qi
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Limin Wang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xingchu Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhao Dang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wenjuan Li
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wei Zhao
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Meilian Tan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Lei Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, China
| | - Zhanhai Dang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China.
| | | | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China.
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Lan S, Zheng C, Hauck K, McCausland M, Duguid SD, Booker HM, Cloutier S, You FM. Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax. Int J Mol Sci 2020; 21:ijms21051577. [PMID: 32106624 PMCID: PMC7084455 DOI: 10.3390/ijms21051577] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/23/2020] [Accepted: 02/23/2020] [Indexed: 01/21/2023] Open
Abstract
Molecular markers are one of the major factors affecting genomic prediction accuracy and the cost of genomic selection (GS). Previous studies have indicated that the use of quantitative trait loci (QTL) as markers in GS significantly increases prediction accuracy compared with genome-wide random single nucleotide polymorphism (SNP) markers. To optimize the selection of QTL markers in GS, a set of 260 lines from bi-parental populations with 17,277 genome-wide SNPs were used to evaluate the prediction accuracy for seed yield (YLD), days to maturity (DTM), iodine value (IOD), protein (PRO), oil (OIL), linoleic acid (LIO), and linolenic acid (LIN) contents. These seven traits were phenotyped over four years at two locations. Identification of quantitative trait nucleotides (QTNs) for the seven traits was performed using three types of statistical models for genome-wide association study: two SNP-based single-locus (SS), seven SNP-based multi-locus (SM), and one haplotype-block-based multi-locus (BM) models. The identified QTNs were then grouped into QTL based on haplotype blocks. For all seven traits, 133, 355, and 1208 unique QTL were identified by SS, SM, and BM, respectively. A total of 1420 unique QTL were obtained by SS+SM+BM, ranging from 254 (OIL, LIO) to 361 (YLD) for individual traits, whereas a total of 427 unique QTL were achieved by SS+SM, ranging from 56 (YLD) to 128 (LIO). SS models alone did not identify sufficient QTL for GS. The highest prediction accuracies were obtained using single-trait QTL identified by SS+SM+BM for OIL (0.929 ± 0.016), PRO (0.893 ± 0.023), YLD (0.892 ± 0.030), and DTM (0.730 ± 0.062), and by SS+SM for LIN (0.837 ± 0.053), LIO (0.835 ± 0.049), and IOD (0.835 ± 0.041). In terms of the number of QTL markers and prediction accuracy, SS+SM outperformed other models or combinations thereof. The use of all SNPs or QTL of all seven traits significantly reduced the prediction accuracy of traits. The results further validated that QTL outperformed high-density genome-wide random markers, and demonstrated that the combined use of single and multi-locus models can effectively identify a comprehensive set of QTL that improve prediction accuracy, but further studies on detection and removal of redundant or false-positive QTL to maximize prediction accuracy and minimize the number of QTL markers in GS are warranted.
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Affiliation(s)
- Samuel Lan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Mathematics and Statistics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
| | - Kyle Hauck
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Mathematics and Statistics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Madison McCausland
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Scott D. Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada;
| | - Helen M. Booker
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Correspondence: (F.M.Y.); (S.C); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Correspondence: (F.M.Y.); (S.C); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Novakovskiy RO, Povkhova LV, Krasnov GS, Rozhmina TA, Zhuchenko AA, Kudryavtseva LP, Pushkova EN, Kezimana P, Kudryavtseva AV, Dmitriev AA, Melnikova NV. The cinnamyl alcohol dehydrogenase gene family is involved in the response to Fusarium oxysporum in resistant and susceptible flax genotypes. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Flax (Linum usitatissimum L.) is used for the production of textile, oils, pharmaceuticals, and composite materials. Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. lini, is a very harmful disease that reduces flax production. Flax cultivars that are resistant to Fusarium wilt have been developed, and the genes that are involved in the host response to F. oxysporum have been identified. However, the mechanisms underlying resistance to this pathogen remain unclear. In the present study, we used transcriptome sequencing data obtained from susceptible and resistant flax genotypes grown under control conditions or F. oxysporum infection. Approximately 250 million reads, generated with an Illumina NextSeq instrument, were analyzed. After filtering to exclude the F. oxysporum transcriptome, the remaining reads were mapped to the L. usitatissimum genome and quantified. Then, the expression levels of cinnamyl alcohol dehydrogenase (CAD) family genes, which are known to be involved in the response to F. oxysporum, were evaluated in resistant and susceptible flax genotypes. Expression alterations in response to the pathogen were detected for all 13 examined CAD genes. The most significant differences in expression between control and infected plants were observed for CAD1B, CAD4A, CAD5A, and CAD5B, with strong upregulation of CAD1B, CAD5A, and CAD5B and strong downregulation of CAD4A. When plants were grown under the same conditions, the expression levels were similar in all studied flax genotypes for most CAD genes, and statistically significant differences in expression between resistant and susceptible genotypes were only observed for CAD1A. Our study indicates the strong involvement of CAD genes in flax response to F. oxysporum but brings no evidence of their role as resistance gene candidates. These findings contribute to the understanding of the mechanisms underlying the response of flax to F. oxysporum infection and the role of CAD genes in stress resistance.
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Affiliation(s)
- R. O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,
| | - L. V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Institute of Physics and Technology
| | - G. S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
| | - T. A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Federal Research Center for Bast Fiber Crops
| | - A. A. Zhuchenko
- Federal Research Center for Bast Fiber Crops; All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery
| | | | - E. N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
| | - P. Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Peoples’ Friendship University of Russia (RUDN University)
| | | | - A. A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
| | - N. V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
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Sertse D, You FM, Ravichandran S, Cloutier S. The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:1483. [PMID: 31798617 PMCID: PMC6878218 DOI: 10.3389/fpls.2019.01483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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46
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Shim YY, Song Z, Jadhav PD, Reaney MJ. Orbitides from flaxseed (Linum usitatissimum L.): A comprehensive review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Tombuloglu H. Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum). Genomics 2019; 112:782-795. [PMID: 31128265 DOI: 10.1016/j.ygeno.2019.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3-86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB141, and MYB146 genes were up-regulated in tissues having higher lignin production capacity. In opposite, MYB012 and MYB113 genes were down-regulated which points out the involvement of those genes in the lignin biosynthesis mechanism. This comprehensive study can provide a basis for understanding the role of MYBs in fiber or lignin production in flax.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441 Dammam, Saudi Arabia.
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48
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Sertse D, You FM, Ravichandran S, Cloutier S. The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation. Mol Phylogenet Evol 2019; 137:22-32. [PMID: 30978393 DOI: 10.1016/j.ympev.2019.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/15/2023]
Abstract
Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 flax growing countries. Population structure analysis resulted in a total of 12 populations that were pooled into four major groups: Temperate, South Asian, Abyssinian and Mediterranean. The vast majority (n = 335) belonged to the Temperate group that comprised eight populations including one dominated by fiber flax. Genetic variation between fiber and oil morphotypes was less pronounced than variation within morphotypes. The genetic variation among groups and populations was attributed in part to eco-geographic and anthropogenic factors. Genetic signatures indicated loci under strong selection by environmental factors such as day length. A high concentration of private haplotypes were observed in the South Asian, Mediterranean and Abyssinian populations despite their low genotype representation, hinting at the long history of the crop in these regions. The addition of genotypes from these three regions would enrich the core collection by capturing a wider genetic breadth for breeding and conservation.
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Affiliation(s)
- Demissew Sertse
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
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49
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Saha D, Mukherjee P, Dutta S, Meena K, Sarkar SK, Mandal AB, Dasgupta T, Mitra J. Genomic insights into HSFs as candidate genes for high-temperature stress adaptation and gene editing with minimal off-target effects in flax. Sci Rep 2019; 9:5581. [PMID: 30944362 PMCID: PMC6447620 DOI: 10.1038/s41598-019-41936-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
Flax (Linum usitatissimum) is a cool season crop commercially cultivated for seed oil and stem fibre production. A comprehensive characterization of the heat shock factor (HSF) candidate genes in flax can accelerate genetic improvement and adaptive breeding for high temperature stress tolerance. We report the genome-wide identification of 34 putative HSF genes from the flax genome, which we mapped on 14 of the 15 chromosomes. Through comparative homology analysis, we classified these genes into three broad groups, and sub-groups. The arrangement of HSF-specific protein motifs, DNA-binding domain (DBD) and hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries substantiated the phylogenetic separation of these genes. Orthologous relationships and evolutionary analysis revealed that the co-evolution of the LusHSF genes was due to recent genome duplication events. Digital and RT-qPCR analyses provided significant evidence of the differential expression of the LusHSF genes in various tissues, at various developmental stages, and in response to high-temperature stress. The co-localization of diverse cis-acting elements in the promoters of the LusHSF genes further emphasized their regulatory roles in the abiotic stress response. We further confirmed DNA-binding sites on the LusHSF proteins and designed guide RNA sequences for gene editing with minimal off-target effects. These results will hasten functional investigations of LusHSFs or assist in devising genome engineering strategies to develop high-temperature stress tolerant flax cultivars.
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Affiliation(s)
- Dipnarayan Saha
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India.
| | - Pranit Mukherjee
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
| | - Sourav Dutta
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
| | - Kanti Meena
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
| | - Surja Kumar Sarkar
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
| | - Asit Baran Mandal
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
| | - Tapash Dasgupta
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, West Bengal, India
| | - Jiban Mitra
- Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, West Bengal, 700121, India
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50
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Bolsheva NL, Melnikova NV, Kirov IV, Dmitriev AA, Krasnov GS, Amosova АV, Samatadze TE, Yurkevich OY, Zoshchuk SA, Kudryavtseva AV, Muravenko OV. Characterization of repeated DNA sequences in genomes of blue-flowered flax. BMC Evol Biol 2019; 19:49. [PMID: 30813893 PMCID: PMC6391757 DOI: 10.1186/s12862-019-1375-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method. RESULTS It was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes. CONCLUSIONS The evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Аlexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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