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Olmedo-Vicente E, Désamoré A, Simón-Porcar VI, Slotte T, Arroyo J. Development of microsatellite markers for sister species Linum suffruticosum and Linum tenuifolium in their overlapping ranges. Mol Biol Rep 2023; 50:7927-7933. [PMID: 37458871 PMCID: PMC10460739 DOI: 10.1007/s11033-023-08471-9] [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: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Microsatellite markers were developed for distylous Linum suffruticosum and tested in the monomorphic sister species Linum tenuifolium. These species are perennial herbs endemic to the western and northwestern Mediterranean, respectively, with a partially overlapping distribution area. METHODS AND RESULTS We developed 12 microsatellite markers for L. suffruticosum using next generation sequencing, and assessed their polymorphism and genetic diversity in 152 individuals from seven natural populations. The markers displayed high polymorphism, with two to 16 alleles per locus and population, and average observed and expected heterozygosities of 0.833 and 0.692, respectively. All loci amplified successfully in the sister species L. tenuifolium, and 150 individuals from seven populations were also screened. The polymorphism exhibited was high, with two to ten alleles per locus and population, and average observed and expected heterozygosities of 0.77 and 0.62, respectively. CONCLUSIONS The microsatellite markers identified in L. suffruticosum and tested in L. tenuifolium are a powerful tool to facilitate future investigations of the population genetics, mating patterns and hybridization between both Linum species in their contact zone.
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Affiliation(s)
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
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Paliwal S, Tripathi MK, Tiwari S, Tripathi N, Payasi DK, Tiwari PN, Singh K, Yadav RK, Asati R, Chauhan S. Molecular Advances to Combat Different Biotic and Abiotic Stresses in Linseed ( Linum usitatissimum L.): A Comprehensive Review. Genes (Basel) 2023; 14:1461. [PMID: 37510365 PMCID: PMC10379177 DOI: 10.3390/genes14071461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Flax, or linseed, is considered a "superfood", which means that it is a food with diverse health benefits and potentially useful bioactive ingredients. It is a multi-purpose crop that is prized for its seed oil, fibre, nutraceutical, and probiotic qualities. It is suited to various habitats and agro-ecological conditions. Numerous abiotic and biotic stressors that can either have a direct or indirect impact on plant health are experienced by flax plants as a result of changing environmental circumstances. Research on the impact of various stresses and their possible ameliorators is prompted by such expectations. By inducing the loss of specific alleles and using a limited number of selected varieties, modern breeding techniques have decreased the overall genetic variability required for climate-smart agriculture. However, gene banks have well-managed collectionns of landraces, wild linseed accessions, and auxiliary Linum species that serve as an important source of novel alleles. In the past, flax-breeding techniques were prioritised, preserving high yield with other essential traits. Applications of molecular markers in modern breeding have made it easy to identify quantitative trait loci (QTLs) for various agronomic characteristics. The genetic diversity of linseed species and the evaluation of their tolerance to abiotic stresses, including drought, salinity, heavy metal tolerance, and temperature, as well as resistance to biotic stress factors, viz., rust, wilt, powdery mildew, and alternaria blight, despite addressing various morphotypes and the value of linseed as a supplement, are the primary topics of this review.
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Affiliation(s)
- Shruti Paliwal
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Devendra K Payasi
- All India Coordinated Research Project on Linseed, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Regional Agricultural Research Station, Sagar 470001, India
| | - Prakash N Tiwari
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Kirti Singh
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Ruchi Asati
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Kaur V, Singh M, Wankhede DP, Gupta K, Langyan S, Aravind J, Thangavel B, Yadav SK, Kalia S, Singh K, Kumar A. Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies - a review. Front Nutr 2023; 10:1165580. [PMID: 37324736 PMCID: PMC10267467 DOI: 10.3389/fnut.2023.1165580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/27/2023] [Indexed: 06/17/2023] Open
Abstract
Linseed or flaxseed is a well-recognized nutritional food with nutraceutical properties owing to high omega-3 fatty acid (α-Linolenic acid), dietary fiber, quality protein, and lignan content. Currently, linseed enjoys the status of a 'superfood' and its integration in the food chain as a functional food is evolving continuously as seed constituents are associated with lowering the risk of chronic ailments, such as heart diseases, cancer, diabetes, and rheumatoid arthritis. This crop also receives much attention in the handloom and textile sectors as the world's coolest fabric linen is made up of its stem fibers which are endowed with unique qualities such as luster, tensile strength, density, bio-degradability, and non-hazardous nature. Worldwide, major linseed growing areas are facing erratic rainfall and temperature patterns affecting flax yield, quality, and response to biotic stresses. Amid such changing climatic regimes and associated future threats, diverse linseed genetic resources would be crucial for developing cultivars with a broad genetic base for sustainable production. Furthermore, linseed is grown across the world in varied agro-climatic conditions; therefore it is vital to develop niche-specific cultivars to cater to diverse needs and keep pace with rising demands globally. Linseed genetic diversity conserved in global genebanks in the form of germplasm collection from natural diversity rich areas is expected to harbor genetic variants and thus form crucial resources for breeding tailored crops to specific culinary and industrial uses. Global genebank collections thus potentially play an important role in supporting sustainable agriculture and food security. Currently, approximately 61,000 germplasm accessions of linseed including 1,127 wild accessions are conserved in genebanks/institutes worldwide. This review analyzes the current status of Linum genetic resources in global genebanks, evaluation for agro-morphological traits, stress tolerance, and nutritional profiling to promote their effective use for sustainable production and nutrition enhancement in our modern diets.
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Affiliation(s)
- Vikender Kaur
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mamta Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kavita Gupta
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jayaraman Aravind
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Boopathi Thangavel
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi, India
| | - Kuldeep Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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Li X, Qiao L, Chen B, Zheng Y, Zhi C, Zhang S, Pan Y, Cheng Z. SSR markers development and their application in genetic diversity evaluation of garlic ( Allium sativum) germplasm. PLANT DIVERSITY 2022; 44:481-491. [PMID: 36187554 PMCID: PMC9512637 DOI: 10.1016/j.pld.2021.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 05/25/2023]
Abstract
Garlic (Allium sativum), an asexually propagated vegetable and medicinal crop, has abundant genetic variation. Genetic diversity evaluation based on molecular markers has apparent advantages since their genomic abundance, environment insensitivity, and non-tissue specific features. However, the limited number of available DNA markers, especially SSR markers, are insufficient to conduct related genetic diversity assessment studies in garlic. In this study, 4372 EST-SSR markers were newly developed, and 12 polymorphic markers together with other 17 garlic SSR markers were used to assess the genetic diversity and population structure of 127 garlic accessions. The averaged polymorphism information content (PIC) of these 29 SSR markers was 0.36, ranging from 0.22 to 0.49. Seventy-nine polymorphic loci were detected among these accessions, with an average of 3.48 polymorphic loci per SSR. Both the clustering analyses based on either the genotype data of SSR markers or the phenotypic data of morphological traits obtained genetic distance divided the 127 garlic accessions into three clusters. Moreover, the Mantel test showed that genetic distance had no significant correlations with geographic distance, and weak correlations were found between genetic distance and the phenotypic traits. AMOVA analysis showed that the main genetic variation of this garlic germplasm collection existed in the within-population or cluster. Results of this study will be of great value for the genetic/breeding studies in garlic and enhance the utilization of these garlic germplasms.
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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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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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Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics. PLoS One 2020; 15:e0231002. [PMID: 32271806 PMCID: PMC7145005 DOI: 10.1371/journal.pone.0231002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sinapis alba is a wild member of the Brassicaceae family reported to possess genetic resistance against major biotic and abiotic stresses of oilseed brassicas. However, the resistance nature of S. alba was not exploited generously due to the unavailability of usable genome sequences in public databases. Therefore, the present study was conducted to assemble the first draft genome from raw whole genome shotgun sequences with annotation and develop simple sequence repeat markers for molecular genetics and marker-assisted breeding. RESULTS The raw genome sequences had 96x coverage on the Illumina platform with 170 Gbp data. The developed assembly by SOAPdenovo2 has ~459 Mbp genome size covered in 403,423 contigs with an average size of 1138.04 bp. The assembly was BLASTX with Arabidopsis thaliana which showed 32.9% positive hits between both plants. The top hit species distribution analysis showed the highest similarity with A. thaliana. A total of 809,597 GO level annotations were recorded after BLASTX results, and 34,012 sequences were annotated with different enzyme codes grouped under seven classes. The gene prediction tool AUGUSTUS identified 113,107 probable genes with an average size of 684 bp. The biochemical pathway annotation assigned 16,119 potential genes to 152 KEGG maps and 1751 enzyme codes. The development of potential SSRs from the de-novo assembly yielded 70731 unique primer pairs. Out of 159 randomly selected SSR markers for validation, 149 successfully amplified in S. alba. However, 10 SSR markers did not amplify during the validation experiment. CONCLUSION The annotated genome assembly with a large number of SSRs was developed in the present study. To the best of our knowledge, this is the first report of S. alba genome assembly development, annotation, and SSRs mining to date. The data presented here will be a very important resource for future crop improvement programs, especially for resistant breeding.
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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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Saha D, Rana RS, Das S, Datta S, Mitra J, Cloutier SJ, You FM. Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes. J Appl Genet 2018; 60:13-25. [PMID: 30368734 DOI: 10.1007/s13353-018-0476-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023]
Abstract
We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions. The panel included 33 accessions from India, including released varieties, dual-purpose lines and landraces, and 60 fiber flax accessions from the global core collection. Thirty-one ReG-SSR markers generated 76 alleles, with an average of 2.5 alleles per primer and a mean allele frequency of 0.77. These markers recorded 0.32 average gene diversity, 0.26 polymorphism information content and 1.35% null alleles. All the 31 ReG-SSR loci were found selectively neutral and showed no evidence of population reduction. A model-based clustering analysis separated the flax accessions into two sub-populations-Indian and global, with some accessions showing admixtures. The distinct clustering pattern of the Indian accessions compared to the global accessions, conforms to the principal coordinate analysis, genetic dissimilarity-based unweighted neighbor-joining tree and analysis of molecular variance. Fourteen flax accessions with 99.3% allelic richness were found optimum to adopt in breeding programs. In summary, the genome-wide ReG-SSR markers will serve as a functional marker resource for genetic and phenotypic relationship studies, marker-assisted selections, and provide a basis for selection of accessions from the Indian and global gene pool in fiber flax breeding programs.
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Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.
| | - Rajeev Singh Rana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Shantanab Das
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.,School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Sylvie J Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
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Soto-Cerda BJ, Cloutier S, Quian R, Gajardo HA, Olivos M, You FM. Genome-Wide Association Analysis of Mucilage and Hull Content in Flax ( Linum usitatissimum L.) Seeds. Int J Mol Sci 2018; 19:ijms19102870. [PMID: 30248911 PMCID: PMC6213135 DOI: 10.3390/ijms19102870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.
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Affiliation(s)
- Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Rocío Quian
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Humberto A Gajardo
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Marcos Olivos
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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Ouyang P, Kang D, Mo X, Tian E, Hu Y, Huang R. Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing. Molecules 2018; 23:molecules23082014. [PMID: 30104467 PMCID: PMC6222658 DOI: 10.3390/molecules23082014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/16/2018] [Accepted: 08/05/2018] [Indexed: 11/16/2022] Open
Abstract
Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10⁻40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.
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Affiliation(s)
- Puyue Ouyang
- Agricultural College, Guangxi University, Nanning 530005, China.
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou 510520, China.
| | - Dali Kang
- College of Medical Technology, Ningbo College of Health Sciences, Ningbo 315100, China.
| | - Xiaolu Mo
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou 510520, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Yanyu Hu
- Agricultural College, Guangxi University, Nanning 530005, China.
| | - Rongshao Huang
- Agricultural College, Guangxi University, Nanning 530005, China.
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Zhang J, Long Y, Wang L, Dang Z, Zhang T, Song X, Dang Z, Pei X. Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2018. [PMID: 30086718 DOI: 10.1186/s128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height. RESULTS In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered. CONCLUSIONS This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.
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Affiliation(s)
- Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liming Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Zhao Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Tianbao Zhang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaxia Song
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanhai Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhang J, Long Y, Wang L, Dang Z, Zhang T, Song X, Dang Z, Pei X. Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2018; 18:160. [PMID: 30086718 PMCID: PMC6081803 DOI: 10.1186/s12870-018-1366-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/16/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height. RESULTS In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered. CONCLUSIONS This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.
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Affiliation(s)
- Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Liming Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Zhao Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Tianbao Zhang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaxia Song
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhanhai Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Hussain T, Plunkett B, Ejaz M, Espley RV, Kayser O. Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata. FRONTIERS IN PLANT SCIENCE 2018; 9:537. [PMID: 29868043 PMCID: PMC5954354 DOI: 10.3389/fpls.2018.00537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/06/2018] [Indexed: 05/06/2023]
Abstract
The liverwort Radula marginata belongs to the bryophyte division of land plants and is a prospective alternate source of cannabinoid-like compounds. However, mechanistic insights into the molecular pathways directing the synthesis of these cannabinoid-like compounds have been hindered due to the lack of genetic information. This prompted us to do deep sequencing, de novo assembly and annotation of R. marginata transcriptome, which resulted in the identification and validation of the genes for cannabinoid biosynthetic pathway. In total, we have identified 11,421 putative genes encoding 1,554 enzymes from 145 biosynthetic pathways. Interestingly, we have identified all the upstream genes of the central precursor of cannabinoid biosynthesis, cannabigerolic acid (CBGA), including its two first intermediates, stilbene acid (SA) and geranyl diphosphate (GPP). Expression of all these genes was validated using quantitative real-time PCR. We have characterized the protein structure of stilbene synthase (STS), which is considered as a homolog of olivetolic acid in R. marginata. Moreover, the metabolomics approach enabled us to identify CBGA-analogous compounds using electrospray ionization mass spectrometry (ESI-MS/MS) and gas chromatography mass spectrometry (GC-MS). Transcriptomic analysis revealed 1085 transcription factors (TF) from 39 families. Comparative analysis showed that six TF families have been uniquely predicted in R. marginata. In addition, the bioinformatics analysis predicted a large number of simple sequence repeats (SSRs) and non-coding RNAs (ncRNAs). Our results collectively provide mechanistic insights into the putative precursor genes for the biosynthesis of cannabinoid-like compounds and a novel transcriptomic resource for R. marginata. The large-scale transcriptomic resource generated in this study would further serve as a reference transcriptome to explore the Radulaceae family.
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Affiliation(s)
- Tajammul Hussain
- Department of Technical Biochemistry, TU Dortmund University, Dortmund, Germany
- *Correspondence: Tajammul Hussain
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Mahwish Ejaz
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard V. Espley
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Oliver Kayser
- Department of Technical Biochemistry, TU Dortmund University, Dortmund, Germany
- Oliver Kayser
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Sudarshan GP, Kulkarni M, Akhov L, Ashe P, Shaterian H, Cloutier S, Rowland G, Wei Y, Selvaraj G. QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax). Sci Rep 2017; 7:15751. [PMID: 29146906 PMCID: PMC5691222 DOI: 10.1038/s41598-017-11565-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/31/2017] [Indexed: 11/08/2022] Open
Abstract
The flowers of flax (linseed) are blue-hued, ephemeral and self-pollinating, and the seeds are typically brown. A century-old interest in natural yellow seed variants and a historical model point to recessive alleles in B1, D and G loci being responsible, but the functional aspects had remained unknown. Here, we characterized the "D" locus by quantitative trait loci (QTL) mapping and identified a FLAVONOID 3'5' HYDROXYLASE (F3'5'H) gene therein. It does not belong to the F3'5'H clade, but resembles biochemically characterized F3'Hs (flavonoid 3' hydroxylase) but without F3'H activity. The genome lacks other F3'H or F3'H-like genes. The apparent neo-functionalization from F3'H is associated with a Thr498 → Ser498 substitution in a substrate recognition site (SRS). The yellow seed and white flower phenotypes of the classical d mutation was found to be due to one nucleotide deletion that would truncate the deduced product and remove three of the six potential SRS, negatively impacting delphinidin synthesis. Delphinidin is sporadic in angiosperms, and flax has no known pollination syndrome(s) with functional pollinator group(s) that are attracted to blue flowers, raising questions on the acquisition of F3'5'H. The appearance of d allele is suggestive of the beginning of the loss of F3'5'H in this species.
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Affiliation(s)
- Gurudatt Pavagada Sudarshan
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Bayer CropScience, Crop Analytics Morrisville, TECHIII 407 Davis Drive, Morrisville, NC, 27560, USA
| | - Manoj Kulkarni
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Leonid Akhov
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Paula Ashe
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Hamid Shaterian
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Gordon Rowland
- Crop Development Centre, Department of Plant Science, University of Saskatchewan, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Gopalan Selvaraj
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
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Saha D, Rana RS, Chakraborty S, Datta S, Kumar AA, Chakraborty AK, Karmakar PG. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Choudhary SB, Sharma HK, Kumar AA, Maruthi RT, Mitra J, Chowdhury I, Singh BK, Karmakar PG. SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions. C R Biol 2017; 340:65-75. [PMID: 28188068 DOI: 10.1016/j.crvi.2016.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/24/2016] [Accepted: 12/24/2016] [Indexed: 11/27/2022]
Abstract
A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm.
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Affiliation(s)
- Shashi Bhushan Choudhary
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India.
| | - Hariom Kumar Sharma
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
| | - Arroju Anil Kumar
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
| | - Rangappa Thimmaiah Maruthi
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
| | - Jiban Mitra
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
| | - Isholeena Chowdhury
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
| | - Binay Kumar Singh
- ICAR - Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Pran Gobinda Karmakar
- ICAR - Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India
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Tanwar UK, Pruthi V, Randhawa GS. RNA-Seq of Guar ( Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. FRONTIERS IN PLANT SCIENCE 2017; 8:91. [PMID: 28210265 PMCID: PMC5288370 DOI: 10.3389/fpls.2017.00091] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/16/2017] [Indexed: 05/24/2023]
Abstract
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained. The quality assessment of assembled unigenes revealed 87.50% of complete and 97.18% partial core eukaryotic genes (CEGs). Sequence similarity analyses and annotation of the unigenes against non-redundant protein (Nr) and Gene Ontology (GO) databases identified 175,882 GO annotations. A total of 11,308 guar unigenes were annotated with various enzyme codes (EC) and categorized in six categories with 55 subclasses. The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1759 enzyme codes. The species distribution analysis of the unigenes showed highest similarity with Glycine max genes. A total of 5773 potential simple sequence repeats (SSRs) and 3594 high-quality single nucleotide polymorphisms (SNPs) were identified. Out of 20 randomly selected SSRs for wet laboratory validation, 13 showed consistent PCR amplification in both guar varieties. In silico studies identified 145 polymorphic SSR markers in two varieties. To the best of our knowledge, this is the first report on transcriptome analysis and SNPs identification in guar till date.
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Wu J, Zhao Q, Wu G, Zhang S, Jiang T. Development of Novel SSR Markers for Flax ( Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 7:2018. [PMID: 28133461 PMCID: PMC5233678 DOI: 10.3389/fpls.2016.02018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/19/2016] [Indexed: 05/29/2023]
Abstract
Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.
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Affiliation(s)
- Jianzhong Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Qian Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Guangwen Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Shuquan Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
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Singh N, Kumar R, Kumar S, Singh PK, Yadav VK, Ranade SA, Yadav HK. Genetic diversity, population structure and association analysis in linseed ( Linum usitatissimum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:207-219. [PMID: 28250596 PMCID: PMC5313412 DOI: 10.1007/s12298-016-0408-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/15/2016] [Accepted: 12/23/2016] [Indexed: 05/16/2023]
Abstract
The present investigation aimed to explore the level of genetic diversity, determine the population structure in a larger set of germplasm of linseed using microsatellite marker and identify linked markers through association mapping. A total of 168 accessions of linseed were evaluated for major agro-economic traits and SSRs markers deployed for diversity assessment. A total of 337 alleles were amplified by 50 SSRs ranging from 2 to 13 with an average of 6.74 ± 2.8 alleles per loci. The neighbor joining based clustering grouped all the accessions into three major clusters that were also confirmed by scatter plot of PCoA. While model based clustering determined four sub-populations (K = 4). Further, analysis of molecular variance analysis considering three population showed that maximum variation (79%) was within the population. We identified one putative SSR marker (Lu_3043) linked with days to 50% flowering through both GLM and MLM analysis of association mapping. The results of this preliminary study revealed genetic diversity, population structure in linseed and linked marker which could be utilized in future breeding program.
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Affiliation(s)
- Neha Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
| | - Rajendra Kumar
- Uttar Pradesh Council of Agricultural Research (UPCAR), Vibhuti Khand, Gomatinagar, Lucknow, 226010 India
| | - Sujit Kumar
- Uttar Pradesh Council of Agricultural Research (UPCAR), Vibhuti Khand, Gomatinagar, Lucknow, 226010 India
| | | | - V. K. Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - S. A. Ranade
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
- Academy of Scientific and Innovative Research, New Delhi, India
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Danchenko M, Klubicova K, Krivohizha MV, Berezhna VV, Sakada VI, Hajduch M, Rashydov NM. Systems biology is an efficient tool for investigation of low-dose chronic irradiation influence on plants in the Chernobyl zone. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716060050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Abstract
New crops are gradually establishing along with cultivation systems to reduce reliance on depleting fossil fuel reserves and sustain better adaptation to climate change. These biological assets could be efficiently exploited as bioenergy feedstocks. Bioenergy crops are versatile renewable sources with the potential to alternatively contribute on a daily basis towards the coverage of modern society's energy demands. Biotechnology may facilitate the breeding of elite energy crop genotypes, better suited for bio-processing and subsequent use that will improve efficiency, further reduce costs, and enhance the environmental benefits of biofuels. Innovative molecular techniques may improve a broad range of important features including biomass yield, product quality and resistance to biotic factors like pests or microbial diseases or environmental cues such as drought, salinity, freezing injury or heat shock. The current review intends to assess the capacity of biotechnological applications to develop a beneficial bioenergy pipeline extending from feedstock development to sustainable biofuel production and provide examples of the current state of the art on future energy crops.
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24
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Zhao YM, Zhou T, Li ZH, Zhao GF. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). Molecules 2015; 20:21214-31. [PMID: 26633323 PMCID: PMC6332360 DOI: 10.3390/molecules201219758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.
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Affiliation(s)
- Yue-Mei Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
- College of Biopharmaceutical and Food Engineering, Shangluo University, Beixin Street, Shangluo 726000, China.
| | - Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
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Zhang L, Li Y, Tao A, Fang P, Qi J. Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp.). PLoS One 2015; 10:e0140861. [PMID: 26512891 PMCID: PMC4626149 DOI: 10.1371/journal.pone.0140861] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/01/2015] [Indexed: 11/19/2022] Open
Abstract
Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively). The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanru Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
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Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). Int J Genomics 2015; 2015:473028. [PMID: 26504770 PMCID: PMC4609433 DOI: 10.1155/2015/473028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/26/2015] [Indexed: 11/17/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.
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Nithin C, Patwa N, Thomas A, Bahadur RP, Basak J. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. BMC PLANT BIOLOGY 2015; 15:140. [PMID: 26067253 PMCID: PMC4464996 DOI: 10.1186/s12870-015-0516-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/29/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. RESULTS We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. CONCLUSIONS There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.
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Affiliation(s)
- Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Nisha Patwa
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India.
| | - Amal Thomas
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India.
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Yue XY, Liu GQ, Zong Y, Teng YW, Cai DY. Development of genic SSR markers from transcriptome sequencing of pear buds. J Zhejiang Univ Sci B 2015; 15:303-12. [PMID: 24711351 DOI: 10.1631/jzus.b1300240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.
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Affiliation(s)
- Xiao-yan Yue
- State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Department of Horticulture, Zhejiang University, Hangzhou 310058, China; College of Agriculture, Guizhou University, Guiyang 550025, China
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Kumar S, You FM, Duguid S, Booker H, Rowland G, Cloutier S. QTL for fatty acid composition and yield in linseed (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:965-84. [PMID: 25748113 DOI: 10.1007/s00122-015-2483-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/11/2015] [Indexed: 05/23/2023]
Abstract
The combined SSR-SNP map and 20 QTL for agronomic and quality traits will assist in marker assisted breeding as well as map-based cloning of key genes in linseed. Flax is an important nutraceutical crop mostly because it is a rich source of omega-3 fatty acids and antioxidant compounds. Canada is the largest producer and exporter of oilseed flax (or linseed), creating a growing need to improve crop productivity and quality. In this study, a genetic map was constructed based on selected 329 single nucleotide polymorphic markers and 362 simple sequence repeat markers using a recombinant inbred line population of 243 individuals from a cross between the Canadian varieties CDC Bethune and Macbeth. The genetic map consisted of 15 linkage groups comprising 691 markers with an average marker density of one marker every 1.9 cM. A total of 20 quantitative trait loci (QTL) were identified corresponding to 14 traits. Three QTL each for oleic acid and stearic acid, two QTL each for linoleic acid and iodine value and one each for palmitic acid, linolenic acid, oil content, seed protein, cell wall, straw weight, thousand seed weight, seeds per boll, yield and days to maturity were identified. The QTL for cell wall, straw weight, seeds per boll, yield and days to maturity all co-located on linkage group 4. Analysis of the candidate gene regions underlying the QTL identified proteins involved in cell wall and fibre synthesis, fatty acid biosynthesis as well as their metabolism and yield component traits. This study provides the foundation for assisting in map-based cloning of the QTL and marker assisted selection of a wide range of quality and agronomic traits in linseed and potentially fibre flax.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB, R3T 2N2, Canada
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Gantait S, Debnath S, Nasim Ali M. Genomic profile of the plants with pharmaceutical value. 3 Biotech 2014; 4:563-578. [PMID: 28324311 PMCID: PMC4235889 DOI: 10.1007/s13205-014-0218-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/01/2014] [Indexed: 12/16/2022] Open
Abstract
There is an ample genetic diversity of plants with medicinal importance around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, identification, characterization and documentation of the gene pool of medicinal plants are essential for this purpose. Genomic information of many a medicinal plant species has increased rapidly since the past decade and genetic resources available for domestication and improvement programs include genome sequencing, expressed sequence tags sequencing, transcript profiling, gene transmit, molecular markers in favor of mapping and breeding. In recent years, multiple endeavors have been undertaken for genomic characterization of medicinal plant species with the aid of molecular markers for sustainable utilization of gene pool, its conservation and future studies. Recent advancement in genomics is so fast that only some researches have been published till date and to a large extent documentation is restricted to electronic resources. Whole genome profiling of the identified medicinal plant species, carried out by several researchers, based on the DNA fingerprinting, is well documented in the present review. This review will facilitate preparing a database of the widely used, economically important medicinal plant species, based on their genomic organization.
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Affiliation(s)
- Saikat Gantait
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Biotechnology, Instrumentation and Environmental Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, West Bengal, India.
| | - Sandip Debnath
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, West Bengal, India
| | - Md Nasim Ali
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
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Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers. PLoS One 2014; 9:e110638. [PMID: 25329551 PMCID: PMC4203809 DOI: 10.1371/journal.pone.0110638] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022] Open
Abstract
Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.
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Soto-Cerda BJ, Diederichsen A, Duguid S, Booker H, Rowland G, Cloutier S. The potential of pale flax as a source of useful genetic variation for cultivated flax revealed through molecular diversity and association analyses. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:2091-2107. [PMID: 26316841 PMCID: PMC4544635 DOI: 10.1007/s11032-014-0165-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/29/2014] [Indexed: 05/25/2023]
Abstract
Pale flax (Linum bienne Mill.) is the wild progenitor of cultivated flax (Linum usitatissimum L.) and represents the primary gene pool to broaden its genetic base. Here, a collection of 125 pale flax accessions and the Canadian flax core collection of 407 accessions were genotyped using 112 genome-wide simple sequence repeat markers and phenotyped for nine traits with the aim of conducting population structure, molecular diversity and association mapping analyses. The combined population structure analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L. usitatissimum convar. crepitans accessions most closely resembled its wild progenitor, both having dehiscent capsules. The unbiased Nei's genetic distance (0.65) confirmed the strong genetic differentiation between cultivated and pale flax. Similar levels of genetic diversity were observed in both species, albeit 430 (48 %) of pale flax alleles were unique, in agreement with their high genetic differentiation. Significant associations were identified for seven and four traits in pale and cultivated flax, respectively. Favorable alleles with potentially positive effect to improve yield through yield components were identified in pale flax. The allelic frequencies of markers associated with domestication-related traits such as capsular dehiscence indicated directional selection with the most common alleles in pale flax being absent or rare in cultivated flax and vice versa. Our results demonstrated that pale flax is a potential source of novel variation to improve multiple traits in cultivated flax and that association mapping is a suitable approach to screening pale flax germplasm to identify favorable quantitative trait locus alleles.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unit, 4791057 Temuco, Chile
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB R6M 1Y5 Canada
| | - Helen Booker
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Gordon Rowland
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Soto-Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S. Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:881-96. [PMID: 24463785 PMCID: PMC3964306 DOI: 10.1007/s00122-014-2264-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/03/2014] [Indexed: 05/20/2023]
Abstract
The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2 Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Km 10 Camino Cajón-Vilcún, Temuco, La Araucania Chile
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, Route 100, Morden, MB R6M 1Y5 Canada
| | - Helen Booker
- Crop Development Centre, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Gordon Rowland
- Crop Development Centre, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2 Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
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Izzah NK, Lee J, Jayakodi M, Perumal S, Jin M, Park BS, Ahn K, Yang TJ. Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map. BMC Genomics 2014; 15:149. [PMID: 24559437 PMCID: PMC3936860 DOI: 10.1186/1471-2164-15-149] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/17/2014] [Indexed: 12/27/2022] Open
Abstract
Background Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction. Results Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F2 population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility. Conclusions This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.
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Affiliation(s)
| | | | | | | | | | | | | | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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Soto-Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S. Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:75-87. [PMID: 24138336 PMCID: PMC4253320 DOI: 10.1111/jipb.12118] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/13/2013] [Indexed: 05/20/2023]
Abstract
The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection.
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Affiliation(s)
- Braulio J Soto-Cerda
- Department of Plant Science, University of Manitoba66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
- Cereal Research Center, Agriculture and Agri-Food Canada195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- † Permanent address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unit, Km 10 Camino Cajón-Vilcún, INIA, Temuco, Chile
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada101 Route 100, Unit 100 Morden, Manitoba, R6M 1Y5, Canada
| | - Helen Booker
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Gordon Rowland
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
- Cereal Research Center, Agriculture and Agri-Food Canada195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- * Correspondence:
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Mudalkar S, Golla R, Ghatty S, Reddy AR. De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers. PLANT MOLECULAR BIOLOGY 2014; 84:159-71. [PMID: 24002439 DOI: 10.1007/s11103-013-0125-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/22/2013] [Indexed: 05/06/2023]
Abstract
Camelina sativa L. is an emerging biofuel crop with potential applications in industry, medicine, cosmetics and human nutrition. The crop is unexploited owing to very limited availability of transcriptome and genomic data. In order to analyse the various metabolic pathways, we performed de novo assembly of the transcriptome on Illumina GAIIX platform with paired end sequencing for obtaining short reads. The sequencing output generated a FastQ file size of 2.97 GB with 10.83 million reads having a maximum read length of 101 nucleotides. The number of contigs generated was 53,854 with maximum and minimum lengths of 10,086 and 200 nucleotides respectively. These trancripts were annotated using BLAST search against the Aracyc, Swiss-Prot, TrEMBL, gene ontology and clusters of orthologous groups (KOG) databases. The genes involved in lipid metabolism were studied and the transcription factors were identified. Sequence similarity studies of Camelina with the other related organisms indicated the close relatedness of Camelina with Arabidopsis. In addition, bioinformatics analysis revealed the presence of a total of 19,379 simple sequence repeats. This is the first report on Camelina sativa L., where the transcriptome of the entire plant, including seedlings, seed, root, leaves and stem was done. Our data established an excellent resource for gene discovery and provide useful information for functional and comparative genomic studies in this promising biofuel crop.
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Affiliation(s)
- Shalini Mudalkar
- Department of Plant Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, Andhra Pradesh, India
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Li X, Luo J, Yan T, Xiang L, Jin F, Qin D, Sun C, Xie M. Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PLoS One 2013; 8:e85480. [PMID: 24392013 PMCID: PMC3877369 DOI: 10.1371/journal.pone.0085480] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022] Open
Abstract
Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.
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Affiliation(s)
- Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Jie Luo
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Tianlian Yan
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Lin Xiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Feng Jin
- College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Dehui Qin
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Ming Xie
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
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Kumar S, Jordan MC, Datla R, Cloutier S. The LuWD40-1 gene encoding WD repeat protein regulates growth and pollen viability in flax (Linum Usitatissimum L.). PLoS One 2013; 8:e69124. [PMID: 23935935 PMCID: PMC3728291 DOI: 10.1371/journal.pone.0069124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/11/2013] [Indexed: 01/22/2023] Open
Abstract
As a crop, flax holds significant commercial value for its omega-3 rich oilseeds and stem fibres. Canada is the largest producer of linseed but there exists scope for significant yield improvements. Implementation of mechanisms such as male sterility can permit the development of hybrids to assist in achieving this goal. Temperature sensitive male sterility has been reported in flax but the leakiness of this system in field conditions limits the production of quality hybrid seeds. Here, we characterized a 2,588 bp transcript differentially expressed in male sterile lines of flax. The twelve intron gene predicted to encode a 368 amino acid protein has five WD40 repeats which, in silico, form a propeller structure with putative nucleic acid and histone binding capabilities. The LuWD40-1 protein localized to the nucleus and its expression increased during the transition and continued through the vegetative stages (seed, etiolated seedling, stem) while the transcript levels declined during reproductive development (ovary, anthers) and embryonic morphogenesis of male fertile plants. Knockout lines for LuWD40-1 in flax failed to develop shoots while overexpression lines showed delayed growth phenotype and were male sterile. The non-viable flowers failed to open and the pollen grains from these flowers were empty. Three independent transgenic lines overexpressing the LuWD40-1 gene had ∼80% non-viable pollen, reduced branching, delayed flowering and maturity compared to male fertile genotypes. The present study provides new insights into a male sterility mechanism present in flax.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Mark C. Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Raju Datla
- National Research Council, Saskatoon, Saskatchewan, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
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Choi HI, Kim NH, Kim JH, Choi BS, Ahn IO, Lee JS, Yang TJ. Development of Reproducible EST-derived SSR Markers and Assessment of Genetic Diversity in Panax ginseng Cultivars and Related Species. J Ginseng Res 2013; 35:399-412. [PMID: 23717085 PMCID: PMC3659560 DOI: 10.5142/jgr.2011.35.4.399] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/08/2011] [Accepted: 07/29/2011] [Indexed: 11/18/2022] Open
Abstract
Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tag-derived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax speciesand 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an F2 population of a cross between two P. ginseng cultivars, 'Yunpoong' and 'Chunpoong', indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar 'Chunpoong', a subgroup with three accessions including two cultivars, 'Gumpoong' and 'Yunpoong' and one landrace 'Hwangsook' and another subgroup with two accessions including one cultivar, 'Gopoong' and one landrace 'Jakyung'. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure.
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Affiliation(s)
- Hong-Il Choi
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University College of Agriculture and Life Sciences, Seoul 151-921, Korea
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Soto-Cerda BJ, Diederichsen A, Ragupathy R, Cloutier S. Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types. BMC PLANT BIOLOGY 2013; 13:78. [PMID: 23647851 PMCID: PMC3656786 DOI: 10.1186/1471-2229-13-78] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 04/26/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. RESULTS Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. CONCLUSIONS Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.
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Affiliation(s)
- Braulio J Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
- Present address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unito, Km 10 Camino Cajón-Vilcún, INIA Temuco, Chile
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatchewan, SK S7N 0X2, Canada
| | - Raja Ragupathy
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
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Liu T, Zhu S, Fu L, Tang Q, Yu Y, Chen P, Luan M, Wang C, Tang S. Development and characterization of 1,827 expressed sequence tag-derived simple sequence repeat markers for ramie (Boehmeria nivea L. Gaud). PLoS One 2013; 8:e60346. [PMID: 23565230 PMCID: PMC3614921 DOI: 10.1371/journal.pone.0060346] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/25/2013] [Indexed: 11/18/2022] Open
Abstract
Ramie (Boehmeria nivea L. Gaud) is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strategies have been hampered by the shortage of simple sequence repeat (SSR) markers. In our previous study, we had assembled de novo 43,990 expressed sequence tags (ESTs). In the present study, we searched these previously assembled ESTs for SSRs and identified 1,685 ESTs (3.83%) containing 1,878 SSRs. Next, we designed 1,827 primer pairs complementary to regions flanking these SSRs, and these regions were designated as SSR markers. Among these markers, dinucleotide and trinucleotide repeat motifs were the most abundant types (36.4% and 36.3%, respectively), whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented <10% of the markers. The motif AG/CT was the most abundant, accounting for 28.74% of the markers. One hundred EST-SSR markers (97 SSRs located in genes encoding transcription factors and 3 SSRs in genes encoding cellulose synthases) were amplified using polymerase chain reaction for detecting 24 ramie varieties. Of these 100 markers, 98 markers were successfully amplified and 81 markers were polymorphic, with 2–6 alleles among the 24 varieties. Analysis of the genetic diversity of all 24 varieties revealed similarity coefficients that ranged from 0.51 to 0.80. The EST-SSRs developed in this study represent the first large-scale development of SSR markers for ramie. These SSR markers could be used for development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping, and cultivar fingerprinting.
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Affiliation(s)
- Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Lili Fu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qingming Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yongting Yu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Ping Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- * E-mail:
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Joy N, Asha S, Mallika V, Soniya EV. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper. PLoS One 2013; 8:e56694. [PMID: 23469176 PMCID: PMC3587635 DOI: 10.1371/journal.pone.0056694] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/13/2013] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L.), an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs) are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs). We used the array of transcripts generated, for the in silico prediction and detection of ‘43 pre-miRNA candidates bearing different types of SSR motifs’. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted ‘pre-miRNA candidates bearing SSRs’. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted ‘pre-miRNA candidates’. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of ‘tandem repeats’ in miRNAs.
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Affiliation(s)
- Nisha Joy
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Srinivasan Asha
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Vijayan Mallika
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Eppurathu Vasudevan Soniya
- Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India
- * E-mail:
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Day A, Fénart S, Neutelings G, Hawkins S, Rolando C, Tokarski C. Identification of cell wall proteins in the flax (Linum usitatissimum
) stem. Proteomics 2013; 13:812-25. [DOI: 10.1002/pmic.201200257] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/08/2012] [Accepted: 11/14/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Arnaud Day
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Stéphane Fénart
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Godfrey Neutelings
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Simon Hawkins
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Christian Rolando
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP); USR CNRS 3290; Villeneuve d'Ascq; France
| | - Caroline Tokarski
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP); USR CNRS 3290; Villeneuve d'Ascq; France
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Soto-Cerda BJ, Cloutier S. Outlier Loci and Selection Signatures of Simple Sequence Repeats (SSRs) in Flax ( Linum usitatissimum L.). PLANT MOLECULAR BIOLOGY REPORTER 2013; 31:978-990. [PMID: 24415843 PMCID: PMC3881565 DOI: 10.1007/s11105-013-0568-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Genomic microsatellites (gSSRs) and expressed sequence tag-derived SSRs (EST-SSRs) have gained wide application for elucidating genetic diversity and population structure in plants. Both marker systems are assumed to be selectively neutral when making demographic inferences, but this assumption is rarely tested. In this study, three neutrality tests were assessed for identifying outlier loci among 150 SSRs (85 gSSRs and 65 EST-SSRs) that likely influence estimates of population structure in three differentiated flax sub-populations (FST = 0.19). Moreover, the utility of gSSRs, EST-SSRs, and the combined sets of SSRs was also evaluated in assessing genetic diversity and population structure in flax. Six outlier loci were identified by at least two neutrality tests showing footprints of balancing selection. After removing the outlier loci, the STRUCTURE analysis and the dendrogram topology of EST-SSRs improved. Conversely, gSSRs and combined SSRs results did not change significantly, possibly as a consequence of the higher number of neutral loci assessed. Taken together, the genetic structure analyses established the superiority of gSSRs to determine the genetic relationships among flax accessions, although the combined SSRs produced the best results. Genetic diversity parameters did not differ statistically (P > 0.05) between gSSRs and EST-SSRs, an observation partially explained by the similar number of repeat motifs. Our study provides new insights into the ability of gSSRs and EST-SSRs to measure genetic diversity and structure in flax and confirms the importance of testing for the occurrence of outlier loci to properly assess natural and breeding populations, particularly in studies considering only few loci.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB Canada R3T 2M9
- Agriaquaculture Nutritional Genomic Center, Genomics and Bioinformatics Unit, CGNA, Km 10 Camino Cajón-Vilcún, INIA, Temuco, Chile
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB Canada R3T 2M9
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Kumar S, You FM, Cloutier S. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 2012; 13:684. [PMID: 23216845 PMCID: PMC3557168 DOI: 10.1186/1471-2164-13-684] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/29/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. RESULTS Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents). Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. CONCLUSIONS Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from flax. The genotyping-by-sequencing approach proved to be efficient for validation. The SNP resources generated in this work will assist in generating high density maps of flax and facilitate QTL discovery, marker-assisted selection, phylogenetic analyses, association mapping and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Santosh Kumar
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
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Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
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Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GKS, Wang J, Deyholos MK. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:461-73. [PMID: 22757964 DOI: 10.1111/j.1365-313x.2012.05093.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
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Affiliation(s)
- Zhiwen Wang
- BGI-Shenzen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
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48
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Fu YB, Diederichsen A, Allaby RG. Locus-specific view of flax domestication history. Ecol Evol 2012; 2:139-52. [PMID: 22408732 PMCID: PMC3297184 DOI: 10.1002/ece3.57] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 11/09/2022] Open
Abstract
Crop domestication has been inferred genetically from neutral markers and increasingly from specific domestication-associated loci. However, some crops are utilized for multiple purposes that may or may not be reflected in a single domestication-associated locus. One such example is cultivated flax (Linum usitatissimum L.), the earliest oil and fiber crop, for which domestication history remains poorly understood. Oil composition of cultivated flax and pale flax (L. bienne Mill.) indicates that the sad2 locus is a candidate domestication locus associated with increased unsaturated fatty acid production in cultivated flax. A phylogenetic analysis of the sad2 locus in 43 pale and 70 cultivated flax accessions established a complex domestication history for flax that has not been observed previously. The analysis supports an early, independent domestication of a primitive flax lineage, in which the loss of seed dispersal through capsular indehiscence was not established, but increased oil content was likely occurred. A subsequent flax domestication process occurred that probably involved multiple domestications and includes lineages that contain oil, fiber, and winter varieties. In agreement with previous studies, oil rather than fiber varieties occupy basal phylogenetic positions. The data support multiple paths of flax domestication for oil-associated traits before selection of the other domestication-associated traits of seed dispersal loss and fiber production. The sad2 locus is less revealing about the origin of winter tolerance. In this case, a single domestication-associated locus is informative about the history of domesticated forms with the associated trait while partially informative on forms less associated with the trait.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Robin G Allaby
- School of Life Sciences, University of WarwickWellesbourne, Warwick CV35 9EF, United Kingdom
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Cloutier S, Miranda E, Ward K, Radovanovic N, Reimer E, Walichnowski A, Datla R, Rowland G, Duguid S, Ragupathy R. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:685-94. [PMID: 22484296 PMCID: PMC3405236 DOI: 10.1007/s00122-012-1860-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 03/21/2012] [Indexed: 05/09/2023]
Abstract
Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
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50
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Nemri A, Barrett LG, Laine AL, Burdon JJ, Thrall PH. Population processes at multiple spatial scales maintain diversity and adaptation in the Linum marginale--Melampsora lini association. PLoS One 2012; 7:e41366. [PMID: 22859978 PMCID: PMC3409196 DOI: 10.1371/journal.pone.0041366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/20/2012] [Indexed: 11/24/2022] Open
Abstract
Host-pathogen coevolution is a major driver of species diversity, with an essential role in the generation and maintenance of genetic variation in host resistance and pathogen infectivity. Little is known about how resistance and infectivity are structured across multiple geographic scales and what eco-evolutionary processes drive these patterns. Across southern Australia, the wild flax Linum marginale is frequently attacked by its rust fungus Melampsora lini. Here, we compare the genetic and phenotypic structure of resistance and infectivity among population pairs from two regions where environmental differences associate with specific life histories and mating systems. We find that both host and pathogen populations are genetically distinct between these regions. The region with outcrossing hosts and pathogens that go through asexual cycles followed by sexual reproduction showed greater diversity of resistance and infectivity phenotypes, higher levels of resistance and less clumped within-population spatial distribution of resistance. However, in the region where asexual pathogens infect selfing hosts, pathogens were more infective and better adapted to sympatric hosts. Our findings largely agree with expectations based on the distinctly different host mating systems in the two regions, with a likely advantage for hosts undergoing recombination. For the pathogen in this system, sexual reproduction may primarily be a survival mechanism in the region where it is observed. While it appears to potentially have adverse effects on local adaptation in the short term, it may be necessary for longer-term coevolution with outcrossing hosts.
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Affiliation(s)
- Adnane Nemri
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Luke G. Barrett
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Anna-Liisa Laine
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jeremy J. Burdon
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Peter H. Thrall
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
- * E-mail:
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