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Ramírez-Parra E, De la Rosa L. Designing Novel Strategies for Improving Old Legumes: An Overview from Common Vetch. PLANTS (BASEL, SWITZERLAND) 2023; 12:1275. [PMID: 36986962 PMCID: PMC10058852 DOI: 10.3390/plants12061275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Common vetch (Vicia sativa L.) is a grain legume used in animal feeding, rich in protein content, fatty acid, and mineral composition that makes for a very adequate component to enrich feedstuff. In addition, relevant pharmacological properties have been reported in humans. The common vetch, similar to other legumes, can fix atmospheric nitrogen, a crucial feature for sustainable agricultural systems. These properties enhance the use of vetch as a cover crop and its sowing in intercropping systems. Moreover, several studies have recently pointed out the potential of vetch in the phytoremediation of contaminated soils. These characteristics make vetch a relevant crop, which different potential improvements target. Varieties with different yields, flowering times, shattering resistance, nutritional composition, rhizobacteria associations, drought tolerance, nitrogen fixation capacity, and other agronomic-relevant traits have been identified when different vetch accessions are compared. Recently, the analysis of genomic and transcriptomic data has allowed the development of different molecular markers to be used for assisted breeding purposes, promoting crop improvement. Here, we review the potential of using the variability of V. sativa genetic resources and new biotechnological and molecular tools for selecting varieties with improved traits to be used in sustainable agriculture systems.
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Affiliation(s)
- Elena Ramírez-Parra
- Centro de Biotecnología y Genómica de Plantas, (CBGP, UPM-INIA/CSIC) Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Lucía De la Rosa
- Centro de Recursos Fitogenéticos, (CRF-INIA/CSIC) Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Alcalá de Henares, 28805 Madrid, Spain
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2
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Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
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Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
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3
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Ouyang Z, Wang Y, Ma T, Kanzana G, Wu F, Zhang J. Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus. PLANTS 2021; 10:plants10050890. [PMID: 33925112 PMCID: PMC8146837 DOI: 10.3390/plants10050890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 01/08/2023]
Abstract
Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.
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De la Rosa L, López-Román MI, González JM, Zambrana E, Marcos-Prado T, Ramírez-Parra E. Common Vetch, Valuable Germplasm for Resilient Agriculture: Genetic Characterization and Spanish Core Collection Development. FRONTIERS IN PLANT SCIENCE 2021; 12:617873. [PMID: 33767716 PMCID: PMC7985455 DOI: 10.3389/fpls.2021.617873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/05/2021] [Indexed: 05/17/2023]
Abstract
Common vetch (Vicia sativa L.) is a legume used for animal feed because of its high protein content and great capacity for nitrogen fixation, making this crop relevant in sustainable agriculture. The Spanish vetch collection, conserved at the Spanish Plant Genetic Resources Center (CRF), is one of the largest collections of this species worldwide, including landraces, wild relatives mainly collected in Spain, and commercial cultivars, but also accessions of international origin. The analysis of the genetic diversity of this material, whose genome has not been sequenced yet, and the assembly of a representative collection could play a pivotal role in conserving and exploiting these genetic resources in breeding programs mainly in those focused on consequences and demands of climate change. In this work, a set of 14 simple sequence repeat (SSR) reference alleles for genetic diversity analysis of the CRF vetch collection has been developed, used for genotyping more than 545 common vetch accessions from all over the world and validated. All the tested markers were polymorphic for the analyzed accessions. Overall, at least 86 different loci were identified with 2-11 alleles per locus with an average of 6.1 alleles per locus. Also, the analyses of the generated SSR database support that most of these SSR markers are transferable across closely related species of Vicia genus. Analysis of molecular variance revealed that wild relatives have a higher genetic diversity than landraces. However, cultivars have similar diversity than landraces, indicating that genetic variability has been barely lost due to the breeding of this legume. Low differences of genetic variations between Spanish and non-Spanish accessions have been observed, suggesting a high degree of diversity within Spanish genotypes, which provide 95% of the total genetic variation, so we have focused our efforts on characterizing genotypes of Spanish origin that were further studied using storage protein profiles. Based on SSR, seed protein profiles, and agromorphological and passport data, a vetch core collection (VCC) containing 47 V. sativa accessions of Spanish origin has been established. In this collection, the characterization has been expanded using ISSR markers, and it has been reevaluated with new agromorphological data, including drought tolerance characters. This VCC presents a minimum loss of genetic diversity concerning the total collection and constitutes an invaluable material that can be used in future breeding programs for direct use in a resilient agricultural system.
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Affiliation(s)
- Lucía De la Rosa
- Centro de Recursos Fitogenéticos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Alcalá de Henares, Spain
| | - María Isabel López-Román
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Juan M. González
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Encarnación Zambrana
- Centro de Recursos Fitogenéticos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Alcalá de Henares, Spain
| | - Teresa Marcos-Prado
- Centro de Recursos Fitogenéticos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Alcalá de Henares, Spain
| | - Elena Ramírez-Parra
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- *Correspondence: Elena Ramírez-Parra,
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Renzi JP, Chantre GR, Smýkal P, Presotto AD, Zubiaga L, Garayalde AF, Cantamutto MA. Diversity of Naturalized Hairy Vetch ( Vicia villosa Roth) Populations in Central Argentina as a Source of Potential Adaptive Traits for Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:189. [PMID: 32180785 PMCID: PMC7059640 DOI: 10.3389/fpls.2020.00189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/07/2020] [Indexed: 05/06/2023]
Abstract
Hairy vetch (Vicia villosa ssp. villosa Roth) is native of Europe and Western Asia and it is the second most cultivated vetch worldwide. Hairy vetch is used as forage species in semiarid environments and as a legume cover crop in sub-humid and humid regions. Being an incompletely domesticated species, hairy vetch can form spontaneous populations in a new environment. These populations might contain novel and adaptive traits valuable for breeding. Niche occupancy based on geographic occurrence and environmental data of naturalized populations in central Argentina showed that these populations were distributed mainly on disturbed areas with coarse soil texture and alkaline-type soils. Low rainfall and warm temperatures during pre- and post-seed dispersal explained the potential distribution under sub-humid and semiarid conditions from Pampa and Espinal ecoregions. Conversely, local adaptation along environmental gradients did not drive the divergence among recently established Argentinian (AR) populations. The highest genetic diversity revealed by microsatellite analysis was observed within accessions (72%) while no clear separation was detected between AR and European (EU) genotypes, although naturalized AR populations showed strong differentiation with the wild EU accessions. Common garden experiments were conducted in 2014-16 in order to evaluate populations' germination, flowering, and biomass traits. European cultivars were characterized by low physical seed dormancy (PY), while naturalized AR accessions showed higher winter biomass production. Detected variation in the quantitative assessment of populations could be useful for selection in breeding for traits that convey favorable functions within specific contexts.
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Affiliation(s)
- Juan P. Renzi
- EEA H. Ascasubi Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Guillermo R. Chantre
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET, Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Palacký University in Olomouc, Olomouc, Czechia
| | - Alejandro D. Presotto
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET, Bahía Blanca, Argentina
| | - Luciano Zubiaga
- EEA H. Ascasubi Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Antonio F. Garayalde
- Departamento de Matemática, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Miguel A. Cantamutto
- EEA H. Ascasubi Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), CONICET, Bahía Blanca, Argentina
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6
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De Novo Assembly and Discovery of Genes That Involved in Drought Tolerance in the Common Vetch. Int J Mol Sci 2019; 20:ijms20020328. [PMID: 30650531 PMCID: PMC6359484 DOI: 10.3390/ijms20020328] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
The common vetch (Vicia sativa) is often used as feed for livestock because of its high nutritional value. However, drought stress reduces forage production through plant damage. Here, we studied the transcriptional profiles of common vetch exposed to drought in order to understand the molecular mechanisms of drought tolerance in this species. The genome of the common vetch has not been sequenced, therefore we used Illumina sequencing to generate de novo transcriptomes. Nearly 500 million clean reads were used to generate 174,636 transcripts, including 122,299 unigenes. In addition, 5313 transcription factors were identified and these transcription factors were classified into 79 different gene families. We also identified 11,181 SSR loci from di- to hexa-nucleotides whose repeat number was greater than five. On the basis of differentially expressed genes, Gene Ontology analysis identified many drought-relevant categories, including “oxidation-reduction process”, “lipid metabolic process” and “oxidoreductase activity”. In addition to these, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified pathways, such as “Plant hormone signal transduction”, “Glycolysis/Gluconeogenesis” and “Phenylpropanoid biosynthesis”, as differentially expressed in the plants exposed to drought. The expression results in this study will be useful for further extending our knowledge on the drought tolerance of common vetch.
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research. Sci Rep 2017; 7:17959. [PMID: 29263338 PMCID: PMC5738344 DOI: 10.1038/s41598-017-18049-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022] Open
Abstract
Melilotus is one of the most important legume forages, but the lack of molecular markers has limited the development and utilization of Melilotus germplasm resources. In the present study, 151 M clean reads were generated from various genotypes of Melilotus albus using Illumina sequencing. A total of 19,263 potential EST-SSRs were identified from 104,358 unigene sequences. Moreover, 18,182 primer pairs were successfully designed, and 550 primer pairs were selected using criteria of base repeat type, fragment length and annealing temperature. In addition, 550 primer pairs were screened by using PCR amplification products and used to assess polymorphisms in 15 M. albus accessions. A total of 114 primer pairs were detected as being highly polymorphic, and the average polymorphism information content (PIC) value was 0.79. Furthermore, those 114 polymorphic primer pairs were used to evaluate the transferability to 18 species of the genus Melilotus, and 70 EST-SSR markers were found to be transferable among the 18 Melilotus species. According to the UPGMA dendrogram and STRUCTURE analysis, the 18 Melilotus species were classified into three clusters. This study offers a valuable resource for the genetic diversity and molecular assisted breeding of germplasm resources in the genus Melilotus.
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9
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Ghasemi N, Secen H, Yılmaz H, Binici B, Goren AC. Determination of neurotoxic agents as markers of common vetch adulteration in lentil by LC-MS/MS. Food Chem 2017; 221:2005-2009. [PMID: 27979192 DOI: 10.1016/j.foodchem.2016.11.079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/08/2016] [Accepted: 11/18/2016] [Indexed: 11/16/2022]
Abstract
Vicia sativa (common vetch), which contains β-cyanoalanine (BCA) and γ-glutamyl β-cyanoalanine (γGBCA) is used for adulteration of lentil and have neuro toxic effects on people and animals. Therefore the determination of BCA and γGBCA analytes in accurate and reliable manner has high importance for human and animal health. LC-IDMS/MS method has been developed and validated for quantitative analyses of β-cyanoalanine and 13C labeled BCA is used as an internal standard in γGBCA analysis. In order to validate the method, linearity, recovery, precision (repeatability), intermediate precision, limit of detection, and limit of quantification parameters were investigated. The correlation coefficient was found to be greater than 0.99 for both analytes. The recoveriess were determined as 95.8% for BCA and 97.4% for γGBCA. The relative expanded measurement uncertainties of β-cyanoalanine and γ-glutamyl-β-cyanoalanine were obtained as 4.6% and 5.8%, respectively with the coverage factor, k, is 2 and at 95% confidence level.
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Affiliation(s)
- Nesa Ghasemi
- Department of Chemistry, Faculty of Sciences, Ataturk University, 25240 Erzurum, Turkey
| | - Hasan Secen
- Department of Chemistry, Faculty of Sciences, Ataturk University, 25240 Erzurum, Turkey
| | - Hasibe Yılmaz
- TUBITAK UME (National Metrology Institute), Chemistry Group, Organic Chemistry Laboratories, P.O. Box 54, 41470 Gebze-Kocaeli, Turkey
| | - Burcu Binici
- TUBITAK UME (National Metrology Institute), Chemistry Group, Organic Chemistry Laboratories, P.O. Box 54, 41470 Gebze-Kocaeli, Turkey
| | - Ahmet C Goren
- TUBITAK UME (National Metrology Institute), Chemistry Group, Organic Chemistry Laboratories, P.O. Box 54, 41470 Gebze-Kocaeli, Turkey.
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Chai X, Dong R, Liu W, Wang Y, Liu Z. Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules 2017; 22:molecules22040567. [PMID: 28362323 PMCID: PMC6154542 DOI: 10.3390/molecules22040567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022] Open
Abstract
Common vetch (Vicia sativa subsp. sativa L.) is a self-pollinating annual forage legume with worldwide importance. Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals. The results showed that the number of alleles and the Polymorphism Information Content (PIC) were different among the four accessions. Cluster analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and STRUCTURE placed the 240 individuals into four distinct clusters. The Expected Heterozygosity (HE) and PIC increased along with an increase in sampling size from 1 to 10 plants but did not change significantly when the sample sizes exceeded 10 individuals. At least 90% of the genetic variation in the four germplasms was represented when the sample size was 10. Finally, we concluded that 10 individuals could effectively represent the genetic diversity of one vetch population based on the SCoT markers. This study provides theoretical support for genetic diversity, cultivar identification, evolution, and marker-assisted selection breeding in common vetch.
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Affiliation(s)
- Xutian Chai
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Rui Dong
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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11
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Dong R, Dong D, Luo D, Zhou Q, Chai X, Zhang J, Xie W, Liu W, Dong Y, Wang Y, Liu Z. Transcriptome Analyses Reveal Candidate Pod Shattering-Associated Genes Involved in the Pod Ventral Sutures of Common Vetch ( Vicia sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:649. [PMID: 28496452 PMCID: PMC5406471 DOI: 10.3389/fpls.2017.00649] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/10/2017] [Indexed: 05/19/2023]
Abstract
The seed dispersion caused by pod shattering is a form of propagation used by many wild species. Loss of seeds from pod shattering is frequent in the common vetch (Vicia sativa L.), an important self-pollinating annual forage legume. However, pod shattering is one of the most important defects that limits the reproduction of the vetch in the field and the usage as a leguminous forage crop. To better understand the vetch pod shattering mechanism, we used high-throughput RNA sequencing to assess the global changes in the transcriptomes of the pod ventral sutures of shattering-susceptible and shattering-resistant vetch accessions screened from 541 vetch germplasms. A total of 1,285 significantly differentially expressed unigenes (DEGs) were detected, including 575 up-regulated unigenes and 710 down-regulated unigenes. Analyses of Gene Ontology and KEGG metabolic enrichment pathways of 1,285 DEGs indicated that 22 DEGs encoding cell wall modifications and hydrolases associated with pod shattering were highly expressed in shattering-susceptible accessions. These genes were mainly enriched in "hydrolase activity," "cytoplasm," and "carbohydrate metabolic process" systems. These cell wall modifications and hydrolases genes included β-glucosidase and endo-polygalacturonase, which work together to break down the glycosidic bonds of pectin and cellulose, and to promote the dissolution and disappearance of the cell wall in the ventral suture of the pod and make the pod more susceptible to shattering. We demonstrated the differences in gene transcription levels between the shattering-susceptible and shattering-resistant vetch accessions for the first time and our results provided valuable information for the identifying and characterizing of pod shattering regulation networks in vetch. This information may facilitate the future identification of pod shattering-related genes and their underlying molecular mechanisms in the common vetch.
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Affiliation(s)
- Rui Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Deke Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Dong Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Qiang Zhou
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Xutian Chai
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Yang Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
- *Correspondence: Yanrong Wang
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
- Zhipeng Liu
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12
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Zhu S, Liu T, Dai Q, Wu D, Zheng X, Tang S, Chen J. Genetic structure and relationships of an associated population in ramie (Boehmeria nivea L. Gaud) evaluated by SSR markers. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1253437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Siyuan Zhu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Touming Liu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Qiuzhong Dai
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Duanqing Wu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Xia Zheng
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Shouwei Tang
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Jianhua Chen
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
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13
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Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Sci Rep 2016; 6:20549. [PMID: 26853106 PMCID: PMC4744933 DOI: 10.1038/srep20549] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/06/2016] [Indexed: 11/09/2022] Open
Abstract
Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.
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14
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Li CY, Chiang TY, Chiang YC, Hsu HM, Ge XJ, Huang CC, Chen CT, Hung KH. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing. Molecules 2016; 21:67. [PMID: 26751439 PMCID: PMC6273106 DOI: 10.3390/molecules21010067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1-4, the polymorphism information content ranged from 0.000-0.692, and the observed and expected heterozygosity were 0.000-1.000 and 0.080-0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.
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Affiliation(s)
- Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou 552, Taiwan.
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Mei Hsu
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Xue-Jun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | | | - Chaur-Tzuhn Chen
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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15
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Kim TS, Raveendar S, Suresh S, Lee GA, Lee JR, Cho JH, Lee SY, Ma KH, Cho GT, Chung JW. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes (Basel) 2015; 6:1164-82. [PMID: 26540077 PMCID: PMC4690033 DOI: 10.3390/genes6041164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.
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Affiliation(s)
- Tae-Sung Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Korea.
| | - Sebastin Raveendar
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Sundan Suresh
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
- Department of Botany, Directorate of Distance Education, Madurai Kamaraj University, Madurai 625 021, India.
| | - Gi-An Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jung-Ro Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Joon-Hyeong Cho
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea.
| | - Sok-Young Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Kyung-Ho Ma
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Gyu-Taek Cho
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jong-Wook Chung
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
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16
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Raveendar S, Lee GA, Jeon YA, Lee YJ, Lee JR, Cho GT, Cho JH, Park JH, Ma KH, Chung JW. Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species. Molecules 2015; 20:1543-50. [PMID: 25608853 PMCID: PMC6272350 DOI: 10.3390/molecules20011543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022] Open
Abstract
The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.
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Affiliation(s)
- Sebastin Raveendar
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Gi-An Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Young-Ah Jeon
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Yun Jeong Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Joon-Hyeong Cho
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea
| | - Jong-Hyun Park
- Food Grain Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong-si 339-012, Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
| | - Jong-Wook Chung
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
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17
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Fu Z, Li Y, Li Y. Isolation and characterization of microsatellite markers for Forsythia suspensa (Thunb.) Vahl (Oleaceae) using 454 sequencing technology. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Zhang J, Ma W, Song X, Lin Q, Gui JF, Mei J. Characterization and development of EST-SSR markers derived from transcriptome of yellow catfish. Molecules 2014; 19:16402-15. [PMID: 25314602 PMCID: PMC6271634 DOI: 10.3390/molecules191016402] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 11/16/2022] Open
Abstract
Yellow catfish (Pelteobagrus fulvidraco) is one of the most important freshwater fish due to its delicious flesh and high nutritional value. However, lack of sufficient simple sequence repeat (SSR) markers has hampered the progress of genetic selection breeding and molecular research for yellow catfish. To this end, we aimed to develop and characterize polymorphic expressed sequence tag (EST)–SSRs from the 454 pyrosequencing transcriptome of yellow catfish. Totally, 82,794 potential EST-SSR markers were identified and distributed in the coding and non-coding regions. Di-nucleotide (53,933) is the most abundant motif type, and AC/GT, AAT/ATT, AAAT/ATTT are respective the most frequent di-, tri-, tetra-nucleotide repeats. We designed primer pairs for all of the identified EST-SSRs and randomly selected 300 of these pairs for further validation. Finally, 263 primer pairs were successfully amplified and 57 primer pairs were found to be consistently polymorphic when four populations of 48 individuals were tested. The number of alleles for the 57 loci ranged from 2 to 17, with an average of 8.23. The observed heterozygosity (HO), expected heterozygosity (HE), polymorphism information content (PIC) and fixation index (FIS) values ranged from 0.04 to 1.00, 0.12 to 0.92, 0.12 to 0.91 and −0.83 to 0.93, respectively. These EST-SSR markers generated in this study could greatly facilitate future studies of genetic diversity and molecular breeding in yellow catfish.
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Affiliation(s)
- Jin Zhang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenge Ma
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaomin Song
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian-Fang Gui
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jie Mei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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20
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Liu Z, Liu P, Luo D, Liu W, Wang Y. Exploiting Illumina sequencing for the development of 95 novel polymorphic EST-SSR markers in common vetch (Vicia sativa subsp. sativa). Molecules 2014; 19:5777-89. [PMID: 24802988 PMCID: PMC6271487 DOI: 10.3390/molecules19055777] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/23/2022] Open
Abstract
The common vetch (Vicia sativa subsp. sativa), a self-pollinating and diploid species, is one of the most important annual legumes in the world due to its short growth period, high nutritional value, and multiple usages as hay, grain, silage, and green manure. The available simple sequence repeat (SSR) markers for common vetch, however, are insufficient to meet the developing demand for genetic and molecular research on this important species. Here, we aimed to develop and characterise several polymorphic EST-SSR markers from the vetch Illumina transcriptome. A total number of 1,071 potential EST-SSR markers were identified from 1025 unigenes whose lengths were greater than 1,000 bp, and 450 primer pairs were then designed and synthesized. Finally, 95 polymorphic primer pairs were developed for the 10 common vetch accessions, which included 50 individuals. Among the 95 EST-SSR markers, the number of alleles ranged from three to 13, and the polymorphism information content values ranged from 0.09 to 0.98. The observed heterozygosity values ranged from 0.00 to 1.00, and the expected heterozygosity values ranged from 0.11 to 0.98. These 95 EST-SSR markers developed from the vetch Illumina transcriptome could greatly promote the development of genetic and molecular breeding studies pertaining to in this species.
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Affiliation(s)
- Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Peng Liu
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Dong Luo
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, School of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
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21
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Fu N, Wang PY, Liu XD, Shen HL. Use of EST-SSR markers for evaluating genetic diversity and fingerprinting celery (Apium graveolens L.) cultivars. Molecules 2014; 19:1939-55. [PMID: 24518809 PMCID: PMC6270925 DOI: 10.3390/molecules19021939] [Citation(s) in RCA: 12] [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: 12/23/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 11/26/2022] Open
Abstract
Celery (Apium graveolens L.) is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting celery molecular breeding are quite limited, thus few studies on celery have been conducted so far. In this study we made use of simple sequence repeat (SSR) markers generated from previous celery transcriptome sequencing and attempted to detect the genetic diversity and relationships of commonly used celery accessions and explore the efficiency of the primers used for cultivars identification. Analysis of molecular variance (AMOVA) of Apium graveolens L. var. dulce showed that approximately 43% of genetic diversity was within accessions, 45% among accessions, and 22% among horticultural types. The neighbor-joining tree generated by unweighted pair group method with arithmetic mean (UPGMA), and population structure analysis, as well as principal components analysis (PCA), separated the cultivars into clusters corresponding to the geographical areas where they originated. Genetic distance analysis suggested that genetic variation within Apium graveolens was quite limited. Genotypic diversity showed any combinations of 55 genic SSRs were able to distinguish the genotypes of all 30 accessions.
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Affiliation(s)
- Nan Fu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Ping-Yong Wang
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Xiao-Dan Liu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Huo-Lin Shen
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
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