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Vishwakarma G, Sanyal RP, Saini A, Sahu PK, Singh Patel RR, Sharma D, Tiwari R, Das BK. GLADS: A gel-less approach for detection of STMS markers in wheat and rice. PLoS One 2019; 14:e0224572. [PMID: 31689318 PMCID: PMC6830750 DOI: 10.1371/journal.pone.0224572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 11/18/2022] Open
Abstract
Sequence tagged microsatellite site (STMS) are useful PCR based DNA markers. Wide genome coverage, high polymorphic index and co-dominant nature make STMS a preferred choice for marker assisted selection (MAS), genetic diversity analysis, linkage mapping, seed genetic purity analysis etc. Routine STMS analysis involving low-throughput, laborious and time-consuming polyacrylamide/agarose gels often limit their full utility in crop breeding experiments that involve large populations. Therefore, convenient, gel-less marker detection methods are highly desirable for STMS markers. The present study demonstrated the utility of SYBR Green dye based melt-profiling as a simple and convenient gel-less approach for detection of STMS markers (referred to as GLADS) in bread wheat and rice. The method involves use of SYBR Green dye during PCR amplification (or post-PCR) of STMS markers followed by generation of a melt-profile using controlled temperature ramp rate. The STMS amplicons yielded characteristic melt-profiles with differences in melting temperature (Tm) and profile shape. These characteristic features enabled melt-profile based detection and differentiation of STMS markers/alleles in a gel-less manner. The melt-profile approach allowed assessment of the specificity of the PCR assay unlike the end-point signal detection assays. The method also allowed multiplexing of two STMS markers with non-overlapping melt-profiles. In principle, the approach can be effectively used in any crop for STMS marker analysis. This SYBR Green melt-profiling based GLADS approach offers a convenient, low-cost (20–51%) and time-saving alternative for STMS marker detection that can reduce dependence on gel-based detection, and exposure to toxic chemicals.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
| | - Ravi Prakash Sanyal
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Ajay Saini
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ravi Raj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ratan Tiwari
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- * E-mail:
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Scollo F, Egea LA, Gentile A, La Malfa S, Dorado G, Hernandez P. Absolute quantification of olive oil DNA by droplet digital-PCR (ddPCR): Comparison of isolation and amplification methodologies. Food Chem 2016; 213:388-394. [DOI: 10.1016/j.foodchem.2016.06.086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 11/28/2022]
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Castillo A, Dorado G, Feuillet C, Sourdille P, Hernandez P. Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilense Roemer et Schultes) as revealed by microsatellite markers. BMC PLANT BIOLOGY 2010; 10:266. [PMID: 21118494 PMCID: PMC3014967 DOI: 10.1186/1471-2229-10-266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Accepted: 11/30/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Multi-allelic microsatellite markers have become the markers of choice for the determination of genetic structure in plants. Synteny across cereals has allowed the cross-species and cross-genera transferability of SSR markers, which constitute a valuable and cost-effective tool for the genetic analysis and marker-assisted introgression of wild related species. Hordeum chilense is one of the wild relatives with a high potential for cereal breeding, due to its high crossability (both interspecies and intergenera) and polymorphism for adaptation traits. In order to analyze the genetic structure and ecogeographical adaptation of this wild species, it is necessary to increase the number of polymorphic markers currently available for the species. In this work, the possibility of using syntenic wheat SSRs as a new source of markers for this purpose has been explored. RESULTS From the 98 wheat EST-SSR markers tested for transferability and polymorphism in the wild barley genome, 53 primer pairs (54.0%) gave cross-species transferability and 20 primer pairs (20.4%) showed polymorphism. The latter were used for further analysis in the H. chilense germplasm. The H. chilense-Triticum aestivum addition lines were used to test the chromosomal location of the new polymorphic microsatellite markers. The genetic structure and diversity was investigated in a collection of 94 H. chilense accessions, using a set of 49 SSR markers distributed across the seven chromosomes. Microsatellite markers showed a total of 351 alleles over all loci. The number of alleles per locus ranged from two to 27, with a mean of 7.2 alleles per locus and a mean Polymorphic Information Content (PIC) of 0.5. CONCLUSIONS According to the results, the germplasm can be divided into two groups, with morphological and ecophysiological characteristics being key determinants of the population structure. Geographic and ecological structuring was also revealed in the analyzed germplasm. A significant correlation between geographical and genetic distance was detected in the Central Chilean region for the first time in the species. In addition, significant ecological influence in genetic distance has been detected for one of the population structure groups (group II) in the Central Chilean region. Finally, the association of the SSR markers with ecogeographical variables was investigated and one marker was found significantly associated with precipitation. These findings have a potential application in cereal breeding.
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Affiliation(s)
- Almudena Castillo
- Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
| | - Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales, C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Catherine Feuillet
- INRA UBP UMR 1095, Genetics, Diversity & Ecophysiology of Cereals, Clermont Ferrand, France
| | - Pierre Sourdille
- INRA UBP UMR 1095, Genetics, Diversity & Ecophysiology of Cereals, Clermont Ferrand, France
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
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Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC PLANT BIOLOGY 2008; 8:97. [PMID: 18822176 PMCID: PMC2569940 DOI: 10.1186/1471-2229-8-97] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 09/28/2008] [Indexed: 05/24/2023]
Abstract
BACKGROUND Hordeum chilense, a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST) derived microsatellites or simple sequence repeat (SSR) markers, commonly called as EST-SSRs, for barley (Hordeum vulgare) represents a promising source to increase the number of genetic markers available for the H. chilense genome. RESULTS All of the 82 barley EST-derived SSR primer pairs tested for transferability to H. chilense amplified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26%) showed polymorphism among H. chilense lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing H. chilense phylogenetic relationships. Triticum aestivum-H. chilense addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group. CONCLUSION From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for diversity analysis of H. chilense, related wild barleys like H. murinum, and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex.
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Affiliation(s)
- Almudena Castillo
- Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
| | - Hikmet Budak
- Sabanci University, Engineering and Natural Sciences, Biological Science and Bioengineering Program, Orhanli 34956 Tuzla-Istanbul, Turkey
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru – 502 324, Andhra Pradesh, India
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales, C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
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Chang SB, de Jong H. Production of alien chromosome additions and their utility in plant genetics. Cytogenet Genome Res 2005; 109:335-43. [PMID: 15753594 DOI: 10.1159/000082417] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Accepted: 02/25/2004] [Indexed: 11/19/2022] Open
Abstract
Breeding programs aiming at transferring desirable genes from one species to another through interspecific hybridization and backcrossings often produce monosomic and disomic additions as intermediate crossing products. Such aneuploids contain alien chromosomes added to the complements of the recipient parent and can be used for further introgression programs, but lack of homoeologous recombination and inevitable segregation of the alien chromosome at meiosis make them often less ideal for producing stable introgression lines. Monosomic and disomic additions can have specific morphological characteristics, but more often they need additional confirmation of molecular marker analyses and assessment by fluorescence in situ hybridization with genomic and chromosome-specific DNA as probes. Their specific genetic and cytogenetic properties make them powerful tools for fundamental research elucidating regulation of homoeologous recombination, distribution of chromosome-specific markers and repetitive DNA sequences, and regulation of heterologous gene expression. In this overview we present the major characteristics of such interspecific aneuploids highlighting their advantages and drawbacks for breeding and fundamental research.
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Affiliation(s)
- S-B Chang
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
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Hernández P, Dorado G, Ramírez MC, Laurie DA, Snape JW, Martín A. Development of cost-effective Hordeum chilense DNA markers: molecular aids for marker-assisted cereal breeding. Hereditas 2003; 138:54-8. [PMID: 12830985 DOI: 10.1034/j.1601-5223.2003.01617.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hordeum chilense is a potential source of useful genes for wheat breeding. The use of this wild species to increase genetic variation in wheat will be greatly facilitated by marker-assisted introgression. In recent years, the search for the most suitable DNA marker system for tagging H. chilense genomic regions in a wheat background has lead to the development of RAPD and SCAR markers for this species. RAPDs represent an easy way of quickly generating suitable introgression markers, but their use is limited in heterogeneous wheat genetic backgrounds. SCARs are more specific assays, suitable for automatation or multiplexing. Direct sequencing of RAPD products is a cost-effective approach that reduces labour and costs for SCAR development. The use of SSR and STS primers originally developed for wheat and barley are additional sources of genetic markers. Practical applications of the different marker approaches for obtaining derived introgression products are described.
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Affiliation(s)
- P Hernández
- Instituto de Agricultura Sostenible (CSIC), Córdoba, Spain.
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