Abstract
Main conclusion
A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers.
The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.
Similar content being viewed by others
Abbreviations
- AFLP:
-
Amplified fragment length polymorphism
- NGS:
-
Next generation sequencing
- PCR:
-
Polymerase chain reaction
- QTL:
-
Quantitative trait loci
- RAPD:
-
Random amplification of polymorphic DNA
- RFLP:
-
Restriction fragment length polymorphism
- SNP:
-
Single-nucleotide polymorphisms
- SSR:
-
Simple sequence repeats
- STR:
-
Short tandem repeats
References
Adal AM, Demissie ZA, Mahmoud SS (2015) Identification, validation and cross-species transferability of novel Lavandula EST-SSRs. Planta 241:987–1004. https://doi.org/10.1007/s00425-014-2226-8
Archambault É, Campbell D, Gingras Y, Larivière V (2009) Comparing bibliometric statistics obtained from the Web of Science and Scopus. J Am Soc Inf Sci Technol 60:1320–1326. https://doi.org/10.1002/asi.21062
Bardakci F (2001) Random amplified polymorphic DNA (RAPD) markers. Turk J Biol 25:185–196
Bohra A, Pandey MK, Jha UC et al (2014) Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. Theor Appl Genet 127:1263–1291
Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890. https://doi.org/10.1093/bioinformatics/btg112
Chung SM, Staub JE (2003) The development and evaluation of consensus chloroplast primer pairs that possess highly variable sequence regions in a diverse array of plant taxa. Theor Appl Genet 107:757–767. https://doi.org/10.1007/s00122-003-1311-3
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363:557–572. https://doi.org/10.1098/rstb.2007.2170
Choi J, Yi S, Lee KC (2011) Analysis of keyword networks in MIS research and implications for predicting knowledge evolution. Inf Manag 48:371–381. https://doi.org/10.1016/j.im.2011.09.004
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510. https://doi.org/10.1038/nrg3012
Eathington SR, Crosbie TM, Edwards MD et al (2007) Molecular markers in a commercial breeding program. Crop Sci 47. https://doi.org/10.2135/cropsci2007.04.0015IPBS
Eckert AJ, Pande B, Ersoz ES et al (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genomes 5:225–234. https://doi.org/10.1007/s11295-008-0183-8
Evans LT (1997) Adapting and improving crops: the endless task. Philos Trans R Soc Lond Ser B Biol Sci 352:901–906. https://doi.org/10.1098/rstb.1997.0069
Fábregas-Ruesgas JJ, Hernández-Abad F, Hernández-Abad V, Rojas-Sola JI (2015) Comparative analysis of a university learning experience: classroom mode versus distance mode. Int J Interact Des Manuf 9:145–157. https://doi.org/10.1007/s12008-014-0205-8
Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217
Ganal MW, Polley A, Graner EM et al (2012) Large SNP arrays for genotyping in crop plants. J Biosci 37:821–828. https://doi.org/10.1007/s12038-012-9225-3
Garrido-Cardenas JA, Manzano-Agugliaro F (2017) The metagenomics worldwide research. Curr Genet. https://doi.org/10.1007/s00294-017-0693-8
Garrido-Cardenas JA, Garcia-Maroto F, Alvarez-Bermejo JA, Manzano-Agugliaro F (2017) DNA sequencing sensors: an overview. Sensors (Basel) 17(3):1–15. https://doi.org/10.3390/s17030588
Gimenez E, Manzano-Agugliaro F (2017) DNA damage repair system in plants: a worldwide research update. Genes (Basel) 8:299. https://doi.org/10.3390/genes8110299
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. https://doi.org/10.1038/nrg.2016.49
Grover A, Sharma PC (2016) Development and use of molecular markers: past and present. Crit Rev Biotechnol 36:290–302. https://doi.org/10.3109/07388551.2014.959891
Gunderson KL, Steemers FJ, Lee G et al (2005) A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 37:549–554. https://doi.org/10.1038/ng1547
Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210:1518–1525. https://doi.org/10.1242/jeb.001370
Hamada H, Kakunaga T (1982) Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature 298:396–398. https://doi.org/10.1038/298396a0
Heller MJ (2002) DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4:129–153. https://doi.org/10.1146/annurev.bioeng.4.020702.153438
Illa-Berenguer E, Van Houten J, Huang Z, van der Knaap E (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet. https://doi.org/10.1007/s00122-015-2509-x
Janssen P, Coopman R, Huys G et al (1996) Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142:1881–1893. https://doi.org/10.1007/s00296-011-2085-6
Kerr MK, Martin M, Churchill GA (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7:819–837. https://doi.org/10.1089/10665270050514954
Kim JJ, Han BG, Lee HI et al (2010) Development of SNP-based human identification system. Int J Legal Med 124:125–131. https://doi.org/10.1007/s00414-009-0389-9
Koornneef M, Meinke D (2010) The development of Arabidopsis as a model plant. Plant J 61:909–921. https://doi.org/10.1111/j.1365-313X.2009.04086.x
Kumar LS (1999) DNA markers in plant improvement: an overview. Biotechnol Adv 17:143–182
Lander ES, Botstein S (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185. https://doi.org/10.1038/hdy.2014.4
Landjeva S, Korzun V, Börner A (2007) Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica 156:271–296
Lateef DD (2015) DNA marker technologies in plants and applications for crop improvements. J Biosci Med 3:7–18. https://doi.org/10.4236/jbm.2015.35002
Lucht JM (2015) Public acceptance of plant biotechnology and GM crops. Viruses 7:4254–4281
Mackill DJ, Nguyen HT, Zhang J (1999) Use of molecular markers in plant improvement programs for rainfed lowland rice. Field Crop Res 64:177–185. https://doi.org/10.1016/S0378-4290(99)00058-1
Mateo-Bonmatí E, Casanova-Sáez R, Candela H, Micol JL (2014) Rapid identification of angulata leaf mutations using next-generation sequencing. Planta 240:1113–1122. https://doi.org/10.1007/s00425-014-2137-8
Mongeon P, Paul-Hus A (2016) The journal coverage of Web of Science and Scopus: a comparative analysis. Scientometrics 106:213–228. https://doi.org/10.1007/s11192-015-1765-5
Montoya FG, Montoya MG, Gómez J et al (2014) The research on energy in Spain: a scientometric approach. Renew Sustain Energy Rev 29:173–183
Montoya FG, Alcayde A, Baños R, Manzano-agugliaro F (2017) Telematics and informatics a fast method for identifying worldwide scientific collaborations using the Scopus database. Telemat Inf. https://doi.org/10.1016/j.tele.2017.10.010
Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394. https://doi.org/10.1016/S0169-5347(99)01659-6
Neves LG, Mc Mamani E, Alfenas AC et al (2011) A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based single feature polymorphisms (SFP) in eucalyptus. BMC Genomics 12:189. https://doi.org/10.1186/1471-2164-12-189
O’Hanlon PC, Peakall R, Briese DT (2000) A review of new PCR-based genetic markers and their utility to weed ecology. Weed Res 40:239–254
Ortiz R (2010) Molecular plant breeding. Crop Sci 50:2196–2197. https://doi.org/10.2135/cropsci2010.12.0004br
Pacheco-Marín R, Melendez-Zajgla J, Castillo-Rojas G et al (2016) Transcriptome profile of the early stages of breast cancer tumoral spheroids. Sci Rep 6:23373. https://doi.org/10.1038/srep23373
Pérez-de-Castro AM, Vilanova S, Cañizares J et al (2012) Application of genomic tools in plant breeding. Curr Genomics 13:179–195. https://doi.org/10.2174/138920212800543084
Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147
Rasheed A, Hao Y, Xia X et al (2017) Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Mol Plant 10:1047–1064
Reynolds MP, Rodomiro O (2010) Adapting crops to climate change: a summary. Clim Chang Crop Prod 51:1–8. https://doi.org/10.1079/9781845936334.0000
Salmerón-Manzano E, Manzano-Agugliaro F (2017) Worldwide scientific production indexed by Scopus on labour relations. Publications 5:25. https://doi.org/10.3390/publications5040025
Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141
Singh V, Perdigones A, García JL et al (2014) Analysis of worldwide research in the field of cybernetics during 1997–2011. Biol Cybern 108:757–776. https://doi.org/10.1007/s00422-014-0617-3
Slonim DK, Yanai I (2009) Getting started in gene expression microarray analysis. PLoS Comput, Biol, p 5
Suwarno WB, Pixley KV, Palacios-Rojas N et al (2015) Genome-wide association analysis reveals new targets for carotenoid biofortification in maize. Theor Appl Genet 128:851–864. https://doi.org/10.1007/s00122-015-2475-3
Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science (80) 327:818–822. https://doi.org/10.1126/science.1183700
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. https://doi.org/10.1038/nature11119
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55
Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. https://doi.org/10.1093/nar/23.21.4407
Vuylsteke M, Peleman JD, van Eijk MJT (2007) AFLP technology for DNA fingerprinting. Nat Protoc 2:1387–1398. https://doi.org/10.1038/nprot.2007.175
Wang Y, Xu J, Deng D et al (2016) A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.). Planta 243:459–471. https://doi.org/10.1007/s00425-015-2419-9
Williams RC (1989) Restriction fragment length polymorphism (RFLP). Am J Phys Anthropol 32:159–184. https://doi.org/10.1002/ajpa.1330320508
Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535. https://doi.org/10.1093/nar/18.22.6531
Xiong J-S, Ding J, Li Y (2015) Genome-editing technologies and their potential application in horticultural crop breeding. Hortic Res 2:15019. https://doi.org/10.1038/hortres.2015.19
Yan J, Yang X, Shah T et al (2010) High-throughput SNP genotyping with the Goldengate assay in maize. Mol Breed 25:441–451. https://doi.org/10.1007/s11032-009-9343-2
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Rights and permissions
About this article
Cite this article
Garrido-Cardenas, J.A., Mesa-Valle, C. & Manzano-Agugliaro, F. Trends in plant research using molecular markers. Planta 247, 543–557 (2018). https://doi.org/10.1007/s00425-017-2829-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00425-017-2829-y