Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)

Kalkidan Shiferaw Abebe

doi:doi:10.11648/j.abb.20190701.11

| Peer-Reviewed

Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)

Kalkidan Shiferaw Abebe

Published in Advances in Bioscience and Bioengineering (Volume 7, Issue 1)

Received: 12 April 2019 Accepted: 3 June 2019 Published: 19 June 2019

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Genotype by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable genotyping of large numbers of individuals at a large number of SNP markers. It is relatively straightforward, robust, and cost-effective method to reduce problems in crop caused by a large genome size, reduced representation libraries are produced using a restriction enzyme that targets genomic regions while multiplexing with barcodes reduces the cost for individual sample. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra- throughput sequences to revolutionize plant genotyping and breeding. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, QTL mapping, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs. GBS will have broad application in genomics-assisted plant breeding programs.

Published in	Advances in Bioscience and Bioengineering (Volume 7, Issue 1)
DOI	10.11648/j.abb.20190701.11
Page(s)	1-7
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2019. Published by Science Publishing Group

Keywords

Single Nucleotide Polymorphism (SNP), Next Generation Sequencing (NGS), Reduced Representation Library (RRL), Marker Assisted Selection (MAS)

References

[1]	Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., & Jiang, R. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465 (7298), 627.
[2]	Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoSONE 3: e3376. doi: 10.1371/journal.pone.0003376.
[3]	Bernatsky, R., and Tanksley, S. D. (1986). Toward a saturated linkage map in tomato based on iso zymes and random cDNA sequences. Genetics 112, 887-898.
[4]	Botstein, D., White, R. L. Skolnick, M., and Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314-331.
[5]	Brown, P. (2011). Genotyping-by sequencing Protocol PstI-MspI Chung, Y. S., Choi, S. C., Jun, T. H., & Kim, C. (2017). Genotyping-by-sequencing: a promising tool for plant genetics research and breeding. Horticulture, Environment, and Biotechnology, 58 (5), 425-431.
[6]	Chutimanitsakun, Y., Nipper, R. W., Cuesta-Marcos, A., Cistue, L., Corey, A., Filichkina, T., et al. (2011). Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4. doi: 10.1186/1471-2164-12-4.
[7]	Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12 (7), 499.
[8]	Deschamps, S., L laca, V. and May G. D. (2012). Genotyping-by-sequencing in plants. Biology 1, 460-483. doi: 10.3390/biology1030460
[9]	Desmarais, D., Zhong, Y., Chakraborty, R., Perreault, C. and Busque, L., 1998. Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). Journal of Forensic Science, 43 (5), pp. 1046-1049.
[10]	Elshire, R. J., Glaubitz, J. C., Sun, Q., Pol, J. A., Kawamoto, K., & Buckler, E. S. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: 19379.
[11]	He, J., Zhao, X., Laroche, A., Lu, Z. X., Liu, H., & Li, Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in plant science, 5, 484.
[12]	Heffner, E. L., Sorrells, M. E., andJannink, J. L. (2009). Genomic selection for crop improvement. Crop Sci. 49, 1-12. doi: 10.2135/cropsci2008.08.0512.
[13]	Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., et al. (2009) High through put genotyping by whole genome resequencing. Genome Res. 19, 1068- 1076. doi: 10.1101/gr.089516.108.
[14]	Hussain, W., Baenziger, P. S., Belamkar, V., Guttieri, M. J., Venegas, J. P., Easterly, A.,... & Poland, J. (2017). Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat. Scientific reports, 7 (1), 16394.
[15]	Jannink, J. L., Lorenz, A. J., andIwata, H. (2010). Genomicselectioninplant breeding from theory to practice. Brief. Funct. Genomics 9, 166-177. doi: 10.1093/bfgp/elq001.
[16]	Jiang, Z., Wang, H., Michal, J. J., Zhou, X., Liu, B., Woods, L. C. S., & Fuchs, R. A. (2016). Genome wide sampling sequencing for SNP genotyping: methods, challenges and future development. International journal of biological sciences, 12 (1), 100.
[17]	Kim, C., Guo, H., Kong, W., Chandnani, R., Shuang, L. S., & Paterson, A. H. (2016). Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science, 242, 14-22.
[18]	Konieczny, A., and Ausubel, F. M. (1993 A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4, 403-410. doi: 10.1046/j.1365-313X.1993.04020403.
[19]	Litt, M., and Luty, J. A. (1986). A hypervariable microsatellite revealed by invitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44, 397-401.
[20]	Liu, H., Bayer, M., Druka, A., Russell, J. R., Hackett, C. A., Poland. J. et al. (2014). An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics 15: 104. doi: 10.1186/1471-2164- 15-104.
[21]	Paran, I., and Michelm ore, R. W. (1993). Development of reliable PCR- based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85, 985-993. doi: 10.1007/BF00215038.
[22]	Peterson, G. W., Dong, Y., Horbach, C., & Fu, Y. B. (2014). Genotyping-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity, 6 (4), 665-680.
[23]	Poland, J., Endelman, J., Dawson, J., Rutkoski, J., Wu, S., Manes, Y.... & Jannink, J. L. (2012). Genomic selection in wheat breeding using genotyping-by-sequencing. The Plant Genome, 5 (3), 103-113.
[24]	Poland, J. A., and Rife T. W (2012), Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5, 92-102. doi: 10.3835/plant genome2012.05.0005
[25]	Salimath S. S., de Oliveira, A. C. Bennetzen, J. and Godwin, I. D. (1995). Assessment of genomic origin and genetic diversity in the genus Eleusine with DNA markers. Genome 38, 757-763. doi: 10.1139/g95-096.
[26]	Scheben, A., Batley, J. and Edwards, D., 2017. Genotyping‐by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant biotechnology journal, 15 (2), pp. 149-161.
[27]	Schneeberger, K., Ossowski, S., Lanz, C., Juul, T., Petersen, A. H. Nielsen, K. L., et al. (2009). SHORE map: simultaneous mapping and mutation identification by deep.
[28]	Sonah, H., Bastien, M., Iquira, E., Tardivel, A., Légaré, G., Boyle, B. & Belzile, F. (2013). An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PloS one, 8 (1), 54603.
[29]	Thomson, M., Zhao, K., Wright, M., McNally, K., Rey, J., Tung, C. W. et al. (2012). High through put single nucleotide polymorphism genotyping for breeding applications in rice using the Bead Xpress platform. Mol. Breed. 29, 875-886. doi: 10.1007/s11032-011-9663-x.
[30]	Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. V. D., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M. and Zabeau, M., 1995. AFLP: a new technique for DNA fingerprinting. Nucleic acids research, 23 (21), pp. 4407-4414.
[31]	Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S. V., 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic acids research, 18 (22), pp. 6531-6535.
[32]	Wickland, Daniel P., et al (2017), a comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GBS BMC bioinformatics, 2017
[33]	Yong, L., Thet, Z. and Zhu, Y., 2017. Genetic editing of the androgen receptor contributes to impaired male courtship behavior in zebrafish. Journal of Experimental Biology, 220 (17), pp. 3017-3021.
[34]	Bastien M., Sonah H. and Belzile F. (2014) Genome wide association mapping of Sclerotinia sclerotiorum resistance in soybean with a genotyping‐by‐sequencing approach. Plant Genome, 7, 1-13.
[35]	Collard B. C. Y., Jahufer M. Z. Z., Brouwer J. B. and Pang E. C. K. (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker‐assisted selection for crop improvement: the basic concepts. Euphytica, 142, 169-196.
[36]	Hwang E. Y., Song Q., Jia G., Specht J. E., Hyten D. L., Costa J. and Cregan P. B. (2014) A genome‐wide association study of seed protein and oil content in soybean. BMC Genom. 15, 1.
[37]	Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA‐MEM. arXiv:1303.3997.
[38]	Meuwissen THT, Hayes BJ and Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps.Genetics 157: 1819-1829
[39]	Mohan M., Nair S., Bhagwat A., Krishna T. G., Yano M., Bhatia C. R. and Sasaki T. (1997) Genome mapping, molecular markers and marker‐assisted selection in crop plants. Mol. Breed. 3, 87-103.
[40]	Morris G. P., Ramu P., Deshpande S. P., Hash C. T., Shah T., Upadhyaya H. D., Riera‐Lizarazu O. et al (2013) Population genomic and genome‐wide association studies of agroclimatic traits in sorghum. Proc. Natl. Acad. Sci. USA, 110, 453-458.
[41]	Lorenz AJ, Chao S, Asoro FG, Heffner EL, Hayashi T, Iwata H, Smith KP, Sorrells ME, Jannink JL (2011) Genomic selection in plant breeding: knowledge and prospects. Adv Agron 10: 77-120.
[42]	Slavov G. T., Nipper R., Robson P., Farrar K., Allison G. G., Bosch M., Clifton‐Brown J. C. et al (2014) Genome‐wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis. New Phytol. 201, 1227-1239.
[43]	Sonah H., Bastien M., Iquira E., Tardivel A., Legare G., Boyle B., Normandeau E. et al (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE, 8, e5460.
[44]	Zhao K., Tung C. W., Eizenga G. C., Wright M. H., Ali M. L., Price A. H., Norton G. J. et al (2011) Genome‐wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2, 467.
[45]	Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S. and Mitchell, S. E., 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one, 6 (5), p. e19379.
[46]	Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M. and Blaxter, M. L., 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12 (7), p. 499.

Cite This Article

Plain Text BibTeX RIS

APA Style

Kalkidan Shiferaw Abebe. (2019). Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Advances in Bioscience and Bioengineering, 7(1), 1-7. https://doi.org/10.11648/j.abb.20190701.11

Copy | Download

ACS Style

Kalkidan Shiferaw Abebe. Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Adv. BioSci. Bioeng. 2019, 7(1), 1-7. doi: 10.11648/j.abb.20190701.11

Copy | Download

AMA Style

Kalkidan Shiferaw Abebe. Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Adv BioSci Bioeng. 2019;7(1):1-7. doi: 10.11648/j.abb.20190701.11

Copy | Download

@article{10.11648/j.abb.20190701.11,
  author = {Kalkidan Shiferaw Abebe},
  title = {Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)},
  journal = {Advances in Bioscience and Bioengineering},
  volume = {7},
  number = {1},
  pages = {1-7},
  doi = {10.11648/j.abb.20190701.11},
  url = {https://doi.org/10.11648/j.abb.20190701.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.abb.20190701.11},
  abstract = {Genotype by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable genotyping of large numbers of individuals at a large number of SNP markers. It is relatively straightforward, robust, and cost-effective method to reduce problems in crop caused by a large genome size, reduced representation libraries are produced using a restriction enzyme that targets genomic regions while multiplexing with barcodes reduces the cost for individual sample. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra- throughput sequences to revolutionize plant genotyping and breeding. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, QTL mapping, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs. GBS will have broad application in genomics-assisted plant breeding programs.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)
AU  - Kalkidan Shiferaw Abebe
Y1  - 2019/06/19
PY  - 2019
N1  - https://doi.org/10.11648/j.abb.20190701.11
DO  - 10.11648/j.abb.20190701.11
T2  - Advances in Bioscience and Bioengineering
JF  - Advances in Bioscience and Bioengineering
JO  - Advances in Bioscience and Bioengineering
SP  - 1
EP  - 7
PB  - Science Publishing Group
SN  - 2330-4162
UR  - https://doi.org/10.11648/j.abb.20190701.11
AB  - Genotype by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable genotyping of large numbers of individuals at a large number of SNP markers. It is relatively straightforward, robust, and cost-effective method to reduce problems in crop caused by a large genome size, reduced representation libraries are produced using a restriction enzyme that targets genomic regions while multiplexing with barcodes reduces the cost for individual sample. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra- throughput sequences to revolutionize plant genotyping and breeding. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, QTL mapping, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs. GBS will have broad application in genomics-assisted plant breeding programs.
VL  - 7
IS  - 1
ER  -

Copy | Download

Author Information

Kalkidan Shiferaw Abebe

Department of Plant Sciences, Gambella University, Gambella, Ethiopia

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Kalkidan Shiferaw Abebe. (2019). Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Advances in Bioscience and Bioengineering, 7(1), 1-7. https://doi.org/10.11648/j.abb.20190701.11

Copy | Download

ACS Style

Kalkidan Shiferaw Abebe. Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Adv. BioSci. Bioeng. 2019, 7(1), 1-7. doi: 10.11648/j.abb.20190701.11

Copy | Download

AMA Style

Kalkidan Shiferaw Abebe. Genotype by Sequencing Method and Its Application for Crop Improvement (A Review). Adv BioSci Bioeng. 2019;7(1):1-7. doi: 10.11648/j.abb.20190701.11

Copy | Download

@article{10.11648/j.abb.20190701.11,
  author = {Kalkidan Shiferaw Abebe},
  title = {Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)},
  journal = {Advances in Bioscience and Bioengineering},
  volume = {7},
  number = {1},
  pages = {1-7},
  doi = {10.11648/j.abb.20190701.11},
  url = {https://doi.org/10.11648/j.abb.20190701.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.abb.20190701.11},
  abstract = {Genotype by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable genotyping of large numbers of individuals at a large number of SNP markers. It is relatively straightforward, robust, and cost-effective method to reduce problems in crop caused by a large genome size, reduced representation libraries are produced using a restriction enzyme that targets genomic regions while multiplexing with barcodes reduces the cost for individual sample. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra- throughput sequences to revolutionize plant genotyping and breeding. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, QTL mapping, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs. GBS will have broad application in genomics-assisted plant breeding programs.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Genotype by Sequencing Method and Its Application for Crop Improvement (A Review)
AU  - Kalkidan Shiferaw Abebe
Y1  - 2019/06/19
PY  - 2019
N1  - https://doi.org/10.11648/j.abb.20190701.11
DO  - 10.11648/j.abb.20190701.11
T2  - Advances in Bioscience and Bioengineering
JF  - Advances in Bioscience and Bioengineering
JO  - Advances in Bioscience and Bioengineering
SP  - 1
EP  - 7
PB  - Science Publishing Group
SN  - 2330-4162
UR  - https://doi.org/10.11648/j.abb.20190701.11
AB  - Genotype by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable genotyping of large numbers of individuals at a large number of SNP markers. It is relatively straightforward, robust, and cost-effective method to reduce problems in crop caused by a large genome size, reduced representation libraries are produced using a restriction enzyme that targets genomic regions while multiplexing with barcodes reduces the cost for individual sample. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra- throughput sequences to revolutionize plant genotyping and breeding. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, QTL mapping, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs. GBS will have broad application in genomics-assisted plant breeding programs.
VL  - 7
IS  - 1
ER  -

Copy | Download