Development of Single Nucleotide Polymorphism (SNP) Markers in Tropical Crops

Yheni Dwiningsih; Miranti Rahmaningsih; Jawaher Alkahtani

doi:10.26877/asset.v2i2.6279

Development of Single Nucleotide Polymorphism (SNP) Markers in Tropical Crops

Yheni Dwiningsih, Miranti Rahmaningsih, Jawaher Alkahtani

Abstract

Understanding genetic diversity, association studies, evolution analysis, quantitative trait loci, marker-assisted selection and genome-wide association in tropical crops are important for improving plant characteristics in order to increase food sustainability in tropical countries. Single nucleotide polymorphism (SNP) marker is becoming the most popular molecular marker for those studies. By using SNP marker, genes associated with important traits can be identified efficiently compared to the other molecular markers. This review describes about how SNP can be discovered in the plant genomes and the application of SNP in plant breeding, especially in tropical crops such as rice, maize, peas, potato, tomato, cassava, taro, etc.

Keywords: food sustainability, plant breeding, SNP marker, tropical crops

Full Text:

PDF

References

McCouch, S. R., Zhao, K., Wright, M., Tung, C. W., Ebana, K., Thomson, M., Reynolds, A., Wang, D., Declerck, G., Ali, M. L., McClung, A., Eizenga, G. & Bustamante, C. Development of genome-wide SNP assays for rice. Breed Sci. 60, 524–535 (2010).

Edwards, D. & Batley, J. Plant genome sequencing: applications for crop improvement. Plant Biotech J. 8, 2–9 (2010).

Thomson, M. J. High-throughput SNP genotyping to accelerate crop improvement. Plant Breed. Biotech. 2, 3, 195–212 (2014). doi:10.9787/PBB.2014.2.3.195

Borlaug, N. E. Contributions of conventional plant breeding to food production. Science. 219, 689–693 (1983).

Tester, M. & Langridge, P. Breeding technologies to increase crop production in a changing world. Science. 327, 818–822 (2010).

Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M. & Blaxer, M. L. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499–510 (2011).

Kim, C., Guo, H., Kong, W., Chandnani, R. & Shuang, L. Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science. 242, 14–22 (2016).

Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PlosOne3. E3376 (2008).

Andolfatto, P., Davison, D., Erezyilmaz, D., Hu, T.T., Mast, J., Sunayama-Morita, T. & Stern, D.L. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 21, 610–617 (2011).

Elshire, R. J., Glaubitz, J. C., Qun, J., Poland, J. A., Kawamoto, K., Buckler, E. S., Mitchell, S. E. & Robust, A. Simple genotyping by sequencing (GBS) approach for high diversity species. PlosOne. e19379 (2011).

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S. & Hoekstra, H. E. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PlosOne. 7. E37135 (2012).

Poland, J. A., Brown, P. J., Sorrells, M. E. & Jannink, J. L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PlosOne. 7. E32253 (2012).

Masher, M., Wu, S., Amand, P. S., Stein, N. & Poland, J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PlosOne. 8. E76925 (2013).

Truong, H. T., Ramos, A. M., Yalcin, F., de Ruiter, H. J., van deer Poel, et al. Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PlosOne. 7. E37565 (2012).

Stolle, E. & Moritz, R. F. RESTseq-efficient benchtop population genomics with RESTriction Fragmentt SEQuencing. PlosOne. 8. E63960 (2013).

Manson-Miller, J., Sanchez-Mendez, D. C., Fass, J., Henry, I. M., Tai, T. H. & Comai, L. Reference genome-independent assessment of mutation density using restriction enzyme-phase sequencing. BMC Genomics. 13, 72 (2012).

Hamilton, J. P., Hansey, C. N., Whitty, B. R., Stoffel, K., Massa, A. N., Deynze, A. V., De Jong, W, S., Douches, D. S. & Buell, C. R. Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics. 12, 302 (2011). doi:10.1186/1471-2164-12-302

Barchi, L., Lanteri, S., Portis, E., Acquadro, A., Vale, G., Toppino, L. & Rotino, G. L. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics. 12, 304 (2011).

Nelson, J. C., Wang, S., Wu, Y., Li, X., Antony, G., White, F. F. & Yu, J. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics. 12, 352 (2011).

Cortes, A. J., Chavarro, M. C. & Blair, M. W. SNP marker diversity in common bean (Phaseolus vulgaris L.). Theoreticl and Applied Genetics. 123, 827–845. (2011). doi:10.1007/s00122-011-1630-8

Gaur, R., Azam, S., Jeena, G., Khan, A. W., Choudhary, S., Jain, M., Yadav, G., Tyagi, A. K., Chattopadhyay, D. & Bhatia, S. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research. 19, 357–373. (2012). doi:10.1093/dnares/dss018

Singh, R., Bollina, V., Higgins, E. E., Clarke, W. E., Eynck, C., Sidebottom, C., Gugel, R., Snowdon, R. & Parkin, I. A. P. Single-nucleotide polymorphism identification and genotyping in Camelina sativa. Molecular Breeding. 35, 35 (2015).

Maughan, P. J., Smith, S. M., Rojas-Beltrian, J. A., Elzinga, D., Raney, J. A., Jellen, E. N., Bonifacio, A., Udall, J. A. & Fairbanks, D. J. Single nucleotide polymorphisms identification, characterization and linkage mapping in Chenopodium quinoa. The Plant Genome (2012). doi:10.3835/plantgenoe2012.06.0011

Yu, H., Xie, W., Li, J., Zhou, F. & Zhang, Q. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J. 12, 28–37 (2014).

Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., Guan, J., Fan, D., Weng, Q., Huang, T., Dong, G., Sang, T. & Han, B. High-throughput genotyping by whole-genome resequencing. Genome Res. 19, 1068–1076 (2009).

Shi, A., Vierling, R., Grazzini, R., Chen, P., Caton, H. & Panthee, D. Molecular Markers for Tm-2 Alleles of Tomato Mosaic Virus Resistance in Tomato. American Journal of Plant Sciences. 2, 180–189 (2011).

Buckler, E. S., Holland, J. B., Bradbury, P. J., et al. The genetic architecture of maize ﬂowering time. Science, 325, 5941: 714-718. (2009).

Poland, J. A., Bradbury, P. J., Buckler, E. S. & Nelson, R. J. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proceedings of the National Academy of Sciences of the United States of America. 108, 17, 6893–6898 (2011).

Zheng, P., Allen, W. B., Roeslar, K., et al. A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nature Genetics. 40, 3, 367–372 (2008).

Kump, K. L., Bradbury, P. J., Wisser, R. J., et al. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics. 43, 2, 163–168 (2011).

Junta, K., Saritnum, O., Juwattanasamran, R., Puddhanon, P., Struss, D., Puttarach, J. & Songchanthiek, S. Identification of single nucleotide polymorphism markers associated with northern corn leaf blight resistance in sweet corn. Chiang Mai University (CMU) Journal of Natural Sciences. 19, 1, 155–162 (2020).

Huang, X., Wei, X., Sang, T. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics. 42, 11, 961–967 (2010).

McNelly, K. L., Childs, K. L., Bohnert, R., Davidson, R. M., Zhao, K., Ulat, V. J., Zeller, G., Clark, R. M., Hoen, D. R., Bureau, T. E., Stokowski, R., Ballinger, D. G., Frazer, K. A., Cox, D. R., Padhukasahasram, B., Bustamante, C. D., Weigel, D., Mackill, D. J., Bruskiewich, R. M., Ratsch, G., Buell, C. R., Leung, H. & Leach, J. E. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. PNAS (2009). doi: 10.1073.pnas.0900992106

Ayres, N. M., Anna, M. M., Larkin, P. D., Bligh, H. F. J., Jonnes, C. et al. Microsatellites and a single nucleotide polymorphism differentiate apparent amylase classes in an extended pedigree of US rice germplasm (2000). http://www.nal.usda.gov/ttic/tektran/data/000007/55/0000075521.html.

Razak, A. S., Nor Azman, N. H. E., Kamaruzaman, R., Saidon, S. A., Mohd Yisof, M. F., Ismail, S. N., Jaafar, M. A. & Abdullah, N. Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers. Czech J. Genet. Plant Breed. 56, 62–70 (2020).

Gupta, P. K., Langridge, P. & Mir, R. R. Marker-assisted wheat breeding: present status and future possibilities. Molecular Breeding. 26, 2, 145–161 (2010).

Wei, O., Peng, Z., Zhou, Y., Yang, Z., Wu, K. & Ouyang, Z. Nucleotide diversity and molecular evolution of the WAG2 gene in common wheat (Triticum aestivum L.) and its relatives. Genetics and Molecular Biology. 34, 4, 606–615 (2011).

Huang, X. & Coder, M. S. Development of SNP assays for genotyping the Puroindoline b gene for grain hardiness in wheat using pyrosequencing. J Agric Food Chem. 53, 2070–2075 (2005).

Ellis, M., Speilmeyer, W., Gale, K., Rebetzke, G. & Richards, R. “Perfect” markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor. Appl. Genet. 105, 1038–1042 (2005).

Kim, K. S., Bellendir, S., Hudson, K. A., et al. Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theoretical and Applied Genetics. 120, 5, 1063–1071 (2010a).

Kim, K. S., Hill, C. B., Hartman, G. L., Hyten, D. L., Hudson, M. E. & Diers, B. W. Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI200538. Theoretical and Applied Genetics. 121, 3, 599–610 (2010b).

Ha, B. K., Hussey, R. S. & Boerma, H. R. Development of SNP assays for marker-assisted selection of two southern root-knot nematode resistance QTL in soybean. Crop Science. 47, 2, 73–82 (2007).

Shi, A., Chen, P., Vierling, R., Cervantes, I. & Shakiba, E. Development of multiplex SNP assays for selection of soybean mosaic virus resistance genes in soybean. World Soybean Research Conference VIII, August 10-15, 2009, Beijing, China (2009).

Gupta, P. K., Roy, J. K. & Prasad, M. Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr. Sci. 80, 524–535 (2001).

Grimmer, M. K., Trybush, S., Hanley, S., Francis, S. A., Karp, A. & Asher, M. J. C. An anchored linkage map for sugar beet based on AFLP, SNP and RAPD markers and QTL mapping of a new source of resistance to Beet necrotic yellow vein virus. Theoretical and Applied Genetics. 114, 7, 1151–1160 (2007).

Grimmer, M. K., Kraft, T., Francis, S. A. & Asher, M. J. C. QTL mapping of BNYVV resistance from the WB258 source in sugar beet. Plant Breeding. 127, 6, 650–652 (2008).

Muchero, W., Diop, N. N., Bhat, P. R., et al. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proceedings of the National Academy of Sciences of the United States of America. 106, 43, 18159–18164 (2009).

Jander, G., Norris, S. R., Rounsley, S. D., Bush, D. F., Levin, I. M. & Last, R. L. Arabidopsis map-based cloning in the post-genome era. Plant Physiology. 129, 2, 440–445. (2002).

Ong, P. W., Maizura, I., Abdullah, N. A. P., Rafii, M. Y., Ooi, L. C. L., Low, E. T. L. & Singh, R. Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis). Genetics and Molecular Research. 14, 4, 12205–12216 (2015).

Maryanto, S. D., Tanjung, Z. A., Sudania, W. M., Kusnandar, A. S., Roberdi, Pujianto, Utomo, C. & Liwang, T. Polymorphism of Fumarate Hydratase 1 (FUM1) gene associated with nitrogen uptake in oil palm (Elaeis guineensis). Biodiversitas, 21, 6, 2462–2466 (2020).

Karim, K. Y., Ifie, B., Dzidzienyo, D., Danquah, E. Y., Blay, E. T., Whyte, J. B. A., Kulakow, P., Rabbi, I., Parkes, E., Omoigui, L., Norman, P. E. and Iluebbey, P. (2020). Genetic characterization of cassava (Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers. Physiol Mol Biol Plants, 26, 2: 317-330.

Helmkampf, M., Wolfgruber, T. K., Bellinger, M. R., Paudel, R., Kantar, M. B., Miyasaka, S. C., Kimball, H. L., Brown, A., Veillet, A., Read, A. and Shintaku, M. (2018). Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping. Journal of Heredity, 272-282. doi:10.1093/jhered/esx070

Boutet, G., Carvalho, S. A., Falque, M., Peterlongo, P., Lhuillier, E., Bouchez, O., Lavaud, C., Pilet-Nayel, M., Riviere, N., and Baranger, A. (2016). SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. Genomics, 17: 121. doi:10.1186/s12864-016-2447-2

DOI: https://doi.org/10.26877/asset.v2i2.6279

Refbacks

There are currently no refbacks.

Advance Sustainable Science, Engineering and Technology (ASSET)

E-ISSN: 2715-4211
Published by Science and Technology Research Centre

Universitas PGRI Semarang, Indonesia

Website: http://journal.upgris.ac.id/index.php/asset/index
Email: asset@upgris.ac.id