A.M., Crooijmans, R.P.M.A., Affara, N.A. et al. (2009). Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: e6524.
72 Richard, I. and Beckman, J.S. (1995). How neutral are synonymous codon mutations? Nature Genetics 10: 259.
73 Roder, M.S., Korzun, V., Wendehake, K. et al. (1998). A microsatellite map of wheat. Genetics 149: 2007–2023.
74 Rosas, J.E., Bonnecarrère, V., and Pérez de Vida, V.F. (2014). One‐step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.). Electronic Journal of Biotechnology 17: 95–101.
75 Sachidanandam, R., Weissman, D., Schmidt, S.C. et al. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (6822): 928–933.
76 Sanger, F., Nicklen, S., and Coulson, A.R. (1977). DNA sequencing with chain chain‐terminating inhibitors. Proceedings of the National Academy Sciences of the United States of America 74: 5463–5467.
77 Semagn, K., Bjornstad, A., and Ndjiondjop, M.N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnology 5 (25): 2540–2568.
78 Semagn, K., Babu, R., Hearne, S., and Olsen, M. (2013). Single nucleotide polymorphism genotyping using Kometitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Molecular Breeding 33: 1–14.
79 Sharopova, N., McMullen, M.D., Schultz, L. et al. (2002). Development and mapping of SSR markers for maize. Plant Molecular Biology 48: 463–481.
80 Shendure, J.A., Porreca, G.J., Church, G.M. et al. (2011). Overview of DNA sequencing strategies. Current Protocols in Molecular Biology 7 (1): 1–7.1.23. https://doi.org/10.1002/0471142727.mb0701s96.
81 Sidhu, G.K., Rustgi, S., Shafqat, M.N. et al. (2008). Fine structure mapping of a gene‐rich region ofwheat carrying Ph1, a suppressor of crossing over between homoeologous chromosomes. Proceedings of the National Academy Sciences of the United States of America 15: 5815–5820.
82 Sim, S.‐C., Durstewitz, G., Plieske, J. et al. (2012). Development of a large SNP genotyping array and generation of high‐density genetic maps in tomato. PLoS One 7 (7): e40563. https://doi.org/10.1371/journal.pone.0040563.
83 Singh, B.D. and Singh, A.K. (2015). Marker‐Assisted Plant Breeding: Principles and Practices. https://doi.org/10.1007/978‐81‐322‐2316‐0. Springer (India) Pvt. Ltd.
84 Singh, S., Sidhu, J.S., Huang, N. et al. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker assisted selection into indica cultivar PR106. Theoretical and Applied Genetics 102: 1011–1015.
85 Smith, J.S.C. and Smith, O.S. (1992). Fingerprinting crop varieties. Advances in Agronomy 47: 85–140.
86 Sobrino, B., Briona, M., and Carracedoa, A. (2005). SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Science International 154: 181–194.
87 Soleimani, V.D., Baum, B.R., and Johnson, D.A. (2003). Efficient validation of single nucleotide polymorphisms in plants by allele‐specific PCR, with an example from barley. Plant Molecular Biology Reporter 21: 281–288.
88 Somers, D.J., Isaac, P., and Edwards, K. (2004). A high‐density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 109: 1105–1114.
89 Song, Q.J., Shi, J.R., Singh, S. et al. (2005). Development and mapping of microsatellite (SSR) markers in wheat. Theoretical and Applied Genetics 110: 550–560.
90 Su, A., Song, W., Xing, J. et al. (2016). Identification of genes potentially associated with the fertility instability of S‐Type cytoplasmic male sterility in maize via bulked segregant RNA‐Seq. PLoS One 11 (9): e0163489.
91 Su, C., Wang, W., Gong, S. et al. (2017). High density linkage map construction and mapping of yield trait QTLs in maize (Zea mays) using the genotyping‐by‐sequencing (GBS) technology. Frontiers in Plant Science 8: 706. https://doi.org/10.3389/fpls.2017.00706.
92 Takagi, H., Tamiru, M., Abe, A. et al. (2015). MutMap accelerates breeding of a salt‐tolerant rice cultivar. Nature Biotechnology 33: 445–449.
93 Tanksley, S.D. and Nelson, J.C. (1996). Advanced backcross QTL analysis: a method for simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theoretical and Applied Genetics 92: 191–203.
94 Tanksley, S.D., Ganal, M.W., Prince, J.P. et al. (1992). High density molecular linkage maps of tomato and potato genomes. Genetics 132: 1141–1160.
95 Tanksley, S.D., Grandillo, S., Fulton, T.M. et al. (1996). Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theoretical and Applied Genetics 92: 213–224.
96 Temnykh, S., Park, W.D., Ayres, N. et al. (2000). Mapping and genome organization of mirosatellite sequences in rice (Oryza sativa) Theor. Applied Genetics 100: 697–712.
97 Tung, C.W., Zhao, K., Wright, M.H. et al. (2010). Development of a research platform for dissecting phenotype genotype associations in rice (Oryza spp.). Rice 3: 205–217.
98 Vos, P., Hogers, R., Bleeker, M. et al. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407–4414.
99 Wang, D.G., Fan, J.B., Siao, C.J. et al. (1998). Large‐scale identification, mapping, and genotyping of single‐nucleotide polymorphisms in the human genome. Science 280: 1077–1082.
100 Wickland, D.P., Battu, G., Hudson, K.A. et al. (2017). A comparison of genotyping‐by‐sequencing analysis methods on low‐coverage crop datasets shows advantages of a new workflow, GB‐eaSy. BMC Bioinformatics 18: 586.
101 Williams, J.G.K., Kublelik, A.R., Livak, K.J. et al. (1990). DNA polymorphism’s amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18: 6531–6535.
102 Xiao, J., Grandillo, S., Ahn, S.N. et al. (1996). Genes from wild rice improved yield. Nature 384: 223–224.
103 Xiao, J., Li, J., Grandillo, S. et al. (1998). Identification of trait improving QTL alleles from a wild rice relative Oryza rufipogon. Genetics 150: 899–909.
104 Yang, G., Chen, S., Chen, L. et al. (2019). Development of a core SNP arrays based on the KASP method for molecular breeding of rice. Rice 12: 21.
105 Yasuda, N., Mitsunaga, T., Hayashi, K. et al. (2015). Effects of pyramiding quantitative resistance genes pi21, Pi34, and Pi35 on rice leaf blast disease. Plant Disease 99: 904–909.
106 Zhang, X., Yang, Q., Rucker, E. et al. (2017). Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis). Theoretical and Applied Genetics 130: 1285–1295.
107 Zhou, Z., Zhang, C., Zhou, Y. et al. (2016). Genetic dissection of maize plant architecture with an ultra‐high density bin map based on recombinant inbred lines. BMC Genomics 17: 178. https://doi.org/10.1186/s12864‐016‐2555‐z.
108 Zhu, M., Liu, D., Liu, W. et al. (2017). QTL mapping using an ultra‐high‐density SNP map reveals a major locus for grain yield in an elite rice restorer R998. Scientific Reports 7: 10914. https://doi.org/10.1038/s41598‐017‐10666‐7.
2 High‐throughput Genotyping Platforms
Sandhya Sharma1, Kuldeep Kumar2, Kishor Tribhuvan3, Rita1, Sandeep Kumar4, Priyanka Jain1, Swati Saxena1,