the designation of GG for Oryza granulata and HHJJ for Oryza ridleyi (Aggarwal et al. 1997 ).
1.7.3 Deployment of Molecular Markers in Plant Variety Protection and Registration
The current system of plant variety protection and registration using assessment of DUS (Distinctness, Uniformity, and Stability) characteristics predominantly relies upon morphological traits which are quite laborious, time‐consuming, requires skills, expertise, and evaluation under special designs for most quantitative traits. With the advent of novel breeding technologies, new varieties differ only for few traits or at few loci which make the process of detecting distinctness in varieties, a challenging task. Even with increasing numbers of plant varieties, DUS testing is becoming quite expensive. In a review by Jamali et al. (2019), DNA‐based molecular markers have been proposed to be a reliable alternative for conducting DUS testing. Molecular markers not only cut cost, time and labor but will also help in the proper sharing of Plant Breeder’s Rights with an assessment of few distinct traits, particularly in essentially derived varieties.
1.8 Summary
The DNA‐based molecular markers are widely recognized for their enormous potential in plant breeding and genetic studies. The past few years have seen remarkable developments in the field of molecular markers technology particularly with the emergence of NGS technologies. SNPs have become the choice of markers of present and future based on their genome‐wide abundance, high polymorphism, amenability to high‐throughput automation, and easier analysis. SNPs can be utilized in different genotyping platforms such as GBS, DArT, WGR, SNP arrays, and KASP. Any genotyping platform can be chosen based on the objective of the study and cost concerns. As an example, GBS, WGR, SNP arrays, and KASP can generate similar type of results for genetic diversity analysis; however, KASP and GBS could be cheaper than others. While the development of KASP will depend upon the availability of SNPs particularly in SNP databases, but GBS can be done without any previous information. It has been observed that these recent marker genotyping technologies have accelerated the crop improvement programs particularly in the identification and utilization of novel genes and QTLs.
References
1 Aggarwal, R.K., Brar, D.S., and Khush, G.S. (1997). Two new genomes in the oryza complex identified on the basis of molecular divergence analysis using total genomic hybridization. Molecular & General Genetics 254: 1–12.
2 Akkurt, M., Welter, L., Maul, E. et al. (2007). Development of SCAR markers linked to powdery mildew (Uncinula necator) resistance in grapevine (Vitis vinifera L. and Vitis sp.). Molecular Breeding 19: 103–111.
3 Bachlava, E., Taylor, C.A., Tang, S. et al. (2012). SNP discovery and development of a high‐density genotyping array for sunflower. PLoS One 7 (1): e29814.
4 Batley, J., Barker, G., O’Sullivan, H. et al. (2003). Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology 132 (1): 84–91.
5 Bhatia, D. (2020). Advanced quantitative genetics technologies for accelerating plant breeding. In: Accelerated Plant Breeding, vol. I (eds. S.S. Gosal and S.H. Wani). Springer Verlag https://doi.org/10.1007/978‐3‐030‐41866‐3_5.
6 Bhatia, D., Sharma, R., Vikal, Y. et al. (2011). Marker assisted development of bacterial blight resistant, dwarf and high yielding versions of two traditional Basmati rice cultivars. Crop Science 51: 759–770.
7 Bhatia, D., Wing, R.A., and Singh, K. (2013). Genotyping by sequencing, its implications and benefits. Crop Improvement 40: 101–111.
8 Bhatia, D., Wing, R.A., Yu, Y. et al. (2018). Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica 214: 41. https://doi.org/10.1007/s10681‐018‐2119‐1.
9 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. American Journal of Human Genetics 32 (314): 331.
10 Brar, D.S. and Dhaliwal, H.S. (1997). Molecular markers and their application in crop improvement. In: Proceedings 3rd Agricultural Science Congress (eds. M.S. Bajwa et al.). New Delhi, India: Natl. Acad. Agr. Sci.
11 Brookes, A.J. (1999). The essence of SNPs. Gene 234: 177–186.
12 Chao, W.Z., Tang, C.H., Zhang, J.S. et al. (2018). Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter‐simple sequence repeat markers. Journal of Integrative Agriculture 17 (1): 130–138.
13 Chen, H., Xie, W., He, H. et al. (2013). A high density SNP genotyping array for rice biology and molecular breeding. Molecular Plant 7: 541–553.
14 Ching, A., Caldwell, K.S., Jung, M.T., and Dolan, M. (2002). SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3 (1): 19. https://doi.org/10.1186/1471‐2156‐3‐19.
15 Cho, Y.G., McCouch, S.R., Kuiper, M. et al. (1997). Integration of AFLP markers into an RFLP and SSLP map of rice (Oryza sativa L.). Rice Genet. Newsletter 14: 106–109.
16 Chung, Y.S., Choi, S.C., Jun, T.‐H., and Kim, C. (2017). Genotyping by sequencing: a promising tool for plant genetics research and breeding. Horticulture, Environment and Biotechnology 58 (5): 425–431.
17 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.
18 Coryell, V.H., Jessen, H., Schupp, J.M. et al. (1999). Allele‐specific hybridization markers for soybean. Theoretical and Applied Genetics 98: 690–696.
19 Ding, C. and Jin, S. (2009, 2003). High‐throughput methods for SNP genotyping. In: Single Nucleotide Polymorphisms, Methods in Molecular Biology, vol. 578 (ed. A.A. Komar). Humana Press, A Part of Springer Science+Business Media, LLC https://doi.org/10.1007/978‐1‐60327‐411‐1_16.
20 Elkot, A.F.A., Chhuneja, P., Kaur, S. et al. (2015). Marker assisted transfer of two powdery mildew resistance genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.). PLoS One 10 (6): e128297.
21 Fang, T., Lei, L., Li, G. et al. (2020). Development and deployment of KASP markers for multiple alleles of Lr34 in wheat. Theoretical and Applied Genetics 133: 2183–2195.
22 Fehr, W. (1984). Genetic Contributions to Yield Gains of Five Major Crop Plants. Madison, Wisconsin: Special publication No. 7 Crop Science Society of America.
23 Fulton, T.M., Nelson, J.C., and Tanksley, S.D. (1997). Introgression and DNA marker analysis of Lycopersicon peruvianum, a wild relative of cultivated tomato into L. esculentum followed through three successive backcross generations. Theoretical and Applied Genetics 95: 895–902.
24 Ganal, M.W., Altmann, T., and Roder, M.S. (2009). SNP identification in crop plants. Current Opinion in Plant Biology 12 (2): 211–217.
25 Ganal, M.W., Durstewitz, G., Polley, A. et al. (2011). A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6.
26 Gibbs, R.A. et al. (2009). Genome‐wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528–532.
27 Grewal, S., Othmeni, M., Walker, J. et al. (2020). Development of Wheat‐Aegilops caudata introgression lines and their characterization using genome‐specific KASP markers. Frontiers in Plant Science 11: 606.
28 Grodzicker, T., Williams,