Marker-assisted selection: A smart biotechnological strategy for modern plant breeding

Authors

  • Shruti Shrestha Agriculture and Forestry University, Rampur, Chitwan, Nepal.
  • Sudeep Subedi Nepal Agricultural Research Council, National Plant Breeding and Genetics Research Centre, Khumaltar, Lalitpur, Nepal.
  • Jiban Shrestha Nepal Agricultural Research Council, National Plant Breeding and Genetics Research Centre, Khumaltar, Lalitpur, Nepal.

DOI:

https://doi.org/10.21704/pja.v4i3.1490

Keywords:

Breeding, Marker Assisted Selection (MAS), Single nucleotide polymorphisms (SNPs)

Abstract

Plant breeders and geneticists use molecular marker-assisted selection also called as MAS as a useful approach for breeding of plant to make selection more efficient and speed up the breeding cycle. MAS can be more efficient, effective, and reliable than phenotypic selection.  Molecular markers are useful to identify the economically important traits in the breeding population for further manipulation in a short time. Due to the applicability of markers at the seedling stage ensuring high precision at the reduced level of cost, marker-assisted selection offer the chances to improve responses from selection. The MAS using DNA level polymorphism accelerate the pace of selection. The main marker technologies applied are chiefly co-dominant markers i.e. microsatellite markers/SSR (Simple Sequence Repeats) marker, RFLP (Restriction Fragment Length Polymorphism) marker and SNPs (Single nucleotide polymorphisms). This review overviews the various MAS technologies and their applications in crop improvement programs.

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References

Abler, B. S. B., Edwards, M. D., & Stuber, C. W. (1991). Isoenzymatic identification of quantitative trait loci in crosses of elite maize inbreds. Crop Science, 31(2), 267–274. https://doi.org/10.2135/cropsci1991.0011183X003100020006x

Adam-Blondon, A.-F., Sévignac, M., Bannerot, H., & Dron, M. (1994). SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theoretical and Applied Genetics, 88(6–7), 865–870. https://doi.org/10.1007/BF01253998

Al-Samarai, F., & Al-Kazaz, A. (2015). Molecular Markers: an Introduction and Applications. European Journal of Molecular Biotechnology, 9. https://doi.org/10.13187/ejmb.2015.9.118

Arshad, H. M. I., Sahi, S. T., Atiq, M., & Wakil, W. (2016). Appraisal of resistant genes and gene pyramid lines of rice against indigenous pathotypes of Xanthomonas oryzae pv. oryzae in Punjab, Pakistan. Pakistan Journal of Agricultural Sciences, 53(2), 365–370. https://doi.org/10.21162/PAKJAS/16.5357

Arunakumari, K., Durgarani, C. V, Satturu, V., Sarikonda, K. R., Chittoor, P. D. R., Vutukuri, B., Laha, G. S., Nelli, A. P. K., Gattu, S., & Jamal, M. (2016). Marker-assisted pyramiding of genes conferring resistance against bacterial blight and blast diseases into Indian rice variety MTU1010. Rice Science, 23(6), 306–316. https://doi.org/10.1016/j.rsci.2016.04.005

Barloy, D., Lemoine, J., Abelard, P., Tanguy, A.-M., Rivoal, R., & Jahier, J. (2007). Marker-assisted pyramiding of two cereal cyst nematode resistance genes from Aegilops variabilis in wheat. Molecular Breeding, 20(1), 31–40. https://doi.org/10.1007/s11032-006-9070-x

Batlle, I., & Alston, F. H. (1996). Genes determining leucine aminopeptidase and mildew resistance from the ornamental apple,‘White Angel.’ Theoretical and Applied Genetics, 93(1–2), 179–182. https://doi.org/10.1007/BF00225743

Bottema, C. D. K., Sarkar, G., Cassady, J. D., Ii, S., Dutton, C. M., & Sommer, S. S. (1993). [29] Polymerase chain reaction amplification of specific alleles: A general method of detection of mutations, polymorphisms, and haplotypes. Methods in Enzymology, 218, 388–402. Elsevier. https://doi.org/10.1016/0076-6879(93)18031-7

Caetano-Anollés, G., Brant J., B., & Peter M., G. (1991). DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers. Bio/Technology, 9(6), 553–557. https://doi.org/10.1038/nbt0691-553

Cao, J., Zhao, J.-Z., Tang, J., Shelton, A., & Earle, E. (2002). Broccoli plants with pyramided cry1Ac and cry1C Bt genes control diamondback moths resistant to Cry1A and Cry1C proteins. Theoretical and Applied Genetics, 105(2–3), 258–264. https://doi.org/10.1007/s00122-002-0942-0

Castro, A. J., Capettini, F., Corey, A. E., Filichkina, T., Hayes, P. M., Kleinhofs, A., Kudrna, D., Richardson, K., Sandoval-Islas, S., & Rossi, C. (2003). Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley. Theoretical and Applied Genetics, 107(5), 922–930. https://doi.org/10.1007/s00122-003-1329-6

Chaitieng, B., Kaga, A., Han, O. K., Wang, X. W., Wongkaew, S., Laosuwan, P., Tomooka, N., & Vaughan, D. A. (2002). Mapping a new source of resistance to powdery mildew in mungbean. Plant Breeding, 121(6), 521–525. https://doi.org/10.1046/j.1439-0523.2002.00751.x

Chhuneja, P., Kaur, S., Garg, T., Ghai, M., Kaur, S., Prashar, M., Bains, N. S., Goel, R. K., Keller, B., & Dhaliwal, H. S. (2008). Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theoretical and Applied Genetics, 116(3), 313–324. https://doi.org/10.1007/s00122-007-0668-0

Chu, Z., Yuan, M., Yao, J., Ge, X., Yuan, B., Xu, C., Li, X., Fu, B., Li, Z., & Bennetzen, J. L. (2006). Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes & Development, 20(10), 1250–1255. https://doi.org/10.1101/gad.1416306

Chukwu, S. C., Rafii, M. Y., Ramlee, S. I., Ismail, S. I., Oladosu, Y., Okporie, E., Onyishi, G., Utobo, E., Ekwu, L., Swaray, S., & Jalloh, M. (2019). Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). Biotechnology & Biotechnological Equipment, 33(1), 440–455. https://doi.org/10.1080/13102818.2019.1584054

Collard, B. C.Y., Jahufer, M. Z. Z., Brouwer, J. B., & 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(1–2), 169–196. https://doi.org/10.1007/s10681-005-1681-5

Collard, Bertrand C.Y., & Mackill, D. J. (2008). Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491), 557–572. https://doi.org/10.1098/rstb.2007.2170

Das, G., & Rao, G. J. N. (2015). Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar. Frontiers in Plant Science, 6(September), 1–18. https://doi.org/10.3389/fpls.2015.00698

Das, G., Patra, J. K., & Baek, K. H. (2017). Insight into MAS: A molecular tool for development of stress resistant and quality of rice through gene stacking. Frontiers in Plant Science, 8(June), 1–9. https://doi.org/10.3389/fpls.2017.00985

De Bustos, A., Rubio, P., Soler, C., Garcia, P., & Jouve, N. (2001). Marker assisted selection to improve HMW-glutenins in wheat. In Wheat in a Global environment (pp. 171–176). Springer. https://doi.org/10.1007/978-94-017-3674-9_19

De Giovanni, C., Dell’Orco, P., Bruno, A., Ciccarese, F., Lotti, C., & Ricciardi, L. (2004). Identification of PCR-based markers (RAPD, AFLP) linked to a novel powdery mildew resistance gene (ol-2) in tomato. Plant Science, 166(1), 41–48. https://doi.org/10.1016/j.plantsci.2003.07.005

Divya, B., Robin, S., Rabindran, R., Senthil, S., Raveendran, M., & Joel, A. J. (2014). Marker assisted backcross breeding approach to improve blast resistance in Indian rice (Oryza sativa) variety ADT43. Euphytica, 200(1), 61–77. https://doi.org/10.1007/s10681-014-1146-9

Dixit, S., Yadaw, R. B., Mishra, K. K., & Kumar, A. (2017). Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal. Euphytica, 213(8), 184. https://doi.org/10.1007/s10681-017-1976-3

Dreher, K., Morris, M., Khairallah, M., Ribaut, J.-M., Pandey, S., & Srinivasan, G. (2002). Is marker-assisted selection cost-effective compared to conventional plant breeding methods? The case of quality protein maize. Proceedings of the 4th Annual Conference of the International Consortium on Agricultural Biotechnology Research (ICABR’00), 203–236.

Evans, K., & James, C. (2003). Identification of SCAR markers linked to Pl-w mildew resistance in apple. Theoretical and Applied Genetics, 106(7), 1178–1183. https://doi.org/10.1007/s00122-002-1147-2

Ghafoor, A., & McPhee, K. (2012). Marker assisted selection (MAS) for developing powdery mildew resistant pea cultivars. Euphytica, 186(3), 593–607. https://doi.org/10.1007/s10681-011-0596-6

Gupta, P. K., Langridge, P., & Mir, R. R. (2010). Marker-assisted wheat breeding: Present status and future possibilities. Molecular Breeding, 26(2), 145–161. https://doi.org/10.1007/s11032-009-9359-7

Hämäläinen, J. H., Watanabe, K. N., Valkonen, J. P. T., Arihara, A., Plaisted, R. L., Pehu, E., Miller, L., & Slack, S. A. (1997). Mapping and marker-assisted selection for a gene for extreme resistance to potato virus Y. Theoretical and Applied Genetics, 94(2), 192–197.

Hasan, M., Rafii, M., Ismail, M., Mahmood, M., Rahim, H., Alam, M. A., Ashkani, S., Malek, M., & A., L. (2015). Marker-assisted backcrossing: A useful method for rice improvement. Biotechnology & Biotechnological Equipment, 29, 1–18. https://doi.org/10.1080/13102818.2014.995920

Hayashi, K., Yoshida, H., & Ashikawa., I. (2006). Development of PCR–based allele specific and InDel marker sets for nine rice blast resistance genes. Theoretical and Applied Genetics, 113, 251–260.

Heikrujam, M., Sharma, K., Kumar, J., & Agrawal, V. (2014). Generation and validation of unique male sex-specific sequence tagged sites (STS) marker from diverse genotypes of dioecious Jojoba-Simmondsia chinensis (Link) Schneider. Euphytica, 199(3), 363–372. https://doi.org/10.1007/s10681-014-1136-y

Hemmat, M., Weedon, N. F., Manganaris, A. G., & Lawson, D. M. (1994). Molecular marker linkage map for apple. Journal of Heredity, 85(1), 4–11. https://doi.org/10.1093/oxfordjournals.jhered.a111390

Hittalmani, S., Parco, A., Mew, T. V, Zeigler, R. S., & Huang, N. (2000). Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theoretical and Applied Genetics, 100(7), 1121–1128. https://doi.org/10.1007/s001220051395

Holland, J. B. (2004). Implementation of molecular markers for quantitative traits in breeding programs-challenges and opportunities. New Directions for a Diverse Planet: Proceedings for the 4th International Crop Science Congress. Regional Institute, Gosford, Australia, Www. Cropscience. Org. Au/Icsc2004.https://doi.org/10.5897/BMBR2010.0006

Hu, J., Li, X., Wu, C., Yang, C., Hua, H., Gao, G., Xiao, J., & He, Y. (2012). Pyramiding and evaluation of the brown planthopper resistance genes Bph14 and Bph15 in hybrid rice. Molecular Breeding, 29(1), 61–69. https://doi.org/10.1007/s11032-010-9526-x

Humphry, M. E., Magner, T., McIntyre, C. L., Aitken, E. A. B., & Liu, C. J. (2003). Identification of a major locus conferring resistance to powdery mildew (Erysiphe polygoni DC) in mungbean (Vigna radiata L. Wilczek) by QTL analysis. Genome, 46(5), 738–744. https://doi.org/10.1139/g03-057

Jamaloddin, M., Durga Rani, C. V., Swathi, G., Anuradha, C., Vanisri, S., Rajan, C. P. D., Krishnam Raju, S., Bhuvaneshwari, V., Jagadeeswar, R., Laha, G.S., Prasad, M.S., Satyanarayana, P.V., Cheralu, C., Rajani, G., Ramprasad, E., Sravanthi, P., Arun Prem Kumar, N., Aruna Kumari, K., ..... Sheshu Madhav, M. (2020). Marker Assisted Gene Pyramiding (MAGP) for bacterial blight and blast resistance into mega rice variety “Tellahamsa”. PloS one, 15(6), e0234088. https://doi.org/10.1371/journal.pone.0234088

Jefferies, S. P., King, B. J., Barr, A. R., Warner, P., Logue, S. J., & Langridge, P. (2003). Marker‐assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley. Plant Breeding, 122(1), 52–56. https://doi.org/10.1046/j.1439-0523.2003.00752.x

Ji, Z., Shi, J., Zeng, Y., Qian, Q., & Yang, C. (2014). Application of a simplified marker-assisted backcross technique for hybrid breeding in rice. Biologia (Poland), 69(4), 463–468. https://doi.org/10.2478/s11756-014-0335-2

Jones J.D.G. , & Dangl J.L. (2006). The plant immune system. Nature, 444, 323–329.

Joshi, B. K., Louws, F. J., Yenco, G. C., Sosinski, B. R., Arellano, C., & Panthee, D. R. (2015). Molecular Markers for Septoria Leaf Spot (Septoria lycopersicii Speg.) Resistance in Tomato (Solanum lycopersicum L.). Nepal Journal of Biotechnology, 3(1), 40–47. https://doi.org/10.3126/njb.v3i1.14230

Joshi, R. K., & Nayak, S. (2010). Gene pyramiding-A broad spectrum technique for developing durable stress resistance in crops. Biotechnology and Molecular Biology Reviews, 5(3), 51-60.

K. Osei, M., Prempeh, R., Adjebeng-Danquah, J., A. Opoku, J., Danquah, A., Danquah, E., Blay, E., & Adu-Dapaah, H. (2019). Marker-Assisted Selection (MAS): A Fast-Track Tool in Tomato Breeding. Recent Advances in Tomato Breeding and Production. https://doi.org/10.5772/intechopen.76007

Kausar, S., Hameed, S., Saleem, K., ul Haque, I., Zamurrad, M., & Ashfaq, M. (2015). Molecular confirmation of Bdv2 gene in wheat germplasm and its field based assessment for resistance against barely yellow dwarf viruses. Advancements in Life Sciences, 3(1), 16–22.

Kelly, J. D., Gepts, P., Miklas, P. N., & Coyne, D. P. (2003). Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Research, 82(2–3), 135–154. https://doi.org/10.1016/S0378-4290(03)00034-0

Khan, G. H., Shikari, A. B., Vaishnavi, R., Najeeb, S., Padder, B. A., Bhat, Z. A., Parray, G. A., Bhat, M. A., Kumar, R., & Singh, N. K. (2018). Marker-assisted introgression of three dominant blast resistance genes into an aromatic rice cultivar Mushk Budji. Scientific Reports, 8(1), 4091. https://doi.org/10.1038/s41598-018-22246-4

Kim, S.-M., Suh, J.-P., Qin, Y., Noh, T.-H., Reinke, R. F., & Jena, K. K. (2015). Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.). Theoretical and Applied Genetics, 128(10), 1933–1943. https://doi.org/10.1007/s00122-015-2557-2

Kloppers, F. J., & Pretorius, Z. A. (1997). Effects of combinations amongst genes Lr13, Lr34 and Lr37 on components of resistance in wheat to leaf rust. Plant Pathology, 46(5), 737–750. https://doi.org/10.1046/j.1365-3059.1997.d01-58.x

Kochert, G. (1994). RFLP technology. In DNA-based markers in plants (pp. 8–38). Springer. https://doi.org/10.1007/978-94-011-1104-1_2

Kottapalli, K. R., Narasu, M. L., & Jena, K. K. (2010). Effective strategy for pyramiding three bacterial blight resistance genes into fine grain rice cultivar, Samba Mahsuri, using sequence tagged site markers. Biotechnology letters, 32(7), 989-996. https://doi.org/10.1007/s10529-010-0249-1

Kumar, N. S., & Gurusubramanian, G. (2011). Random amplified polymorphic DNA (RAPD) markers and its applications. Science Vision, 11(3), 116–124.

Kumar, V. A., Balachiranjeevi, C. H., Naik, S. B., Rambabu, R., Rekha, G., Madhavi, K. R., Harika, G., Vijay, S., Pranathi, K., Hajira, S. K., Srivastava, A., Mahadevaswamy, H. K., Anila, M., Yugander, A., Aruna, J., Prasad, A. S. H., Madhav, M. S., Laha, G. S., Viraktamath, B. C., & Prasad, M. S. (2016). Marker-assisted introgression of the major bacterial blight resistance gene, Xa21 and blast resistance gene, Pi54 into RPHR-1005, the restorer line of the popular rice hybrid, DRRH3. Journal of Plant Biochemistry and Biotechnology, 25(4), 400–409. https://doi.org/10.1007/s13562-016-0352-z

Kumar, V. A., Balachiranjeevi, C. H., Naik, S. B., Rekha, G., Rambabu, R., Harika, G., ... & Kale, R. (2017). Marker-assisted pyramiding of bacterial blight and gall midge resistance genes into RPHR-1005, the restorer line of the popular rice hybrid DRRH-3. Molecular Breeding, 37(7), 86. https://doi.org/10.1007/s11032-017-0687-8

Kurokawa, Y., Noda, T., Yamagata, Y., Angeles-Shim, R., Sunohara, H., Uehara, K., ... & Yoshimura, A. (2016). Construction of a versatile SNP array for pyramiding useful genes of rice. Plant Science, 242, 131-139. https://doi.org/10.1016/j.plantsci.2015.09.008

Kurth, J., Kolsch, R., Simons, V., & Schulze-Lefert, P. (2001). A high-resolution genetic map and a diagnostic RFLP marker for the Mlg resistance locus to powdery mildew in barley. Theoretical and Applied Genetics, 102(1), 53–60. https://doi.org/10.1007/s001220051617

Lema, M. (2018). Marker Assisted Selection in Comparison to Conventional Plant Breeding: Review Article. Agricultural Research and Technology: Open Access Journal, 14(2). https://doi.org/10.19080/artoaj.2018.14.555914

Liebhard, R., Gianfranceschi, L., Koller, B., Ryder, C. D., Tarchini, R., Van de Weg, E., & Gessler, C. (2002). Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.). Molecular Breeding, 10(4), 217–241. https://doi.org/10.1023/A:1020525906332

Linde, M., & Debener, T. (2003). Isolation and identification of eight races of powdery mildew of roses (Podosphaera pannosa)(Wallr.: Fr.) de Bary and the genetic analysis of the resistance gene Rpp1. Theoretical and Applied Genetics, 107(2), 256–262. https://doi.org/10.1007/s00122-003-1240-1

Linde, M., Hattendorf, A., Kaufmann, H., & Debener, T. (2006). Powdery mildew resistance in roses: QTL mapping in different environments using selective genotyping. Theoretical and Applied Genetics, 113(6), 1081–1092. https://doi.org/10.1007/s00122-006-0367-2

Liu, J., Liu, D., Tao, W., Li, W., Wang, S., Chen, P., Cheng, S., & Gao, D. (2000). Molecular marker‐facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breeding, 119(1), 21–24. https://doi.org/10.1046/j.1439-0523.2000.00431.x

Mackill, D. J., Nguyen, H. T., & Zhang, J. (1999). Use of molecular markers in plant improvement programs for rainfed lowland rice. Field Crops Research, 64(1), 177–185. https://doi.org/10.1016/S0378-4290(99)00058-1

Malav, A. K., Indu., & Chandrawat, K. S. (2016). Gene pyramiding: An overview. International Journal of Current Research in Biosciences and Plant Biology, 3, 22–28. http://dx.doi.org/10.20546/ijcrbp.2016.307.004

Maphosa, M., Talwana, H., & Tukamuhabwa, P. (2012). Enhancing soybean rust resistance through Rpp2, Rpp3 and Rpp4 pair wise gene pyramiding. African Journal of Agricultural Research, 7(30), 4271–4277.

McCouch, S. R., Chen, X., Panaud, O., Temnykh, S., Xu, Y., Cho, Y. G., Huang, N., Ishii, T., & Blair, M. (1997). Microsatellite marker development, mapping and applications in rice genetics and breeding. In Oryza: From Molecule to Plant (pp. 89–99). Springer. https://doi.org/10.1007/978-94-011-5794-0_9

McCough, S. R., & Doerge, R. W. (1995). QTL mapping in rice. Trends in Genetics, 11(12), 482–487. https://doi.org/10.1016/S0168-9525(00)89157-X

Mehlenbacher, S. A. (1995). Classical and molecular approaches to breeding fruit and nut crops for disease resistance. HortScience, 30(3), 466–477.

Meksem, K., Leister, D., Peleman, J., Zabeau, M., Salamini, F., & Gebhardt, C. (1995). A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers. Molecular and General Genetics MGG, 249(1), 74–81. https://doi.org/10.1007/BF00290238

Miedaner, T., Wilde, F., Steiner, B., Buerstmayr, H., Korzun, V., & Ebmeyer, E. (2006). Stacking quantitative trait loci (QTL) for Fusarium head blight resistance from non-adapted sources in an European elite spring wheat background and assessing their effects on deoxynivalenol (DON) content and disease severity. Theoretical and Applied Genetics, 112(3), 562–569.

Miyagi, M., Humphry, M., Ma, Z. Y., Lambrides, C. J., Bateson, M., & Liu, C. J. (2004). Construction of bacterial artificial chromosome libraries and their application in developing PCR-based markers closely linked to a major locus conditioning bruchid resistance in mungbean (Vigna radiata L. Wilczek). Theoretical and Applied Genetics, 110(1), 151–156. https://doi.org/10.1007/s00122-004-1821-7

Mohan, M., Nair, S., Bhagwat, A., Krishna, T. G., Yano, M., Bhatia, C. R., & Sasaki, T. (1997). Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding, 3(2), 87–103. https://doi.org/10.1023/A:1009651919792

Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N., Özkan, H., Chung, G., & Baloch, F. S. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2), 261–285. https://doi.org/10.1080/13102818.2017.1400401

Niño-Liu D.O., Ronald P.C., & Bogdanove A.J. (2006). Xanthomonas oryzae pathovars: Model pathogen of a model crop. Molecular Plant Pathology, 7, 303–324.

Nocente, F., Gazza, L., & Pasquini, M. (2007). Evaluation of leaf rust resistance genes Lr1, Lr9, Lr24, Lr47 and their introgression into common wheat cultivars by marker-assisted selection. Euphytica, 155(3), 329–336. https://doi.org/10.1007/s10681-006-9334-x

Nogoy, F. M., Song, J.-Y., Ouk, S., Rahimi, S., Kwon, S. W., Kang, K.-K., & Cho, Y.-G. (2016). Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.) . Plant Breeding and Biotechnology, 4(3), 271–284. https://doi.org/10.9787/pbb.2016.4.3.271

Ogbonnaya, F. C., Subrahmanyam, N. C., Moullet, O., De Majnik, J., Eagles, H. A., Brown, J. S., Eastwood, R. F., Kollmorgen, J., Appels, R., & Lagudah, E. S. (2001). Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Australian Journal of Agricultural Research, 52(12), 1367–1374. https://doi.org/10.1071/AR01031

Panaud, O., Chen, X., & McCouch, S. R. (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular and General Genetics MGG, 252(5), 597–607. https://doi.org/10.1007/BF02172406

Patocchi, A., Frei, A., Frey, J. E., & Kellerhals, M. (2009). Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes. Molecular Breeding, 24(4), 337. https://doi.org/10.1007/s11032-009-9295-6

Patroti, P., Vishalakshi, B., Umakanth, B., Suresh, J., Senguttuvel, P., & Madhav, M. S. (2019). Marker-assisted pyramiding of major blast resistance genes in Swarna-Sub1, an elite rice variety (Oryza sativa L.). Euphytica, 215(11). https://doi.org/10.1007/s10681-019-2487-1

Pradhan, S. K., Nayak, D. K., Mohanty, S., Behera, L., Barik, S. R., Pandit, E., Lenka, S., & Anandan, A. (2015). Pyramiding of three bacterial blight resistance genes for broad-spectrum resistance in deepwater rice variety, Jalmagna. Rice, 8(1), 19. https://doi.org/10.1186/s12284-015-0051-8

Pumphrey, M. O., Bernardo, R., & Anderson, J. A. (2007). Validating the Fhb1 QTL for Fusarium head blight resistance in near‐isogenic wheat lines developed from breeding populations. Crop Science, 47(1), 200–206. https://doi.org/10.2135/cropsci2006.03.0206

Ramalingam, J., Savitha, P., Alagarasan, G., Saraswathi, R., & Chandrababu, R. (2017). Functional marker assisted improvement of stable cytoplasmic male sterile lines of rice for bacterial blight resistance. Frontiers in Plant Science, 8(June), 1–9. https://doi.org/10.3389/fpls.2017.01131

Rana, M., Sood, A., Hussain, W., Kaldate, R., Sharma, T.R., Gill, R.K., Kumar, S., & Singh, S. (2019). Gene pyramiding and multiple character breeding. In Lentils. pp. 83-124. Academic Press.

Rani, P. J., Satyanarayana, P. V., Chamundeswari, N., & Rani, M. G. (2014). A review on marker assisted selection in crop improvement. https://www.semanticscholar.org/paper/Review-article-A-REVIEW-ON-MARKER-ASSISTED-IN-CROP-Rani-Satyanarayana/6b036be9086540c5193c70633c95a8bee68d7ee5

Ranade, S. A., Srivastava, A. P., Rana, T. S., Srivastava, J., & Tuli, R. (2008). Easy assessment of diversity in Jatropha curcas L. plants using two single-primer amplification reaction (SPAR) methods. Biomass and Bioenergy, 32(6), 533–540. https://doi.org/10.1016/j.biombioe.2007.11.006

Sarika, K., Hossain, F., Muthusamy, V., Zunjare, R. U., Baveja, A., Goswami, R., Bhat, J. S., Saha, S., & Gupta, H. S. (2018). Marker-assisted pyramiding of opaque2 and novel opaque16 genes for further enrichment of lysine and tryptophan in sub-tropical maize. Plant Science, 272, 142–152.

Schütte, U. M. E., Abdo, Z., Bent, S. J., Shyu, C., Williams, C. J., Pierson, J. D., & Forney, L. J. (2008). Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Applied Microbiology and Biotechnology, 80(3), 365–380. https://doi.org/10.1007/s00253-008-1565-4

Servin, B., Martin, O. C., & Mézard, M. (2004). Toward a theory of marker-assisted gene pyramiding. Genetics, 168(1), 513–523. https://doi.org/10.1534/genetics.103.023358

Shanti, M. L., George, M. L. C., Cruz, C. M. V., Bernardo, M. A., Nelson, R. J., Leung, H., Reddy, J. N., & Sridhar, R. (2001). Identification of resistance genes effective against rice bacterial blight pathogen in eastern India. Plant Disease, 85(5), 506–512. https://doi.org/10.1094/PDIS.2001.85.5.506

Shavrukov, Y. N. (2016). CAPS markers in plant biology. Russian Journal of Genetics: Applied Research, 6(3), 279–287. https://doi.org/10.1134/S2079059716030114

Shi, A., Chen, P., Li, D., Zheng, C., Zhang, B., & Hou, A. (2009). Pyramiding multiple genes for resistance to soybean mosaic virus in soybean using molecular markers. Molecular Breeding, 23(1), 113. https://doi.org/10.1007/s11032-008-9219-x

Singh S., Sidhu J.S., Huang N., Vikal Y., Li Z., Brar D.S., Dhaliwal H.S., & Khush G.S. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker assisted selection into indica rice cultivar PR106. Theoretical and Applied Genetics, 102, 1011–1015.

Singh, M., Mallick, N., Chand, S., Kumari, P., Sharma, J. B., Sivasamy, M., Jayaprakash, P., Prabhu, K. V, & Jha, S. K. (2017). Marker-assisted pyramiding of Thinopyrum-derived leaf rust resistance genes Lr19 and Lr24 in bread wheat variety HD2733. Journal of Genetics, 96(6), 951–957.

Singh, R., Datta, D., Singh, S., & Tiwari, R. (2004). Marker-assisted selection for leaf rust resistance genes Lr19 and Lr24 in wheat (Triticum aestivum L.). Journal of Applied Genetics, 45(4), 399–404.

Singh, S., Sidhu, J. S., Huang, N., Vikal, Y., Li, Z., Brar, D. S., Dhaliwal, H. S., & Khush, G. S. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theoretical and Applied Genetics, 102(6–7), 1011–1015. https://doi.org/10.1007/s001220000495

Snowdon, R. J., & Friedt, W. (2004). Molecular markers in Brassica oilseed breeding: current status and future possibilities. Plant Breeding, 123(1), 1–8. https://doi.org/10.1111/j.1439-0523.2003.00968.x

Somers, D. J., Thomas, J., DePauw, R., Fox, S., Humphreys, G., & Fedak, G. (2005). Assembling complex genotypes to resist Fusarium in wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 111(8), 1623–1631. https://doi.org/10.1007/s00122-005-0094-0

Spielmeyer, W., Sharp, P. J., & Lagudah, E. S. (2003). Identification and validation of markers linked to broad‐spectrum stem rust resistance gene Sr2 in wheat (Triticum aestivum L.). Crop Science, 43(1), 333–336. https://doi.org/10.2135/cropsci2003.3330

Sun, X., Cao, Y., Yang, Z., Xu, C., Li, X., Wang, S., & Zhang, Q. (2004). Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase‐like protein. The Plant Journal, 37(4), 517–527. https://doi.org/10.1046/j.1365-313X.2003.01976.x

Swathi, G., Durga Rani, C. V., Md, J., Madhav, M. S., Vanisree, S., Anuradha, C., Kumar, N. R., Kumar, N. A. P., Kumari, K. A., Bhogadhi, S. C., Ramprasad, E., Sravanthi, P., Raju, S. K., Bhuvaneswari, V., Rajan, C. P. D., & Jagadeeswar, R. (2019). Marker-assisted introgression of the major bacterial blight resistance genes, Xa21 and xa13, and blast resistance gene, Pi54, into the popular rice variety, JGL1798. Molecular Breeding, 39(4). https://doi.org/10.1007/s11032-019-0950-2

Tabien, R. E., Li, Z., Paterson, A. H., Marchetti, M. A., Stansel, J. W., Pinson, S. R. M., & Park, W. D. (2000). Mapping of four major rice blast resistance genes from’Lemont’and’Teqing’and evaluation of their combinatorial effect for field resistance. Theoretical and Applied Genetics, 101(8), 1215–1225. https://doi.org/10.1007/s001220051600

Tanksley, S. D., Young, N. D., Paterson, A. H., & Bonierbale, M. W. (1989). RFLP mapping in plant breeding: new tools for an old science. Bio/Technology, 7(3), 257–264. https://doi.org/10.1038/nbt0389-257

Tao, C., Hao, W., Ya-dong, Z., Zhen, Z., Qi-yong, Z., Li-hui, Z., Shu, Y., Ling, Z., Xin, Y., Chun-fang, Z., & Cai-lin, W. (2016). Genetic Improvement of Japonica Rice Variety Wuyujing 3 for Stripe Disease Resistance and Eating Quality by Pyramiding Stv-bi and Wx-mq. Rice Science, 23(2), 69–77. https://doi.org/10.1016/j.rsci.2016.02.002

Thomas, W. T. B. (2003). Prospects for molecular breeding of barley. Annals of Applied Biology, 142(1), 1–12. https://doi.org/10.1111/j.1744-7348.2003.tb00223.x

Tucker, D. M., Griffey, C. A., Liu, S., & Saghai Maroof, M. A. (2006). Potential for effective marker‐assisted selection of three quantitative trait loci conferring adult plant resistance to powdery mildew in elite wheat breeding populations. Plant Breeding, 125(5), 430–436. https://doi.org/10.1111/j.1439-0523.2006.01233.x

Vuylsteke, M., Peleman, J. D., & van Eijk, M. J. T. (2007). AFLP technology for DNA fingerprinting. Nature Protocols, 2(6), 1387–1398. https://doi.org/10.1038/nprot.2007.175

Waghmare, S., P Dr, S., Shylaja, M., Mathew, D., Francies, R., Abida, P., & Sivarajan, S. (2018). Analysis of simple sequence repeat (SSR) polymorphism between N22 and Uma rice varieties for marker assisted selection. Electronic Journal of Plant Breeding, 9, 511–517. https://doi.org/10.5958/0975-928X.2018.00062.5

Walker, D., Boerma, H. R., All, J., & Parrott, W. (2002). Combining cry1Ac with QTL alleles from PI 229358 to improve soybean resistance to lepidopteran pests. Molecular Breeding, 9(1), 43–51. https://doi.org/10.1023/A:1018923925003

Wang, D., Lin, Z., Kai, L. I., Ying, M. A., Wang, L., Yang, Y., YangG, Y., & Zhi, H. (2017). Marker-assisted pyramiding of soybean resistance genes RSC4, RSC8, and RSC14Q to soybean mosaic virus. Journal of Integrative Agriculture, 16(11), 2413–2420. https://doi.org/10.1016/S2095-3119(17)61682-4

Welsh, J., & McClelland, M. (1991). Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Research, 19(19), 5275–5279. https://doi.org/10.1093/nar/19.19.5275

Wilde, F., Korzun, V., Ebmeyer, E., Geiger, H. H., & Miedaner, T. (2007). Comparison of phenotypic and marker-based selection for Fusarium head blight resistance and DON content in spring wheat. Molecular Breeding, 19(4), 357–370. https://doi.org/10.1007/s11032-006-9067-5

Wilde, F., Schön, C. C., Korzun, V., Ebmeyer, E., Schmolke, M., Hartl, L., & Miedaner, T. (2008). Marker-based introduction of three quantitative-trait loci conferring resistance to Fusarium head blight into an independent elite winter wheat breeding population. Theoretical and Applied Genetics, 117(1), 29–35. https://doi.org/10.1007/s00122-008-0749-8

Willcox, M. C., Khairallah, M. M., Bergvinson, D., Crossa, J., Deutsch, J. A., Edmeades, G. O., Gonzalez‐de‐Leon, D., Jiang, C., Jewell, D. C., & Mihm, J. A. (2002). Selection for resistance to Southwestern corn borer using marker‐assisted and conventional backcrossing. Crop Science, 42(5), 1516–1528. https://doi.org/10.2135/cropsci2002.1516

Williams, M. N. V, Pande, N., Nair, S., Mohan, M., & Bennett, J. (1991). Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA. Theoretical and Applied Genetics, 82(4), 489–498.

Xu, J. (2013). Pyramiding of two BPH resistance genes and Stv-b i gene using marker-assisted selection in japonica rice. Crop Breeding and Applied Biotechnology, 13(2), 99–106. https://doi.org/10.1590/S1984-70332013000200001

Yang, R., Yan, Z., Wang, Q., Li, X., & Feng, F. (2018). Marker-assisted backcrossing of lcyE for enhancement of proA in sweet corn. Euphytica, 214(8), 130. https://doi.org/10.1007/s10681-018-2212-5

Ye, C., Tenorio, F. A., Argayoso, M. A., Laza, M. A., Koh, H.-J., Redoña, E. D., Jagadish, K. S. V, & Gregorio, G. B. (2015). Identifying and confirming quantitative trait loci associated with heat tolerance at flowering stage in different rice populations. BMC Genetics, 16(1), 41. https://doi.org/10.1186/s12863-015-0199-7

Yu, J., Gu, W. K., Weeden, N. F., & Provvidenti, R. (1996). Development of an ASAP marker for resistance to bean yellow mosaic virus in Pisum sativum. Pisum Genet, 28, 31–32.

Yugander, A., Sundaram, R. M., Singh, K., Ladhalakshmi, D., Subba Rao, L. V., Madhav, M. S., Badri, J., Prasad, M. S., & Laha, G. S. (2018). Incorporation of the novel bacterial blight resistance gene Xa38 into the genetic background of elite rice variety Improved Samba Mahsuri. PLoS ONE, 13(5), 1–16. https://doi.org/10.1371/journal.pone.0198260

Zhang, F., Zhuo, D. L., Zhang, F., Huang, L. Y., Wang, W. S., Xu, J. L., Vera Cruz, C., Li, Z. K., & Zhou, Y. L. (2015). Xa39, a novel dominant gene conferring broad-spectrum resistance to Xanthomonas oryzae pv. oryzae in rice. Plant Pathology, 64(3), 568–575. https://doi.org/10.1111/ppa.12283

Zhou, P., Tan, Y., He, Y., Xu, C., & Zhang, Q. (2003). Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theoretical and Applied Genetics, 106(2), 326–331. https://doi.org/10.1007/s00122-002-1023-0

Zhou, R., Zhu, Z., Kong, X., Huo, N., Tian, Q., Li, P., Jin, C., Dong, Y., & Jia, J. (2005). Development of wheat near-isogenic lines for powdery mildew resistance. Theoretical and Applied Genetics, 110(4), 640–648. https://doi.org/10.1007/s00122-004-1889-0

Zietkiewicz, E., Rafalski, A., & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20(2), 176–183. https://doi.org/10.1006/geno.1994.1151

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2020-12-30

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Shrestha, S., Subedi, S., & Jiban, J. (2020). Marker-assisted selection: A smart biotechnological strategy for modern plant breeding. Peruvian Journal of Agronomy, 4(3), 104-120. https://doi.org/10.21704/pja.v4i3.1490