GENOMIC ASSISTED CROP BREEDING APPROACHES FOR DESIGNING FUTURE CROPS TO COMBAT FOOD PRODUCTION CHALLENGES

M BABAR; MS NAWAZ; AAA SHAHANI; MN KHALID; A LATIF; K KANWAL; M IJAZ; Z MAQSOOD; I AMJAD; A KHAN; NH KHAN; S SHAUKAT

doi:10.54112/bcsrj.v2022i1.143

Authors

M BABAR Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
MS NAWAZ Vegetable Research Station Karor Laal Eason District Layyah, Pakistan
AAA SHAHANI Crop Sciences Plant Breeding and Genetics, College of Agriculture, Yanbian University, Yanji Jilin, China
MN KHALID Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
A LATIF Vegetable Research Station Karor Laal Eason District Layyah, Pakistan
K KANWAL Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
M IJAZ Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
Z MAQSOOD Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
I AMJAD Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
A KHAN Maize and Millets Research Institute Yusafwala, Sahiwal, Pakistan
NH KHAN Department of Continuing Education, University of Agriculture Faisalabad, Pakistan
S SHAUKAT Department of Plant Breeding and Genetics, Lasbela University of Agriculture Water and Marine Sciences, Uthal, Pakistan

DOI:

https://doi.org/10.54112/bcsrj.v2022i1.143

Keywords:

plant breeding, selection, breeding methods, genomics

Abstract

Improvement of crop species has been a fundamental goal of mankind since the dawn of agriculture. The key to increasing agricultural productivity and improving other attributes has been plant breeding. The foundations of conventional breeding are the utilization of diversity, which occurs naturally in the form of land races and wild relatives, and the development of diverse selection and breeding techniques. Selection, which was the first strategy identified and is currently utilized by the majority of breeding programs, is the most fundamental aspect of plant breeding. There is a need to boost global food production in order to meet the rising demand of a growing population as a result of a growing human population and a changing environment, which have both heightened concerns about global food security. Conventional breeding methods are inadequate to supply this rising need. In the past few decades, numerous advancements in genetic engineering and molecular biology have led to the emergence of novel approaches that rely on phenotypic characterization. Now, the wide availability of molecular markers has facilitated the identification of variation sources and selection. Specifically, genomics played a crucial part in the revolution of plant breeding. Because genomics enabled the extended study of genotype and its relationship to phenotype for multigenic characteristics, allowing for a greater understanding of genotype and phenotype. In this overview, we will address conventional breeding methods and contemporary genomics techniques, and their function in crop improvement.

Downloads

Download data is not yet available.

1660

References

Abbas, M. S. T. (2018). Genetically engineered (modified) crops (Bacillus thuringiensis crops) and the world controversy on their safety. Egyptian Journal of Biological Pest Control28, 1-12. DOI: https://doi.org/10.1186/s41938-018-0051-2

Acquaah, G. (2009). Principles of plant genetics and breeding. John Wiley & Sons.

Adlak, T., Tiwari, S., Tripathi, M., Gupta, N., Sahu, V. K., Bhawar, P., & Kandalkar, V. (2019). Biotechnology: An advanced tool for crop improvement. Current Journal of Applied Science and Technology33, 1-11. DOI: https://doi.org/10.9734/cjast/2019/v33i130081

Aharoni, A., & Vorst, O. (2002). DNA microarrays for functional plant genomics. Plant molecular biology48, 99-118. DOI: https://doi.org/10.1023/A:1013734019946

Araus, J. L., Slafer, G. A., Royo, C., & Serret, M. D. (2008). Breeding for yield potential and stress adaptation in cereals. Critical Reviews in Plant Science27, 377-412. DOI: https://doi.org/10.1080/07352680802467736

Batley, J., & Edwards, D. (2016). The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current opinion in plant biology30, 78-81. DOI: https://doi.org/10.1016/j.pbi.2016.02.002

Bisognin, D. A. (2002). Origin and evolution of cultivated cucurbits. Ciência Rural32, 715-723. DOI: https://doi.org/10.1590/S0103-84782002000400028

Breseghello, F., & Coelho, A. S. G. (2013). Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.). Journal of agricultural and food chemistry61, 8277-8286. DOI: https://doi.org/10.1021/jf305531j

Brown, N. M., & Fedoroff, N. V. (2004). Mendel in the kitchen: a scientist's view of genetically modified foods. Joseph Henry Press.

Cao, G., Zhu, J., He, C., Gao, Y., Yan, J., & Wu, P. (2001). Impact of epistasis and QTL× environment interaction on the developmental behavior of plant height in rice (Oryza sativa L.). Theoretical and Applied Genetics103, 153-160. DOI: https://doi.org/10.1007/s001220100536

Carroll, D. (2011). Genome engineering with zinc-finger nucleases. Genetics188, 773-782. DOI: https://doi.org/10.1534/genetics.111.131433

Ceccarelli, S. (2009). Evolution, plant breeding and biodiversity. Journal of Agriculture and Environment for International Development (JAEID)103, 131-145.

Chai, L., Chen, Z., Bian, R., Zhai, H., Cheng, X., Peng, H., Yao, Y., Hu, Z., Xin, M., & Guo, W. (2018). Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.). Theoretical and Applied Genetics131, 2621-2637. DOI: https://doi.org/10.1007/s00122-018-3177-4

Eathington, S. R., Crosbie, T. M., Edwards, M. D., Reiter, R. S., & Bull, J. K. (2007). Molecular markers in a commercial breeding program. Crop Science47, S-154-S-163. DOI: https://doi.org/10.2135/cropsci2007.04.0015IPBS

Fedoroff, N. V. (2010). The past, present and future of crop genetic modification. New Biotechnology27, 461-465. DOI: https://doi.org/10.1016/j.nbt.2009.12.004

Gelvin, S. B. (2003). Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiology and molecular biology reviews67, 16-37. DOI: https://doi.org/10.1128/MMBR.67.1.16-37.2003

Hallauer, A. R. (2011). Evolution of plant breeding. Crop breeding and applied biotechnology11, 197-206. DOI: https://doi.org/10.1590/S1984-70332011000300001

Hedden, P. (2003). The genes of the Green Revolution. Trends in Genetics19, 5-9. DOI: https://doi.org/10.1016/S0168-9525(02)00009-4

Heffner, E. L., Lorenz, A. J., Jannink, J. L., & Sorrells, M. E. (2010). Plant breeding with genomic selection: gain per unit time and cost. Crop Science50, 1681-1690. DOI: https://doi.org/10.2135/cropsci2009.11.0662

Huang, X., & Han, B. (2014). Natural variations and genome-wide association studies in crop plants. Annual review of plant biology65, 531-551. DOI: https://doi.org/10.1146/annurev-arplant-050213-035715

Jelili, T. O. (2006). Agrobacterium-mediated transformation of plants: emerging factors that influence efficiency. Biotechnology and Molecular Biology Reviews1, 12-20.

Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., & Weeks, D. P. (2013). Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic acids research41, e188-e188. DOI: https://doi.org/10.1093/nar/gkt780

Khush, G. S. (2001). Green revolution: the way forward. Nature reviews genetics2, 815-822. DOI: https://doi.org/10.1038/35093585

Lambert, B., Denolf, P., Engelen, S., Golds, T., Haesendonckx, B., Ruiter, R., Robbens, S., Bots, M., & Laga, B. (2015). Omics-directed reverse genetics enables the creation of new productivity traits for the vegetable oil crop canola. Procedia Environmental Sciences29, 77-78. DOI: https://doi.org/10.1016/j.proenv.2015.07.167

Leng, P.-f., Lübberstedt, T., & Xu, M.-l. (2017). Genomics-assisted breeding–a revolutionary strategy for crop improvement. Journal of integrative agriculture16, 2674-2685. DOI: https://doi.org/10.1016/S2095-3119(17)61813-6

Liu, R., Xiao, X., Gong, J., Li, J., Zhang, Z., Liu, A., Lu, Q., Shang, H., Shi, Y., & Ge, Q. (2020). QTL mapping for plant height and fruit branch number based on RIL population of upland cotton. Journal of Cotton Research3, 1-9. DOI: https://doi.org/10.1186/s42397-020-0046-x

McGonigle, B., Keeler, S. J., Lau, S.-M. C., Koeppe, M. K., & O'Keefe, D. P. (2000). A genomics approach to the comprehensive analysis of the glutathione S-transferase gene family in soybean and maize. Plant Physiology124, 1105-1120. DOI: https://doi.org/10.1104/pp.124.3.1105

Mohanta, T. K., Bashir, T., Hashem, A., Abdullah, E. F., & Bae, H. (2017). Genome editing tools in plants. Genes8, 399. DOI: https://doi.org/10.3390/genes8120399

Moose, S. P., & Mumm, R. H. (2008). Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiology147, 969-977. DOI: https://doi.org/10.1104/pp.108.118232

Morrell, P. L., Buckler, E. S., & Ross-Ibarra, J. (2012). Crop genomics: advances and applications. Nature reviews genetics13, 85-96. DOI: https://doi.org/10.1038/nrg3097

Nakaya, A., & Isobe, S. N. (2012). Will genomic selection be a practical method for plant breeding? Annals of botany110, 1303-1316. DOI: https://doi.org/10.1093/aob/mcs109

Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J. D., & Kamoun, S. (2013). Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature biotechnology31, 691-693. DOI: https://doi.org/10.1038/nbt.2655

Oladosu, Y., Rafii, M. Y., Abdullah, N., Hussin, G., Ramli, A., Rahim, H. A., Miah, G., & Usman, M. (2016). Principle and application of plant mutagenesis in crop improvement: a review. Biotechnology & Biotechnological Equipment30, 1-16. DOI: https://doi.org/10.1080/13102818.2015.1087333

Prohens, J. (2011). Plant breeding: a success story to be continued thanks to the advances in genomics. Frontiers in plant science2, 51. DOI: https://doi.org/10.3389/fpls.2011.00051

Ray, S., & Satya, P. (2014). Next generation sequencing technologies for next generation plant breeding. In (Vol. 5, pp. 367): Frontiers Media SA. DOI: https://doi.org/10.3389/fpls.2014.00367

Redman, M., King, A., Watson, C., & King, D. (2016). What is CRISPR/Cas9? Archives of Disease in Childhood-Education and Practice101, 213-215. DOI: https://doi.org/10.1136/archdischild-2016-310459

Reif, J. C., Zhang, P., Dreisigacker, S., Warburton, M. L., van Ginkel, M., Hoisington, D., Bohn, M., & Melchinger, A. E. (2005). Wheat genetic diversity trends during domestication and breeding. Theoretical and Applied Genetics110, 859-864. DOI: https://doi.org/10.1007/s00122-004-1881-8

Rensink, W. A., & Buell, C. R. (2005). Microarray expression profiling resources for plant genomics. Trends in plant science10, 603-609. DOI: https://doi.org/10.1016/j.tplants.2005.10.003

Sattler, M. C., Carvalho, C. R., & Clarindo, W. R. (2016). The polyploidy and its key role in plant breeding. Planta243, 281-296. DOI: https://doi.org/10.1007/s00425-015-2450-x

Scheben, A., Yuan, Y., & Edwards, D. (2016). Advances in genomics for adapting crops to climate change. Current Plant Biology6, 2-10. DOI: https://doi.org/10.1016/j.cpb.2016.09.001

Singsit, C., Adang, M. J., Lynch, R. E., Anderson, W. F., Wang, A., Cardineau, G., & Ozias-Akins, P. (1997). Expression of a Bacillus thuringiensis cryIA (c) gene in transgenic peanut plants and its efficacy against lesser cornstalk borer. Transgenic research6, 169-176. DOI: https://doi.org/10.1023/A:1018481805928

Takahagi, K., Uehara-Yamaguchi, Y., Yoshida, T., Sakurai, T., Shinozaki, K., Mochida, K., & Saisho, D. (2016). Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Scientific reports6, 1-11. DOI: https://doi.org/10.1038/srep33199

Takeda, S., & Matsuoka, M. (2008). Genetic approaches to crop improvement: responding to environmental and population changes. Nature reviews genetics9, 444-457. DOI: https://doi.org/10.1038/nrg2342

Tester, M., & Langridge, P. (2010). Breeding technologies to increase crop production in a changing world. Science327, 818-822. DOI: https://doi.org/10.1126/science.1183700

Upadhyay, S. K., Kumar, J., Alok, A., & Tuli, R. (2013). RNA-guided genome editing for target gene mutations in wheat. G3: Genes, Genomes, Genetics3, 2233-2238. DOI: https://doi.org/10.1534/g3.113.008847

Vaeck, M., Reynaerts, A., Höfte, H., Jansens, S., De Beuckeleer, M., Dean, C., Zabeau, M., Montagu, M. V., & Leemans, J. (1987). Transgenic plants protected from insect attack. Nature328, 33-37. DOI: https://doi.org/10.1038/328033a0

Valliyodan, B., Ye, H., Song, L., Murphy, M., Shannon, J. G., & Nguyen, H. T. (2017). Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. Journal of experimental botany68, 1835-1849. DOI: https://doi.org/10.1093/jxb/erw433

Varshney, R. K., Hoisington, D. A., & Tyagi, A. K. (2006). Advances in cereal genomics and applications in crop breeding. Trends in Biotechnology24, 490-499. DOI: https://doi.org/10.1016/j.tibtech.2006.08.006

Varshney, R. K., Nayak, S. N., May, G. D., & Jackson, S. A. (2009). Next-generation sequencing technologies and their implications for crop genetics and breeding. TRENDS in Biotechnology27, 522-530. DOI: https://doi.org/10.1016/j.tibtech.2009.05.006

Watson, A., Ghosh, S., Williams, M. J., Cuddy, W. S., Simmonds, J., Rey, M.-D., Asyraf Md Hatta, M., Hinchliffe, A., Steed, A., & Reynolds, D. (2018). Speed breeding is a powerful tool to accelerate crop research and breeding. Nature plants4, 23-29. DOI: https://doi.org/10.1038/s41477-017-0083-8

Wu, J., McCarty, J., Jenkins, J., & Meredith, W. (2010). Breeding potential of introgressions into upland cotton: genetic effects and heterosis. Plant Breeding129, 526-532. DOI: https://doi.org/10.1111/j.1439-0523.2009.01715.x

Wu, Y., Yin, J., Guo, W., Zhu, X., & Zhang, T. (2004). Heterosis performance of yield and fibre quality in F1 and F2 hybrids in upland cotton. Plant Breeding123, 285-289. DOI: https://doi.org/10.1111/j.1439-0523.2004.00990.x

Wullschleger, S. D., & Difazio, S. P. (2003). Emerging use of gene expression microarrays in plant physiology. Comparative and Functional Genomics4, 216-224. DOI: https://doi.org/10.1002/cfg.277

Yang, H., Jian, J., Li, X., Renshaw, D., Clements, J., Sweetingham, M. W., Tan, C., & Li, C. (2015). Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC genomics16, 1-17. DOI: https://doi.org/10.1186/s12864-015-1878-5