BREEDING CROP PLANTS USING MOLECULAR GENETICS, GENOMICS, AND BIOTECHNOLOGY
Keywords:
genetic alteration, F1 hybrids, QTL, CRISPR/Cas9 site-directed mutagenesis, ddRAD sequencing, genotyping-by-sequencing, genomic selection, genetic modificationAbstract
Over the previous nearly 40 years, several different kinds of molecular markers techniques have been developed and successfully applied to breeding several important crops. Now that they have been reduced to a few favoured DNA-based marker types, the focus is on modifying the technologies to work with various crop plants and trees. This Special Issue features research and review papers that highlight the power of molecular breeding by combining genetic markers with other conventional breeding techniques to improve crop quality. The ongoing improvement and upkeep of quality through breeding is challenged by a changing climate and the use of molecular markers to enable the direct introgression of traits into elite breeding lines. Precise plant phenotyping in various environments and seasons is necessary for increased fertilizer efficiency, but this was previously costly. It is now less expensive thanks to genetic engineering, DNA sequencing, and PCR-based marker-assisted selection. New techniques like next-generation sequencing can target crop development that responds to climate change.
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References
Aaliya, K., Qamar, Z., Ahmad, N. I., Ali, Q., Munim, F. A., and Husnain, T. (2016). Transformation, evaluation of gtgene and multivariate genetic analysis for morpho-physiological and yield attributing traits in Zea mays. Genetika 48, 423-433.
Aguilar, F. V. (2005). "Rice in the Filipino diet and culture." PIDS discussion paper series.
Aguirre, N. C., Filippi, C. V., Zaina, G., Rivas, J. G., Acuña, C. V., Villalba, P. V., García, M. N., González, S., Rivarola, M., and Martínez, M. C. (2019). Optimizing ddRADseq in non-model species: A case study in Eucalyptus dunnii Maiden. Agronomy 9, 484.
Ahmar, S., Gill, R. A., Jung, K.-H., Faheem, A., Qasim, M. U., Mubeen, M., and Zhou, W. (2020). Conventional and molecular techniques from simple breeding to speed breeding in crop plants: recent advances and future outlook. International journal of molecular sciences 21, 2590.
Ahmar, S., Hensel, G., and Gruszka, D. (2023). CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals–current status, improvements, and perspectives. Biotechnology Advances, 108248.
Ali, A., Cao, J., Jiang, H., Chang, C., Zhang, H.-P., Sheikh, S. W., Shah, L., and Ma, C. (2019). Unraveling molecular and genetic studies of wheat (Triticum aestivum L.) resistance against factors causing pre-harvest sprouting. Agronomy 9, 117.
Ali, F., Ahsan, M., Ali, Q., and Kanwal, N. (2017). Phenotypic stability of Zea mays grain yield and its attributing traits under drought stress. Frontiers in plant science 8, 1397.
Ali, F., Kanwal, N., Ahsan, M., Ali, Q., Bibi, I., and Niazi, N. K. (2015). Multivariate analysis of grain yield and its attributing traits in different maize hybrids grown under heat and drought stress. Scientifica 2015.
Ali, Q., Ahsan, M., Ali, F., Aslam, M., Khan, N. H., Munzoor, M., Mustafa, H. S. B., and Muhammad, S. (2013). Heritability, heterosis and heterobeltiosis studies for morphological traits of maize (Zea mays L.) seedlings. Advancements in Life sciences 1.
Ali, Q., Ahsan, M., Kanwal, N., Ali, F., Ali, A., Ahmed, W., Ishfaq, M., and Saleem, M. (2016). Screening for drought tolerance: comparison of maize hybrids under water deficit condition. Advancements in Life Sciences 3, 51-58.
Ali, Q., Ahsan, M., and Saleem, M. (2010a). Genetic variability and trait association in chickpea (Cicer arietinum L.). Electronic Journal of Plant Breeding 1, 328-333.
Ali, Q., Ahsan, M., Tahir, M. H. N., Elahi, M., Farooq, J., Waseem, M., and Sadique, M. (2011). Genetic variability for grain yield and quality traits in chickpea. International Journal of Agro-Veterinary and Medical Sciences 5, 201-208.
Ali, Q., Ali, A., Ahsan, M., Nasir, I. A., Abbas, H. G., and Ashraf, M. A. (2014). Line× Tester analysis for morpho-physiological traits of Zea mays L seedlings. Advancements in Life sciences 1, 242-253.
Ali, Q., and Malik, A. (2021). Genetic response of growth phases for abiotic environmental stress tolerance in cereal crop plants. Genetika 53, 419-456.
Ali, Q., Muhammad, A., and Farooq, J. (2010b). Genetic variability and trait association in chickpea (Cicer arietinum L.) genotypes at seedling stage. Electronic Journal of Plant Breeding 1, 334-341.
Ashraf, M. (2010). Inducing drought tolerance in plants: recent advances. Biotechnology advances 28, 169-183.
Ashraf, M., and Akram, N. A. (2009). Improving salinity tolerance of plants through conventional breeding and genetic engineering: an analytical comparison. Biotechnology advances 27, 744-752.
Auxcilia, J., and Shabha, N. (2017). Breeding of Fruit and Plantation Crops. Agrimoon publications.
Basile, S. M. L., Burrell, M. M., Walker, H. J., Cardozo, J. A., Steels, C., Kallenberg, F., Tognetti, J. A., DallaValle, H. R., and Rogers, W. J. (2018). Metabolic Profiling of Phloem Exudates as a Tool to Improve Bread-Wheat Cultivars. Agronomy 8, 45.
Berry, C. D. (1969). "Genetic diversity, natural and controlled crossing, and inheritance in Vernonia anthelmintica (L.) Willd," Purdue University.
Bhargava, S., and Sawant, K. (2013). Drought stress adaptation: metabolic adjustment and regulation of gene expression. Plant breeding 132, 21-32.
Brown, D., and Thorpe, T. (1995). Crop improvement through tissue culture. World Journal of Microbiology and Biotechnology 11, 409-415.
Brown, J. (1996). The choice of molecular marker methods for population genetic studies of plant pathogens. New Phytologist 133, 183-195.
Brunelle, D. C. (2018). "Morphological and Genetic Analysis of Embryo Specific Mutants in Maize," The University of North Dakota.
Cheng, A., Chai, H. H., Ho, W. K., Bamba, A. S. A., Feldman, A., Kendabie, P., Halim, R. A., Tanzi, A., Mayes, S., and Massawe, F. (2017). Molecular marker technology for genetic improvement of underutilised crops. Crop Improvement: Sustainability Through Leading-Edge Technology, 47-70.
Costa, J. M., Marques da Silva, J., Pinheiro, C., Barón, M., Mylona, P., Centritto, M., Haworth, M., Loreto, F., Uzilday, B., and Turkan, I. (2019). Opportunities and limitations of crop phenotyping in southern European countries. Frontiers in plant science 10, 1125.
Daun, J. K., Eskin, M. N., and Hickling, D. (2015). "Canola: chemistry, production, processing, and utilization," Elsevier.
Dixon, R. A., and Srinivasa Reddy, M. (2003). Biosynthesis of monolignols. Genomic and reverse genetic approaches. Phytochemistry Reviews 2, 289-306.
Dolferus, R. (2014). To grow or not to grow: a stressful decision for plants. Plant Science 229, 247-261.
Eriksson, D., Kershen, D., Nepomuceno, A., Pogson, B. J., Prieto, H., Purnhagen, K., Smyth, S., Wesseler, J., and Whelan, A. (2019). A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward. New Phytologist 222, 1673-1684.
Fanucci, G. E., and Cafiso, D. S. (2006). Recent advances and applications of site-directed spin labeling. Current opinion in structural biology 16, 644-653.
Feng, X., Zhao, Y., Nie, W., Zhang, Q., Liu, Z., Jiang, Y., Chen, K., Yu, N., Luan, X., and Li, W. (2023). Historical Trends Analysis of Main Agronomic Traits in South China Inbred Indica Rice Varieties since Dwarf Breeding. Agronomy 13, 2159.
Fortuny, A. P., Bueno, R. A., Pereira da Costa, J. H., Zanor, M. I., and Rodríguez, G. R. (2021). Tomato fruit quality traits and metabolite content are affected by reciprocal crosses and heterosis. Journal of Experimental Botany 72, 5407-5425.
Gao, P., Kasama, T., Godonoga, M., Ogawa, A., Sone, C., Komine, M., Endo, Y., Koide, T., and Miyake, R. (2021). A needle-type micro-sampling device for collecting nanoliter sap sample from plants. Analytical and Bioanalytical Chemistry 413, 3081-3091.
Grattapaglia, D., Silva-Junior, O. B., Kirst, M., de Lima, B. M., Faria, D. A., and Pappas, G. J. (2011). High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC plant biology 11, 1-18.
Han, Y., Luo, D., Usman, B., Nawaz, G., Zhao, N., Liu, F., and Li, R. (2018). Development of high yielding glutinous cytoplasmic male sterile rice (Oryza sativa L.) lines through CRISPR/Cas9 based mutagenesis of Wx and TGW6 and proteomic analysis of anther. Agronomy 8, 290.
Heffner, E. L., Sorrells, M. E., and Jannink, J. L. (2009). Genomic selection for crop improvement. Crop Science 49, 1-12.
Hong, T., Feng, X., Tong, W., and Xu, W. (2019). Bibliometric analysis of research on the trends in autophagy. PeerJ 7, e7103.
Hu, D., Jing, J., Snowdon, R. J., Mason, A. S., Shen, J., Meng, J., and Zou, J. (2021). Exploring the gene pool of Brassica napus by genomics‐based approaches. Plant Biotechnology Journal 19, 1693-1712.
Hu, Q., Hua, W., Yin, Y., Zhang, X., Liu, L., Shi, J., Zhao, Y., Qin, L., Chen, C., and Wang, H. (2017). Rapeseed research and production in China. The Crop Journal 5, 127-135.
Hubert, B., Rosegrant, M., Van Boekel, M. A., and Ortiz, R. (2010). The future of food: scenarios for 2050. Crop Science 50, S-33-S-50.
Ibáñez, C., Simó, C., García-Cañas, V., Acunha, T., and Cifuentes, A. (2015). The role of direct high-resolution mass spectrometry in foodomics. Analytical and bioanalytical chemistry 407, 6275-6287.
Irina, A., and Evgeny, R. (2020). The ideas of n. I. Vavilov and current problems of crop Genetics. Biological Communications 65, 3-14.
Jennings, P. R. (1979). "Rice improvement," Int. Rice Res. Inst.
Kher, A., Mulholland, M., Green, E., and Reedy, B. (2006). Forensic classification of ballpoint pen inks using high performance liquid chromatography and infrared spectroscopy with principal components analysis and linear discriminant analysis. Vibrational spectroscopy 40, 270-277.
Kole, C., Muthamilarasan, M., Henry, R., Edwards, D., Sharma, R., Abberton, M., Batley, J., Bentley, A., Blakeney, M., and Bryant, J. (2015). Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Frontiers in plant science 6, 563.
Krishnappa, G., Tyagi, B. S., Gupta, V., Gupta, A., Venkatesh, K., Kamble, U. R., Singh, G., and Singh, G. P. (2022). Wheat Breeding. In "Fundamentals of Field Crop Breeding", pp. 39-111. Springer.
Kulwal, P., Singh, R., Balyan, H., and Gupta, P. (2004). Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analyses in bread wheat. Functional & Integrative Genomics 4, 94-101.
Langridge, P., and Reynolds, M. (2021). Breeding for drought and heat tolerance in wheat. Theoretical and Applied Genetics 134, 1753-1769.
Licht, K., and Jantsch, M. F. (2016). Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications. Journal of Cell Biology 213, 15-22.
Lv, S., Feng, K., Peng, S., Wang, J., Zhang, Y., Bian, J., and Nie, X. (2018). Comparative analysis of the transcriptional response of tolerant and sensitive wheat genotypes to drought stress in field conditions. Agronomy 8, 247.
Mackay, I., Piepho, H. P., and Garcia, A. A. F. (2019). Statistical methods for plant breeding. Handbook of Statistical Genomics: Two Volume Set, 501-20.
Mackay, T. F., Stone, E. A., and Ayroles, J. F. (2009). The genetics of quantitative traits: challenges and prospects. Nature Reviews Genetics 10, 565-577.
Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., and Jin, S. (2020). CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off‐target evaluation, and strategies to mitigate off‐target effects. Advanced science 7, 1902312.
Meena, H., Sujatha, M., and Reddy, A. V. (2022). Advances in Male Sterility Systems and Hybrid Breeding in Sunflower. In "Plant Male Sterility Systems for Accelerating Crop Improvement", pp. 91-147. Springer.
Mir, R. R., Reynolds, M., Pinto, F., Khan, M. A., and Bhat, M. A. (2019). High-throughput phenotyping for crop improvement in the genomics era. Plant Science 282, 60-72.
Mongi, H., Majule, A. E., and Lyimo, J. G. (2010). Vulnerability and adaptation of rain fed agriculture to climate change and variability in semi-arid Tanzania. African Journal of Environmental Science and Technology 4.
Pandita, D., Pandita, A., and Wani, S. H. (2022). Transgenic approach: A Key to Enrich Soybean Oil Quality. In "Soybean Improvement: Physiological, Molecular and Genetic Perspectives", pp. 203-213. Springer.
Rasmussen, S. K. (2020). Molecular genetics, genomics, and biotechnology in crop plant breeding. Vol. 10, pp. 439. MDPI.
Reddy, N., Pierson, M., Sathe, S., and Salunkhe, D. (1985). Dry bean tannins: a review of nutritional implications. Journal of the American Oil Chemists Society 62, 541-549.
Regitano Neto, A., Miguel, A. M. R. d. O., Mourad, A. L., Henriques, E. A., and Alves, R. M. V. (2016). Environmental effect on sunflower oil quality. Crop Breeding and Applied Biotechnology 16, 197-204.
Romero, F. M., and Gatica-Arias, A. (2019). CRISPR/Cas9: development and application in rice breeding. Rice Science 26, 265-281.
Sahu, P. K., Sao, R., Mondal, S., Vishwakarma, G., Gupta, S. K., Kumar, V., Singh, S., Sharma, D., and Das, B. K. (2020). Next generation sequencing based forward genetic approaches for identification and mapping of causal mutations in crop plants: A comprehensive review. Plants 9, 1355.
Saini, P., Saini, P., Kaur, J. J., Francies, R. M., Gani, M., Rajendra, A. A., Negi, N., Jagtap, A., Kadam, A., and Singh, C. (2020). Molecular approaches for harvesting natural diversity for crop improvement. Rediscovery of genetic and genomic resources for future food security, 67-169.
Sarwar, M., Anjum, S., Alam, M. W., Ali, Q., Ayyub, C., Haider, M. S., Ashraf, M. I., and Mahboob, W. (2022). Triacontanol regulates morphological traits and enzymatic activities of salinity affected hot pepper plants. Scientific Reports 12, 1-8.
Shabalina, S. A., Spiridonov, N. A., and Kashina, A. (2013). Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic acids research 41, 2073-2094.
Singh, P., Pandey, V. K., Sultan, Z., Singh, R., and Dar, A. H. (2023). Classification, benefits, and applications of various anti-nutritional factors present in edible crops. Journal of Agriculture and Food Research 14, 100902.
Taranto, F., Nicolia, A., Pavan, S., De Vita, P., and D’Agostino, N. (2018). Biotechnological and digital revolution for climate-smart plant breeding. Agronomy 8, 277.
Tuan, P. A., Kumar, R., Rehal, P. K., Toora, P. K., and Ayele, B. T. (2018). Molecular mechanisms underlying abscisic acid/gibberellin balance in the control of seed dormancy and germination in cereals. Frontiers in Plant Science 9, 668.
Vandenberg, A., and Khazaei, H. (2023). Faba bean in North America–Status and potential. Legume perspectives 24, 26.
Wang, C. M., Bai, Z. Y., He, X. P., Lin, G., Xia, J. H., Sun, F., Lo, L. C., Feng, F., Zhu, Z. Y., and Yue, G. H. (2011). A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. Bmc Genomics 12, 1-18.
Wenzl, P., Li, H., Carling, J., Zhou, M., Raman, H., Paul, E., Hearnden, P., Maier, C., Xia, L., and Caig, V. (2006). A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. Bmc Genomics 7, 1-22.
Yan, S., Zou, G., Li, S., Wang, H., Liu, H., Zhai, G., Guo, P., Song, H., Yan, C., and Tao, Y. (2011). Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theoretical and applied genetics 123, 1173-1181.
Zanotto, S. (2018). Genetics and Biochemistry of the Low Tannin Characteristic in Vicia faba L. and Development of a Molecular Marker for the zt2 Gene, University of Saskatchewan.
Zenda, T., Liu, S., Dong, A., and Duan, H. (2021). Advances in cereal crop genomics for resilience under climate change. Life 11, 502.
Zhu, M., Monroe, J. G., Suhail, Y., Villiers, F., Mullen, J., Pater, D., Hauser, F., Jeon, B. W., Bader, J. S., and Kwak, J. M. (2016). Molecular and systems approaches towards drought‐tolerant canola crops. New Phytologist 210, 1169-1189.
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