Maize Genomics and Genetics 2024, Vol.15, No.5, 247-256 http://cropscipublisher.com/index.php/mgg 247 Feature Review Open Access High-Throughput Sequencing in Maize: A Gateway to Precision Breeding Lan Zhou, Long Jiang College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, Jilin, China Corresponding author: jlnykjxyjl@163.com Maize Genomics and Genetics, 2024, Vol.15, No.5 doi: 10.5376/mgg.2024.15.0024 Received: 15 Aug., 2024 Accepted: 26 Sep., 2024 Published: 13 Oct., 2024 Copyright © 2024 Zhou and Jiang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhou L., and Jiang L., 2024, High-throughput sequencing in maize: a gateway to precision breeding, Maize Genomics and Genetics, 15(5): 247-256 (doi: 10.5376/mgg.2024.15.0024) Abstract High-throughput sequencing (HTS) technologies have revolutionized maize breeding by enabling precise genomic analysis and the identification of beneficial traits. This review explores the impact of HTS on maize, highlighting its role in discovering quantitative trait loci (QTL), genes, and alleles that contribute to crop improvement. The integration of multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, has significantly advanced our understanding of maize's response to abiotic stresses. HTS has facilitated the assembly of complex genomes, identification of genetic variations, and the development of molecular markers for precision breeding. Despite challenges such as data analysis and cost, HTS remains a cornerstone in the pursuit of enhanced maize productivity and resilience. Keywords High-throughput sequencing (HTS); Maize breeding; Multi-omics; Quantitative trait loci (QTL); Abiotic stress tolerance 1 Introduction Maize (Zea mays) is one of the most significant staple crops globally, serving as a crucial source of food, animal feed, and industrial raw materials. Its importance is underscored by its extensive cultivation and the diverse applications it supports, from human consumption to biofuel production (Wang et al., 2022; Jafari et al., 2023). The crop's adaptability and high yield potential have made it a cornerstone of global food security and agricultural sustainability (Andorf et al., 2019; Wang et al., 2022). Historically, maize has undergone significant genetic and phenotypic transformations since its domestication from teosinte, which has contributed to its current status as a vital agricultural commodity (Liu et al., 2019). The advent of high-throughput sequencing (HTS) technologies has revolutionized the field of plant genomics, providing unprecedented insights into the genetic makeup of crops like maize. These technologies enable the rapid sequencing of large genomes, facilitating the identification of genetic variations and the understanding of complex traits (Andorf et al., 2019). HTS has been instrumental in advancing maize breeding programs by allowing for the precise manipulation of genetic material, thereby accelerating the development of new varieties with desirable traits such as increased yield, stress resistance, and improved nutritional content. The integration of HTS with other biotechnological tools, such as CRISPR-Cas genome editing, has further enhanced the potential for precision breeding in maize (Dong et al., 2019; Wang et al., 2022). This study provides a comprehensive overview of the impact of high-throughput sequencing on maize breeding, explores the historical context and current applications of HTS in maize genomics, highlighting key advancements and breakthroughs. Additionally, this study will discuss the integration of HTS with other genomic tools and its implications for future breeding strategies. By examining the technological progress and its practical applications, this study seeks to underscore the transformative potential of HTS in achieving precision breeding in maize, ultimately contributing to global food security and sustainable agriculture. 2 Fundamentals of High-Throughput Sequencing Technology 2.1 Principles and types of high-throughput sequencing High-throughput sequencing (HTS) technologies have revolutionized the field of genomics by enabling the rapid sequencing of large amounts of DNA and RNA. The fundamental principle of HTS involves the parallel
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