Molecular Plant Breeding 2024, Vol.15, No.2, 52-62 http://genbreedpublisher.com/index.php/mpb 52 Review and Progress Open Access The Current Situation and Future of Using GWAS Strategies to Accelerate the Improvement of Crop Stress Resistance Traits Wenzhong Huang Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: Wenzhonghuang@126.com Molecular Plant Breeding, 2024, Vol.15, No.2 doi: 10.5376/mpb.2024.15.0007 Received: 26 Jan., 2024 Accepted: 01 Mar., 2024 Published: 15 Mar., 2024 Copyright © 2024 Huang, 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: Huang W.Z., 2024, The current situation and future of using GWAS strategies to accelerate the improvement of crop stress resistance traits, Molecular Plant Breeding, 15(2): 52-62 (doi: 10.5376/mpb.2024.15.0007) Abstract This study explores the current state and future prospects of accelerating crop resistance trait improvement through Genome-Wide Association Studies (GWAS) strategies. With the rapid development of high-throughput sequencing technology and bioinformatics, GWAS has emerged as a powerful tool for linking DNA variations to important crop traits. This research particularly emphasizes the strategies for integrating multi-omics data, as well as the application of precision breeding and gene editing technologies based on GWAS findings, offering new directions and strategies for the improvement of crop resistance traits. Additionally, the emergence of methods such as Transcriptome-Wide Association Studies (TWAS) provides robust tools for identifying genes associated with complex traits, suggesting a more comprehensive understanding of genomic regulation and genetically regulated genes in the future. These advancements not only propel the scientific research of crop genetic improvement but also provide a solid scientific foundation for the sustainable development of crop production and food safety. Keywords Genome-wide association studies (GWAS); High-throughput sequencing technology; Bioinformatics; Crop resistance traits; Transcriptome-wide association studies (TWAS) 1 Introduction The genetic diversity of crops is the basis of breeding efforts, and by identifying beneficial alleles and useful variations in target traits, new varieties can be developed that can meet global agricultural challenges (Alison et al., 2022). In this context, technologies such as whole-genome resequencing, genome excerpts, partial-genome sequencing strategies, and high-density genotyping arrays have enabled large-scale assessment of the genetic diversity of a wide range of species, including major and “orphan” crops (Alison et al., 2022). However, unless these technologies are combined with adaptive and functional improvements in crops, their value will be limited. With the advancement of high-throughput phenotyping technology, the “phenotypic bottleneck” has been overcome, making powerful phenotypic data points that accurately characterize crop agronomic and physiological attributes available (Alison et al., 2022). A growing number of studies are leveraging these scientific advances and data science techniques to reveal the relationship between the genome and phenotype, unlocking the breeding potential of plant genetic resources. Genome -wide association studies (GWAS) and genomic selection (GS) are methods to explore marker - trait associations, The powerful data science method of MTAs can accelerate the rate of genetic gain of crops and shorten the breeding cycle in a cost-effective manner (Xu et al., 2021). For example, a GWAS analysis of 217 upland cotton varieties revealed genetic variation and candidate genes for traits related to salt tolerance (Rafael et al., 2021). These findings provide breeders with a rich toolbox for developing new varieties. In addition, new methods using new library preparation technologies and single-molecule long-read sequencing technologies (such as PacBio and Oxford Nanopore Technologies) have rapidly developed, making it possible to align sequences from multiple individuals, and due to the read length and be able to characterize missing sequences in the reference genome (Rafael et al., 2021). Furthermore, the creation of pan-genome references enables the characterization of structural variation in a non-reference-biased manner. Access to multiple reference-quality genome assemblies provides the opportunity for analysis of SVs (structural variation) in crop species, although doing so is problematic in some crop species. Its large and complex genome is costly.
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