Bioscience Method 2024, Vol.15, No.1, 8-19 http://bioscipublisher.com/index.php/bm 14 Figure 3 SV-based GWAS identifies additional correlation signals of tomato fruit flavor Note: a: Modeling of pan-genome and core genome sizes when incorporating additional genomes into the clustering and composition of the tomato super-pangenome; b: Different types of structures within each genome compared to the S. galapagense reference genome Number of variations; c: distribution of structural variations in 12 tomato genomes on 12 chromosomes; d: wild-specific genome fragment on chromosome1. The 8kb sequence is present in the genomes of all 9 wild tomatoes, but this sequence is not present in domesticated tomato and the 8 kb wild-specific region containing both genes is boxed in red; e: Dot plot showing alignment of chromosome 3 between 12 tomato genomes and the S. galapagense genome Further research highlights the use of wild relatives in modern breeding, particularly in meeting the challenges posed by future food demands and climate change. By exploring rare and valuable wild species conserved in genetic banks, botanical gardens, national parks, conservation hotspots, and inventories, researchers can discover CWRs carrying agronomically important traits (Soodeh et al., 2022). In addition, by adopting modern breeding experimental methods (such as de novo domestication, genome editing and speed breeding) and computational methods (such as machine learning), the utilization of CWR seeds in breeding programs can be accelerated to improve crop adaptability and yield. These research examples demonstrate that beneficial genetic variants can be successfully identified and exploited from CWRs using GWAS and other genomic tools, which is of great significance for enhancing crop stress resistance, increasing yield, and improving nutritional quality. Through these methods, researchers can expand the sources of genetic variation in breeding programs and select those traits and genes that contribute to crop improvement, thereby increasing the sustainability of agriculture and global food security. 3 Challenges and Limitations of GWAS 3.1 Challenges of GWAS in crop genetic research GWAS have become a powerful tool in genetics research, especially in uncovering associations between genetic variations and complex traits. Although GWAS has made significant progress in multiple fields, it still faces a series of challenges and limitations.
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