Triticeae Genomics and Genetics, 2024, Vol.15, No.2, 66-76 http://cropscipublisher.com/index.php/tgg 71 5 Case Studies 5.1 Successful examples in wheat improvement Recent advancements in genomic tools have significantly contributed to the improvement of wheat (Triticum aestivumL.). One notable example is the development of TRITEX, an open-source computational workflow that has enhanced the assembly of chromosome-scale genome sequences in wheat. This tool has been instrumental in constructing high-quality reference genome sequences, which are crucial for pan-genomic studies and have facilitated the identification of genomic regions associated with important agronomic traits (Monat et al., 2019) (Figure 2). Figure 2 TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools (Adopted from Monat et al., 2019) Image caption: Morex V1 pseudomolecules, an improved BAC-by-BAC assembly, and a genome-wide optical map; Panel (a) shows a dot plot alignment revealing high collinearity at a megabase scale but discordance at finer resolutions; Panel (b) presents a more consistent alignment with the improved Dovetail BAC-by-BAC assembly, showing a higher correlation and concordance in orientations; Panel (c) aligns optical map contigs to TRITEX scaffolds, indicating high-confidence matches but highlighting some unaligned restriction sites (Adapted from Monat et al., 2019) Monat et al. (2019) validates the TRITEX assembly method by comparing it with various genomic resources, demonstrating its high accuracy and reliability. The TRITEX super-scaffolds showed strong concordance with the Morex V1 pseudomolecules, improved BAC-by-BAC assemblies, and the genome-wide optical map, indicating robust sequence alignment and improved assembly quality. This validation highlights TRITEX's effectiveness in producing precise and comprehensive genome sequences, addressing previous assembly issues, and enhancing our understanding of the Triticeae genomes. The findings emphasize TRITEX's potential to significantly advance genomic studies and breeding programs in Triticeae crops, contributing to more accurate and efficient genetic research and crop improvement strategies. Additionally, a high-resolution genome-wide association study (GWAS) identified 395 quantitative trait loci (QTL) for 12 traits in wheat, using a panel of 768 cultivars. This study not only pinpointed known genes and QTL but also identified eight putative candidate genes that enhance spike seed-setting and grain size. These findings are pivotal for genomics-based breeding programs aimed at improving wheat yield (Pang et al., 2020). Moreover, the integration of wild genetic resources into wheat breeding programs has been explored to introduce new diversity for genes or alleles of agronomical interest. This approach has the potential to accelerate the development of new improved cultivars, although it is often hampered by the genetic background of the recipient varieties or the donor (Laugerotte et al., 2022). 5.2 Advances in barley genomics Barley (Hordeum vulgare) has also seen significant advancements in genomic research. The TRITEX workflow has been applied to barley, resulting in an improved annotated reference genome sequence assembly of the barley cultivar Morex. This assembly serves as a valuable community resource for further genomic studies (Monat et al., 2019).
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