Molecular Plant Breeding 2024, Vol.15, No.4, 155-166 http://genbreedpublisher.com/index.php/mpb 157 RNA-Seq has provided a comprehensive view of the sugarcane transcriptome, capturing full-length transcript isoforms and enhancing gene model predictions (Hoang et al., 2017). These advancements underscore the critical role of HTS technologies in overcoming the challenges posed by the sugarcane genome's polyploidy and heterozygosity (Manimekalai et al., 2020). 3.2 Innovations in genome assembly Innovative genome assembly methods, including long-read sequencing and hybrid approaches, have been pivotal in addressing the complexity of the sugarcane genome. Long-read sequencing technologies, such as PacBio and Oxford Nanopore, have been instrumental in generating more contiguous and complete genome assemblies (Lang et al., 2020). For example, the assembly of the SP80-3280 sugarcane variety using PacBio technology resulted in the identification of 373 869 putative genes and their regulatory regions, providing insights into gene family evolution and functional diversity (Souza et al., 2019). Shearman et al. (2022) used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of Khon Kaen 3, and genome annotation produced 242 406 genes from 30 927 orthogroups. Hybrid assembly strategies, combining long-read and short-read sequencing data, have also proven effective. The assembly of 19 Mb of the sugarcane genome using a hybrid approach with Illumina and PacBio reads demonstrated high collinearity with the sorghum genome, highlighting the utility of hybrid methods in constructing reference scaffold maps (Okura et al., 2016). These innovations are crucial for advancing our understanding of the sugarcane genome and improving breeding programs (Mikheenko et al., 2018). 3.3 Published genomic resources The current state of sugarcane genomic resources includes several reference sequences and databases that serve as valuable tools for researchers. A notable example is the BAC-based monoploid reference sequence for sugarcane, which was constructed by exploiting colinearity with sorghum and sequencing a minimum tiling path of 4 660 BAC clones, resulting in a SNP-based sugarcane genetic map (Figure 1) (Garsmeur et al., 2018). This comparative genomic analysis by Garsmeur et al. (2018) highlights the genetic complexity and polyploidy of sugarcane, revealing conserved synteny and evolutionary links with sorghum. These insights are crucial for understanding the genetic architecture of sugarcane, aiding in the identification of functional genes and enhancing breeding programs through marker-assisted selection. By leveraging syntenic relationships, it is possible to identify and transfer desirable traits such as disease resistance and yield improvement from sorghum to sugarcane. Additionally, two tetraploid genomes of S. spontaneumclones AP85-441 and Np-X have been published, provides a foundational resource for understanding the genetic architecture of sugarcane and its progenitors (Zhang et al., 2018; Zhang et al., 2022). The representative genomic assembly of the SP80-3280 genome sequence reveals differences in promoter regions associated with distinct gene expression patterns and transposable elements (TEs), contributing to fine tuning of the sugarcane genome (Souza et al., 2019). Recent publications of the genomes of the commercial variety KK3 and the modern hybrid sugarcane ZZ1 provide a solid foundation for future research in sugarcane genomics and molecular breeding, paving the way for advancements in these fields (Shearman et al., 2022; Bao et al., 2024). These genomic resources, along with extensive collections of expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) libraries, have opened new avenues for functional genomic analyses and the development of molecular markers for breeding (Thirugnanasambandam et al., 2018). The availability of these comprehensive genomic datasets is instrumental in facilitating comparative genomics, gene discovery, and the improvement of sugarcane cultivars. 4 Functional Genomics in Sugarcane 4.1 Gene expression profiling Gene expression profiling through transcriptome analysis has been instrumental in linking specific genes to phenotypic traits in sugarcane. Singh and Singh (2015) discussed how transcriptome resources, encompassing both specific and overlapping gene expression patterns, are used to elucidate functions related to important traits such as sucrose accumulation and stress responses. By comparing the transcriptomic expression differences
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