Plant Gene and Trait 2024, Vol.15, No.2, 62-72 http://genbreedpublisher.com/index.php/pgt 66 4.3 Exploring the integration of gene duplication studies with functional genomics Integrating gene duplication studies with functional genomics is essential for a comprehensive understanding of sugarcane biology and for the development of improved cultivars. Functional genomics approaches, such as genome-wide association studies (GWAS) and transcriptome analysis, can identify candidate genes and elucidate their roles in important traits (Barreto et al., 2019). For example, GWAS has been used to identify loci associated with yield component traits in sugarcane, providing valuable insights into the genetic basis of these traits and the potential role of duplicated genes (Barreto et al., 2019). Moreover, the integration of genomic, transcriptomic, and genetic mapping data can reveal the complex interactions between duplicated genes and their regulatory networks (Barreto et al., 2019). This holistic approach can facilitate the identification of key genes involved in sugarcane's response to biotic and abiotic stresses, ultimately aiding in the development of more resilient and high-yielding sugarcane varieties. By leveraging the power of functional genomics, researchers can better understand the evolutionary patterns and functional significance of gene duplication in sugarcane, paving the way for innovative breeding strategies and crop improvement (Sforça et al., 2019). 5 Case Studies 5.1 Detailed analysis of specific duplicated genes in sugarcane Gene duplication plays a significant role in the evolution and trait diversity of sugarcane. One notable example is the duplication of the HP600 and Centromere Protein C (CENP-C) genes. These genes are found in two different homeologous chromosome groups with ploidies of eight and ten. The first region, orthologous to Sorghum bicolor, showed all haplotypes of HP600 and CENP-C expressed, although HP600 exhibited unbalanced haplotype expression. The second region, a scrambled sugarcane sequence, contained partial duplications of HP600 and CENP-C, resulting in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C (Figure 3) (Sforça et al., 2019). Figure 3 Representation of each sugarcane BAC from Region01 and Region02 (Adopted from Sforça et al., 2019) Image caption: The image depicts two genomic regions, labeled “Region01” and “Region02” each illustrating the comparative genomics of different haplotypes (Adopted from Sforça et al., 2019) Another example involves the Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) gene family. In Saccharum spontaneum, 48 CIPK genes were identified, which likely underwent six gene duplication events. These duplications, driven by whole-genome duplications (WGDs), have been under strong purifying selection pressure, indicating their functional importance (Su et al., 2020). 5.2 Impacts of gene duplications on sugarcane trait development Gene duplications have profound impacts on sugarcane trait development. For instance, the genome-wide association study (GWAS) identified 23 marker-trait associations (MTAs) for yield component traits such as soluble solid content, stalk height, stalk number, stalk weight, and cane yield (Li et al., 2020). These MTAs can be
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