Plant Gene and Trait 2024, Vol.15, No.5, 220-229 http://genbreedpublisher.com/index.php/pgt 220 Review Article Open Access Genome-Wide Association Studies in Sugarcane: Unlocking the Genetic Basis of Yield and Agronomic Traits WanruWang1,2, Xiping Yang1,2 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China 2 College of Agricultural, Guangxi University, Nanning, 530005, Guangxi, China Corresponding email: xipingyang@gxu.edu.cn Plant Gene and Trait, 2024, Vol.15, No.5 doi: 10.5376/pgt.2024.15.0022 Received: 11 Aug., 2024 Accepted: 18 Sep., 2024 Published: 26 Sep., 2024 Copyright © 2024 Wang and Yang, 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: Wang W.R., and Yang X.P., 2024, Genome-wide association studies in sugarcane: unlocking the genetic basis of yield and agronomic traits, Plant Gene and Trait, 15(5): 220-229 (doi: 10.5376/pgt.2024.15.0022) Abstract This study provides a comprehensive overview of genome-wide association studies (GWAS) applications in sugarcane, highlighting the key findings related to yield and agronomic traits. Major GWAS studies conducted in sugarcane have identified numerous genetic markers associated with important traits. Significant loci linked to high sucrose content, overall yield, disease resistance, and abiotic stress tolerance have been discovered, offering valuable insights for breeding programs. The integration of these findings into marker-assisted selection (MAS) and genomic selection (GS) has enhanced breeding efficiency, leading to the development of superior sugarcane varieties. A detailed case study on the Brazilian Panel of Sugarcane Genotypes (BPSG) study exemplifies the practical application of GWAS in sugarcane research. The BPSG study identified key genetic regions associated with yield and disease resistance, demonstrating the potential of GWAS to accelerate genetic improvements. In the future, it is expected to improve the resolution and applicability of GWAS, address current challenges in translating findings to field applications, and unleash the full potential of GWAS in improving sugarcane yield and agronomic traits. Keywords Sugarcane (Saccharumspp.); Genome-wide association studies (GWAS); Genetic basis; Yield; Agronomic traits 1 Introduction Sugarcane (Saccharumspp.) is a vital crop globally, contributing significantly to the production of sugar, ethanol, and electricity. It is a C4 plant known for its high biomass production and is cultivated extensively in tropical and subtropical regions (Budeguer et al., 2021; Mahadevaiah et al., 2021). Modern sugarcane varieties are complex hybrids derived from interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. The crop's economic importance is underscored by its role in supplying up to 80% of the world's sugar and approximately 60% of biofuel (Yang et al., 2020; Zan et al., 2020). The yield and agronomic traits of sugarcane are critical for meeting the growing global demand for sugar and biofuels, especially in the context of climate change. Key agronomic traits include cane yield, sucrose content, disease resistance, and tolerance to abiotic stresses such as drought and salinity (Racedo et al., 2016; Fickett et al., 2019). Improving these traits is essential for enhancing sugarcane productivity and sustainability. However, the genetic complexity of sugarcane, characterized by its polyploidy and high heterozygosity, poses significant challenges to traditional breeding methods (Budeguer et al., 2021; Meena et al., 2022). Genome-wide association studies (GWAS) have emerged as a powerful tool for dissecting the genetic basis of complex traits in sugarcane. Unlike biparental mapping, GWAS leverages natural genetic variation within a population to identify marker-trait associations (MTAs) (Fickett et al., 2019; Yang et al., 2020). This approach is particularly advantageous in sugarcane due to its large linkage disequilibrium, which allows for the identification of markers associated with important agronomic traits. Recent studies have successfully utilized GWAS to identify markers linked to yield, sucrose traits, and other agronomic characteristics, providing valuable genetic resources for sugarcane improvement (Racedo et al., 2016; Yang et al., 2020). The objective of this study is to summarize recent advances in sugarcane genomics and the identification of favorable alleles for superior agronomic traits, highlight the challenges and limitations associated with GWAS in
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