Allelic expression and subgenome bias influence plant height in cultivated hybrid sugarcane

Optimizing plant height to enhance lodging resistance and facilitate mechanized harvesting is a critical breeding objective for cultivated hybrid sugarcane. However, the genetic dissection of this trait has been impeded by the complexity of the aneuploid sugarcane genome. To address this issue, we performed a k-mer-based genome-wide association study (GWAS) of 603 re-sequenced sugarcane accessions. We identified 138 quantitative trait loci (QTLs) linked to plant height. These included well-known regulators in the gibberellin and brassinosteroid pathways (e.g., GID1, DWF1) and genes involved in less-studied processes that might contribute to differences in plant height, such as sucrose and fatty acid biosynthesis (e.g., SUS6, ACC2). Using transcriptome data, we documented widespread, stable, allele-specific expression of plant height-related genes and unequal contributions among alleles: 35.02% of alleles accounted for 80% of total gene expression. We also detected substantial imbalances in both gene copy number and expression between the two progenitor-derived subgenomes. The expression bias between subgenomes was typically much smaller than the imbalance suggested by copy number alone, indicating partial buffering at the expression level. Crucially, at the population level, changes in both the dominant allele and subgenome bias of specific genes were associated with differences in plant height in cultivated sugarcane. Finally, we inferred an expression-based regulatory network for plant height-related genes and identified hub genes with possible direct and indirect roles in regulating plant height. Our findings shed light on the regulation of plant height in cultivated sugarcane and offer breeding targets for improved plant architecture.