Integrated BSA-seq and RNA-seq analysis to identify candidate genes controlling plant height in soybean

Soybean ( Glycine max L.) is a globally important crop that provides vegetable oil and protein. Plant height, a key component of soybean plant architecture, significantly affects lodging resistance, planting density, and mechanized harvesting efficiency. Elucidating the genetic basis of soybean plant height is therefore essential for yield improvement. In this study, two varieties that differed only in plant height were analyzed using BSA-seq and RNA-seq. BSA-seq analyses based on G′ value, ΔSNP-index, and Euclidean distance (ED) identified candidate regions of 1.2 Mb and 3.3 Mb on chromosomes 10 and 18, containing 108 genes, including three genes with missense mutations: GmWRI1 , GmEXPA23 , and GmPPR . Additionally, RNA-seq identified 5,019 differentially expressed genes, which were mainly enriched in plant hormone signaling, MAPK signaling pathways, and metabolic processes. Furthermore, integrating both datasets with tissue-specific expression analysis identified five additional putative genes: GmSEC22 , GmFLS2-1 , GmFLS2-2 , GmPSYR , and GmPHO1-H9 . Integration of haplotype analysis in the natural population and haplotype sequencing of the parental lines revealed that four of the above eight genes showed significant differences in plant height among haplotypes. These results provide a prioritized set of candidate genes and a valuable foundation for elucidating the complex genetic architecture underlying soybean plant height.