Genome-wide identification and transcriptome analysis revealed candidate genes controlling plant height in soybean using YHSBLP

Plant height (PH) is a vital agronomic trait in soybean breeding, exemplifying a classic quantitative trait controlled by multiple genes and significantly influenced by environmental factors. In this study, we undertook an extensive phenotypic assessment of 339 soybean breeding lines adapted to the Yangtze-Huai region of China, evaluated across six different environments over a period of five years. To identify genomic regions associated with PH, we conducted a genome-wide association study (GWAS) utilizing two robust statistical models: the compressed mixed linear model (CMLM) and the Fixed and Random Model Circulating Probability Unification model (FarmCPU). This analysis employed a high-density marker set comprising over 60,000 single nucleotide polymorphism (SNP) markers, facilitating the detection of significant quantitative trait nucleotide (QTN) regions associated with PH. As a result, five stable QTN regions were identified in association with PH. Among these, two regions overlapped with previously reported quantitative trait loci or well-known soybean PH genes, specifically Dt1 on and E2 . To identify candidate genes for qPh08-1 loci significantly associated with PH, we identified 135 putative genes within the Gm08_15013896 block. Transcriptome data analysis revealed that the expression levels of Glyma.08g192700 were significantly higher in three extremely short lines (SLs) compared to high lines (HLs) during the V2 developmental stage of the stem apical meristem (SAM) in soybean. DNA sequencing analysis successfully determined the nucleotide sequences of the initial six promoter regions of Glyma.08g192700 . A 7-base pair insertion (TG→CGCCTGCCG) was identified at position 153 of the third exon, distinguishing HLs from SLs. This insertion introduces a premature termination codon (TAA) at position 50 of the fourth exon, resulting in the HLs variant encoding a truncated protein of only 136 amino acid residues. Therefore, Glyma.08g192700 is likely the most probable gene involved in qPh08-1 .