Fine mapping and candidate gene analysis of qPH19.1, a locus for soybean (Glycine max L.) plant height

A new height locus qPH19.1 was identified, and Glyma.19G206100 was verified as the key gene regulating soybean plant height. Plant height stands as a pivotal component of the plant ideotype and has a substantial influence on crop yield. However, the genetic basis of this trait in soybean plant height remains poorly understood. To identify the genetic determinants of plant height, a BC₁F₂ segregating population was developed by crossing the super-dwarf soybean line F02 (derived from recombinant inbred lines, RILs) as the paternal parent with ZB (a progenitor of the RIL population) as the maternal parent. Genetic analysis of the BC₁F₂ population revealed that the ultra-dwarf trait was controlled by a single recessive gene, designated qPH19.1. The candidate gene was initially mapped to chromosome 19 via bulked segregant analysis (BSA-seq) combined with whole-genome sequencing and then fine-mapped to a 53.7-kb region using 2662 BC₁F_2:3 individuals. Comprehensive sequence analysis, expression profiling, gene annotation, and haplotype analysis identified Glyma.19G206100, which encoded an auxin response factor, as the most probable candidate gene for qPH19.1. Four single-nucleotide polymorphisms (SNPs) in the promoter, coding, and 3' UTR regions differentiated between the parental lines F02 and ZB, collectively defining five distinct haplotypes. Among them, Hap-2 (ZB type) and Hap-4 (F02 type) predominated in landraces and cultivars, and plants carrying these haplotypes showed significant differences in plant height. These findings provide new perspectives for understanding the genetic mechanisms underlying soybean plant height and offer valuable genetic resources for breeding improved plant architecture.