Soybean (Glycine max) variety Heihe 54 has played a crucial role in the Heihe soybean breeding program in China, contributing to the development of over 85 cultivars. To elucidate the genetic changes that have occurred across multiple generations of selection during soybean breeding, we conducted comprehensive genotyping analysis using the 180K Axiom SoyaSNP array on 42 varieties from the Heihe breeding program, as well as eight parental lines. Cluster analysis revealed four distinct groups, reflecting various breeding phases that incorporated diverse genetic resources as parental lines within the pedigree. A detailed examination of the graphical genotype profile across the genome identified preferred chromosome segments for specific breeding phases. These conserved blocks, which have been consistently maintained in descendant varieties during the extensive breeding period, likely harbor genes related to critical agronomic traits. This is exemplified by the consistent transmission of two segments located on chromosomes 18 and 20, which harbor the stem growth habit-related gene Dt2 and the leaflet shape-related gene Ln, respectively. The widespread cultivation of Heihe 43, a soybean cultivar developed within this pedigree, is attributed to its broad genetic base and the pyramiding of elite alleles from its parental lines. The identification of favorable chromosome segments provides valuable insight for agronomic trait-related gene mining and targeted breeding in the future.

Stem growth habit is an important agronomic trait in soybean and is subject to artificial selection. This study aimed to provide a theory for genotypic selection of stem growth habit for breeding purposes by analyzing the alleles of GmTfl1 gene in Chinese soybean varieties and establishing a database of GmTfl1 variation. Using knowledge of insertion and deletion (Indel) in the non-coding region and four single-nucleotide polymorphisms (SNPs) in the coding sequences of the GmTfl1 gene, four CAPS and one Indel markers were developed and used to test 1120 Chinese soybean varieties. We found that the dominant GmTfl1 allele was prevalent in accessions from the Northern ecoregion, whereas the recessive allele, Gmtfl1, was more common in the Southern ecoregion, and the proportions of GmTfl1 and recessive alleles were respectively 40.1% and 59.9% in the Huang-Huai ecoregion. The proportion of GmTfl1 decreased and that of Gmtfl1 increased, gradually from north to south. Allele GmTfl1-a was present in higher proportions in the Huang-Huai spring, Huang-Huai summer, and Northern spring sub-ecoregions than that in the other sub-ecoregions. GmTfl1-b was common in the Northeast spring, Northern spring and Southern summer sub-ecoregions. Gmtfl1-ta was found mainly in the Huang-Huai spring, Huang-Huai summer and Southern spring sub-ecoregions. The Gmtfl1-ab allele was distributed in all six soybean sub-ecoregions. The Gmtfl1-bb allele was distributed mainly in the Huang-Huai spring and summer and Southern spring and summer sub-ecoregions, but the Gmtfl1-tb allele was detected only in the Huang-Huai summer sub-ecoregion. The distributions of GmTfl1 and Gmtfl1 have shown no large changes in nearly 60 years of breeding, but the frequency of the recessive genotype Gmtfl1 has shown a rising trend in the last 20 years. This study provides a theoretical foundation for breeding new soybean varieties for different ecoregions.