# High‐resolution quantitative trait loci mapping and pyramiding effects of candidate genes for plant height in soybean

## TL;DR

Researchers identified key genes and genetic regions that influence soybean plant height, which can help breed plants with better architecture and yield.

## Contribution

The study identified three candidate genes and four stable QTL for plant height with pyramiding effects across soybean germplasm.

## Key findings

- Four QTL (qPH-5, qPH6-1, qPH18, and qPH19-2) were consistently detected across multiple environments.
- TCP13, Dt2, and Dt1 were identified as strong candidate genes influencing plant height.
- Haplotype combinations of these genes showed a pyramiding effect on plant height.

## Abstract

Plant height is a crucial agronomic trait that significantly influences plant architecture and yield in soybean (Glycine max (L.) Merr.). Identifying major genes regulating plant height and developing closely linked molecular markers are crucial for breeding soybean cultivars with ideal architecture. In this study, a recombinant inbred line (RIL) population (F2:7‐8) developed from a cross between two soybean cultivars with contrasting plant heights was used to conduct quantitative trait loci (QTL) mapping for plant height across five environments based on a high‐density genetic linkage map. As a result, 13 QTL associated with plant height were identified on seven chromosomes. Among these, four QTL (qPH‐5, qPH6‐1, qPH18, and qPH19‐2) were consistently detected across multiple environments. Candidate genes for three stable QTL (qPH6‐1, qPH18, and qPH19‐2) with major effects on plant height were identified by annotating single‐nucleotide polymorphisms within the parental haplotypes, combined with analyses of gene expression patterns and biological functions. Consequently, TCP13, Dt2, and Dt1 were predicted as strong candidate genes influencing plant height within these loci, respectively. Haplotype analyses within RIL population and across diverse soybean germplasm revealed that allelic variation in each of these genes significantly affected plant height. Moreover, different haplotype combinations of the three genes exhibited distinct phenotypic effects, indicating a pyramiding effect of these three genes on plant height. These findings will facilitate molecular breeding of soybean cultivars with ideal plant architecture.

Thirteen quantitative trait loci (QTL) associated with soybean plant height were identified using 192 recombinant inbred lines.Four stable QTL for plant height were consistently detected across environments.
TCP13, Dt2, and Dt1 were predicted as strong candidate genes affecting plant height in soybean.Haplotype analyses revealed pyramiding effect of TCP13, Dt2, and Dt1 on plant height.These findings facilitated developing cultivars with ideal plant architecture in soybean breeding programs.

Thirteen quantitative trait loci (QTL) associated with soybean plant height were identified using 192 recombinant inbred lines.

Four stable QTL for plant height were consistently detected across environments.

TCP13, Dt2, and Dt1 were predicted as strong candidate genes affecting plant height in soybean.

Haplotype analyses revealed pyramiding effect of TCP13, Dt2, and Dt1 on plant height.

These findings facilitated developing cultivars with ideal plant architecture in soybean breeding programs.

Plant height is a key trait influencing plant architecture and crop yield. In this study, we utilized a recombinant inbred line (RIL) population derived from two soybean cultivars with contrasting heights to perform quantitative trait loci (QTL) mapping for plant height across five environments, employing a high‐density genetic linkage map. We identified four stable QTL (qPH‐5, qPH6‐1, qPH18, and qPH19‐2) over multiple environments. Within three of these QTL (qPH6‐1, qPH18, and qPH19‐2), which exhibited high phenotypic variance contributions, we predicted TCP13, Dt2, and Dt1 as strong candidate genes. Haplotype analyses within the RIL population and across diverse soybean germplasm demonstrated that allelic variation in each gene significantly affected plant height. Furthermore, different combinations of haplotypes for these genes indicated a pyramiding effect on soybean plant height. These findings will facilitate the molecular breeding of soybean cultivars with ideal plant architecture.