# Genome-wide detection of superior haplotypes for seed oil and protein content in Northeast China soybean (Glycine max L.) germplasm

## TL;DR

This study identifies genetic factors influencing oil and protein content in soybeans from Northeast China, offering insights for breeding improvements.

## Contribution

The study identifies novel QTLs and haplotypes associated with seed oil and protein content in Northeast China soybean germplasm.

## Key findings

- 105 and 59 significant SNPs were detected for SOC and SPC across four environments.
- Five novel QTLs were identified, including qSOC1, qSPC1, qSOC9, qSOC_SPC15.1, and qSOC_SPC15.2.
- 80 candidate genes were prioritized, with 12 showing distinct selection signatures between populations.

## Abstract

Seed oil content (SOC) and seed protein content (SPC) are the crucial traits determining the economic importance of soybeans. However, the molecular mechanism underlying the high SOC and low SPC of Northeast China soybeans is still limited. To address this, we elucidated the genetic basis of SOC and SPC in soybean germplasm adapted to Northeast China by employing an integrated genomic analysis. The genome-wide association study (GWAS) detected 105 and 59 significant SNPs associated with the SOC and SPC, respectively across four environments plus combined environment (CE). The haplotype allele number in the 15 identified haplotype blocks varied from 2–4 regulating the SOC and SPC in the range of 16.68-21.15% and 38.63-42.69%, respectively. Five quantitative trait loci (QTLs) among the total 17 identified QTLs were novel that include qSOC1, qSPC1, qSOC9, qSOC_SPC15.1 and qSOC_SPC15.2 associated with SOC or/and SPC. Based on the in-silico, variant annotation and haplotype analysis, the 80 genes were prioritized as potential candidates. The haplotype alleles of these genes varied from 2–8 regulating SOC and SPC in the range of 15.98-21.23% and 37.69%-43.30%, respectively. Twelve of 80 genes showed distinct selection signatures between the two populations, suggesting their key roles in shaping the specific seed quality profiles of soybean germplasm in Northeast China. Hence, the current study provides novel insights on divergent breeding influencing the local adaptation and seed quality difference between different regional soybean populations. Besides, the stable QTLs, superior haplotypes and candidate genes identified can be used for soybean improvement.