ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
This article is part of the Research TopicTraits Evaluation and Gene Mining of Plant Germplasm ResourcesView all 9 articles
Genome-wide detection of superior haplotypes for seed oil and protein content in Northeast China soybean (Glycine max L.) germplasm
Provisionally accepted
Moran Bu1
Ye Zhang1,2Weitao Xu1,2Yanhua Li1,2
Hui Yu1
Yaohua Zhang1
Suxin Yang1,2
Javaid Akhter Bhat1*
Xianzhong Feng1,2*- 1Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology Chinese Academy of Sciences, Changchun, China
- 2University of Chinese Academy of Sciences, Beijing, China
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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 varies 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 of 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.
Keywords: GWAS, haplotype, Northeast China, oil content, protein content, Soybean
Received: 14 Dec 2025; Accepted: 26 Jan 2026.
Copyright: © 2026 Bu, Zhang, Xu, Li, Yu, Zhang, Yang, Bhat and Feng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Javaid Akhter Bhat
Xianzhong Feng
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