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Journal of Integrative Agriculture
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A near-gapless genome assembly of soybean line Zhongpin 03-5373 enables structural variation based dissection of SCN3 resistance

Xueqing Wang1, Jiajun Wang2, Lichun Huang3, Yu Tian1, Yinghui Li1#, Lijuan Qiu1#

1 State Key Laboratory of Crop Gene Resources and Breeding/The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

2 Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China

3 Hinngan League Academy of Agricultural and Animal Husbandry Sciences (Inner Mongolia Innovation Center of Biological Breeding Technology).

 Highlights 

l Near-gapless de novo genome assembly of elite SCN3-resistant soybean ZP03.

l Identification of novel QTL qSCN3-16 and candidate SNARE gene SYP16.

l A favorable SYP16 promoter SV is significantly associated with SCN3 resistance.

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摘要  

栽培大豆(Glycine max [L.] Merr.)是全球重要的植物蛋白和食用油来源,其产量受大豆胞囊线虫(Soybean Cyst Nematode, SCN严重制约,3号生理小种(SCN3)是我国分布最广、危害最重的小种之一。中品03-5373ZP03)是一个优良的中国大豆品系,兼具对SCN3的稳定抗性和优良农艺性状。本研究利用PacBio RevioHiFi)长读长测序结合Hi-C染色质互作图谱技术,对ZP03进行了近无缺口从头基因组组装。组装基因组总长度1,067.68 MbContig N5035.36 Mb,其中95.24%的序列锚定到20条染色体上。比较基因组分析揭示了ZP03中与SCN3抗性相关的大量结构变异(Structural Variations, SV,并鉴定到一个位于GmSNAP11启动子区域的393 bp缺失型结构变异,该变异与SCN3侵染后基因表达升高相关,提示其可能参与病原胁迫下的差异转录调控。进一步基于ZP03×中黄13ZH13)重组自交系群体构建的SV遗传图谱,定位到一个新的与SCN3抗性相关的QTL-qSCN3-16,可解释7.51%的表型变异(LOD=3.42)。在该位点内,优先筛选到抗性候选基因Glyma.16G045900SYP16,其编码一个t-SNARE蛋白。对2,214大豆材料进行单倍型分析表明,SYP16启动子中的一个SVSCN3抗性显著相关。综上所述,本研究揭示SV在大豆免疫应答中的关键作用,并为SCN3抗性大豆品种的分子育种提供了高分辨率基因组资源和功能标记。



Abstract  

Cultivated soybean (Glycine max [L.] Merr.) is a major global source of vegetable protein and edible oil, yet its production is severely constrained by soybean cyst nematode (SCN, Heterodera glycines), with race 3 being the most prevalent and destructive pathotype in China. Zhongpin 03-5373 (ZP03) is an elite Chinese soybean line characterized by stable resistance to SCN3 (race 3, HG type 0) and superior agronomic performance. Here, we report a near-gapless de novo genome assembly of ZP03 generated using PacBio Revio (HiFi) long-read sequencing combined with Hi-C chromatin interaction mapping. The assembled genome spans 1,067.68 Mb with a Contig N50 of 35.36 Mb, anchoring 95.24% of sequences onto 20 chromosomes. Comparative genomic analyses revealed an extensive structural variation (SV) landscape associated with SCN3 resistance in ZP03. A 393-bp deletion-type SV located in the promoter region of GmSNAP11 was identified and was associated with increased gene expression following SCN3 infection. This allelic variation may contribute to differential transcriptional regulation under pathogen challenge. Using an SV-based genetic map constructed from a ZP03×Zhonghuang 13 (ZH13) recombinant inbred line population, we further identified a novel QTL qSCN3-16 contributing to SCN3 resistance, which explaining 7.51% of the phenotypic variance (LOD=3.42). Within this locus, Glyma.16G045900 (SYP16), encoding a t-SNARE protein, was prioritized as the candidate gene. Haplotype analysis across 2,214 diverse soybean accessions demonstrated that a favorable promoter SV in SYP16 is significantly associated with enhanced SCN3 resistance. Together, these results highlight the critical role of structural variation in shaping soybean immune responses and provide high-resolution genomic resources and functional markers, specifically the novel QTL qSCN3-16, to support precision breeding of SCN3-resistant soybean cultivars.

Keywords:  soybean       de novo assembly              soybean cyst nematode              structural variation              QTL mapping  
Online: 25 April 2026  
Fund: 

This work was supported by the Inner Mongolia Autonomous Region Science and Technology Program (2023DXZD0001) and State Key Laboratory of Crop Gene Resources and Breeding, China (CGRB-2026-05).

About author:  #Correspondence Yinghui Li, E-mail: liyinghui@caas.cn; Lijuan Qiu, E-mail: qiulijuan@caas.cn

Cite this article: 

Xueqing Wang, Jiajun Wang, Lichun Huang, Yu Tian, Yinghui Li, Lijuan Qiu. 2026. A near-gapless genome assembly of soybean line Zhongpin 03-5373 enables structural variation based dissection of SCN3 resistance. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.04.032

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