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Journal of Integrative Agriculture  2022, Vol. 21 Issue (9): 2521-2537    DOI: 10.1016/j.jia.2022.07.005
Special Issue: 油料作物合辑Oil Crops
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean
ZHANG Hua*, WU Hai-yan*, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying
State Key Laboratory of North China Crop Improvement and Regulation/Hebei Agricultural University, Baoding 071001, P.R.China
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Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean.  The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem.  In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line (RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the T1 stage, and the six-leaf stage as the flowering critical stage was designated as the T2 stage.  In total, 200 single nucleotide polymorphism (SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the T1 stage, and 109 detected at the T2 stage.  Among these SNP loci, one SNP cluster (s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the T1 stage, and the elite haplotype showed significantly greater plant height than the others.  Meanwhile, one pleiotropic SNP cluster (ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the T2 stage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition.  Furthermore, four co-associated SNP loci (ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the T1 and T2 stages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population.  More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by qRT-PCR.  Thus, these genetic loci and candidate genes could be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

Keywords:  soybean        phosphorus utilization        GWAS        linkage mapping        genetic loci        candidate genes  
Received: 16 December 2020   Accepted: 01 April 2021
Fund: This research was funded by the Project of Hebei Province Science and Technology Support Program, China (17927670H and 16227516D-1).
About author:  ZHANG Hua, Mobile: +86-15733202069, E-mail: zhanghua0316@; WU Hai-yan, E-mail:; Correspondence LI Xi-huan, Tel: +86-312-7528122, E-mail:; ZHANG Cai-ying, Tel: +86-312-7521558, E-mail: * These authors contributed equally to this study.

Cite this article: 

ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying. 2022. Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean. Journal of Integrative Agriculture, 21(9): 2521-2537.

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