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Volume 14
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10.3390/plants14030357
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study

by
Xinjing Yang
1,2,
Ye Zhang
1,2,
Javaid Akhter Bhat
3,
Mingjing Wang
3,
Huanbin Zheng
1,
Moran Bu
1,2,
Beifang Zhao
1,
Suxin Yang
1,2,* and
Xianzhong Feng
1,2,*
1
Key Laboratory of Soybean Molecular Design Breeding, National Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
2
College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
3
Zhejiang Lab, Hangzhou 310012, China
*
Authors to whom correspondence should be addressed.
Plants 2025, 14(3), 357; https://doi.org/10.3390/plants14030357
Submission received: 29 December 2024 / Revised: 17 January 2025 / Accepted: 21 January 2025 / Published: 24 January 2025
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
Versions Notes

Abstract

Alkaline stress is one of the major abiotic constraints that limits plant growth and development. However, the genetic basis underlying alkaline tolerance in soybean [Glycine max (L.) Merr.] remains largely unexplored. In this study, an integrated genomic analysis approach was employed to elucidate the genetic architecture of alkaline tolerance in a diverse panel of 326 soybean cultivars. Through association mapping, we detected 28 single nucleotide polymorphisms (SNPs) significantly associated with alkaline tolerance. By examining the genomic distances around these significant SNPs, five genomic regions were characterized as stable quantitative trait loci (QTLs), which were designated as qAT1, qAT4, qAT14, qAT18, and qAT20. These QTLs are reported here for the first time in soybean. Seventeen putative candidate genes were identified within the physical intervals of these QTLs. Haplotype analysis indicated that four of these candidate genes exhibited significant allele variation associated with alkaline tolerance-related traits, and the haplotype alleles for these four genes varied in number from two to four. The findings of this study may have important implications for soybean breeding programs aimed at enhancing alkaline tolerance.
Keywords: soybean; alkaline tolerance; GWAS; haplotype; candidate gene soybean; alkaline tolerance; GWAS; haplotype; candidate gene

Share and Cite

MDPI and ACS Style

Yang, X.; Zhang, Y.; Bhat, J.A.; Wang, M.; Zheng, H.; Bu, M.; Zhao, B.; Yang, S.; Feng, X. Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study. Plants 2025, 14, 357. https://doi.org/10.3390/plants14030357

AMA Style

Yang X, Zhang Y, Bhat JA, Wang M, Zheng H, Bu M, Zhao B, Yang S, Feng X. Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study. Plants. 2025; 14(3):357. https://doi.org/10.3390/plants14030357

Chicago/Turabian Style

Yang, Xinjing, Ye Zhang, Javaid Akhter Bhat, Mingjing Wang, Huanbin Zheng, Moran Bu, Beifang Zhao, Suxin Yang, and Xianzhong Feng. 2025. "Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study" Plants 14, no. 3: 357. https://doi.org/10.3390/plants14030357

APA Style

Yang, X., Zhang, Y., Bhat, J. A., Wang, M., Zheng, H., Bu, M., Zhao, B., Yang, S., & Feng, X. (2025). Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study. Plants, 14(3), 357. https://doi.org/10.3390/plants14030357

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