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Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)

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Abstract

Main conclusion

A total of 41 SNPs were identified as significantly associated with five yield-related traits in wild soybean populations across multiple environments, and the candidate gene GsCID1 was found to be associated with seed weight. These results may facilitate improvements in cultivated soybean.

Abstract

Crop-related wild species contain new sources of genetic diversity for crop improvement. Wild soybean (Glycine soja Sieb. and Zucc.) is the progenitor of cultivated soybean [Glycine max (L.) Merr.] and can be used as an essential genetic resource for yield improvements. In this research, using genome-wide association study (GWAS) in 96 out of 113 wild soybean accessions with 114,090 single nucleotide polymorphisms (SNPs) (with minor allele frequencies ≤ 0.05), SNPs associated with five yield-related traits were identified across multiple environments. In total, 41 SNPs were significantly associated with the traits in two or more environments (significance threshold P ≤ 8.76 × 10–6), with 29, 7, 3, and 2 SNPs detected for 100-seed weight (SW), maturity time (MT), seed yield per plant (SY) and flowering time (FT), respectively. BLAST search against the Glycine soja W05 reference genome was performed, 20 candidate genes were identified based on these 41 significant SNPs. One candidate gene, GsCID1 (Glysoja.04g010563), harbored two significant SNPs—AX-93713187, with a non-synonymous mutation, and AX-93713188, with a synonymous mutation. GsCID1 was highly expressed during seed development based on public information resources. The polymorphisms in this gene were associated with SW. We developed a derived cleaved amplified polymorphic sequence (dCAPS) marker for GsCID1 that was highly associated with SW and was validated as a functional marker. In summary, the revealed SNPs/genes are useful for understanding the genetic architecture of yield-related traits in wild soybean, which could be used as a potential exotic resource to improve cultivated soybean yields.

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Abbreviations

DAF:

Days after flowering

dCAPS:

Derived cleaved amplified polymorphic sequence

FT:

Flowering time

GWAS:

Genome-wide association study

h 2 :

Broad-sense heritability

LD:

Linkage disequilibrium

MT:

Maturity time

PN:

Number of effective pods

SNP:

Single nucleotide polymorphism

SW:

100-Seed weight

SY:

Seed yield per plant

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Acknowledgements

This work was supported in part by the Ministry of Science and Technology (2016YFD0100304, 2017YFE0111000), the Key Transgenic Breeding Program of China (2016ZX08004-003, 2016ZX08009003-004), and the National Natural Science Foundation of China (31871649, 31671715).

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  1. Dezhou Hu and Huairen Zhang contributed equally to this work

Authors and Affiliations

  1. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China

    Dezhou Hu, Huairen Zhang, Qing Du, Zhongyi Yang, Xiao Li, Jiao Wang, Fang Huang, Deyue Yu, Hui Wang & Guizhen Kan

  2. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Huairen Zhang

  3. Department of Agronomy, Kansas State University, Manhattan, KS, USA

    Zhenbin Hu

  4. School of Life Sciences, Guangzhou University, Guangzhou, 510006, China

    Deyue Yu

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  1. Dezhou Hu
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Hu, D., Zhang, H., Du, Q. et al. Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.). Planta 251, 39 (2020). https://doi.org/10.1007/s00425-019-03329-6

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