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Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans

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Abstract

The main stem node number (MSN) is a trait related to geographic adaptation, plant architecture and yield potential of soybean. The QTL-allele constitution of the Chinese Cultivated Soybean Population (CCSP) was identified using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) procedure, from which a QTL-allele matrix was established and then separated into submatrices to explore the genetic structure, evolutionary differentiation, breeding potential and candidate genes of MSN in CCSP. The MSN of 821 accessions varied from 8.8 to 31.1, with an average of 16.3 in Nanjing, China (32.07° N, 118.62° E), where the MSNs of all the materials could be evaluated in a standardized manner. Among the six geo-seasonal subpopulations, the MSN varied from 21.7 in a southern summer-autumn-sowing subpopulation (SA-IV) down to 13.5 in a northeastern spring-sowing subpopulation (SP-I). The materials were genotyped with restriction site-associated DNA-sequencing. Totally 142 main-effect QTLs (73.24% new) with 560 alleles contributing 72.98% to the phenotypic variance were identified. The evolutionary QTL-allele changes in MSN from SA-IV through SP-I showed that inheritance (78.93% of alleles) was the primary factor influencing the evolution of this trait, followed by allele emergence (19.64% alleles), allele exclusion (1.43% alleles), and recombination among retained alleles. In the evolutionary changes, 70 QTLs, including 12 newly emerged QTLs, with 118 alleles were involved. An increase potential of 2–8 nodes was predicted and 112 candidate genes were annotated and preliminarily verified with χ2-tests in the CCSP. The RTM-GWAS showed powerful in detecting QTL-allele system, assessing evolution factors, predicting optimal crosses and identifying candidate genes in a germplasm population.

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Funding

This work was supported by the China National Key R & D Program for Crop Breeding (2016YFD0100201, 2017YFD0100500), the Natural Science Foundation of China (31601325, 31701447), the MOE 111 Project (B08025), Program for Changjiang Scholars, and Innovative Research Team in University (PCSIRT_17R55), the MARA CARS-04 program, the Fundamental Research Funds for the Central Universities (KYT201801) and the Jiangsu JCIC-MCP Program. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.

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Author notes

  1. Abbas Muhammad Fahim and Fangdong Liu have contribute to this work equally.

Authors and Affiliations

  1. Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing & Junyi Gai

  2. MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing & Junyi Gai

  3. MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing & Junyi Gai

  4. State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing & Junyi Gai

  5. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Abbas Muhammad Fahim, Fangdong Liu, Jianbo He, Wubing Wang, Guangnan Xing & Junyi Gai

Authors
  1. Abbas Muhammad Fahim
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  2. Fangdong Liu
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  3. Jianbo He
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  4. Wubing Wang
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  5. Guangnan Xing
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Contributions

JG designed the methods and experiments. FL, AMF, and WW performed the field experiments. AMF, FL, JH, and GX analyzed the data. AMF, FL, and JG drafted the manuscript.

Corresponding author

Correspondence to Junyi Gai.

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The authors have declared that no competing or conflicts of interest exist.

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The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher.

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Communicated by Stefan Hohmann.

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Fahim, A.M., Liu, F., He, J. et al. Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans. Mol Genet Genomics 296, 313–330 (2021). https://doi.org/10.1007/s00438-020-01748-9

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  • DOI: https://doi.org/10.1007/s00438-020-01748-9

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