Theoretical and Applied Genetics

, Volume 130, Issue 11, pp 2297–2314 | Cite as

Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure

  • Shuguang Li
  • Yongce Cao
  • Jianbo He
  • Tuanjie ZhaoEmail author
  • Junyi GaiEmail author
Original Article


Key message

The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected.


Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments. Using restriction-site-associated DNA sequencing the population was genotyped with SNP markers. The restricted two-stage multi-locus (RTM) genome-wide association study (GWAS) (RTM-GWAS) with SNP linkage disequilibrium block (SNPLDB) as multi-allele genomic markers performed the best among the five mapping procedures with software publicly available. It identified the greatest number of quantitative trait loci (QTLs) (139) and alleles (496) on 20 chromosomes covering almost all of the QTLs detected by four other mapping procedures. The RTM-GWAS provided the detected QTLs with highest genetic contribution but without overflowing and missing heritability problems (81.7% genetic contribution vs. heritability of 97.6%), while SNPLDB markers matched the NAM population property of multiple alleles per locus. The 139 QTLs with 496 alleles were organized into a QTL-allele matrix, showing the corresponding DTF genetic architecture of the five parents and the NAM population. All lines and parents comprised both positive and negative alleles, implying a great potential of recombination for early and late DTF improvement. From the detected QTL-allele system, 126 candidate genes were annotated and χ 2 tested as a DTF candidate gene system involving nine biological processes, indicating the trait a complex, involving several biological processes rather than only a handful of major genes.



This work was supported by the National Key Research and Development Program of China for Crop Breeding (2016YFD0100304), the National Key Basic Research Program of China (2011CB1093), the National Hightech Research and Development Program of China (2012AA101106), the Natural Science Foundation of China (31571691, 31571695), the MOE 111 Project (B08025), the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT13073), the MOA Public Profit Program (201203026-4), the MOA CARS-04 program, the Jiangsu Higher Education PAPD Program 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.

Author contribution statement

TZ and JG conceived and designed the study. SL and YC performed the field experiments. JH developed the mapping procedure RTM-GWAS. TZ provided the mapping population. SL and JH analyzed and interpreted the results. SL, TZ and JG drafted the manuscript.

Compliance with ethical standards

Conflict of interest

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

Supplementary material

122_2017_2960_MOESM1_ESM.pdf (1.9 mb)
Supplementary material 1 (PDF 1925 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Soybean Research InstituteNanjing Agricultural UniversityNanjingChina
  2. 2.National Center for Soybean ImprovementMinistry of AgricultureNanjingChina
  3. 3.Key Laboratory of Biology and Genetic Improvement of Soybean (General)Ministry of AgricultureNanjingChina
  4. 4.State Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
  5. 5.Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina

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