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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (6): 852-858.doi: 10.3724/SP.J.1006.2018.00852


Mapping Main-effect and Epistatic QTL for Hard Seededness in Soybean

Li-Juan AI1,2,Qiang CHEN2,Chun-Yan YANG2,Long YAN2,Feng-Min WANG2,Rong-Chao GE1,*(),Meng-Chen ZHANG2,*()   

  1. 1 College of Life Science, Hebei Normal University, Shijiazhuang 050024, Hebei, China
    2 Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences / Shijiazhuang Branch of National Soybean Improvement Center / Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture / Hebei Key Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, Hebei, China
  • Received:2017-09-05 Accepted:2018-01-08 Online:2018-06-12 Published:2018-01-23
  • Contact: Rong-Chao GE,Meng-Chen ZHANG E-mail:grcgp@sina.com;mengchenzhang@hotmail.com
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0100201);the China Agriculture Research System(CARS-004-PS06);Key Research and Development Projects of Hebei Provence(16227516D)


Hardness is a common characteristic of plant seeds, which is an important quantitative trait affecting germination rate, viability and storage life, and also processing quality of soybean seeds. In this study QTL analysis of the additive and epistatic interaction was used to reveal the important loci and effects controlling soybean hard seededness, and to provide theoretical basis for further analysis of the complex genetic mechanism of hard seededness. F6:8 and F6:9 populations of 186 recombinant inbred lines (RIL) derived from a cross of Jidou 12 and native variety Heidou (ZDD03651) were used to determine the additive QTLs for hard seededness in different years by the composite interval mapping (CIM) method in WinQTL Cartographer V. 2.5 software. The inclusive complete interval mapping (ICIM) method in IciMapping 4.1 software was used for analysing the interaction of additive and epistatic QTLs for hard seededness. Three QTLs for hard seededness were identified on Chr. 02, Chr. 06, and Chr. 14, respectively, with the genetic contribution rate of 5.54%-12.94%. Four pairs of epistatic interaction QTLs were detected on Chr. 02, Chr. 06, Chr. 09, Chr. 12, and Chr. 14, respectively, with explained 2.53%-3.47% of the phenotypic variation. The QTLs of additive and epistatic interactions were also detected in the hard seeds of soybean, and the epistasis was performed between the main effect QTLs or between the main effect QTL and the non-main effect QTL. The results indecate that the epistatic interaction effect plays an important role in the genetic basis of hard seededness of soybean.

Key words: soybean, hard seededness, QTL, epistasis

Fig. 1

Change of hard seededness rate"

Table 1

Phenotypic values of the hard seededness of soybean parents and RILs populations under different environments"

亲本Parents 重组自交系群体RILs population
Jidou 12 (%)
Heidou (%)
Mean (%)
Maximum (%)
Minimum (%)
CV (%)
2011 0 71.65 9.78 90.00 0 17.52 56 2.07 4.27
2013 0 83.33 16.85 96.67 0 22.45 75 1.42 1.29

Fig. 2

Frequency distributions for hard seededness in 186 soybean RILs"

Table 2

QTLs for hardness of soybean seeds under different environments by different methods"

Name of QTL
Marker interval
WinQTL Cart 2.5 IciMapping 4.1
R2 (%)
Additive effect
R2 (%)
qHS-2-1 Chr.02/D1b Sat_069-Sat_183 2011 2.94 6.82 4.62 2011 2.99 5.57 4.57
2013 2.51 5.54 5.16
qHS-6-1 Chr.06/C2 Sat_402-Satt460 2011 6.02 11.99 6.09 2011 5.87 11.04 6.47
2013 6.64 12.94 7.92 2013 2.77 6.52 6.29
qHS-14-1 Chr.14/B2 Satt577-Sat_287 2013 3.34 8.25 -6.26 2013 3.31 9.39 -7.47

Table 3

Epistasis effect of QTLs for hardness of soybean seeds under different environments"

Name of QTL
Marker interval
Name of QTL
Marker interval
R2 (%)
Add by add
qHS-6-1 Sat_402-Satt460 qHS-2-1 Sat_069-Sat_183 2011 10.41 2.69 8.66
qHS-9-1 Sat_399-Satt273 2011 10.93 2.74 8.82
2013 7.24 3.36 11.64
qHS-12-1 Barcsoyssr_12_1-Satt353 2011 6.22 2.53 -8.15
2013 7.50 3.47 -10.08
qHS-14-1 Satt577-Sat_287 qHS-12-1 Barcsoyssr_12_1-Satt353 2013 5.87 3.13 10.10

Fig. 3

Location of additive QTLs and epistatic effects QTLs on linkage groups The black bars show the support interval of QTL position, the dotted line represents epistatic QTLs."

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