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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (5): 1091-1102.doi: 10.3724/SP.J.1006.2022.14063


Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height

YU Chun-Miao1,3(), ZHANG Yong2, WANG Hao-Rang3, YANG Xing-Yong2, DONG Quan-Zhong2, XUE Hong2, ZHANG Ming-Ming2, LI Wei-Wei2, WANG Lei2, HU Kai-Feng2, GU Yong-Zhe3, QIU Li-Juan1,3,*()   

  1. 1College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161606, Heilongjiang, China
    3National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-04-16 Accepted:2021-09-09 Online:2022-05-12 Published:2021-10-18
  • Contact: QIU Li-Juan E-mail:17709858735@163.com;qiulijuan@caas.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31601326);Central Public-interest Scientific Institution Basal Research Fund(S2021ZD02);Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences;Protection and Utilization of Soybean Germplasm Resources(2019NWB036-05)


In this study, 252 plants and their parents of Fengshou 24 × Tongjiao 83-611 were genotyped by SNP160K DNA-chip. A high-density genetic linkage map with a total length of 3661.46 cM was constructed, composing of 5861 SNP markers. Seven QTLs of plant height were detected by inclusive composite interval mapping (ICIM), and each one explained 2.56%-10.41% of the variation in plant height. qPH-6-1 had the highest contribution rate of phenotypic variation and dominant effect, explaining 10.41% of plant height variation, and the additive and dominant effects are -1.72 and 18.94, respectively. The contribution rate of qPH-18-1 was the second, explaining 9.64% of plant height variation, but qPH-18-1 has the highest additive effect, reaching -12.42. 11 plants with qPH-6-1 and qPH-18-1 genotypes Q6Q6/Q18Q18 were screened in F2 population with an average plant height of 167.00 cm, and 16 plants with 2-locus genotypes q6q6/q18q18 were screened out with an average plant height of 91.25 cm. The addition of 23 SNP markers inside and outside the qPH-18-1 locus interval narrowed the locus interval from 766.97 kb to 66.03 kb, containing eight genes. Combined with gene annotation and relative expression difference analysis, it was hypothesized that Glyma.18G279800 and Glyma.18G280200 might be associated with plant height of soybean. This study provides a molecular reference base and genetic basis for the improvement of soybean plant architecture.

Key words: soybean, plant height, SNP, genetic linkage map, QTLs mapping, candidate gene

Table 1

Primers of candidate genes and internal reference genes"

Primer name
Gene ID
Forward primer (5'-3')
Reverse primer (5'-3')
Product length (bp)

Table 2

SSR marker information for qPH-18-1 genotype identification"

Marker name
Forward sequence (5'-3')
Reverse sequence (5'-3')
Physical position (bp)

Fig. 1

Phenotypic distribution of plant height per plant in F2 population"

Table 3

Statistical analysis of plant height of parents and populations"

亲本Parent 群体Population
Fengshou 24
Tongjiao 83-611
株高Plant height (cm) 90.67±3.67 191.17±6.91 60.00-230.00 144.28 30.65 0.36 -0.54

Fig. 2

Distribution of 5861 SNP markers in soybean genetic linkage map The black horizontal line in the picture indicates the marker position; the color in the figure indicates the marker density, and the gradual change from red to blue indicates that the marker density is from dense to sparse."

Table 4

Distribution of SNP markers on the constructed genetic map"

Number of markers
Total distance (cM)
Average distance (cM)
1 277 170.23 0.61
2 338 220.66 0.65
3 344 158.81 0.46
4 379 195.95 0.52
5 312 176.98 0.57
6 310 209.66 0.68
7 236 170.11 0.72
8 250 203.31 0.81
9 304 192.14 0.63
10 354 200.50 0.57
11 268 195.60 0.73
12 150 118.50 0.79
13 261 227.96 0.87
14 276 152.34 0.55
15 272 162.66 0.60
16 244 177.84 0.73
17 455 185.47 0.41
18 285 195.06 0.68
19 240 177.67 0.74
20 306 170.02 0.56
合计Total 5861 3661.46 0.62

Table 5

QTL of plant height of soybean mapped by inclusive composite interval mapping"

QTL 染色体
Marker flanking
Position (cM)
LOD 贡献率
PVE (%)
qPH-6-1 6 Gm06_18957454-Gm06_17916496 57 3.00 9.24 10.41 -1.72 18.94 Rossi et al., 2013[4]
qPH-8-1 8 Gm08_9294990-Gm08_9210707 143 10.00 2.57 2.56 2.45 -9.12
qPH-10-1 10 Gm10_8606306-Gm10_7981987 134 7.00 3.00 2.95 4.30 -8.25
qPH-13-1 13 Gm13_38753560-Gm13_37989992 56 6.00 4.16 4.73 -9.04 3.38 Pathan et al., 2013[25]
qPH-13-2 13 Gm13_28621502-Gm13_28455484 115 3.00 2.70 2.67 -2.20 9.56 Li et al., 2009[26]
qPH-18-1 18 Gm18_56044812-Gm18_56811782 16 6.00 8.58 9.64 -12.42 1.84 Kim et al., 2012[12]
qPH-20-1 20 Gm20_33777405-Gm20_33894103 56 1.00 3.77 4.05 -8.10 -1.49 Chapman et al., 2003[27]

Table 6

Effects of polymerizing plant height QTLs of different genotypes on plant height"

QTL of polymerized homozygous genotypes with increase plant height
QTL of polymerized homozygous genotypes with reduce plant height
No. of QTL
No. of plants
Average height (cm)
No. of QTL
No. of plants
Average height (cm)
0 36 131.39±4.48 AC 对照Control 0 35 170.86±3.30 a 对照Control
1 64 139.45±3.89 AB 0.548 1 61 154.18±3.19 b 0.013*
2 74 146.49±3.28 BD 0.043* 2 70 137.14±3.18 c 0.000*
3 26 154.23±4.78 DE 0.010* 3 33 125.00±4.99 d 0.000*
4 15 166.67±5.66 E 0.000* 4 15 133.00±7.49 cd 0.000*
5 3 160.00±10.00 5 4 115.00±10.41 cd 0.000*

Fig. 3

New qPH-18-1 mapped by Fengshou 24 and Tongjiao 83-611 F2 population"

Table 7

Gene annotation and homologous genes in mapping interval"

Gene ID
Gene annotation
Homologous gene
Glyma.18G279500 后期促进复合物3 (APC3, CDC27)
Anaphase-promoting complex subunit 3 (APC3, CDC27)
Glyma.18G279800 在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶)
GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase);
PMR5 N terminal Domain (PMR5N)
Glyma.18G279900 在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶)
GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase);
PMR5 N terminal Domain (PMR5N)
Glyma.18G280100 与F27J15.22相关; 油质蛋白
F27J15.22-RELATED; Oleosin
Glyma.18G280200 富脯氨酸受体样蛋白激酶perk8
Proline-rich receptor-like protein kinase perk8

Fig. 4

Correlation analysis between plant genotype and phenotype in population *, **, and ** denote significant difference at the 0.05, 0.01, and 0.001 probability levels, respectively. The upper and lower borders of the square bar indicate the location of the upper and lower quartiles, respectively, and the black line in the middle is the median of the data set."

Fig. 5

Relative expression patterns of genes in the interval *: P<0.05; **: P<0.01."

Table 8

Comparison of genetic maps constructed by SNP microarray detection markers"

SNP-chip name
No. of parental SNPs
No. of markers
Total distance (cM)
Average distance (cM)
BARCSoySNP6K 1133-2585 1063-2283 1908.7-2834 1.10-1.80
SoyaSNP180K 23,429-28,385 1570-8967 3454-5050 0.50-2.2
SNP160K 48,248 5861 3661.46 0.62
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