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

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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)

Abstract:

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"

引物名称
Primer name
基因编号
Gene ID
上游引物
Forward primer (5'-3')
下游引物
Reverse primer (5'-3')
产物长度
Product length (bp)
Fbox Glyma.12G051100 CTAATGGCAATTGCAGCTCTC AGATAGGGAAATTGTGCAGGT 93
Q2795 Glyma.18G279500 GTAGCAGCCATGGAAGCGATAC AGATTTGTCTCGGTGGGGAAC 122
Q2796 Glyma.18G279600 CTGCTGGCTATGATGCACAGTCA AGGTTCATATCCACCTCCACTACG 122
Q2797 Glyma.18G279700 TACATGCGTGGTTCGCCTTGC TGTATGTTAGAGGGTGGGGAAAGG 135
Q2798 Glyma.18G279800 CCTTGATGAGCCAGATGAGAAATG CATAGTACATGGTTAAGTCAGGAAC 170
Q2799 Glyma.18G279900 CATCACCACCACAAGTAGTTTGG GATTTTGAGAGTTCATTGGAACTG 132
Q2800 Glyma.18G280000 GATCCTCTCCAGAAACATTGAGATG GGGTTATTATGTGGCTCTACTTGTG 128
Q2802 Glyma.18G280200 GTACATGCAAGGACCCTCTTGG TCACTGCTCTAACACACTGGCG 124

Table 2

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

标记名称
Marker name
上游引物
Forward sequence (5'-3')
下游引物
Reverse sequence (5'-3')
物理位置
Physical position (bp)
BARCSOYSSR_18_1842 TGAAATGGAGGAGAAAATGGA GTCCGGGGAAACTGAACC 56,015,746-56,015,789
BARCSOYSSR_18_1843 TCGTTCGCAAAGAAAAATCC TTGGCAACAATGGAGTCTCA 56,035,543-56,035,596
BARCSOYSSR_18_1844 TGCAAGGCATTGATCTGATT AGAGGCGTCCTTCTGTTGTT 56,063,881-56,063,916
BARCSOYSSR_18_1845 TCATTGAGCCGAATCTTTTAAT CGTGCACATGGTGAGACATA 56,066,436-56,066,463
BARCSOYSSR_18_1846 CTTTTAACGATTGGGTTGGG CTTCGGCCTTAGACTTTTCG 56,068,160-56,068,221
BARCSOYSSR_18_1848 CGGTGTTGCTGACTATTGTCCT GGCTTTTGTAAACTGCTGGC 56,110,310-56,110,343
BARCSOYSSR_18_1849 TCTCGTCCCCGTATAAGGCT GGCGGATTGGAGAGAACATA 56,110,482-56,110,503
BARCSOYSSR_18_1850 AAATGCATTCGTGGCTTTCT TGGGTATTATTTGGCAAGCAC 56,138,357-56,138,410

Fig. 1

Phenotypic distribution of plant height per plant in F2 population"

Table 3

Statistical analysis of plant height of parents and populations"

性状
Trait
亲本Parent 群体Population
丰收24
Fengshou 24
通交83-611
Tongjiao 83-611
幅度
Range
均值
Mean
标准差
SD
峰度
Kurtosis
偏度
Skewness
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"

染色体号
Chromosome-ID
标记数量
Number of markers
总图距
Total distance (cM)
平均图矩
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
Chr.
标记区间
Marker flanking
位置
Position (cM)
区间长度
Length
(cM)
LOD 贡献率
PVE (%)
加性效应
Add
显性效应
Dmo
已报道位点
Reported
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"

聚合纯合提升株高基因型的QTL
QTL of polymerized homozygous genotypes with increase plant height
聚合纯合降低株高基因型的QTL
QTL of polymerized homozygous genotypes with reduce plant height
位点数
No. of QTL
植株数量
No. of plants
平均株高
Average height (cm)
分组
Group
P
P-value
位点数
No. of QTL
植株数量
No. of plants
平均株高
Average height (cm)
分组
Group
P
P-value
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"

基因编号
Gene ID
基因注释
Gene annotation
同源基因
Homologous gene
Glyma.18G279500 后期促进复合物3 (APC3, CDC27)
Anaphase-promoting complex subunit 3 (APC3, CDC27)
Phvul.008G021500
AT2G20000
Glyma.18G279600
Glyma.18G279700
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)
Phvul.008G021200
AT5G15900
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)
Phvul.008G021100
Glyma.18G280000
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
AL7G52030

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"

芯片名称
SNP-chip name
亲本间SNP数
No. of parental SNPs
图谱标记数
No. of markers
图谱总长
Total distance (cM)
标记间平均距离
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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