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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (3): 341-353.doi: 10.3724/SP.J.1006.2020.94076

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

QTL analysis for relative contents of glycinin and β-conglycinin fractions from storage protein in soybean seeds under monoculture and relay intercropping

Dai-Ling LIU,Jun-Feng XIE,Qian-Rui HE,Si-Wei CHEN,Yue HU,Jia ZHOU,Yue-Hui SHE,Wei-Guo LIU,Wen-Yu YANG(),Xiao-Ling WU()   

  1. College of Agronomy, Sichuan Agricultural University / Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu 611130, Sichuan, China
  • Received:2019-05-20 Accepted:2019-09-26 Online:2020-03-12 Published:2019-10-09
  • Contact: Wen-Yu YANG,Xiao-Ling WU E-mail:mssiyangwy@sicau.edu.cn;wulx@sicau.edu.cn
  • Supported by:
    the Crops Breeding Project in Sichuan Province(2017YFD0101500);the Crops Breeding Project in Sichuan Province(2016NYZ0031)

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Abstract:

The relative contents of glycinin and β-conglycinin from storage protein are closely related to the quality and function of soybean seeds. However, it is not clear whether or how glycinin and β-conglycinin contents change in maize-soybean strip intercropping system. The glycinin and β-conglycinin relative contents of the recombinant inbred lines (RILs) derived from the cross of ‘Nandou 12’ and ‘Jiuyuehuang’ were measured under different environments (E1: 2017, Renshou; E2: 2017, Ya’an; E3: 2016, Renshou) and planting patterns (M: monoculture; RI: relay intercropping), among which the differences were significant or extremely significant in parents and RILs. Based on a genetic linkage map with 6366 SNP markers, we detected ten QTLs for glycinin and β-conglycinin relative contents which were distributed in nine linkage groups with the phenotypic variation of 5.63%-9.68%. According to the soybean genomic information, 65 candidate genes were screened in the region of above-mentioned QTLs. These results lay a theoretical foundation for soybean quality breeding.

Key words: Soybean (Glycine max L.), storage protein, shade, QTL mapping

Table 1

Glycinin and β-conglycinin relative content of ‘Nandou 12’ (ND12) and ‘Jiuyuehuang’ (JYH) under different environments and planting patterns"

性状
Trait		 种植方式
Planting pattern		 E1 E2 E3
南豆12
ND12		 九月黄
JYH		 Sig. 南豆12
ND12		 九月黄
JYH		 Sig. 南豆12
ND12		 九月黄
JYH		 Sig.
7S (%) M 20.18±0.22 b 24.47±0.30 a ** 21.77±1.28 a 21.55±0.63 a NS 22.84±0.20 a 22.96±0.47 a NS
RI 23.42±1.40 a 25.25±2.05 a NS 23.36±1.64 a 21.25±1.16 a NS 22.43±2.21 a 22.21±1.45 a NS
11S (%) M 33.74±0.29 a 42.47±0.31 A ** 36.80±2.06 a 38.05±0.97 a NS 37.99±0.69 a 36.08±0.76 a *
RI 35.57±1.64 a 36.63±0.30 B NS 38.09±1.37 a 35.35±1.02 b * 33.30±3.60 a 38.12±2.03 a NS
11S+7S (%) M 53.92±0.51 b 66.94±0.27 a ** 58.58±3.33 a 59.60±1.59 a NS 60.84±0.88 a 59.04±1.18 a NS
RI 58.99±3.04 a 61.88±2.16 b NS 61.45±1.01 a 56.60±2.15 a * 55.73±5.80 a 60.33±3.48 a NS
11S/7S M 1.67±0.00 a 1.74±0.03 A * 1.69±0.01 a 1.77±0.01 a ** 1.66±0.02 A 1.57±0.02 B **
RI 1.52±0.02 b 1.46±0.11 B NS 1.64±0.16 a 1.67±0.05 b NS 1.48±0.02 B 1.72±0.02 A **
α' (%) M 6.67±0.03 B 8.35±0.06 a ** 7.06±0.22 a 7.12±0.17 a NS 7.08±0.54 a 8.01±0.16 A *
RI 7.66±0.26 A 8.84±0.96 a NS 7.29±0.83 a 6.74±0.83 a NS 7.68±0.94 a 6.90±0.36 B NS
Α (%) M 6.84±0.18 a 9.49±0.28 a ** 7.92±0.75 a 7.63±0.69 a NS 8.38±0.50 a 8.14±0.81 a NS
RI 8.29±0.93 a 9.89±0.89 a NS 8.50±0.92 a 7.25±0.15 a NS 8.45±0.92 a 7.72±0.72 a NS
Β (%) M 6.67±0.20 B 6.63±0.42 a NS 6.80±0.38 b 6.81±0.12 b NS 7.39±0.91 a 6.81±0.30 b NS
RI 7.47±0.23 A 6.52±0.66 a NS 7.57±0.27 a 7.26±0.19 a NS 6.30±0.60 a 7.59±0.37 a *
A3 (%) M 5.27±0.15 a 7.43±0.76 a ** 5.04±0.71 a 4.79±0.11 a NS 5.61±0.23 a 5.28±1.24 a NS
RI 4.71±0.61 a 6.52±1.07 a NS 5.47±0.21 a 4.65±0.31 a * 5.37±0.15 a 6.00±0.46 a NS
Acid (%) M 13.01±0.88 a 17.17±0.78 a ** 15.79±2.58 a 14.68±1.07 a NS 17.46±1.65 a 15.77±1.65 a NS
RI 14.14±0.65 a 16.35±2.29 a NS 16.98±1.68 a 14.56±1.20 a NS 13.72±1.33 b 17.39±0.44 a **
Basic (%) M 8.65±0.44 a 12.48±1.28 a ** 8.93±0.08 B 9.82±0.57 a NS 8.27±0.47 a 8.66±0.11 a NS
RI 9.36±1.42 a 9.45±2.24 a NS 9.90±0.15 A 9.24±0.96 a NS 8.95±0.71 a 9.13±0.45 a NS
A5 (%) M 6.81±0.34 a 5.39±0.66 a * 7.04±0.91 a 8.75±1.31 a NS 6.71±2.71 a 6.37±1.59 a NS
RI 7.36±0.92 a 4.42±1.10 a * 5.74±0.58 a 6.9±0.94 a NS 5.27±2.86 a 5.60±1.65 a NS

Fig. 1

SDS-PAGE results of storage protein subunits in soybean seeds 1: Nandou 12; 2: Jiuyuehuang; 3: RIL158; 4: RIL104. Abbreviations are the same as those given in Table 1."

Fig. 2

Frequency distribution profiles of glycinin and β-conglycinin from seed storage protein in RILs population Abbreviations are the same as those given in Table 1."

Table 2

Statistic analysis of the glycinin and β-conglycinin relative content of seed storage protein in RILs population"

性状
Trait		 环境
E		 种植方式
Planting
pattern		 平均数±标准差
Mean±SD		 最大值
Max.		 最小值
Min.		 极差
Range		 变异系数
CV (%)		 偏度
Skew.		 峰度
Kurt.		 P (S-W)
7S (%) E1 M 22.34±1.81 30.03 19.73 10.30 8.11 1.73 4.07 0.00
RI 24.30±2.67 29.35 19.17 10.18 10.99 -0.10 -1.30 0.00
E2 M 21.74±1.63 26.88 17.49 9.39 7.52 0.49 0.33 0.01
RI 22.44±1.45 26.24 18.16 8.08 6.45 0.03 0.06 0.74
E3 M 24.67±1.92 29.92 19.60 10.32 7.78 0.23 -0.37 0.21
RI 25.22±1.92 30.18 19.89 10.29 7.60 0.14 -0.04 0.35
11S (%) E1 M 36.16±2.68 42.62 30.03 12.59 7.42 0.14 -0.79 0.01
RI 35.65±2.27 41.83 29.24 12.59 6.37 0.15 -0.17 0.75
E2 M 37.73±2.05 42.69 32.39 10.30 5.43 0.26 -0.35 0.05
RI 36.57±2.30 44.09 29.91 14.18 6.28 0.25 0.52 0.20
E3 M 37.47±2.62 46.31 30.46 15.85 6.99 0.14 0.01 0.34
RI 36.22±2.74 44.36 30.87 13.49 7.56 0.81 0.48 0.00
11S+7S (%) E1 M 58.50±2.81 65.08 52.05 13.03 4.80 -0.03 -0.79 0.00
RI 59.95±2.85 67.16 53.25 13.91 4.76 -0.01 -0.30 0.59
E2 M 59.46±2.23 65.27 54.60 10.67 3.75 0.05 -0.74 0.04
RI 59.01±2.59 65.31 51.99 13.32 4.39 -0.04 0.01 0.30
E3 M 62.15±2.65 72.35 55.68 16.67 4.27 0.21 0.28 0.10
RI 61.45±2.76 69.69 55.35 14.34 4.49 0.66 0.08 0.00
11S/7S E1 M 1.63±0.19 2.10 1.10 1.00 11.67 -0.17 0.01 0.11
RI 1.49±0.22 2.03 1.06 0.97 14.67 0.29 -0.99 0.00
E2 M 1.75±0.18 2.37 1.32 1.05 10.36 0.26 0.35 0.06
RI 1.64±0.16 2.08 1.26 0.82 9.46 0.31 -0.13 0.22
E3 M 1.53±0.18 2.17 1.10 1.07 12.07 0.22 0.19 0.47
RI 1.45±0.18 1.93 1.09 0.84 12.32 0.30 -0.42 0.03
α' (%) E1 M 7.45±0.79 9.99 6.10 3.89 10.59 1.19 1.71 0.00
RI 8.35±1.22 11.12 6.02 5.10 14.61 -0.07 -1.06 0.00
E2 M 7.10±0.65 10.01 5.61 4.40 9.09 0.57 1.79 0.00
RI 7.43±0.61 9.87 5.81 4.06 8.18 0.24 1.72 0.00
E3 M 8.39±0.77 10.46 6.66 3.80 9.21 0.42 -0.32 0.00
RI 8.53±0.85 11.05 5.98 5.07 9.95 0.01 0.41 0.14
α (%) E1 M 8.12±0.73 11.71 6.81 4.90 9.00 1.91 5.37 0.00
RI 9.03±1.17 11.33 6.73 4.60 12.94 -0.17 -1.10 0.00
E2 M 7.92±0.72 10.24 6.20 4.04 9.09 0.60 0.36 0.00
RI 8.04±0.63 9.81 6.32 3.49 7.87 -0.03 -0.02 0.61
E3 M 9.28±0.89 11.93 6.81 5.12 9.59 0.22 -0.27 0.13
RI 9.43±0.94 12.60 6.97 5.63 9.98 0.29 0.47 0.14
β (%) E1 M 6.77±0.58 9.48 5.31 4.17 8.54 1.72 5.30 0.00
RI 6.92±0.61 8.33 4.97 3.36 8.78 0.07 0.08 0.02
E2 M 6.72±0.61 8.73 5.46 3.27 9.13 0.30 0.02 0.11
RI 6.97±0.60 8.95 5.49 3.46 8.63 0.46 0.80 0.01
E3 M 7.01±0.76 9.37 5.23 4.14 10.85 0.11 -0.05 0.75
RI 7.26±0.59 8.71 5.54 3.17 8.15 0.03 0.09 0.64
A3 (%) E1 M 5.50±0.38 6.48 4.25 2.23 6.92 -0.28 0.39 0.21
RI 5.06±0.55 6.25 3.71 2.54 10.89 -0.41 -0.24 0.00
E2 M 5.64±0.61 8.20 4.30 3.90 10.86 0.77 1.84 0.00
RI 5.35±0.54 7.02 3.16 3.86 10.11 -0.37 1.65 0.00
E3 M 5.42±0.62 7.15 3.45 3.70 11.35 -0.36 0.34 0.04
RI 5.60±0.72 7.56 3.94 3.62 12.85 0.33 -0.14 0.10

"

性状
Trait		 环境
E		 种植方式
Planting
pattern		 平均数±标准差
Mean±SD		 最大值
Max		 最小值
Min		 极差
Range		 变异系数
CV (%)		 偏度
Skew.		 峰度
Kurt.		 P (S-W)
Acid (%) E1 M 15.64±1.54 20.78 12.51 8.27 9.83 0.69 0.11 0.00
RI 14.38±1.52 17.99 8.70 9.29 10.57 -0.60 0.90 0.00
E2 M 15.86±1.92 21.60 11.33 10.27 12.10 0.50 0.26 0.01
RI 15.16±1.68 19.19 9.57 9.62 11.08 -0.07 0.07 0.43
E3 M 15.38±1.25 18.93 10.92 8.01 8.15 -0.29 0.98 0.04
RI 14.90±1.38 19.04 11.33 7.71 9.26 -0.19 -0.19 0.22
Basic (%) E1 M 10.36±1.95 16.15 6.46 9.69 18.79 0.56 -0.26 0.00
RI 10.18±2.83 20.32 5.35 14.97 27.78 0.84 1.50 0.00
E2 M 10.77±2.21 16.66 6.33 10.33 20.52 0.16 -0.62 0.03
RI 9.89±2.25 20.84 5.37 15.47 22.75 1.78 4.17 0.00
E3 M 8.82±2.31 23.59 4.81 18.78 26.24 1.90 7.63 0.00
RI 8.09±1.79 15.48 4.50 10.98 22.09 0.96 2.47 0.00
A5 (%) E1 M 4.66±1.53 11.43 2.88 8.55 32.86 1.95 4.15 0.00
RI 6.02±2.32 15.45 0.88 14.57 38.44 1.21 1.57 0.00
E2 M 5.45±1.63 11.61 3.01 8.60 29.84 1.22 1.56 0.00
RI 6.17±1.76 11.42 2.83 8.59 28.56 0.30 -0.21 0.00
E3 M 7.85±3.36 17.74 1.09 16.65 42.85 0.65 -0.13 0.00
RI 7.64±3.94 18.83 1.75 17.08 51.52 1.03 0.31 0.00

Table 3

Analysis of variance of glycinin and β-conglycinin from seed storage protein in soybean"

性状
Trait		 变异来源 Variability source
E P G E×P E×G P×G E×P×G
7S (%) 2719.17** 1130.16** 16.35** 198.05** 12.31** 15.24** 9.05**
11S (%) 232.79** 390.23** 9.34** 22.11** 9.01** 8.57** 6.90**
11S+7S (%) 577.47** 1.81 5.13** 90.72** 4.71** 4.39** 4.42**
11S/7S 3509.46** 3081.43** 34.63** 68.89** 29.83** 35.37** 20.09**
α' (%) 1534.95** 670.80** 10.08** 169.27** 6.65** 8.86** 6.62**
α (%) 1726.56** 423.291** 8.68** 181.27** 6.97** 7.90** 5.07**
β (%) 131.30** 162.88** 6.03** 4.20* 4.76** 4.04** 3.80**
A3 (%) 60.23** 91.30** 3.89** 93.41** 3.23** 2.47** 2.70**
Acid (%) 43.73** 324.46** 5.05** 26.16** 3.87** 3.09** 4.02**
Basic (%) 490.46** 116.33** 7.57** 14.65** 5.40** 5.82** 4.28**
A5 (%) 541.06** 97.84** 5.93** 52.02** 6.24** 5.73** 4.71**

Table 5

QTLs for glycinin and β-conglycinin from storage protein in soybean seeds"

环境
Environ.		 种植方式
Planting pattern		 QTL 标记区间
Marker interval		 LOD 贡献率
PVE(%)		 加性效应
Add. effect		 置信区间
Confidence
interval
E1 M qAcid-6-131 Marker359561-Marker361355 5.63 8.06 0.53 130.5-131.5
qAcid-10-80 Marker584033-Marker584037 4.03 5.63 -0.46 79.5-80.5
qAcid-14-155 Marker713356-Marker710168 4.06 5.81 -0.47 153.5-158.0
RI qGpC-18-85 Marker1158309-Marker1157431 5.61 6.62 1.06 84.5-85.5
qBeta-19-5 Marker1175558-Marker1175562 4.03 9.01 -0.18 4.5-5.5
E2 M qBeta-1-135 Marker69562-Marker69768 3.21 7.49 -0.18 134.5-135.5
RI qAlpha-8-27 Marker460291-Marker460320 4.40 9.68 0.20 26.5-27.5
qBeta-1-13 Marker2130-Marker2656 3.22 7.14 -0.17 11.5-15.5
E3 M qAcid-4-67 Marker270606-Marker271196 3.68 8.20 -0.40 66.5-70.5
RI qGpC-20-110 Marker1242459-Marker1242433 3.65 8.60 0.82 109.5-110.5

Table 6

Candidate gene classification related to glycinin and β-conglycinin relative content from storage protein"

分组
Group		 生物过程
Biological process		 基因ID (净作/套作)
Gene ID (Monoculture/Relay intercropping)		 注释信息
Annotation description
I 激素调节
Regulation of
hormone		 Glyma.01G179900; Glyma.14G193800, 060300, 195200, 195300, 196000, 196600, 197100, 197200, 197500, 197600, 198000, 198100, 198300, 198600, 199200, 200200, 202000, 202600, 202700, 203000 / Glyma.01G025300, 025400, 025500, 025600, 027400; Glyma.18G251800, 252200, 252300, 252400 脱落酸激活的信号通路、激素介导的信号通路、乙烯激活的信号通路、生长素反应、脱落酸反应
Abscisic acid-activated signaling pathway, hormone-mediated signaling pathway, ethylene-activated signaling pathway, response to auxin, response to abscisic acid
II 氨基酸合成
Amino acid
synthesis		 Glyma.01G180100; Glyma.04G211400; Glyma.06G243800; Glyma.14G195300, 196600, 197100, 198700, 202000, 202700, 203000, 203700 / Glyma.01G025600, 027100, 027400, 028100, 028700; Glyma.08G210500; Glyma.18G250600, 251800 蛋白丝氨酸/苏氨酸激酶活性、丝氨酸家族氨基酸代谢过程
Protein serine/threonine kinase activity, serine family amino acid metabolic process
III 蛋白质磷酸化
Protein
phosphorylation		 Glyma.06G243800; Glyma.14G195200, 196600, 202700, 203000 / Glyma.01G027100, 028000, 028700; Glyma.18G249400, 249700, 249900, 250500, 250600, 251800 蛋白质磷酸化、蛋白质丝氨酸/苏氨酸磷酸酶活性、蛋白质脱磷酸
Protein phosphorylation, protein serine/threonine phosphatase activity, protein dephosphorylation
IV 细胞器生物过程
Organelle
biological process		 Glyma.04G212200, 212400; Glyma.14G194300, 194500, 196600, 197600, 198000, 198100, 198600, 199000, 202000, 202400, 203000 / Glyma.01G025200, 026000, 026200, 026700, 028100; Glyma.18G248400, 251300, 251800, 253200 内质网、液泡、内质网膜
E ndoplasmic reticulum, vacuole, endoplasmic reticulum membrane
V 种子发育
Seed development		 Glyma.01G179800; Glyma.14G197100, 197500, 199000, 202100 / Glyma.01G025200, 025300, 025400, 026200, 027400; Glyma.18G249400, 249700, 249800, 250000, 250100, 250600, 250700, 251200, 251800 子叶发育、以种子休眠结束的胚胎发育
Cotyledon development, embryo development ending in seed dormancy

Table 7

Meteorological data for E1, E2, and E3 from June to October (℃)"

月
Month		 旬
Ten-day periods		 日平均温度
Daily mean temperature		 日最高温度
Daily maximum temperature		 日最低温度
Daily minimum temperature
E1 E2 E3 E1 E2 E3 E1 E2 E3
6月
June		 上旬 The first ten days 25.40 23.13 25.80 30.47 28.02 31.86 21.59 19.87 20.99
中旬 The middle ten days 23.94 22.68 27.40 28.07 26.92 32.54 21.12 19.82 22.43
下旬 The last ten days 25.77 24.24 25.90 30.39 29.45 30.41 22.08 20.61 22.53
7月
July		 上旬 The first ten days 27.83 26.09 27.20 33.93 31.38 31.26 23.67 22.73 23.57
中旬 The middle ten days 29.23 27.78 27.80 35.00 34.31 32.80 24.45 23.50 23.20
下旬 The last ten days 30.41 28.08 27.90 36.13 35.23 32.84 25.88 24.15 24.23
8月
August		 上旬 The first ten days 29.41 28.11 27.00 35.17 34.20 31.98 25.55 24.43 23.79
中旬 The middle ten days 27.71 26.10 30.40 32.25 31.20 35.66 24.23 23.24 26.33
下旬 The last ten days 26.16 24.36 28.20 29.99 28.63 33.05 23.40 21.88 24.72
9月
September		 上旬 The first ten days 23.95 22.54 23.10 27.66 27.38 27.12 21.31 19.81 20.43
中旬 The middle ten days 23.68 22.29 22.00 27.40 26.03 25.40 21.22 20.30 19.82
下旬 The last ten days 23.04 21.55 22.30 26.43 25.89 25.95 20.94 19.24 19.88
10月
October		 上旬 The first ten days 19.97 18.77 22.00 23.73 23.03 25.59 17.70 16.85 19.47
中旬 The middle ten days 17.07 15.75 18.30 19.41 18.36 20.94 15.65 14.28 16.55
下旬 The last ten days 16.02 14.97 17.70 18.60 17.70 20.75 14.33 13.58 15.76
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