Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (15): 3168-3182.doi: 10.3864/j.issn.0578-1752.2021.15.003

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

Mapping QTL for Soybean Fatty Acid Composition Based on RIL and CSSL Population

QU KeXin(),HAN Lu,XIE JianGuo,PAN WenJing,ZHANG ZeXin,XIN DaWei,LIU ChunYan,CHEN QingShan(),QI ZhaoMing()   

  1. Soybean Genetic Improvement Laboratory, College of Agriculture, Northeast Agricultural University, Harbin 150030
  • Received:2021-02-03 Accepted:2021-03-22 Online:2021-08-01 Published:2021-08-10
  • Contact: QingShan CHEN,ZhaoMing QI E-mail:18145648226@163.com;qshchen@126.com;qizhaoming1860@126.com

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Abstract:

【Objective】 Soybeans (Glycine max) originated from China. High-quality soybeans are widely used in various processing industries such as food, feeding, textiles, etc. Therefore, high-quality soybean breeding is a key point for soybean breeders and producers. This study conducted QTL mapping of each component of soybean fatty acid and screening of candidate genes, which would lay the molecular foundation for soybean quality improvement. 【Method】 A recombinant inbred lines (RILs) population crossed by Charleston (American soybean varieties ) and Dongnong 594, and a chromosome segment substitution lines (CSSLs) population crossed by Suinong 14 (cultivated soybean) and ZYD00006 (wild soybean) were used for QTL mapping. We used gas chromatography to determine the fatty acid content of these two populations. As the genetic maps have been published by the soybean genetic improvement laboratory of the Agricultural College of Northeast Agricultural University before, QTL mapping of soybean fatty acid components in RIL and CSL populations were performed by the Windows QTL Cartographer 2.5 and ICIMapping software. And the candidate genes were screened from the QTL interval. 【Result】 Based on 2017 to 2018 years data, 34 and 20 QTLs related to fatty acid components were mapped in the RIL population and the CSSL population, respectively. These QTLs distribute in 13 linkage groups except B2, C1, G, H, J, M, and O. QTL mapping of the two populations was compared that ten pairs of QTLs were detected in the two populations. We found that QTLs distributed in the A1, C2, D1a, F, K, and N linkage groups were related to the content of multiple fatty acids components. An overlapping QTL related to linoleic acid and oil content was detected on the A1 linkage group, QTL related to stearic acid and oil content on the C2, QTL related to stearic acid and oil content on the D1a, QTLs related to palmitic acid, stearic acid and oil content on the F, QTLs related to linoleic acid and linolenic acid content on the K, QTLs related to palmitic acid and oil content, and QTL related to oleic acid and linoleic acid content on the N. Candidate genes were screened out from QTL intervals. In total, 485 candidate genes were screened from the gene annotation data set and 271 of them annotated within GO annotations. GO enrichment analysis showed that 15 candidate genes involved in fatty acids pathway. These genes affect synthesis of fatty acids mainly through encoding plant acyl carrier protein (ACP) thioesterase, fatty acid desaturase, phospholipase D1, fatty acid-hydroxylase and pyruvate kinase, participating in the biosynthesis of acyl-CoA, and regulating the extension of fatty acid chain. 【Conclusion】 54 QTLs related to soybean fatty acid were detected, and 10 pairs QTLs were stable detected from the two mapping populations. We used the confidence intervals from QTL mapping to screen candidate genes, and 15 candidate genes related to fatty acids pathway were screened out. These stable QTLs and candidate genes can be used for molecular marker-assisted selection of soybean fatty acid improvement.

Key words: soybean, introduction line, gas chromatography, QTL mapping, gene mining, enrichment analysis

Fig. 1

Distribution histogram of the 5 fatty acids content in the RILs population in 2017 The X-axis represents the percentage of each fatty acid component to the total oil content, the Y-axis represents the plant coefficient of the percentage of each fatty acid component in the total oil content, and the black solid line represents the normal curve of the RILs population. The frequency distribution of the five fatty acid content of the RILs population in 2018 is the same as the 2017 results, showing continuous normal distribution, so only the 2017 results are shown here. The same as below"

Fig. 2

Distribution histogram of the 5 fatty acids content in the CSSLs population in 2017 Black solid line means normal curve of the CSSLs population"

Fig. 3

Distribution histogram of total oil in the RILs and CSSLs populations in 2017-2018 The black arrow represents the oil content of the male parent Charleston and wild bean (ZYD00006) in the RILs and CSSLs populations, and the red arrow represents the oil content of the female parent Dongnong 594 and Suinong 14 of the RILs and CSSLs groups"

Table 1

Descriptive statistics of fatty acids content for parents and individuals in two population"

性状
Trait		 群体
Population		 亲本Parent 群体Population
父本
Male		 母本
Female		 最小值
Minimum		 最大值
Maximum		 平均值
Mean		 标准差
SD		 变异系数
CV		 偏度
Skewness		 峰度
Kurtosis
棕榈酸
PA (%)		 17-RIL 12.80 13.15 11.48 13.98 13.05 0.42 3.21 -0.76 1.82
17-CSSL 12.75 13.17 12.62 13.33 13.03 0.15 1.13 -0.18 -0.61
18-RIL 12.74 13.09 12.11 13.27 12.90 0.18 1.42 -0.63 -1.04
18-CSSL 12.81 13.12 12.70 13.60 13.05 0.15 1.16 -0.09 -0.05
硬脂酸
SA (%)		 17-RIL 4.09 4.28 3.59 5.19 4.40 0.31 6.99 -0.43 0.15
17-CSSL 3.94 4.17 3.64 4.95 4.19 0.17 4.17 0.21 1.19
18-RIL 4.03 4.23 3.92 4.99 4.53 0.27 5.88 -0.28 -0.86
18-CSSL 4.04 4.15 3.80 4.68 4.23 0.17 3.91 0.28 -0.01
油酸
OA (%)		 17-RIL 19.19 20.35 17.00 23.53 19.33 1.12 5.78 0.84 1.59
17-CSSL 19.10 20.71 17.00 22.20 19.61 1.17 5.94 0.16 -0.63
18-RIL 19.13 20.06 18.09 22.25 19.53 0.83 4.25 0.64 0.59
18-CSSL 19.29 20.72 17.03 22.25 19.45 0.98 5.03 0.43 -0.13
亚油酸
LA (%)		 17-RIL 54.81 53.35 51.15 57.37 54.28 1.16 2.13 0.12 0.46
17-CSSL 55.17 53.19 51.59 57.37 54.20 1.25 2.31 -0.07 -0.62
18-RIL 54.97 53.76 51.47 56.12 54.10 0.95 1.76 -0.14 -0.06
18-CSSL 54.85 53.14 51.65 57.09 54.27 1.06 1.95 -0.29 -0.29
亚麻酸
LNA (%)		 17-RIL 9.11 8.87 7.75 10.87 8.94 0.40 4.51 0.47 3.93
17-CSSL 9.04 8.76 8.52 9.63 8.98 0.20 2.25 0.22 -0.42
18-RIL 9.13 8.86 8.29 9.34 8.93 0.19 2.11 -0.81 0.37
18-CSSL 9.01 8.87 8.30 9.63 8.99 0.19 2.12 -0.26 0.96
油分
OIL (%)		 17-RIL 20.25 21.62 19.82 24.26 21.94 0.99 4.53 -0.08 -0.44
17-CSSL 20.79 21.34 19.74 23.35 21.70 0.96 4.40 -0.24 -0.97
18-RIL 20.11 21.46 19.66 23.38 21.58 1.04 4.83 -0.11 -1.04
18-CSSL 20.53 21.19 19.87 23.33 21.74 1.00 4.59 -0.36 -0.93

Table 2

Correlation analysis of fatty acid content in RILs population"

性状 Traits 棕榈酸PA 硬脂酸SA 油酸OA 亚油酸LA 亚麻酸LNA
棕榈酸PA 1 0.388** -0.387** 0.582** 0.261**
硬脂酸SA 0.301** 1 -0.561** 0.714** 0.605**
油酸OA -0.015 -0.171* 1 -0.939** -0.790**
亚油酸LA 0.336** 0.398** -0.853** 1 0.717**
亚麻酸LNA 0.301** 0.275** -0.352** 0.230** 1

Table 3

Correlation analysis of fatty acid content in CSSLs population"

性状 Traits 棕榈酸PA 硬脂酸SA 油酸OA 亚油酸LA 亚麻酸LNA
棕榈酸PA 1 0.649** -0.846** 0.873** 0.855**
硬脂酸SA 0.815** 1 -0.651** 0.726** 0.684**
油酸OA -0.862** -0.778** 1 -0.987** -0.883**
亚油酸LA 0.895** 0.830** -0.991** 1 0.868**
亚麻酸LNA 0.843** 0.771** -0.881** 0.864** 1

Table 4

QTL mapping of fatty acid content in RIL population"

性状
Trait		 年份
Year		 QTL名称
QTL name		 染色体
Chromosome		 起始位置
Start position (Mb)		 终止位置
End position (Mb)		 距离
Size (Mb)		 LOD 贡献率
R2 (%)		 加性效应
Additive effect
棕榈酸
PA		 2017 qPA-N-1 3 14.80 18.50 3.70 4.00 9.56 0.15
2017 qPA-C2-1 6 20.47 21.61 1.14 4.44 10.51 -0.05
2017 qPA-C2-2 6 27.37 27.84 0.46 3.74 8.95 -0.04
2017 qPA-E-1 15 33.29 33.49 0.21 2.64 6.66 -0.06
2017 qPA-E-2 15 32.53 32.61 0.07 5.60 13.50 -0.09
2017 qPA-E-3 15 28.34 28.72 0.37 3.84 9.05 0.07
2017 qPA-E-4 15 22.73 22.77 0.04 2.70 6.47 0.05
2018 qPA-D1b-1 2 42.46 42.49 0.03 3.73 8.99 -0.05
2018 qPA-A1-1 5 34.54 34.55 0.01 2.89 6.96 -0.04
2018 qPA-F-1 13 15.74 15.83 0.09 5.32 13.16 0.09
硬脂酸
SA		 2017 qSA-N-1 3 40.50 44.10 3.60 2.98 7.62 -0.03
2018 qSA-D1b-1 2 42.61 42.62 0.01 2.84 6.90 -0.03
2018 qSA-F-1 13 15.74 15.83 0.09 4.51 11.11 0.06
2018 qSA-D2-1 17 38.23 38.91 0.68 3.20 7.73 0.03
油酸
OA		 2017 qOA-D1a-1 1 13.87 14.26 0.39 3.24 7.71 0.10
2017 qOA-N-1 3 23.25 23.29 0.04 3.86 9.09 -0.11
2017 qOA-N-2 3 24.72 24.96 0.24 3.89 9.17 -0.11
2017 qOA-A1-1 5 38.94 39.09 0.15 2.65 5.64 0.10
2017 qOA-D2-1 17 36.95 37.10 0.16 2.94 7.40 0.10
2018 qOA-A1-2 5 38.94 39.09 0.15 3.65 7.64 0.13
2018 qOA-D2-2 17 36.95 37.10 0.16 3.94 9.43 0.12
亚油酸
LA		 2017 qLA-N-1 3 23.05 23.11 0.06 2.76 6.99 -0.24
2017 qLA-N-2 3 28.10 28.27 0.17 3.25 8.29 0.26
2017 qLA-K-1 9 33.51 33.52 0.01 3.26 8.34 -0.19
2017 qLA-L-1 19 42.92 43.49 0.57 2.86 7.26 0.19
2018 qLA- A1-1 5 0.03 0.80 0.77 3.10 8.03 0.17
2018 qLA-I-1 20 24.43 24.44 0.02 2.54 6.40 -0.16
亚麻酸
LNA		 2017 qLNA-N-1 3 37.15 37.22 0.07 4.19 10.13 0.05
2017 qLNA-K-1 9 33.51 33.52 0.01 5.46 13.49 -0.05
2017 qLNA-B1-1 11 38.31 38.71 0.39 3.25 7.74 -0.04
2018 qLNA -B1-2 11 38.31 38.71 0.39 4.25 9.89 -0.07
2018 qLNA-I-1 20 45.55 45.74 0.19 3.20 8.16 0.03
油分
OIL		 2017 qOIL- D1b-1 2 6.25 6.51 0.25 2.67 6.95 -0.60
2018 qOIL-F-1 13 15.74 15.83 0.09 3.79 10.04 0.58

Table 5

QTL mapping of fatty acid content in CSSL population"

性状
Trait		 年份
Year		 QTL名称
QTL name		 染色体
Chromosome		 起始位置
Start position (Mb)		 终止位置
End position (Mb)		 距离
Size （Mb)		 LOD值
LOD		 贡献率
PVE (%)		 加性效应
Additive effect
棕榈酸
PA		 2017 qPA-N-2 3 18.57 19.23 0.66 2.86 4.62 0.16
2018 qPA-N-3 3 18.57 19.23 0.66 6.87 7.75 0.16
硬脂酸
SA		 2017 qSA-C2-1 6 49.19 49.24 0.05 1.78 3.21 0.41
2018 qSA-D1a-1 1 5.71 5.79 0.08 2.95 5.00 0.27
油酸
OA		 2017 qOA-F-1 13 13.72 13.81 0.09 9.60 8.80 0.30
2017 qOA-E-1 15 40.66 40.67 0.01 3.98 5.22 0.29
2018 qOA-D2-3 17 14.17 14.25 0.09 2.75 4.49 0.22
亚油酸
LA		 2017 qLA-A1-2 5 0.51 0.53 0.02 11.65 22.09 0.33
2018 qLA-A1-3 5 0.51 0.53 0.02 2.59 4.28 1.02
亚麻酸
LNA		 2017 qLNA-A1-1 5 34.40 34.44 0.04 3.80 3.93 0.05
2017 qLNA-A2-1 8 2.45 2.49 0.03 4.43 4.73 0.03
2018 qLNA-K-2 9 2.35 2.40 0.05 2.31 2.92 0.23
2018 qLNA-F-1 13 0.80 0.82 0.02 2.96 2.97 0.07
2018 qLNA-F-2 13 11.48 11.55 0.07 5.51 5.86 -0.04
2018 qLNA-E-1 15 49.40 49.44 0.03 2.97 3.01 0.04
油分
OIL		 2017 qOIL- D1a-1 1 5.71 5.79 0.08 3.59 7.96 0.43
2017 qOIL-N-1 3 18.57 19.23 0.66 3.37 7.44 0.31
2017 qOIL-C2-1 6 49.19 49.24 0.05 3.67 8.14 0.52
2018 qOIL-A1-1 5 0.51 0.53 0.02 1.84 3.02 1.43
2018 qOIL-F-2 13 31.17 31.19 0.02 2.74 3.71 0.36

Fig. 4

The linkage group distribution of QTLs of RILs and CSSLs population in 2017-2018 : QTLs mapped to the RIL population in 2017; : QTLs mapped to the RIL population in 2018; : QTLs mapped to the CSSL population in 2017; : QTLs mapped to the CSSL population in 2018"

Table 6

Annotation of candidate genes"

基因
Gene		 KO注释
KO annotation		 GO注释
GO annotation		 同源基因
Homologous gene		 基因功能
Gene description
Glyma.02G073800 GO:0016747 Glyma.06G211200 乙醇-乙酰基转移酶Alcohol-acetyltransferase
Glyma.13G044100
Glyma.02G074000 GO:0008080 酰基辅酶a/酰基转移酶Acyl-CoA/N-acyltransferases (NAT)
Glyma.03G070200 K00167 GO:0008152 α-酮酸脱羧酶E1β亚基Alpha-keto acid decarboxylase E1 beta subunit
Glyma.05G007700 GO:0016788 Glyma.13G044500 脂肪酶/酰基水解酶Lipase/Acyl hydrolase
Glyma.19G171000
Glyma.20G221200
Glyma.05G008100 K00326 GO:0016491 FAD/NAD（P）结合氧化还原酶 FAD/NAD(P)-binding oxidoreductase
Glyma.05G208900 K15398 GO:0055114 脂肪酸ω-羟化酶（CYP86A4S）Fatty acid omega-hydroxylase (CYP86A4S)
Glyma.05G000700 K00873 GO:0030955 丙酮酸激酶家族蛋白Pyruvate kinase family protein
Glyma.06G211300 K10781 GO:0006633 脂肪酰基-ACP硫酯酶B Fatty acyl-ACP thioesterases B
Glyma.17G219100 磷脂酶D1 Phospholipase D1
Glyma.17G228400 K13076 GO:0006629 脂肪酸去饱和酶Fatty acid desaturase
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