| Literature DB >> 28389769 |
Bin Li1, Shengxü Fan1, Fukuan Yu1, Ying Chen1, Shengrui Zhang1, Fenxia Han1, Shurong Yan1, Lianzheng Wang1, Junming Sun2.
Abstract
KEY MESSAGE: We constructed a high-density linkage map comprising 3541 markers developed by specific-locus amplified fragment sequencing, and identified 26 stable QTL including nine novel loci, for fatty acid composition in soybean. Soybean oil quality and stability are mainly determined by the fatty acid composition of the seed. In the present study, we constructed a high-density genetic linkage map using 200 recombinant inbred lines derived from a cross between cultivated soybean varieties Luheidou2 and Nanhuizao, and SNP markers developed by specific-locus amplified fragment sequencing (SLAF-seq). This map comprises 3541 markers on 20 linkage groups and spans a genetic distance of 2534.42 cM, with an average distance of 0.72 cM between adjacent markers. Inclusive composite interval mapping revealed 26 stable QTL for five fatty acids, explaining 0.4-37.0% of the phenotypic variance for individual fatty acids across environments. Of these QTL, nine are novel loci (qLA1, qLNA2_1, qPA4_1, qLA4_1, qPA6_1, qSA12_1, qPA16_1, qOA18_1, and qFA19_1). These stable QTL harbor three fatty acid biosynthesis genes (GmFabG, GmACP, and GmFAD8), and 66 genes encoding lipid-related transcription factors. These stable QTL and tightly linked SNP markers can be used for marker-assisted selection in soybean breeding programs.Entities:
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Year: 2017 PMID: 28389769 PMCID: PMC5487593 DOI: 10.1007/s00122-017-2902-8
Source DB: PubMed Journal: Theor Appl Genet ISSN: 0040-5752 Impact factor: 5.699
The characteristics of five fatty acids in 200 soybean RILs from 2009 to 2011
| Trait | Environment | Mean ± SD (%) | Minimum (%) | Maximum (%) | CVa | Variance |
|
|
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|---|---|---|---|---|---|---|---|---|---|
| Pamitic | 2009 | 10.24 ± 0.57 | 8.78 | 13.25 | 0.056 | 0.33 | 0.563 | 0.81 | 0.75 |
| 2010 | 10.89 ± 0.54 | 9.29 | 13.75 | 0.049 | 0.29 | 0.568 | 0.76 | ||
| 2011 | 10.75 ± 0.68 | 9.23 | 12.96 | 0.064 | 0.47 | 0.500 | 0.57 | ||
| Stearic | 2009 | 3.84 ± 0.48 | 2.57 | 5.11 | 0.124 | 0.23 | 0.099 | 0.87 | 0.74 |
| 2010 | 3.75 ± 0.43 | 2.62 | 4.95 | 0.113 | 0.18 | 0.968 | 0.77 | ||
| 2011 | 3.68 ± 0.66 | 2.22 | 7.06 | 0.178 | 0.43 | 0.515 | 0.63 | ||
| Oleic | 2009 | 24.06 ± 2.67 | 19.61 | 35.07 | 0.111 | 7.11 | 0.216 | 0.88 | 0.81 |
| 2010 | 26.47 ± 4.39 | 17.71 | 39.13 | 0.166 | 19.24 | 0.369 | 0.87 | ||
| 2011 | 22.26 ± 3.05 | 17.67 | 36.28 | 0.137 | 9.29 | 0.001 | 0.86 | ||
| Linoleic | 2009 | 53.27 ± 2.31 | 45.95 | 57.50 | 0.043 | 5.32 | 0.744 | 0.88 | 0.80 |
| 2010 | 51.40 ± 3.53 | 41.64 | 59.00 | 0.069 | 12.44 | 0.190 | 0.87 | ||
| 2011 | 55.05 ± 2.51 | 43.64 | 59.46 | 0.046 | 6.28 | 0.003 | 0.69 | ||
| Linolenic | 2009 | 8.58 ± 0.69 | 6.72 | 10.56 | 0.081 | 0.48 | 0.830 | 0.78 | 0.88 |
| 2010 | 7.48 ± 0.88 | 5.47 | 10.57 | 0.117 | 0.77 | 0.910 | 0.84 | ||
| 2011 | 8.26 ± 0.80 | 5.74 | 10.05 | 0.097 | 0.65 | 0.825 | 0.89 |
aCoefficient of variance
b P value in Kolmogorov–Smirnov test
cBroad-sense heritability in each environment
dBroad-sense heritability in combined environments (2009, 2010, and 2011)
Fig. 1Frequency distributions of five fatty acid contents in 200 RIL seeds from 2009 to 2011. The arrows indicate the fatty acid compositions in two parental lines (cv. LHD2 and NHZ)
Fig. 2High-density genetic map for soybean and 26 stable QTL for fatty acids. The SLAF marker distributions were depicted on the 20 linkage groups (Gm01–Gm20) based on their genetic positions in centiMorgans (cM). The 26 stable QTL for fatty acids, along with their interval distances (cM) are shown between the tightly linked SLAF markers on the right side of each linkage group. The three fatty acid biosynthesis genes are indicated within the QTL intervals in red color by comparing their physical positions with that of SLAF markers in the soybean reference genome (color figure online)
Description of characteristics of the 20 linkage groups (LGs) in the soybean genetic map
| LGa | No. of SLAFs | Distance (cM) | Average distance between markers (cM) | Largest gap (cM) |
|---|---|---|---|---|
| Gm01 | 228 | 130.35 | 0.57 | 5.27 |
| Gm02 | 154 | 140.93 | 0.92 | 13.74 |
| Gm03 | 231 | 147.28 | 0.64 | 15.40 |
| Gm04 | 260 | 94.18 | 0.36 | 5.95 |
| Gm05 | 86 | 99.60 | 1.17 | 8.20 |
| Gm06 | 196 | 143.70 | 0.74 | 7.10 |
| Gm07 | 142 | 118.42 | 0.84 | 14.89 |
| Gm08 | 152 | 137.60 | 0.91 | 4.37 |
| Gm09 | 147 | 151.62 | 1.04 | 13.95 |
| Gm10 | 167 | 110.81 | 0.67 | 5.75 |
| Gm11 | 69 | 112.48 | 1.65 | 8.71 |
| Gm12 | 100 | 96.85 | 0.98 | 8.86 |
| Gm13 | 178 | 176.98 | 1.00 | 7.02 |
| Gm14 | 209 | 136.25 | 0.66 | 12.63 |
| Gm15 | 237 | 99.96 | 0.42 | 6.97 |
| Gm16 | 172 | 110.83 | 0.65 | 8.10 |
| Gm17 | 217 | 120.51 | 0.56 | 4.82 |
| Gm18 | 339 | 187.47 | 0.55 | 6.32 |
| Gm19 | 161 | 120.24 | 0.75 | 7.18 |
| Gm20 | 96 | 98.36 | 1.04 | 7.38 |
| Maximum | 339 | 187.47 | 1.65 | 15.40 |
| Minimum | 69 | 94.18 | 0.36 | 4.37 |
| Total | 3541 | 2534.42 | 0.72 | – |
aLinkage group
The stable QTL for specific fatty acids in soybean seed across multiple environments
| QTLa | Traitb | Environmentc | Chrd | Marker interval | LOD | PVEe (%) | Novelty | Reported QTL or QTN | Gene annotationf |
|---|---|---|---|---|---|---|---|---|---|
|
| PA | 2009/2011 | 4 | Gm04_47098–Gm04_44762 | 5.1–16.3 | 1.7–7.7 | Novel | ||
|
| 2009/2010 | 6 | Gm06_8091–Gm06_2457 | 8.0–14.4 | 4.1–6.1 | Novel | |||
|
| 2010/2011 | 8 | Gm08_9171–Gm08_38849 | 43.8–48.5 | 28.0–37.0 | Bachlava et al. ( | |||
|
| 2009/2010 | 16 | Gm16_28849–Gm16_52098 | 5.9–13.5 | 2.2–7.5 | Novel | |||
|
| SA | 2009/2011 | 8 | Gm08_53938–Gm08_3252 | 34.2–39.8 | 22.4–28.7 | Li et al. ( | ||
|
| 2009/2011 | 12 | Gm12_1782–Gm12_30904 | 18.0–32.6 | 9.9–11.9 | Novel |
| ||
|
| 2009/2010 | 14 | Gm14_21994–Gm14_55450 | 3.8–28.8 | 3.0–7.0 | Xie et al. ( | |||
|
| 2009/2011 | 18 | Gm18_84824–Gm18_77518 | 6.0–32.0 | 2.8–11.6 | Fan et al. ( | |||
|
| OA | 2010/2011 | 7 | Gm07_58581–Gm07_29390 | 13.0–54.0 | 1.3–33.6 | Fan et al. ( | ||
|
| 2009/2010 | 8 | Gm08_13258–Gm08_43422 | 6.0–6.1 | 1.1–6.5 | Bachlava et al. ( | |||
|
| 2009/2010 | 9 | Gm09_45996–Gm09_5152 | 6.9–23.1 | 1.3–14.9 | Fan et al. ( |
| ||
|
| 2009/2011 | 13 | Gm13_25899–Gm13_9722 | 11.9–28.9 | 2.3–3.5 | Fan et al. ( | |||
|
| 2009/2010 | 17 | Gm17_33278–Gm17_7573 | 8.9–15.0 | 1.5–1.7 | Xie et al. ( | |||
|
| 2009/2011 | 18 | Gm18_79781–Gm18_53964 | 52.1–68.1 | 8.6–27.4 | Novel | |||
|
| 2009/2011 | 19 | Gm19_67930–Gm19_42890 | 10.4–20.5 | 1.0–4.4 | Novel | |||
|
| 2009/2010 | 19 | Gm19_58422–Gm19_16080 | 3.6–20.9 | 1.8–4.4 | Fan et al. ( | |||
|
| LA | 2009/2010 | 19 | Gm19_67930–Gm19_42890 | 7.9–26.0 | 0.7–12.0 | Novel | ||
|
| 2009/2010 | 19 | Gm19_58422–Gm19_16080 | 28.3–40.3 | 13.6–19.3 | Fan et al. ( | |||
|
| 2009/2011 | 1 | Gm01_79467–Gm01_15147 | 6.7–25.9 | 3.0–4.4 | Novel | |||
|
| 2009/2010 | 4 | Gm04_67180–Gm04_61504 | 7.6–27.4 | 2.7–4.8 | Novel | |||
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| 2010/2011 | 5 | Gm05_27463–Gm05_53236 | 3.9–4.1 | 0.4–1.3 | Bachlava et al. ( | |||
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| 2009/2010/2011 | 8 | Gm08_47647–Gm08_8866 | 7.9–33.6 | 1.3–16.9 | Fan et al. ( | |||
|
| LNA | 2009/2011 | 2 | Gm02_57581–Gm02_69905 | 6.2–9.1 | 2.5–3.6 | Novel | ||
|
| 2010/2011 | 3 | Gm03_40606–Gm03_10118 | 13.1–42.1 | 3.7–21.7 | Fan et al. ( |
| ||
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| 2009/2010 | 15 | Gm15_4886–Gm15_16198 | 7.9–35.2 | 3.0–17.6 | Li et al. ( | |||
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| 2010/2011 | 16 | Gm16_11545–Gm16_47706 | 8.6–9.9 | 2.8–3.0 | Diers and Shoemaker ( | |||
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| 2010/2011 | 19 | Gm19_45448–Gm19_57039 | 48.3–50.1 | 28.2–32.3 | Fan et al. ( | |||
|
| 2009/2010/2011 | 20 | Gm20_19811–Gm20_41673 | 14.9–44.4 | 3.6–26.0 | Fan et al. ( |
aThe name of QTL, is a composite of the influenced trait: PA (palmitic acid), SA (stearic acid), OA (oleic acid), LA (linoleic acid), and LNA (linolenic acid), followed by the chromosome number. For QTL underlying multiple fatty acids across various environments, the name is designated as a composite of FA (fatty acid) followed by the chromosome number
bThe five predominant fatty acids are designated as follows: palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LNA)
cThe three environments are designated as follows: 2009, 2010, and 2011
dChromosome
ePVE indicates the phenotypic variance explained by individual QTL
fGene annotation shows the essential genes involved in fatty acid biosynthesis discovered within the additive QTL intervals
Epistatic QTL for fatty acid contents in soybean seeds
| Traita | Chrb1 | Pc1 (cM) | Marker interval 1 | Chr2 | P2 (cM) | Marker interval 2 | LOD(E)d | PVEe (%) | A1f (%) | A2 g (%) | A1byA2 h (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PA_2011 | 10 | 100 | Gm10_49818–Gm10_38521 | 19 | 65 | Gm19_62762–Gm19_39258 | 5.3 | 10.4 | 0.0001 | −0.0882 | −0.2088 |
| SA_2009 | 6 | 0 | Gm06_27520–Gm06_53504 | 7 | 115 | Gm07_85356–Gm07_21186 | 5.2 | 5.6 | −0.0353 | 0.0005 | −0.1149 |
| SA_2009 | 8 | 75 | Gm08_54434–Gm08_14077 | 12 | 15 | Gm12_67387–Gm12_12747 | 5.1 | 4.7 | −0.0001 | 0.0033 | −0.1036 |
| SA_2011 | 6 | 0 | Gm06_27520–Gm06_53504 | 10 | 90 | Gm10_74377–Gm10_25475 | 5.1 | 7.2 | −0.0141 | 0.0001 | −0.1768 |
| LNA_2011 | 2 | 30 | Gm02_14960–Gm02_48191 | 13 | 140 | Gm13_52660–Gm13_55424 | 5.1 | 3.4 | −0.0011 | 0.0373 | 0.1473 |
aThe five predominant fatty acids are designated as follows: PA (palmitic acid), SA (stearic acid), OA (oleic acid), LA (linoleic acid), and LNA (linolenic acid); the three environments are three continuous years from 2009 to 2011
bChromosome
cPosition in linkage groups in centiMorgans
dLOD score of epistatic QTL
ePhenotypic variance explained by epistatic QTL
fAdditive effect of the first QTL
gAdditive effect of the second QTL
hEpistatic effect between two QTL
Number of QTL in soybean detected using different population sizes and marker densities
| Population size | Marker density | Total QTL number |
|---|---|---|
| 100 | 161 | 54 |
| 100 | 3541 | 149 |
| 150 | 3541 | 193 |
| 200 | 3541 | 316 |