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Table 1 Peak SNP, beneficial allele and candidate genes associated with unsaturated FA identified by GWAS

From: Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions

Trait Year Chr. Peak SNP Peak SNP position Number of significant SNPs -log (P-value) of Peak SNP R2 (%) of Peak SNP Allele 1 Allele 2 Average trait value of accessions with allele 1 Average trait value of accessions with allele 2 Average value of population IDs of FA related genes Known QTL Reference
Oleic acid 2013 1 rs18996061 18,996,061 1 4.05 16.08 T A 20.28 31.46 20.42    
2013 3 rs6779592 6,779,592 1 4.58 17.65 A C 20.31 29.22 20.42    
2013 6 rs10058820 10,058,820 1 3.87 15.53 G C 20.25 25.68 20.42    
2013 8 rs35562739 35,562,739 1 3.96 15.81 A T 20.26 28.49 20.42    
2013 10 rs30082069 30,082,069 1 4.12 16.27 C T 20.23 23.24 20.42    
2013 14 rs39135305 39,135,305 1 3.73 15.11 C T 20.26 26.03 20.42    
2013 15 rs259146 259,146 2 4.77 18.25 A T 20.23 23.61 20.42    
2013 15 rs18512918 18,512,918 1 4.43 17.19 T C 20.20 24.44 20.42    
2013 15 rs47976104 47,976,104 1 3.80 15.34 G T 20.21 23.96 20.42    
2013 16 rs6724381 6,724,381 1 4.01 15.95 T C 20.33 35.33 20.42    
2013 16 rs36081420 36,081,420 1 5.80 21.44 T G 18.79 20.77 20.42 Glyma.16G200200Glyma.16G003500   
2013 17 rs7339569 7,339,569 1 4.12 16.27 C A 20.26 27.85 20.42    
2013 17 rs10758737 10,758,737 1 3.93 15.71 G T 20.25 27.28 20.42    
2013 20 rs47531251 47,531,251 1 4.67 17.92 G A 20.26 28.44 20.42 Glyma.20G158300Glyma.20G245500   
2014 3 rs35644650 35,644,650 2 5.01 23.46 G T 21.21 25.89 21.42    
2014 6 rs8371282 8,371,282 1 4.24 21.62 G T 21.31 24.07 21.42    
2014 7 rs18395919 18,395,919 1 4.13 21.38 G T 21.27 24.73 21.42 Glyma.07G151300   
2014 8 rs20308530 20,308,530 3 5.14 23.76 A C 21.20 25.89 21.42 Glyma.08G233200   
2014 9 rs34018579 34,018,579 5 3.77 20.56 C A 21.19 24.22 21.42    
2014 15 rs33757180 33,757,180 1 3.68 20.34 C A 21.28 24.35 21.42    
2014 16 rs33751855 33,751,855 1 3.63 20.24 A G 21.36 26.92 21.42    
2014 18 rs5683686 5,683,686 1 3.60 20.16 G T 21.28 27.54 21.42 Glyma.18G062000 Ole 3–2  
2014 19 rs31881460 31,881,460 1 4.45 22.11 G T 21.16 23.78 21.42   Ole 2–2  
2015 1 rs50012108 50,012,108 1 4.39 11.38 T A 19.05 22.51 19.19    
2015 3 rs35817332 35,817,332 2 3.76 9.71 G A 18.95 22.22 19.19    
2015 4 rs29355727 29,355,727 1 5.66 14.79 C T 18.95 27.66 19.19    
2015 6 rs50110801 50,110,801 2 4.05 10.45 T A 18.96 21.08 19.19    
2015 7 rs3937684 3,937,684 1 3.64 9.40 G T 19.07 25.48 19.19 Glyma.07G046200 Ole 7–1  
2015 11 rs24645193 24,645,193 1 4.16 10.75 G T 19.07 21.62 19.19    
2015 12 rs32443263 32,443,263 1 3.96 10.23 G T 18.94 22.04 19.19    
2015 13 rs16802809 16,802,809 2 4.32 11.17 T C 18.88 21.57 19.19 Glyma.13G068600Glyma.13G069100   
2015 15 rs1748955 1,748,955 1 4.58 11.86 C A 19.01 26.82 19.19   Ole 1–4  
2015 16 rs36081420 36,081,420 2 6.29 16.53 T C 19.10 34.81 19.19 Glyma.16G200200Glyma.16G003500   
2015 17 rs35024325 35,024,325 2 3.92 10.12 C A 18.93 22.96 19.19    
2015 18 rs12585602 12,585,602 1 4.09 10.56 T A 19.04 28.45 19.19    
2015 19 rs43329219 43,329,219 1 4.04 10.46 G A 18.90 22.40 19.19   Ole 2–2  
2015 20 rs47531251 47,531,251 4 4.84 12.56 G A 18.96 27.37 19.19 Glyma.20G158300Glyma.20G245500   
Linoleic acid 2013 4 rs29355727 29,355,727 1 4.24 20.13 T C 46.08 55.59 55.34    Reinprecht et al. 2006
2013 13 rs20383965 20,383,965 1 4.40 20.61 T G 48.18 55.57 55.34    Hyten et al. 2004
2013 16 rs4446239 4,446,239 1 3.88 19.13 T G 52.43 55.64 55.34    
2013 17 rs28191708 28,191,708 1 4.12 19.79 C T 54.12 55.81 55.34    
2013 17 rs28979581 28,979,581 1 3.68 18.55 G T 54.18 55.80 55.34    
2013 17 rs34633822 34,633,822 1 4.52 20.96 C T 52.36 55.70 55.34    
2013 17 rs35259287 35,259,287 1 3.85 19.02 T C 51.76 55.53 55.34    Kim et al. 2010
2013 18 rs21573804 21,573,804 1 3.90 19.18 A T 52.35 55.58 55.34    
2013 19 rs577646 577,646 1 3.90 19.18 A G 54.00 55.63 55.34    
2013 20 rs1608443 1,608,443 1 3.81 18.90 G C 54.76 57.56 55.34    
2013 16 rs36081420 36,081,420 1 3.67 18.52 C T 43.10 55.41 55.34 Glyma.16G200200Glyma.16G003500   Diers and Shoemaker 1992
2013 20 rs47531251 47,531,251 1 4.19 20.01 A G 50.96 55.51 55.34 Glyma.20G158300Glyma.20G245500   
2014 1 rs49504957 49,504,957 1 3.90 19.01 G T 54.09 55.35 54.26    
2014 2 rs4953186 4,953,186 1 4.23 18.40 G T 54.11 55.78 54.26    
2014 3 rs6481810 6,481,810 1 4.11 18.10 C T 53.16 54.43 54.26    Hyten et al. 2004
2014 8 rs39589269 39,589,269 3 3.82 17.42 G T 54.15 55.47 54.26    
2014 9 rs20595231 20,595,231 1 3.70 17.14 T C 51.27 54.31 54.26    
2014 10 rs10278177 10,278,177 1 3.70 17.14 A T 51.93 54.41 54.26    
2014 13 rs31318746 31,318,746 1 3.70 17.13 T C 50.54 54.40 54.26   Linole 2–1  
2014 15 rs1064298 1,064,298 1 3.65 17.02 C T 54.07 55.64 54.26    
2014 16 rs18741800 18,741,800 1 3.60 16.90 A C 52.28 54.37 54.26    
2015 1 rs50012108 50,012,108 3 6.40 17.63 A T 53.42 56.38 56.26    
2015 2 rs7975863 7,975,863 1 5.16 14.25 T C 53.36 56.44 56.26    Hyten et al. 2004
2015 3 rs35817332 35,817,332 1 4.80 13.29 A G 53.24 56.48 56.26    
2015 4 rs29355727 29,355,727 1 4.73 13.11 T C 49.13 56.93 56.26    
2015 5 rs26200085 26,200,085 2 4.67 12.70 C T 52.23 56.33 56.26    
2015 6 rs50110801 50,110,801 3 4.52 12.56 A T 50.03 56.46 56.26    
2015 7 rs22961030 22,961,030 2 4.41 12.28 T C 53.64 56.41 56.26    
2015 8 rs35562739 35,562,739 1 4.26 11.87 T A 49.76 56.37 56.26    
2015 9 rs30794068 30,794,068 1 4.26 11.86 T G 53.05 56.36 56.26    
2015 11 rs6577617 6,577,617 1 4.24 11.82 T G 52.42 56.39 56.26    
2015 13 rs16802831 16,802,831 2 4.20 11.72 T C 54.59 56.48 56.26   Linole 6–9  
2015 14 rs39135305 39,135,305 1 4.16 11.62 T C 52.44 56.41 56.26   Linole 2–1  
2015 15 rs35324780 35,324,780 2 3.97 11.12 T C 52.96 56.43 56.26    
2015 16 rs36081420 36,081,420 4 3.83 10.43 C T 44.07 56.33 56.26 Glyma.16G200200Glyma.16G003500   
2015 17 rs34339550 34,339,550 1 3.68 10.40 G A 49.88 56.33 56.26    Bachlava et al. 2009
2015 18 rs39638216 39,638,216 1 3.67 10.37 T G 52.95 56.38 56.26    Hyten et al. 2004
2015 19 rs14807896 14,807,896 1 3.59 10.16 T T 53.69 56.36 56.26    
2015 20 rs47531251 47,531,251 1 3.58 10.14 A G 50.47 56.36 56.26 Glyma.20G158300Glyma.20G245500   
Linolenic acid 2013 1 rs37146219 37,146,219 1 3.68 10.98 T C 6.69 8.82 8.73    
2013 16 rs3989930 3,989,930 1 4.33 13.01 G T 8.59 10.37 8.73    
2013 16 rs15449450 15,449,450 1 3.81 11.39 A G 8.23 9.05 8.73    
2013 20 rs3008708 3,008,708 1 3.63 10.85 G A 5.01 8.83 8.73    
2014 2 rs35057707 35,057,707 23 3.66 30.58 G A 8.09 10.52 8.13    
2014 4 rs48837377 48,837,377 1 3.77 30.79 T C 7.26 8.21 8.13    
2014 7 rs43158730 43,158,730 1 3.60 30.44 C T 8.10 10.40 8.13 Glyma.07G254500   
2014 10 rs41662636 41,662,636 1 4.16 31.58 G T 8.00 10.04 8.13    
2014 12 rs16701034 16,701,034 1 3.81 30.88 G A 8.05 9.13 8.13    
2014 16 rs5443771 5,443,771 3 4.01 31.27 G T 8.02 8.27 8.13    
2014 18 rs52833743 52,833,743 4 3.85 30.94 A C 8.02 8.79 8.13   Linolen 4–2 Panthee et al. 2006
2014 19 rs21750320 21,750,320 1 3.83 30.90 G C 8.05 9.66 8.13    
2015 13 rs14900419 14,900,419 1 3.98 10.27 A T 9.10 10.93 9.19    
2015 14 rs45949815 45,949,815 4 3.81 9.83 T A 9.11 11.59 9.19 Glyma.14G194300   
2015 17 rs35024325 35,024,325 1 4.06 10.48 C T 9.12 10.62 9.19    
2015 19 rs13718585 13,718,585 1 3.94 10.17 A C 7.97 9.27 9.19    
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