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