Table 3 Significant SNPs associated with leaf chlorophyll content for plants without SCN infestation, leaf chlorophyll content for SCN-infested plants, decrease in leaf chlorophyll content due to SCN, genes within 10 kb genomic region harboring the SNPs, and functional annotation of the genes
Trait | SNP_ID | Chromosome | Position (bp) | MAF (%) | LOD (−log10(p-value))a | Gene nameb | Functional annotation |
|---|---|---|---|---|---|---|---|
Leaf chlorophyll content undernon-SCN infestation | Gm04_2,574,201_T_G | 4 | 2,574,201 | 14.11 | 2.54 | Glyma.04 g032100 | Predicted membrane protein |
Gm04_7,672,403_A_G | 4 | 7,672,403 | 39.88 | 3.99 | Glyma.04 g088800 | Serine/threonine protein kinase | |
Gm05_40,299,923_A_G | 5 | 40,299,923 | 7.1 | 5.65 | Glyma.05 g224000 | Aspartyl/lysyl-trna synthetase | |
Gm06_11,948,808_G_A | 6 | 11,948,808 | 31.25 | 6.16 | Glyma.06 g146400 | 4-alpha-glucanotransferase | |
Gm06_16,792,113_T_C | 6 | 16,792,113 | 6.62 | 8.63 | Glyma.06 g191200 | IQ-domain 31 | |
Gm06_43,980,786_G_A | 6 | 43,980,786 | 6.02 | 3.31 | NAc | NA | |
Gm06_47,439,414_C_T | 6 | 47,439,414 | 35.58 | 5.80 | Glyma.06 g285800 | Vascular plant one zinc finger protein | |
Gm07_3,953,270_T_C | 7 | 3,953,270 | 38.51 | 2.57 | Glyma.07 g047100 | Calcineurin-like metallo-phosphoesterase superfamily protein | |
Gm07_3,990,308_A_G | 7 | 3,990,308 | 37.42 | 2.52 | Glyma.07 g047600 | Chlorophyll A-B binding protein | |
Gm10_4,458,104_G_A | 10 | 4,458,104 | 30.62 | 2.51 | Glyma.10 g049600 | ROP interactive partner 3 | |
Gm10_41,610,215_C_T | 10 | 41,610,215 | 17.58 | 4.88 | Glyma.10 g183000 | Phytoene dehydrogenase | |
Gm11_3,641,716_A_C | 11 | 3,641,716 | 26.41 | 2.87 | Glyma.11 g048600 | Formin-related | |
Gm11_4,702,578_C_A | 11 | 4,702,578 | 25.95 | 2.89 | Glyma.11 g062300 | Homeobox protein transcription factors | |
Gm11_15,558,504_T_C | 11 | 15,558,504 | 21.81 | 4.21 | Glyma.11 g164300 | Serine/threonine protein phosphatase | |
Gm11_37,978,746_G_T | 11 | 37,978,746 | 11.11 | 3.82 | NA | NA | |
Gm11_38,183,607_G_A | 11 | 38,183,607 | 13.09 | 3.04 | LOC106795218 | NA | |
Gm12_1,460,019_T_C | 12 | 1,460,019 | 12.65 | 3.68 | Glyma.12 g020500 | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | |
Gm13_38,032,737_G_A | 13 | 38,032,737 | 38.6 | 3.40 | Glyma.13 g279200 | Asparagine synthetase | |
Gm19_42,195,616_G_A | 19 | 42,195,616 | 28.05 | 2.72 | Glyma.19 g161200 | Uridine kinase | |
Gm19_48,074,289_A_C | 19 | 48,074,289 | 40 | 6.35 | Glyma.19 g229800 | Karyopherin (importin) alpha | |
Gm20_1,621,036_T_C | 20 | 1,621,036 | 26.06 | 7.90 | Glyma.20 g017100 | Sulfate transporter | |
Gm20_33,580,029_C_T | 20 | 33,580,029 | 16.97 | 5.70 | Glyma.20 g092200 | 40S ribosomal protein | |
Leaf chlorophyll conent for SCN-infested plants | Gm02_207,506_A_G | 2 | 207,506 | 4.76 | 3.09 | Glyma.02 g001700 | Protein of unknown function |
Gm02_2,246,479_A_G | 2 | 2,246,479 | 33.33 | 4.82 | Glyma.02 g025200 | Protein of unknown function | |
Gm03_36,634,361_G_A | 3 | 36,634,361 | 5.36 | 2.64 | Glyma.03 g151400 | NA | |
Gm05_39,995,603_C_T | 5 | 39,995,603 | 7.74 | 4.27 | Glyma.05 g220300 | Formin binding protein and related proteins | |
Gm06_50,593,128_T_G | 6 | 50,593,128 | 22.84 | 9.01 | Glyma.06 g317100 | Predicted transporter | |
Gm07_11,956,773_T_C | 7 | 11,956,773 | 34.18 | 2.54 | Glyma.07 g114300 | Ethylene-responsive element binding factor 13 | |
Gm10_6,196,864_T_G | 10 | 6,196,864 | 34.18 | 4.13 | Glyma.10 g064900 | Sequence-specific DNA binding transcription factors | |
Gm13_39,378,998_G_A | 13 | 39,378,998 | 5.81 | 3.97 | Glyma.13 g294200 | Putative signaling peptide similar to TAX1 | |
Gm14_49,357,738_A_G | 14 | 49,357,738 | 6.55 | 2.52 | NA | NA | |
Gm15_43,797,502_G_T | 15 | 43,797,502 | 23.75 | 5.94 | Glyma.15 g233100 | Leucine-rich repeat-containing protein | |
Gm18_1,620,585_T_C | 18 | 1,620,585 | 9.2 | 5.15 | Glyma.18 g022100 | BTB/POZ domain-containing protein | |
Gm19_38,917,571_A_G | 19 | 38,917,571 | 19.02 | 2.60 | Glyma.19 g129700 | F-box family protein | |
Gm19_39,863,286_G_T | 19 | 39,863,286 | 24.69 | 5.02 | Glyma.19 g137300 | Det1 complexing ubiquitin ligase | |
Gm19_48,074,289_A_C | 19 | 48,074,289 | 40 | 4.39 | Glyma.19 g229800 | Karyopherin (importin) alpha | |
Decrease in chlorophyll content | Gm02_6,340,233_C_A | 2 | 6,340,233 | 4.19 | 2.83 | Glyma.02 g072300 | Methyltransferase-like protein |
Gm03_3,334,303_C_A | 3 | 3,334,303 | 35.03 | 4.47 | Glyma.03 g029900 | Cytochrome P450 | |
Gm03_39,574,966_T_C | 3 | 39,574,966 | 27.85 | 2.67 | Glyma.03 g183700 | NA | |
Gm04_5,172,181_A_G | 4 | 5,172,181 | 23.27 | 5.50 | Glyma.04 g062600 | NA | |
Gm06_16,315,206_A_G | 6 | 16,315,206 | 39.26 | 5.26 | Glyma.06 g187300 | Lipase (class 3) | |
Gm06_50,593,128_T_G | 6 | 50,593,128 | 22.84 | 7.22 | Glyma.06 g317100 | Predicted transporter | |
Gm07_35,908,169_T_C | 7 | 35,908,169 | 17.5 | 6.37 | Glyma.07 g191600 | Secretory carrier membrane protein | |
Gm08_9,848,168_T_C | 8 | 9,848,168 | 4.71 | 2.69 | Glyma.08 g127700 | Phosphatidylinositol-4-phosphate 5-kinase | |
Gm08_10,116,360_C_T | 8 | 10,116,360 | 5.32 | 2.75 | Glyma.08 g132000 | Protein of unknown function | |
Gm08_11,501,419_A_C | 8 | 11,501,419 | 5.36 | 5.70 | Glyma.08 g149800 | Iron/ascorbate family oxidoreductases | |
Gm08_43,787,988_G_A | 8 | 43,787,988 | 12.05 | 2.60 | Glyma.08 g318600 | NA | |
Gm09_6,664,095_T_C | 9 | 6,664,095 | 38.22 | 2.50 | LOC106794327 | NA | |
Gm13_5,211,326_T_C | 13 | 5,211,326 | 12.12 | 2.90 | NA | NA | |
Gm13_39,378,998_G_A | 13 | 39,378,998 | 5.81 | 10.33 | Glyma.13 g294200 | Putative signaling peptide similar to TAX1 | |
Gm15_43,797,502_G_T | 15 | 43,797,502 | 23.75 | 4.79 | Glyma.15 g233100 | Leucine-rich repeat-containing protein | |
Gm18_1,427,298_G_T | 18 | 1,427,298 | 5.29 | 3.29 | Glyma.18 g019300 | Copper transport protein ATOX1-related |