Table 3.
Details of 49 pleiotropic SNPs of agronomic and yield-related traits detected from genome-wide association study (GWAS).
| SNP name | Chr | Allele | Number | Phenotype | Traits | Near locus previously reported in the same chromosome | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bn-A02-p8191099 | A02 | AA | AC | CC | 15 | 20 | 83 | 186.0 | 182.3 | 183.0 | DTF | New |
| 193.8 | 189.4 | 190.7 | DTSD | |||||||||
| Bn-A02-p8284992 | A02 | AA | AG | GG | 15 | 18 | 84 | 186.0 | 181.5 | 183.2 | DTF | New |
| 193.8 | 189.1 | 190.8 | DTSD | |||||||||
| Bn-A02-p8323616 | A02 | AA | AC | CC | 16 | 19 | 84 | 185.8 | 181.8 | 183.1 | DTF | New |
| 193.5 | 189.0 | 190.8 | DTSD | |||||||||
| Bn-A02-p8440451 | A02 | AA | AG | GG | 24 | 31 | 54 | 185.1 | 181.3 | 183.5 | DTF | New |
| 192.7 | 188.9 | 191.1 | DTSD | |||||||||
| Bn-A02-p8660632 | A02 | AA | AG | GG | 18 | 25 | 76 | 185.4 | 182.1 | 184.4 | DTF |
BnaA02g12130D, BnaA02g12260D
(Zheng et al., 2017) |
| 186.8 | 189.5 | 191.6 | DTSD | |||||||||
| Bn-A02-p8934537 | A02 | AA | AG | GG | 18 | 20 | 81 | 185.2 | 182.5 | 183.0 | DTF | Bn-A02-p3539297 (Xu et al., 2015) |
| 193.1 | 190.0 | 190.6 | DTSD | |||||||||
| Bn-A02-p8999771 | A02 | AA | AC | CC | 19 | 21 | 79 | 185.1 | 182.4 | 183.0 | DTF | Bn-A02-p3539297 (Xu et al., 2015) |
| 192.9 | 189.8 | 190.6 | DTSD | |||||||||
| Bn-A02-p9000921 | A02 | AA | AG | GG | 79 | 21 | 19 | 183.0 | 182.4 | 185.1 | DTF | Bn-A02-p3539297 (Xu et al., 2015) |
| 190.6 | 189.8 | 192.9 | DTSD | |||||||||
| Bn-A02-p8190375 | A02 | AA | AG | GG | 15 | 20 | 83 | 168.0 | 182.3 | 183.0 | DTF | New |
| 193.8 | 189.4 | 190.7 | DTSD | |||||||||
| Bn-A10-p13390065 | A10 | AA | AG | GG | 6 | 14 | 98 | 179.5 | 178.96 | 184.0 | DTF | BnaA10g18420D, BnaA10g18480D, BnaA10g22080D, BnaA10g24300D (Helal et al., 2021) |
| 187.3 | 187.26 | 191.5 | DTSD | |||||||||
| Bn-A10-p15668415 | A10 | AA | AG | GG | 12 | 17 | 89 | 179.8 | 180.5 | 184.1 | DTF | New |
| 187.6 | 188.7 | 191.7 | DTSD | |||||||||
| Bn-A01-p17377721 | A01 | AA | AC | CC | 4 | 25 | 88 | 187.0 | 190.7 | 191.2 | DTSD | New |
| 121.0 | 116.2 | 118.2 | PH | |||||||||
| Bn-A01-p27079797 | A01 | AA | AG | GG | 33 | 83 | 2 | 192.0 | 190.4 | 191.9 | DTSD | New |
| 117.8 | 118.1 | 121.3 | PH | |||||||||
| Bn-A01-p21758046 | A01 | AA | AG | GG | 51 | 42 | 25 | 191.2 | 190.4 | 191.0 | DTSD | BnaA01g26410D-BnaA01g26530D (Lu et al., 2017) |
| 118.3 | 117.6 | 117.7 | PH | |||||||||
| 9.5 | 8.7 | 9.1 | HI | |||||||||
| Bn-A01-p5715141 | A01 | AA | AG | GG | 27 | 28 | 62 | 191.9 | 190.7 | 190.5 | DTSD | Bna.QRT3 (BnaA01g10390D) (Lu et al., 2017) |
| 118.4 | 117.5 | 117.7 | PH | |||||||||
| 9.3 | 8.8 | 9.1 | HI | |||||||||
| Bn-A01-p6678914 | A01 | AA | AG | GG | 93 | 16 | 6 | 266.8 | 266.5 | 266.3 | DTR | Bn-A01-p7430311 (Sun et al., 2016b) |
| 117.8 | 116.8 | 118.2 | PH | |||||||||
| Bn-A01-p9203096 | A01 | AA | AG | GG | 8 | 19 | 90 | 265.6 | 266.1 | 266.8 | DTR | New |
| 118.1 | 117.8 | 117.9 | PH | |||||||||
| Bn-scaff_18936_1-p102755 | C03 | AA | AG | GG | 75 | 27 | 13 | 266.8 | 266.5 | 266.4 | DTR | New |
| 118.2 | 116.6 | 117.1 | PH | |||||||||
| Bn-scaff_18936_1-p240670 | C03 | AA | AG | GG | 16 | 29 | 72 | 266.4 | 266.4 | 266.8 | DTR | New |
| 116.9 | 117.4 | 118.3 | PH | |||||||||
| Bn-scaff_18936_1-p269153 | C03 | AA | AC | CC | 95 | 19 | 4 | 266.7 | 266.4 | 267.7 | DTR | New |
| 118.3 | 116.6 | 113.7 | PH | |||||||||
| Bn-scaff_18936_1-p472353 | C03 | AA | AG | GG | 17 | 36 | 65 | 266.9 | 266.4 | 266.7 | DTR | New |
| 116.8 | 118.2 | 118.0 | PH | |||||||||
| Bn-scaff_18936_1-p93643 | C03 | AA | AG | GG | 13 | 27 | 76 | 266.4 | 266.5 | 266.8 | DTR | New |
| 117.1 | 117.0 | 118.2 | PH | |||||||||
| Bn-scaff_18936_1-p97644 | C03 | AA | AC | CC | 76 | 28 | 13 | 266.8 | 266.5 | 266.4 | DTR | New |
| 118.2 | 117.0 | 117.1 | PH | |||||||||
| Bn-scaff_18936_1-p274133 | C03 | AA | AG | GG | 5 | 17 | 95 | 267.3 | 266.4 | 266.7 | DTR | New |
| 114.4 | 116.5 | 118.3 | PH | |||||||||
| Bn-A01-p7619726 | A01 | AA | AG | GG | 102 | 12 | 5 | 265.6 | 265.7 | 266.8 | DTR | New |
| 117.8 | 117.0 | 122.0 | PH | |||||||||
| 9.1 | 9.0 | 9.8 | HI | |||||||||
| Bn-A01-p8014995 | A01 | AA | AG | GG | 4 | 9 | 104 | 266.9 | 265.6 | 266.7 | DTR | BnvaA0107152286 (Han et al., 2022) |
| 118.7 | 115.6 | 118.0 | PH | |||||||||
| 9.1 | 8.7 | 9.2 | HI | |||||||||
| Bn-scaff_18936_1-p439378 | C03 | AA | AG | GG | 5 | 17 | 96 | 267.3 | 265.8 | 266.8 | DTR | New |
| 114.4 | 117.1 | 118.2 | PH | |||||||||
| 1,762.8 | 1,875.1 | 1,905.8 | PW | |||||||||
| Bn-scaff_18936_1-p440619 | C03 | AA | AG | GG | 5 | 17 | 96 | 266.8 | 265.8 | 267.3 | DTR | New |
| 114.4 | 117.1 | 118.2 | PH | |||||||||
| 1,762.8 | 1,875.1 | 1,905.8 | PW | |||||||||
| Bn-scaff_18936_1-p559490 | C03 | AA | AC | CC | 3 | 20 | 95 | 267.4 | 265.9 | 266.8 | DTR | New |
| 112.8 | 116.3 | 118.4 | PH | |||||||||
| 1,539.0 | 1,878.7 | 1908.4 | PW | |||||||||
| Bn-scaff_18936_1-p610540 | C03 | AA | AG | GG | 94 | 20 | 4 | 267.8 | 266.1 | 266.7 | DTR | New |
| 118.4 | 116.2 | 114.4 | PH | |||||||||
| 1,911.3 | 1,867.0 | 1662.0 | PW | |||||||||
| Bn-scaff_18936_1-p611810 | C03 | AA | AC | CC | 94 | 20 | 4 | 267.8 | 266.1 | 266.7 | DTR | New |
| 118.4 | 116.2 | 114.4 | PH | |||||||||
| 1,911.3 | 1,867.0 | 1662.0 | PW | |||||||||
| Bn-scaff_18936_1-p618378 | C03 | AA | AG | GG | 4 | 20 | 94 | 267.8 | 266.1 | 266.7 | DTR | BnaC03g45540D (Zhang et al., 2023a) |
| 114.4 | 116.2 | 118.4 | PH | |||||||||
| 1,662.0 | 1,867.0 | 1911.3 | PW | |||||||||
| Bn-scaff_18936_1-p622547 | C03 | AA | AC | CC | 94 | 20 | 4 | 266.7 | 266.1 | 267.8 | DTR | New |
| 118.4 | 116.2 | 114.4 | PH | |||||||||
| 1,911.3 | 1,867.0 | 1662.0 | PW | |||||||||
| Bn-scaff_18936_1-p643990 | C03 | AA | AG | GG | 94 | 20 | 4 | 266.7 | 266.1 | 267.8 | DTR | New |
| 118.4 | 116.2 | 114.4 | PH | |||||||||
| 1,911.3 | 1,867.0 | 1662.0 | PW | |||||||||
| Bn-A08-p12555227 | A08 | AA | AG | GG | 11 | 20 | 86 | 1,936.4 | 1,903.4 | 1882.5 | PW | New |
| 197.6 | 177.1 | 174.9 | SWPP | |||||||||
| 9.9 | 9.0 | 9.0 | HI | |||||||||
| 2,507.1 | 2,172.5 | 2196.8 | SY | |||||||||
| Bn-A08-p15782077 | A08 | AA | AG | GG | 70 | 29 | 20 | 1,822.2 | 1954.1 | 2041.1 | PW | New |
| 168.1 | 182.7 | 204.7 | SWPP | |||||||||
| 9.1 | 9.0 | 9.5 | HI | |||||||||
| 2,127.5 | 2,255.8 | 2520.0 | SY | |||||||||
| Bn-A08-p15782229 | A08 | AA | AG | GG | 70 | 28 | 20 | 1,822.2 | 1,947.9 | 2041.1 | PW | New |
| 168.1 | 182.1 | 204.7 | SWPP | |||||||||
| 9.1 | 9.0 | 9.5 | HI | |||||||||
| 2,127.5 | 2,234.1 | 2520.0 | SY | |||||||||
| Bn-A08-p12556455 | A08 | AA | AG | GG | 88 | 10 | 11 | 1,887.5 | 1,832.9 | 2098.3 | PW | New |
| 175.0 | 179.7 | 264.3 | SWPP | |||||||||
| 2,201.0 | 2,151.8 | 3177.8 | SY | |||||||||
| Bn-A08-p13626189 | A08 | AA | AG | GG | 72 | 31 | 15 | 1,890.8 | 1,870.0 | 1932.4 | PW | New |
| 175.3 | 175.7 | 189.7 | SWPP | |||||||||
| 2,191.0 | 2,198.2 | 2368.3 | SY | |||||||||
| Bn-A08-p13626982 | A08 | AA | AG | GG | 16 | 32 | 70 | 1,906.0 | 1,895.2 | 1885.0 | PW | New |
| 188.7 | 175.6 | 175.4 | SWPP | |||||||||
| 2,339.1 | 2,190.0 | 2198.8 | SY | |||||||||
| Bn-A08-p13638847 | A08 | AA | AC | CC | 69 | 33 | 16 | 1,889.1 | 1,886.3 | 1906.0 | PW | New |
| 175.8 | 174.8 | 188.7 | SWPP | |||||||||
| 2,201.5 | 2,184.7 | 2339.1 | SY | |||||||||
| Bn-A08-p13670107 | A08 | AA | AG | GG | 15 | 28 | 72 | 1,932.4 | 1,880.5 | 1890.8 | PW | New |
| 189.7 | 176.0 | 175.3 | SWPP | |||||||||
| 2,368.3 | 2,217.4 | 2191.0 | SY | |||||||||
| Bn-A08-p14538807 | A08 | AA | AG | GG | 87 | 19 | 8 | 1,873.6 | 1,955.0 | 1930.9 | PW | New |
| 171.6 | 193.4 | 185.4 | SWPP | |||||||||
| 2,163.2 | 2,330.7 | 2371.0 | SY | |||||||||
| Bn-A08-p15994149 | A08 | AA | AC | CC | 29 | 25 | 63 | 1,988.2 | 1,901.6 | 1839.1 | PW |
Bna.BBX20 (BnaA08g16780D, AT4G39070) (Lu et al., 2017) Bna.BBX15 (BnaA08g19420D) (Lu et al., 2017) |
| 198.4 | 178.7 | 167.3 | SWPP | |||||||||
| 2,432.6 | 2,196.9 | 2132.8 | SY | |||||||||
| Bn-scaff_19208_1-p78898 | C04 | AA | AG | GG | 66 | 32 | 20 | 1,883.9 | 1,828.8 | 2002.8 | PW | New |
| 178.4 | 161.4 | 200.9 | SWPP | |||||||||
| 2,196.2 | 2,098.2 | 2489.5 | SY | |||||||||
| Bn-scaff_19208_1-p82535 | C04 | AA | AG | GG | 66 | 31 | 20 | 1,883.9 | 1,827.1 | 2002.8 | PW | New |
| 178.4 | 161.5 | 200.9 | SWPP | |||||||||
| 2,196.2 | 2,103.9 | 2489.5 | SY | |||||||||
| Bn-scaff_19208_1-p93814 | C04 | AA | AC | CC | 66 | 31 | 21 | 1,883.9 | 1,827.1 | 2002.8 | PW | New |
| 178.4 | 161.5 | 200.9 | SWPP | |||||||||
| 2,196.2 | 2,103.9 | 2489.5 | SY | |||||||||
| Bn-scaff_19208_1-p94498 | C04 | AA | AC | CC | 66 | 32 | 21 | 1,883.9 | 1,828.8 | 2002.8 | PW | New |
| 178.4 | 161.4 | 200.9 | SWPP | |||||||||
| 2,196.2 | 2,098.2 | 2489.5 | SY | |||||||||
| Bn-scaff_19208_1-p94501 | C04 | AA | AG | GG | 20 | 31 | 66 | 2,002.8 | 1,827.1 | 1883.9 | PW | New |
| 200.9 | 161.5 | 178.4 | SWPP | |||||||||
| 2,489.5 | 2,103.9 | 2196.2 | SY | |||||||||
DTF, DTSD, DTR, PH, PW, SWPP, HI, and SY are the abbreviations of days to flowering, days to silique development, days to ripening, plant height, plant weight, seed weight/plant, harvest index, and seed yield, respectively.