Table 2.
List of significant SNPs associated with dark green color index (DGCI) in three environments, Pine Tree (PT), Rohwer (RH), and Fayetteville (FY), and averaged across all environments (AVG) using the FarmCPU model with the threshold P value of (−Log10 (P) ≥ 3.5; P ≤ 0.0003).
| Locus | SNP | CHR | Position | −Log10 (P) | Allelesa | Allelic effectb | %Changec | Environment |
|---|---|---|---|---|---|---|---|---|
| 1 | ss715579060 | 1 | 3,390,236 | 3.6 | T/C | −0.006 | 1.5 | PT |
| ss715579430 | 1 | 4,267,470 | 3.6 | A/G | 0.003 | 0.7 | PT | |
| 2 | ss715580803 | 1 | 7,659,177 | 4.8 | T/C | 0.049 | 17.5 | RH, PT, AVG |
| 3 | ss715581591 | 2 | 2,458,205 | 3.7 | G/A | 0.011 | 3.9 | FY |
| 4 | ss715583531 | 2 | 51,429,037 | 3.5 | C/T | 0.029 | 10.4 | FY, PT |
| 5 | ss715584636 | 3 | 1,866,786 | 3.5 | C/A | 0.029 | 7.1 | PT |
| 6 | ss715588053 | 4 | 40,982,329 | 4 | C/T | 0.002 | 0.5 | PT |
| ss715588055 | 4 | 40,996,359 | 3.6 | C/A | 0.001 | 0.2 | PT | |
| 7 | ss715591018 | 5 | 34,211,795 | 8.4 | T/C | 0.071 | 17.3 | PT |
| 8 | ss715594787 | 6 | 47,315,808 | 5.6 | C/T | 0.001 | 0.4 | FY, PT |
| ss715594897 | 6 | 47,843,257 | 4.2 | G/T | 0.003 | 1.2 | AVG | |
| ss715594979 | 6 | 48,475,049 | 3.5 | C/T | −0.03 | 7.3 | PT | |
| 9 | ss715598313 | 7 | 5,226,366 | 7.1 | C/T | 0.026 | 9.3 | FY, RH |
| 10 | ss715595750 | 7 | 10,234,156 | 4 | A/G | 0.032 | 7.8 | PT |
| ss715595919 | 7 | 11,956,773 | 3.9 | T/C | 0.051 | 16.5 | RH | |
| 11 | ss715597487 | 7 | 36,972,752 | 4.1 | C/T | 0.061 | 23.5 | AVG |
| 12 | ss715599860 | 8 | 16,790,002 | 3.8 | C/A | 0.014 | 5.4 | AVG |
| 13 | ss715601931 | 8 | 41,504,420 | 4.3 | T/C | 0.05 | 17.9 | RH, AVG |
| 14 | ss715602501 | 8 | 46,430,924 | 3.7 | C/T | 0.053 | 18.9 | FY |
| 15 | ss715604985 | 9 | 4,612,586 | 4.5 | C/T | −0.004 | 1.4 | FY |
| 16 | ss715603006 | 9 | 12,240,541 | 4.2 | C/A | −0.002 | 0.5 | PT |
| 17 | ss715605048 | 9 | 46,800,908 | 3.5 | G/A | 0.025 | 8.9 | RH |
| 18 | ss715606249 | 10 | 3,268,393 | 5.6 | T/C | −0.005 | 1.9 | AVG |
| 19 | ss715608369 | 10 | 6,104,071 | 4.3 | T/C | 0.044 | 15.7 | FY, RH, AVG |
| 20 | ss715608656 | 10 | 9,026,417 | 5.5 | A/G | −0.029 | 10.4 | FY |
| 21 | ss715605790 | 10 | 19,202,280 | 3.5 | T/G | 0.008 | 2.9 | RH |
| ss715605845 | 10 | 21,174,006 | 3.7 | C/T | 0.008 | 2.9 | RH, AVG | |
| 22 | ss715611154 | 11 | 7,846,048 | 6.7 | A/C | 0.04 | 14.3 | FY |
| 23 | ss715613653 | 12 | 896,036 | 6.1 | G/T | −0.003 | 1.1 | FY |
| 24 | ss715613628 | 12 | 8,844,839 | 3.7 | T/G | −0.019 | 4.6 | PT |
| 25 | ss715612526 | 12 | 35,036,533 | 4.2 | G/T | −0.006 | 1.5 | PT |
| 26 | ss715614254 | 13 | 24,708,738 | 4.3 | A/G | 0.009 | 2.2 | PT |
| 27 | ss715614615 | 13 | 27,196,435 | 3.5 | G/A | 0.001 | 0.4 | AVG |
| 28 | ss715615227 | 13 | 30,738,046 | 3.6 | C/A | 0.013 | 5.0 | AVG |
| ss715615232 | 13 | 30,771,524 | 10.3 | A/G | −0.019 | 6.8 | FY | |
| 29 | ss715615582 | 13 | 33,591,479 | 5.6 | T/C | −0.02 | 4.9 | PT |
| 30 | ss715619978 | 14 | 8,185,171 | 4.2 | A/C | 0.035 | 12.5 | FY |
| ss715620046 | 14 | 8,951,951 | 5.6 | A/G | 0.028 | 10.0 | FY | |
| 31 | ss715618272 | 14 | 30,760,829 | 3.6 | C/T | −0.012 | 4.6 | AVG |
| 32 | ss715618984 | 14 | 44,846,030 | 4.7 | C/T | 0.046 | 16.4 | RH |
| ss715618985 | 14 | 44,854,103 | 3.5 | A/G | 0.038 | 14.6 | AVG | |
| 33 | ss715623028 | 15 | 7,522,072 | 3.5 | C/T | −0.015 | 5.4 | FY, PT |
| 34 | ss715622385 | 15 | 47,961,687 | 13.5 | A/G | 0.109 | 26.6 | PT |
| 35 | ss715623939 | 16 | 2,824,073 | 4.9 | G/T | 0.039 | 13.9 | FY, PT,RH |
| ss715624366 | 16 | 3,067,762 | 4.6 | C/A | 0.053 | 12.9 | PT | |
| 36 | ss715625423 | 16 | 7,214,372 | 4.8 | T/C | −0.022 | 7.9 | FY |
| ss715625453 | 16 | 7,364,708 | 3.6 | G/A | 0.02 | 7.7 | AVG | |
| 37 | ss715624500 | 16 | 31,945,745 | 4.9 | G/A | −0.014 | 5.4 | AVG |
| 38 | ss715627213 | 17 | 37,456,348 | 3.7 | G/A | −0.032 | 7.8 | PT |
| ss715627253 | 17 | 37,879,524 | 10.3 | A/G | 0.021 | 5.1 | PT, RH | |
| 39 | ss715631221 | 18 | 51,574,691 | 3.7 | T/C | −0.019 | 6.8 | FY |
| 40 | ss715636405 | 19 | 845,338 | 3.8 | G/A | 0.059 | 22.7 | AVG |
| 41 | ss715635925 | 19 | 49,266,400 | 3.5 | A/C | 0.012 | 2.9 | PT |
| ss715635935 | 19 | 49,341,559 | 3.6 | T/C | 0.003 | 0.7 | PT | |
| ss715635938 | 19 | 49,388,460 | 3.7 | T/G | 0.004 | 1.0 | PT | |
| 42 | ss715637471 | 20 | 33,559,707 | 5 | C/T | −0.037 | 14.2 | AVG |
| 43 | ss715638047 | 20 | 38,616,560 | 8.7 | C/T | −0.045 | 11.0 | PT |
CHR: Glycine max chromosome number.
aAllele: Major/Minor alleles of Single Nucleotide Polymorphism.
bAllelic effect: Difference in mean DGCI between genotypes with the major allele and those with the minor allele. Positive sign indicates that the major allele is associated with increased DGCI. Negative sign indicates that the minor allele is associated with increased DGCI.
c% Change: percentage change in DGCI due to allelic effect.