Table 4.
Significant novel SNPs identified from this study associated with CW for the 12 environments, Columbia (CO18), Maricopa (MC18 and 19), Pine Tree (PT18 and 19), and Rohwer (RH18) under IR and DR treatments, and for CW scores averaged across site-years for irrigated (Ave_IR) and drought (Ave_DR) treatments, and averaged across all environments (AAE) at the significant threshold P-value [–Log10 (P) ≥ 3.5; P ≤ 0.0003].
| Locus | SNP_ID | CHR | Position | –Log10 (P) | Allelea | Allelic effectb | Env | Common ENVc |
|---|---|---|---|---|---|---|---|---|
| Irrigated (IR) | ||||||||
| 1 | ss715579037 | 1 | 3318347 | 9.5 | G/A | −5.0 | RH18IR | AAE/Ave_IR/PT19DR/Ave_DR/PT18IR/CO18DR |
| 2 | ss715582188 | 2 | 4076323 | 4.3 | T/C | −3.6 | CO18IR | PT19DR/AAE |
| 3 | ss715583267 | 2 | 4909353 | 5.2 | T/C | 0.3 | CO18IR | |
| 4 | ss715583177 | 2 | 48286454 | 4.3 | C/T | −2.4 | PT19IR | |
| 5 | ss715589211 | 4 | 6979721 | 4.3 | A/G | −0.2 | RH18IR | AAE |
| 6 | ss715599166 | 8 | 10308372 | 3.9 | A/G | 0.4 | PT19IR | |
| 7 | ss715601604 | 8 | 38203165 | 9.2 | C/T | −3.5 | CO18IR | PT19DR |
| 8 | ss715603362 | 9 | 24238724 | 3.9 | T/C | −0.8 | MC18IR | |
| 9 | ss715603732 | 9 | 35730340 | 4.7 | C/T | −1.2 | PT19IR | |
| 10 | ss715604821 | 9 | 44523441 | 3.5 | G/A | <0.1 | CO18IR | |
| 11 | ss715609311 | 11 | 1617883 | 3.7 | C/T | −0.6 | MC18IR | |
| 12 | ss715613244 | 12 | 6151953 | 4.5 | C/T | 1.2 | PT19IR | AAE/RH18IR/RH18DR |
| 13 | ss715612970 | 12 | 39465759 | 4.9 | C/T | 0.7 | RH18IR | |
| 14 | ss715616824 | 13 | 5766019 | 4.1 | G/T | 1.3 | RH18IR | PT18IR |
| 15 | ss715614097 | 13 | 22446130 | 7.9 | T/C | −1.5 | PT19IR | |
| 16 | ss715620897 | 15 | 15081653 | 6.0 | T/C | −2.2 | CO18IR | AAE |
| 17 | ss715621830 | 15 | 40160334 | 4.1 | G/A | −0.8 | MC18IR | |
| 18 | ss715621869 | 15 | 41427016 | 4.0 | A/G | −0.9 | MC18IR | |
| 19 | ss715621873 | 15 | 41570902 | 4.0 | T/C | −0.8 | MC18IR | |
| 20 | ss715621877 | 15 | 41711821 | 4.0 | A/G | −0.8 | MC18IR | |
| 21 | ss715623751 | 16 | 2320279 | 5.0 | C/T | −0.9 | MC18IR | |
| 22 | ss715626698 | 17 | 311571 | 8.8 | C/A | −6.5 | CO18IR | Ave_IR/PT19IR/CO18DR/PT19DR/AAE/PT18IR |
| 23 | ss715632608 | 18 | 7138173 | 3.9 | C/T | −4.1 | PT18IR | RH18DR/PT19DR |
| 24 | ss715633673 | 19 | 30020611 | 5.4 | C/A | −7.7 | CO18IR | CO18DR/AAE/Ave_IR/PT19DR/PT18IR/Ave_DR/MC18IR |
| 25 | ss715636922 | 20 | 20831971 | 4.2 | A/C | −0.9 | MC18IR | PT18DR |
| ss715636931 | 20 | 21123471 | 4.2 | G/A | −0.9 | MC18IR | PT18DR | |
| ss715636938 | 20 | 21317230 | 4.1 | T/C | −0.8 | MC18IR | ||
| 26 | ss715636958 | 20 | 22132466 | 4.1 | C/T | −0.8 | MC18IR | PT19IR |
| 27 | ss715637018 | 20 | 23693436 | 3.5 | C/A | −0.8 | MC18IR | |
| ss715637021 | 20 | 23754062 | 3.8 | A/G | −0.9 | MC18IR | PT18DR | |
| ss715637031 | 20 | 23941995 | 3.8 | G/A | −0.9 | MC18IR | PT18DR | |
| ss715637033 | 20 | 23971966 | 3.8 | A/C | −0.9 | MC18IR | PT18DR | |
| ss715637037 | 20 | 23996839 | 3.8 | T/C | −0.9 | MC18IR | PT18DR | |
| ss715637047 | 20 | 24131410 | 3.8 | C/T | −0.9 | MC18IR | PT18DR | |
| ss715637052 | 20 | 24202089 | 3.8 | A/G | −0.9 | MC18IR | PT18DR | |
| ss715637062 | 20 | 24571057 | 3.8 | C/T | −0.9 | MC18IR | PT18DR | |
| 28 | ss715637093 | 20 | 25746345 | 3.8 | C/T | −0.9 | MC18IR | PT18DR |
| Drought (DR) | ||||||||
| 1 | ss715578838 | 1 | 2675653 | 4.5 | C/T | −3.1 | RH18DR | MC18IR/RH18IR/PT18IR |
| ss715578860 | 1 | 2747136 | 5.0 | A/C | −2.2 | MC19DR | PT19DR | |
| 2 | ss715578432 | 1 | 11047155 | 4.8 | T/C | −4.1 | MC18DR | MC18IR/PT18IR/PT19DR |
| 3 | ss715578452 | 1 | 12231584 | 4.4 | G/A | −7.0 | PT19DR | PT18IR/MC18IR |
| 4 | ss715586000 | 3 | 40950687 | 5.3 | G/T | <0.1 | CO18DR | |
| 5 | ss715586264 | 3 | 43838447 | 4.1 | C/T | −6.2 | PT19DR | CO18DR/PT18IR |
| ss715586270 | 3 | 43992877 | 3.9 | A/C | −5.8 | PT19DR | PT18IR | |
| ss715586272 | 3 | 44011106 | 3.7 | G/T | −5.5 | PT19DR | CO18DR/PT18IR | |
| 6 | ss715589774 | 5 | 1068534 | 4.1 | C/T | −8.8 | CO18DR | PT19DR/PT18IR |
| 7 | ss715598333 | 7 | 5382683 | 4.1 | T/C | 1.1 | RH18DR | |
| 8 | ss715599966 | 8 | 17718826 | 7.9 | A/G | 1.3 | CO18DR | MC19IR |
| 9 | ss715601844 | 8 | 40735987 | 3.6 | T/C | −1.1 | CO18DR | CO18IR/RH18IR |
| ss715601899 | 8 | 41163228 | 4.1 | C/A | −5.0 | CO18DR | Ave_DR/CO18IR | |
| ss715601932 | 8 | 41533120 | 3.9 | A/G | −4.4 | CO18DR | AAE/Ave_DR | |
| 10 | ss715603337 | 9 | 22917889 | 6.4 | G/A | −5.4 | CO18DR | MC18IR/PT18DR/AAE |
| 11 | ss715604653 | 9 | 42974503 | 4.1 | G/T | −1.6 | RH18DR | Ave_DR |
| 12 | ss715604845 | 9 | 44799336 | 5.9 | T/C | 4.2 | MC19DR | CO18IR |
| 13 | ss715605772 | 10 | 18658872 | 10.2 | A/G | 1.2 | PT18DR | MC19DR/PT18IR/MC19IR/Ave_IR |
| 14 | ss715607829 | 10 | 47946637 | 4.4 | C/A | 0.2 | MC18DR | |
| 15 | ss715607984 | 10 | 48811357 | 5.1 | G/A | −1.1 | PT18DR | |
| 16 | ss715609728 | 11 | 24299777 | 4.7 | A/G | −3.1 | PT18DR | PT18IR |
| 17 | ss715611451 | 12 | 12635492 | 5.4 | A/G | −3.2 | MC18DR | |
| 18 | ss715612366 | 12 | 34102452 | 4.2 | A/G | 0.5 | PT18DR | PT18IR |
| 19 | ss715617261 | 13 | 852961 | 4.7 | T/C | −2.9 | MC19DR | |
| 20 | ss715616860 | 13 | 5993892 | 4.1 | T/C | −0.6 | PT18DR | CO18IR/MC19DR/AAE |
| ss715616861 | 13 | 5994977 | 4.1 | A/G | −0.6 | PT18DR | CO18IR/MC19DR/AAE | |
| 21 | ss715614911 | 13 | 28880849 | 4.6 | C/T | 2.2 | CO18DR | MC18R/CO18IR/PT18IR/RH18IR |
| 22 | ss715619422 | 14 | 48312276 | 5.0 | T/G | −0.9 | PT18DR | MC19DR |
| ss715619486 | 14 | 48836596 | 3.9 | G/A | −2.4 | PT18DR | PT19DR/PT18IR | |
| 23 | ss715622900 | 15 | 6272006 | 3.7 | T/C | 0.1 | RH18DR | Ave_DR/CO18DR |
| 24 | ss715625245 | 16 | 5866453 | 5.7 | A/G | 2.2 | MC19DR | Ave_IR/PT19DR |
| 25 | ss715623895 | 16 | 27521057 | 5.1 | T/G | −0.1 | MC18DR | |
| 26 | ss715623938 | 16 | 28238331 | 4.4 | G/A | 2.7 | MC19DR | PT18DR/CO18DR |
| 27 | ss715626698 | 17 | 311571 | 3.6 | C/A | −9.1 | CO18DR | Ave_IR/PT19IR/CO18IR/PT19DR/AAE/PT18IR |
| 28 | ss715626021 | 17 | 13252195 | 3.8 | G/A | 1.1 | MC18DR | |
| 29 | ss715626252 | 17 | 15616539 | 4.6 | C/T | 3.7 | MC18DR | MC19DR |
| 30 | ss715630859 | 18 | 48314296 | 5.2 | C/T | −3.4 | PT18DR | PT18IR/PT19DR |
| 31 | ss715631739 | 18 | 56124763 | 5.5 | T/C | 3.3 | MC18DR | PT19DR/Ave_DR |
| 32 | ss715632215 | 18 | 59814051 | 4.9 | T/C | 4.3 | RH18DR | MC18DR/PT19DR |
| ss715633191 | 19 | 1502707 | 4.1 | C/T | 3.1 | PT19DR | ||
| 33 | ss715636101 | 19 | 5205785 | 4.9 | T/C | 0.1 | PT18DR | MC18IR/CO18IR |
| 34 | ss715633673 | 19 | 30020611 | 5.3 | C/A | −12.6 | CO18DR | CO18IR/AAE/Ave_IR/PT19DR/PT18IR/Ave_DR/MC18IR |
| 35 | ss715634898 | 19 | 39686084 | 6.1 | C/T | −0.4 | MC18DR | |
| Average irrigated (Ave_IR) | ||||||||
| 1 | ss715579037 | 1 | 3318347 | 4.3 | G/A | −3.3 | Ave_IR | RH18IR/AAE/PT19DR/Ave_DR/PT18IR/CO18DR |
| 2 | ss715583262 | 2 | 49079505 | 6.7 | T/C | 1.2 | Ave_IR | PT18IR |
| 3 | ss715586436 | 3 | 45668212 | 5.4 | G/A | 0.9 | Ave_IR | CO18IR/CO18DR/AAE |
| 4 | ss715587848 | 4 | 36908862 | 3.6 | T/C | 0.3 | Ave_IR | |
| 5 | ss715597242 | 7 | 34279212 | 4.6 | C/T | −1.1 | Ave_IR | PT18IR/Ave_DR |
| 6 | ss715614457 | 13 | 26279705 | 4.0 | G/A | 0.1 | Ave_IR | PT18DR |
| 7 | ss715625320 | 16 | 6483232 | 3.8 | C/T | 0.0 | Ave_IR | PT19IR |
| 8 | ss715626698 | 17 | 311571 | 6.4 | C/A | −3.8 | Ave_IR | CO18IR/PT19IR/CO18DR/PT19DR/AAE/PT18IR |
| 9 | ss715633673 | 19 | 30020611 | 3.6 | C/A | −4.5 | Ave_IR | CO18IR/CO18DR/AAE/PT19DR/PT18IR/Ave_DR/MC18IR |
| Average drought (Ave_DR) | ||||||||
| 1 | ss715585976 | 3 | 40874888 | 8.0 | C/T | −1.8 | Ave_DR | AAE/PT19DR/Ave_IR/RH18IR |
| 2 | ss715597294 | 7 | 35103803 | 4.1 | G/A | 1.7 | Ave_DR | AAE |
| 3 | ss715601736 | 8 | 40012659 | 8.6 | C/T | −2.2 | Ave_DR | PT19DR |
| 4 | ss715603468 | 9 | 2799750 | 3.7 | T/G | 0.9 | Ave_DR | |
| 5 | ss715631039 | 18 | 49432890 | 3.5 | C/T | −4.8 | Ave_DR | PT19DR/RH18IR/MC18DR/CO18IR |
| Average across environments (AAE) | ||||||||
| 1 | ss715579037 | 1 | 3318347 | 6.9 | G/A | −5.0 | AAE | RH18IR/Ave_IR/PT19DR/Ave_DR/PT18IR/CO18DR |
| 2 | ss715585976 | 3 | 40874888 | 6.1 | C/T | −1.6 | AAE | Ave_DR/PT19DR/Ave_IR/RH18IR |
| 3 | ss715597294 | 7 | 35103803 | 4.2 | G/A | 1.2 | AAE | Ave_DR |
| 4 | ss715604906 | 9 | 4542201 | 4.3 | T/G | 1.6 | AAE | Ave_DR/PT19IR |
| 5 | ss715603638 | 9 | 32987730 | 4.9 | G/A | 1.7 | AAE | Ave_IR/Ave_DR/MC19DR/MC18DR |
| 6 | ss715613260 | 12 | 6268063 | 6.2 | A/G | −0.6 | AAE | PT19DR |
| 7 | ss715633673 | 19 | 30020611 | 5.2 | C/A | −5.9 | AAE | CO18IR/CO18DR/Ave_IR/PT19DR/PT18IR/Ave_DR/MC18IR |
For each SNP, the following information is reported: locus number, CHR in base pairs, –log10(P), allele and allelic effect, ENV where the SNP was significant, and common ENV where the SNP was also significant.
a
Major/minor alleles of SNP.
b
Allelic effect: Difference in mean CW between genotypes with major allele and minor allele. Negative sign indicates that major allele is favorable for CW. Positive sign indicates that minor allele is favorable for CW.
c
Common Env: Indicates that SNP was significant (P ≤ 0.05) in additional environments.