Table 3.
Significant coincident single-nucleotide polymorphisms (SNPs) with previous studies associated with CW with the 12 environments, Columbia (CO18), Maricopa (MC18 and 19), Pine Tree (PT18 and 19), and Rohwer (RH18) under IR and DR treatments, and for averaged across site-years for irrigated (Ave_IR) and drought (Ave_DR) treatments, and averaged across all environments (AAE) at the significance threshold of –Log10 (P) ≥ 3.5; P ≤ 0.0003.
| Locus | SNP_ID | CHR | Position | -Log10 (P) | Allelea | Allelic effectb | ENV | Common ENVc | Coincident genomic regions with previous studiesd |
|---|---|---|---|---|---|---|---|---|---|
| Irrigated (IR) | |||||||||
| 1 | ss715580748 | 1 | 595259 | 3.6 | T/C | −2.7 | PT18IR | GWAS-δ18O QTL2 | |
| 2 | ss715581576 | 2 | 2391001 | 5.0 | T/C | 2.3 | PT19IR | PT18IR | CT-QTL7 |
| 3 | ss715584835 | 3 | 2359805 | 3.6 | G/A | 0.9 | RH18IR | MC19DR | GWAS-CT QTL3 |
| 4 | ss715589557 | 4 | 8924261 | 3.9 | T/C | −0.8 | MC18IR | GWAS-δ13C QTL2, Canopy_wilt_2_29 | |
| 5 | ss715590117 | 5 | 1983770 | 3.6 | T/C | −1.3 | CO18IR | mqCanopy_wilt_007 and mqCanopy_wilt_0198, Canopy_wilt_2_39 | |
| 6 | ss715591559 | 5 | 37839978 | 4.8 | C/T | 1.3 | PT19IR | AAE/MC19IR | GWAS-CW QTL1 |
| 7 | ss715598790 | 7 | 8267191 | 4.4 | A/C | 1.4 | CO18IR | δ13C-QTL5 | |
| 8 | ss715602950 | 9 | 1066026 | 6.6 | T/C | −1.8 | CO18IR | CO18DR | GWAS-CW QTL1, GWAS-δ13C and δ18O QTL2 |
| 9 | ss715605115 | 9 | 5057308 | 4.0 | T/C | −2.7 | CO18IR | GWAS-CT QTL3 | |
| 10 | ss715606242 | 10 | 3253404 | 4.3 | A/C | −0.1 | RH18IR | RH18DR/PT18DR/MC19IR | GWAS-CW QTL4 |
| 11 | ss715611329 | 11 | 9912187 | 4.2 | G/A | −3.8 | PT18IR | AAE/CO18DR | mqCanopy_wilt_0208 |
| 12 | ss715612746 | 12 | 37356120 | 8.1 | C/T | −2.7 | RH18IR | RH18DR/PT18DR/PT18IR/MC19IR | GWAS-CW QTL1 |
| 13 | ss715614917 | 13 | 28949836 | 5.5 | A/G | 1.3 | CO18IR | Ave_IR/PT18IR | GWAS-δ13C QTL2 |
| 14 | ss715617331 | 14 | 10092238 | 3.6 | G/A | 0.7 | PT19IR | PT18IR | GWAS-CW QTL4 |
| 15 | ss715620301 | 15 | 11228851 | 7.4 | A/G | −3.2 | PT19IR | PT19DR/PT18IR | GWAS-CW QTL1 |
| 16 | ss715622635 | 15 | 49582581 | 5.8 | A/G | 1.2 | RH18IR | PT18IR/Ave_IR/PT19IR | GWAS-CW QTL4 |
| 17 | ss715627700 | 17 | 40335241 | 4.3 | G/A | −1.1 | RH18IR | PT19DR/CO18IR | mqCanopy_wilt_0158 |
| 18 | ss715630654 | 18 | 46111574 | 6.2 | A/C | −3.3 | RH18IR | AAE/PT19DR/MC18DR/PT18IR | GWAS-CT QTL3 |
| 19 | ss715632103 | 18 | 59162269 | 4.1 | C/T | −5.1 | PT18IR | Ave_IR/PT18DR/Ave_DR/AAE/PT19IR/MC18IR/CO18DR/PT19DR | GWAS-CW QTL1, δ13C-QTL6 |
| 20 | ss715632312 | 18 | 60577930 | 3.8 | C/T | −0.7 | CO18IR | GWAS-CT QTL3, CT-QTL7 | |
| 21 | ss715632502 | 18 | 62056969 | 3.6 | T/C | −0.5 | CO18IR | RH18IR/Ave_IR | GWAS-CW QTL1 |
| 22 | ss715634991 | 19 | 40220231 | 3.8 | G/A | 1.0 | CO18IR | GWAS-CW QTL1 | |
| 23 | ss715635419 | 19 | 44955912 | 4.0 | G/T | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL4, δ13C-QTL6 |
| ss715635420 | 19 | 44964042 | 4.0 | T/C | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR | GWAS-CW QTL4, δ13C-QTL6 | |
| ss715635421 | 19 | 44969187 | 4.0 | G/T | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL4, δ13C-QTL6 | |
| ss715635422 | 19 | 44974132 | 4.0 | T/C | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR | GWAS-CW QTL4, δ13C-QTL6 | |
| ss715635432 | 19 | 45046164 | 4.0 | T/G | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR | GWAS-CW QTL4 | |
| ss715635433 | 19 | 45062248 | 4.0 | C/T | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL4 | |
| ss715635435 | 19 | 45064787 | 3.7 | C/T | −0.5 | MC18IR | PT19DR | GWAS-CW QTL4 | |
| ss715635436 | 19 | 45066028 | 3.7 | T/C | −0.5 | MC18IR | PT19DR | GWAS-CW QTL4 | |
| ss715635437 | 19 | 45067155 | 3.6 | T/C | −0.5 | MC18IR | PT19DR/AAE | GWAS-CW QTL4 | |
| ss715635439 | 19 | 45072668 | 3.7 | C/A | −0.5 | MC18IR | PT19DR | GWAS-CW QTL4 | |
| ss715635442 | 19 | 45080661 | 4.0 | C/T | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL4 | |
| ss715635447 | 19 | 45099890 | 4.0 | A/G | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL1, 4 | |
| ss715635448 | 19 | 45101232 | 4.0 | A/G | −0.5 | MC18IR | PT19DR/MC18DR/AAE/PT18IR/MC19IR | GWAS-CW QTL1, 4 | |
| 24 | ss715639090 | 20 | 96607 | 4.7 | G/A | −5.1 | CO18IR | CO18DR/PT19DR | GWAS-CW QTL4 |
| 25 | ss715636929 | 20 | 2106131 | 4.0 | C/T | −0.5 | MC18IR | MC18DR/RH18DR | GWAS-CW QTL1, GWAS-δ18O QTL2 |
| ss715636930 | 20 | 2109330 | 4.1 | T/G | −0.5 | MC18IR | MC18DR/RH18DR | GWAS-CW QTL1, GWAS-δ18O QTL2 | |
| Drought (DR) | |||||||||
| 1 | ss715580188 | 1 | 51097931 | 4.1 | C/A | −2.7 | MC18DR | GWAS-CW QTL4 | |
| ss715580224 | 1 | 51398886 | 6.6 | G/A | −9.0 | CO18DR | PT19DR | GWAS-CW QTL4 | |
| 2 | ss715582745 | 2 | 4438645 | 5.8 | A/G | −1.1 | PT18DR | Ave_IR/PT18IR/MC19IR | GWAS-δ13C QTL2 |
| ss715582949 | 2 | 4611848 | 5.2 | T/C | 2.1 | RH18DR | AAE/Ave_IR/PT18IR | GWAS-δ13C QTL2 | |
| 3 | ss715584310 | 2 | 9896652 | 5.4 | T/C | 1.7 | PT18DR | RH18DR/Ave_IR | GWAS-δ13C QTL2, GWAS-CT QTL3 |
| ss715580895 | 2 | 10064424 | 7.8 | C/T | 4.5 | MC19DR | MC19IR | GWAS-δ13C QTL2, GWAS-CT QTL3 | |
| 4 | ss715592981 | 6 | 12999522 | 4.7 | T/G | 4.4 | RH18DR | AAE | GWAS-CW QTL4 |
| 5 | ss715593221 | 6 | 14321140 | 8.2 | C/T | 4.2 | CO18DR | AAE/PT18IR | GWAS-CW QTL4 |
| 6 | ss715594542 | 6 | 46074664 | 4.5 | A/G | 0.7 | PT18DR | GWAS-CW QTL1 | |
| 7 | ss715595238 | 6 | 50038514 | 4.1 | C/T | −0.2 | RH18DR | Ave_DR/AAE | δ13C-QTL6 |
| 8 | ss715597447 | 7 | 36678744 | 4.0 | C/T | 1.2 | MC18DR | GWAS-δ13C QTL2 | |
| 9 | ss715606242 | 10 | 3253404 | 3.7 | A/C | 0.6 | RH18DR | RH18IR/PT18DR/MC19IR | GWAS-CW QTL4 |
| 10 | ss715611163 | 11 | 7934621 | 4.0 | A/G | −5.1 | CO18DR | PT19DR/PT18IR | GWAS-δ13C QTL2 |
| 11 | ss715611278 | 11 | 9063628 | 6.1 | A/G | −1.0 | MC19DR | RH18IR | GWAS-CW QTL1 |
| 12 | ss715610265 | 11 | 36484015 | 4.1 | C/T | 1.8 | MC19DR | Ave_DR | GWAS-CT QTL3, GWAS-CW QTL4 |
| 13 | ss715611782 | 12 | 2146126 | 8.4 | C/T | 2.3 | CO18DR | GWAS-CW QTL4 | |
| 14 | ss715612746 | 12 | 37356120 | 9.5 | C/T | −3.4 | RH18DR | RH18IR/PT18DR/PT18IR/MC19IR | GWAS-CW QTL1 |
| 15 | ss715620072 | 14 | 915942 | 5.5 | T/G | −2.4 | CO18DR | GWAS-CW QTL1, Canopy_wilt_1_210 | |
| 16 | ss715618057 | 14 | 2311158 | 4.7 | G/A | 0.8 | MC18DR | GWAS-CT QTL3 | |
| 17 | ss715618585 | 14 | 3819249 | 4.1 | A/G | −2.2 | RH18DR | MC19IR | GWAS-CT QTL3 |
| 18 | ss715623062 | 15 | 7718600 | 8.7 | A/G | 2.1 | CO18DR | GWAS-δ13C QTL2 | |
| 19 | ss715624261 | 16 | 30036170 | 4.3 | A/G | 3.0 | MC18DR | GWAS-CW QTL1 | |
| 20 | ss715628231 | 17 | 8248213 | 4.1 | G/T | −4.6 | MC19DR | PT18IR | GWAS-δ18O QTL2, δ13C-QTL5, mqCanopy_wilt_0218 |
| 21 | ss715626991 | 17 | 36586178 | 4.7 | C/T | −4.4 | PT18DR | PT19DR/PT18IR | GWAS-δ13C QTL2, GWAS-CW QTL4 |
| 22 | ss715632594 | 18 | 702847 | 3.8 | T/C | 0.0 | MC19DR | Ave_DR | GWAS-δ13C QTL2 |
| 23 | ss715632103 | 18 | 59162269 | 6.0 | C/T | −5.4 | PT18DR | Ave_IR/Ave_DR/PT18IR/AAE/PT19IR/MC18IR/CO18DR/PT19DR | GWAS-CW QTL1, δ13C-QTL6 |
| 24 | ss715633103 | 19 | 1252510 | 4.0 | T/C | 1.6 | MC18DR | AAE/Ave_DR/PT19DR | GWAS-δ13C QTL2 |
| 25 | ss715635396 | 19 | 44705794 | 6.5 | T/C | 0.7 | CO18DR | PT18IR | δ13C-QTL6 |
| ss715635416 | 19 | 44938831 | 6.2 | G/A | −4.0 | RH18DR | PT19DR/MC18IR/PT18IR/AAE | GWAS-CW QTL4, δ13C-QTL6 | |
| ss715635458 | 19 | 45178132 | 10.6 | T/C | −3.5 | CO18DR | PT18IR/PT19DR/AAE | GWAS-CW QTL1, 4 | |
| 26 | ss715638951 | 20 | 46752502 | 5.3 | G/A | 4.6 | MC19DR | MC18DR/PT19DR | GWAS-CW QTL1 |
| Average irrigated (Ave_IR) | |||||||||
| 1 | ss715614827 | 13 | 28425391 | 4.3 | T/C | −0.1 | Ave_IR | MC18IR | GWAS-CW QTL4 |
| 2 | ss715614963 | 13 | 29130244 | 3.7 | C/T | 1.0 | Ave_IR | GWAS-δ13C QTL2 | |
| ss715615031 | 13 | 29565886 | 3.7 | G/A | 1.1 | Ave_IR | CO18IR/PT18IR | GWAS-δ13C QTL2 | |
| 3 | ss715617562 | 14 | 1219464 | 5.3 | A/G | −1.3 | Ave_IR | PT18IR/MC19IR | GWAS-CW QTL1 |
| 4 | ss715632103 | 18 | 59162269 | 8.5 | C/T | −4.0 | Ave_IR | PT18DR/Ave_DR/PT18IR/AAE/PT19IR/MC18IR/CO18DR/PT19DR | GWAS-CW QTL1, δ13C-QTL6 |
| 5 | ss715635361 | 19 | 44462578 | 9.0 | A/G | −1.3 | Ave_IR | PT18IR/MC18IR | δ13C-QTL6 |
| Average drought (Ave_DR) | |||||||||
| 1 | ss715580947 | 2 | 1073084 | 5.7 | C/T | −1.4 | Ave_DR | MC18DR/AAE/PT19DR | GWAS-CW QTL1 |
| 2 | ss715588382 | 4 | 43699749 | 3.7 | A/G | −2.3 | Ave_DR | PT19DR | GWAS-CW QTL1, GWAS-CT QTL3 |
| 3 | ss715588984 | 4 | 48593967 | 7.3 | T/C | 0.9 | Ave_DR | AAE/RH18DR/CO18IR/CO18DR/PT18IR | GWAS-CW QTL1 |
| 4 | ss715591524 | 5 | 37592814 | 7.5 | C/A | 1.7 | Ave_DR | RH18DR/PT19DR/MC18IR | GWAS-CW QTL1, δ13C-QTL6 |
| 5 | ss715598277 | 7 | 4921108 | 3.6 | A/G | −0.8 | Ave_DR | AAE/PT19DR | GWAS-δ18O QTL2 |
| 6 | ss715599784 | 8 | 16250528 | 6.2 | T/G | −2.4 | Ave_DR | MC18IR/PT19DR/PT18IR | GWAS-CW QTL1 |
| 7 | ss715604779 | 9 | 43958999 | 6.0 | A/G | 1.6 | Ave_DR | RH18DR | GWAS-CW QTL1 |
| 8 | ss715632103 | 18 | 59162269 | 4.8 | C/T | −4.7 | Ave_DR | PT18DR/Ave_IR/PT18IR/AAE/PT19IR/MC18IR/CO18DR/PT19DR | GWAS-CW QTL1, δ13C-QTL6 |
| Average across environments (AAE) | |||||||||
| 1 | ss715590862 | 5 | 33130272 | 3.8 | G/A | 0.9 | AAE | PT19IR | GWAS-CW QTL1 |
| 2 | ss715598845 | 7 | 8518123 | 5.5 | G/T | 1.1 | AAE | PT19DR/CO18IR | δ13C-QTL5 |
| 3 | ss715611329 | 11 | 9912187 | 4.5 | G/A | −3.1 | AAE | PT18IR/CO18DR | mqCanopy_wilt_0208 |
| 4 | ss715632103 | 18 | 59162269 | 3.8 | C/T | −5.0 | AAE | Ave_IR/PT18DR/Ave_DR/PT18IR/PT19IR/MC18IR/CO18DR/PT19DR | GWAS-CW QTL1, δ13C-QTL6 |
For each SNP, the following information is reported: locus number, chromosomal position (CHR) in base pairs, –log10(P), allele and allelic effect, environment (ENV) where the SNP was significant, common environments (common ENV) where the SNP was also significant, and quantitative trait loci (QTL) that was coincident from previous studies. Green highlighted areas represent genomic regions in this study that were exactly coincident with Kaler et al. (2017a) genomic regions for CW.
Major/minor alleles of SNP.
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.
Common Env: Indicates that SNP was significant (P ≤ 0.05) in additional environments.
Coincident genomic regions with previous studies: (1) Kaler et al. (2017a) (CW); (2) Kaler et al. (2017b) (C13 and O18); (3) Kaler et al. (2018) (CT); (4) Steketee et al. (2020) (CW); (5) Bazzer et al. (2020a) (C13); (6) Bazzer et al. (2020b) (C13); (7) Bazzer and Purcell (2020) (CT); (8) Hwang et al. (2016) (CW); (9) Abdel Haleem et al. (2012) (CW); (10) Charlson et al. (2009) (CW). CW, canopy wilting; CT, canopy temperature; C13, carbon isotope ratio; O18, oxygen isotope ratio. For QTL naming: genome-wide association (GWAS) followed by trait name means its association mapping QTL (for example, GWAS-O18 QTL). If a GWAS prefix was not included, the QTL was identified from biparental mapping.