Table 4. Marker-traits associations based haplotype-GWAS identified in water-limited conditions.
| P-valuesc | ||||||||
|---|---|---|---|---|---|---|---|---|
| Traita | Haplotype block | Chr | Positionb | Haplo-group | WW | WL | Diff | Co-localizationd |
| Chl | Hap1B-Chl-1 | 1B | 4320839 | GATACT | 7.93E-06 | |||
| Chl | Hap3B-Chl-1 | 3B | 480341620 | TT | 2.05E-06 | |||
| Chl | Hap4A-Chl-1 | 4A | 12399327 | CC | 8.00E-06 | |||
| Chl | Hap4A-Chl-2 | 4A | 726215255 | GA | 1.64E-07 | |||
| Chl | Hap4A-Chl-2 | 4A | 726215255 | AG | 2.48E-07 | |||
| Chl | Hap4B-Chl-1 | 4B | 651800378 | TCGGCCC | 1.61E-08 | |||
| Chl | Hap6A-Chl-1 | 6A | 4427440 | CA | 5.26E-06 | |||
| CT | Hap4A-CT-1 | 4A | 614870817 | CC | 8.91E-06 | |||
| GS | Hap1B-GS-1 | 1B | 548536105 | TTTTCTGCCAATTGGCGTGTCAG | 2.68E-06 | |||
| GS | Hap4A-GS-1 | 4A | 631922510 | TTAT | 9.28E-06 | |||
| GY | Hap1A-GY-1 | 1A | 12306177 | CT | 2.63E-06 | 1.16E-46 | ||
| GY | Hap1B-GY-1 | 1B | 20589424 | ACG | 6.17E-06 | |||
| GY | Hap5B-GY-1 | 5B | 10888795 | CC | 5.33E-06 | |||
| GY | Hap7B-GY-1 | 7B | 3148623 | AC | 5.74E-06 | |||
| PH | Hap1B-PH-1 | 1B | 15166232 | GCA | 3.04E-06 | |||
| PH | Hap1B-PH-1 | 1B | 15166232 | AAG | 3.04E-06 | |||
| PH | Hap2A-PH-1 | 2A | 118446554 | TC | 4.54E-06 | Sus2-2A | ||
| PH | Hap2A-PH-2 | 2A | 319042351 | CC | 8.94E-06 | |||
| PH | Hap2A-PH-3 | 2A | 712706867 | TGC | 6.67E-09 | 1.56E-25 | ||
| PH | Hap2A-PH-3 | 2A | 712706867 | CAT | 1.88E-08 | 1.56E-25 | ||
| PH | Hap2B-PH-3 | 2B | 683003143 | TGCTTTAT | 4.41E-08 | |||
| PH | Hap2D-PH-1 | 2D | 9826098 | GG | 9.75E-09 | |||
| PH | Hap2D-PH-3 | 2D | 572074690 | CTTTC | 3.09E-08 | |||
| PH | Hap2D-PH-3 | 2D | 572074690 | TCGCT | 3.09E-08 | |||
| PH | Hap3B-PH-1 | 3B | 24940169 | TAG | 8.74E-06 | |||
| PH | Hap4A-PH-1 | 4A | 732511707 | GACAT | 4.22E-07 | 1.74E-31 | ||
| PH | Hap5A-PH-1 | 5A | 679489793 | GAGAAA | 2.15E-06 | AWN | ||
| PH | Hap5B-PH-1 | 5B | 580085162 | GG | 8.42E-06 | |||
| PH | Hap6B-PH-1 | 6B | 15781175 | CCG | 6.64E-06 | |||
| PH | Hap6B-PH-2 | 6B | 709531181 | GTT | 8.41E-06 | |||
| Proline | Hap4D-Proline-1 | 4D | 42538561 | GT | 1.60E-06 | 4.70E-07 | ||
| RWC | Hap2A-RWC-1 | 2A | 41232496 | ACTCCG | 5.10E-06 | Ppd-A1 | ||
| RWC | Hap2B-RWC-2 | 2B | 643682900 | CGTGGGG | 7.48E-06 | 4.94E-06 | ||
| RWC | Hap3B-RWC-1 | 3B | 40184024 | TGTAGGGC | 3.01E-06 | |||
| RWC | Hap7A-RWC-1 | 7A | 701493027 | GACTAAC | 8.85E-06 | |||
| SDW | Hap2D-SDW-1 | 2D | 64190307 | AG | 7.56E-06 | 1.19E-07 | ||
| SFW | Hap2A-SFW-1 | 2A | 709836654 | ATAG | 8.35E-06 | |||
| SFW | Hap2D-SFW-1 | 2D | 571077641 | GCAATTAGT | 7.27E-07 | 2.19E-21 | ||
| SFW | Hap3A-SFW-1 | 3A | 666229575 | CG | 1.81E-06 | |||
| SFW | Hap3A-SFW-1 | 3A | 666229575 | TA | 1.88E-06 | |||
| Sugar | Hap4B-Sugar-1 | 4B | 535049503 | TTGCGAAA | 4.23E-06 | |||
| Sugar | Hap4B-Sugar-1 | 4B | 535049503 | CCAAAGGG | 4.23E-06 | |||
| TGW | Hap5B-TGW-2 | 5B | 603881835 | ATTCTCGTT | 4.18E-06 | |||
a
Chl: chlorophyll contents (mg/g); CCI: chlorophyll content index; CT: Canopy temperature (°C); GS: grains per spike; GY: grain yield (g m-2); PH: plant height (cm); Proline (µmol/g); RWC: relative water contents (%); SDW: shoot dry weight (g); SFW: shoot fresh weight (g); Sugar (µg/g); TGW: thousand grain weight (g).
b
Position of SNP based on IWGSC Ref sequence version 1.0 (https://urgi.versailles.inra.fr/blast_iwgsc/blast.php)
c
P-value significance for marker-trait associations in well-watered (WW), water-limited (WL) and difference between well-watered and water-limited (DIFF) conditions.
d
Co-localization of marker-trait associations with divergent selective sweeps (the numeric values are the p-value of selection sweep) and functional genes.