Table 9 The effect of favorable alleles on agronomic traits of Iranian wheat accessions exposed to the rain-fed conditions
SNPs | Trait | Marker | ai | Typical accession | Allele | Favorable allele | MAF | p(−log10) | R2 |
|---|---|---|---|---|---|---|---|---|---|
Original | SW | rs63808 rs15903 rs51526 | 0.02 0.03 0.03 | 623,125 BAHAR 623,125 | A/G A/G A/G | G A A | 0.15 0.32 0.19 | 3.60 3.47 3.26 | 0.32 0.32 0.32 |
SL | rs2237 | −0.53 | 627,057 | A/G | G | 0.17 | 4.62 | 0.13 | |
TKW | rs26577 rs61706 | 1.57 1.90 | 625,123 623,909 | C/T A/G | T G | 0.48 0.21 | 3.57 3.82 | 0.09 0.09 | |
SN | rs57846 | 0.58 | Bahar | A/T | T | 0.22 | 3.43 | 0.37 | |
GY | rs51526 rs56337 | 0.03 0.03 | 627,410 625,047 | A/G G/T | A G | 0.19 0.25 | 3.44 3.91 | 0.21 0.22 | |
PH | rs25700 | −11.06 | 623,318 | C/G | G | 0.14 | 3.93 | 0.24 | |
PL | rs46075 | −1.76 | 623,139 | C/T | C | 0.19 | 3.51 | 0.09 | |
GFP | rs46504 rs53016 | 1.31 1.57 | 626,360 623,905 | A/C G/T | C T | 0.19 0.16 | 3.63 5.21 | 0.09 0.11 | |
DE | rs30520 | −0.28 | 626,825 | A/G | G | 0.13 | 3.41 | 0.07 | |
LG | rs33549 | 1.69 | Gascogne | A/G | G | 0.19 | 3.65 | 0.10 | |
Imputed | SL | rs50187 rs44154 | −0.39 − 0.14 | 626,924 627,057 | A/G A/G | A G | 0.22 0.21 | 4.04 3.42 | 0.14 0.13 |
SW | rs736 | 0.29 | Alvand | A/G | G | 0.11 | 3.81 | 0.32 | |
PL | rs11116 rs25700 | −2.66 −4.56 | 627,410 623,344 | C/T C/G | C G | 0.12 0.11 | 3.55 3.65 | 0.08 0.08 | |
DH | rs59282 rs17806 | −4.24 −7.59 | Dastjerdi Kavir 624,818 | A/C C/T | C T | 0.23 0.11 | 3.45 3.69 | 0.36 0.36 | |
DA | rs17806 | −7.04 | Shanghai7 Kavir | C/T | T | 0.11 | 3.30 | 0.38 | |
DM | rs17806 | −6.78 | Frontana 624,818 | C/T | T | 0.11 | 3.44 | 0.32 | |
CT | rs64750 rs55557 | −2.61 −0.39 | 624,315 622,105 | A/G A/T | G T | 0.03 0.49 | 4.32 3.58 | 0.11 0.09 | |
LG | rs41689 | 0.82 | Roshan 623,344 | C/G | C | 0.24 | 3.83 | 0.12 |