TABLE 6.
Haplotypes associated with resistance to Pst at seedling and adult plant stages in SYN-DER wheats using 90K and GBS markers.
| Genotype (Frequency) | ||||||||
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| Trait | Haplotype ID | Chr | Position | SNPs/ block | −log10(p) | Hap-I | Hap-II | Hap-III |
| ISB.16 | LDB_1_25490035_25490120 | 1A | 25490035 | 2 | 1.45E-06 | GA (0.68) | AG (0.30) | GG (0.019) |
| Pst.571242 | LDB_1_575215721_575228785 | 1A | 575215721 | 2 | 1.00E-08 | GG (0.59) | AA (0.18) | AG (0.15) |
| NWS.15 | LDB_3_19112718_19129042 | 1D | 19112718 | 2 | 1.19E-06 | AA (0.74) | TG (0.25) | |
| ISB.15 | LDB_3_488576303_488577792 | 1D | 488576303 | 4 | 4.00E-07 | ATGT (0.55) | GGAC:0.37 | GGGT (0.02) |
| NWS.15 | LDB_3_488576303_488577792 | 1D | 488576303 | 4 | 1.00E-08 | ATGT (0.55) | GGAC:0.37 | GGGT (0.02) |
| ISB.15 | LDB_4_30830742_30831056 | 2A | 30830742 | 2 | 7.00E-08 | CA (0.92) | TG:0.06 | CG (0.01) |
| NWS.15 | LDB_5_6258683_6338084 | 2B | 6258683 | 9 | 3.00E-12 | CATTCTTCA (0.43) | CACCCTTCA (0.18) | TGTTCCTCG (0.14) |
| Pst.140202 | LDB_8_125880000_125930410 | 3B | 125880000 | 4 | 6.91E-06 | GACT (0.67) | GGTC (0.15) | AGTC (0.15) |
| NWS.16 | LDB_10_111292188_111292941 | 4A | 111292188 | 2 | 2.00E-09 | GC (0.47) | AT (0.44) | GT (0.046) |
| NWS.15 | LDB_13_465541110_465541233 | 5A | 465541110 | 2 | 5.00E-07 | CG (0.58) | TA (0.35) | TG (0.02) |
| ISB.16 | LDB_13_465541110_465541233 | 5A | 465541110 | 2 | 1.00E-08 | CG (0.58) | TA (0.35) | TG (0.02) |
| NWS.15 | LDB_16_584678556_584680439 | 6A | 584678556 | 2 | 8.00E-06 | GT (0.60) | TG (0.31) | GG (0.025 |
| NWS.16 | LDB_17_15781175_15781777 | 6B | 15781175 | 3 | 1.00E-07 | CCG (0.34) | CTG (0.31) | TCT (0.25) |
| Pst.173262 | LDB_21_627325333_627325482 | 7D | 627325333 | 2 | 6.00E-07 | GC (0.79) | AT (0.103) | GT (0.06) |
*Bold haplotype blocks are the loci also identified by SNP-GWAS. Only the top three most frequent haplotypes in each LD block are mentioned, and the values in parentheses are the frequencies of the relevant haplotypes in the diversity panel.