Table 3.
Candidate genes containing top significant single nucleotide polymorphisms detected using integrated extended haplotype homozygosity and cross-population extended haplotype homozygosity analyses.
| Top significant SNP | chr | Candidate gene | Putative function | Detection analysis | Max statistic | Log p-value |
|---|---|---|---|---|---|---|
| solcap_snp_c1_5209 | 4 | Soltu.DM.04G019230 | D-aminoacid aminotransferase-like PLP-dependent enzymes superfamily protein | iHS_sk | 3.6 | 3.5 |
| XPEHH_sk_us | 4.0 | 4.2 | ||||
| solcap_snp_c2_16722 | 4 | Soltu.DM.04G020490 | Protein Ycf2 | XPEHH_sk_us | 5.4 | 7.1 |
| XPEHH_sk_jp | 3.4 | 3.1 | ||||
| solcap_snp_c2_16712 | 4 | Soltu.DM.04G020520 | Conserved hypothetical protein | iHS_sk, | 3.3 | 3.0 |
| XPEHH_sk_us | 5.4 | 7.1 | ||||
| XPEHH_sk_jp | 3.5 | 3.4 | ||||
| solcap_snp_c2_16718 | 4 | Soltu.DM.04G020610 | Cytochrome P450, family 71, subfamily A, polypeptide | iHS_sk | 3.5 | 3.3 |
| XPEHH_sk_us | 5.8 | 8.1 | ||||
| XPEHH_sk_jp | 3.6 | 3.5 | ||||
| solcap_snp_c2_16744 | 4 | Soltu.DM.04G020750 | Cystathionine beta-synthase (CBS) family protein | XPEHH_sk_us | 3.6 | 3.5 |
| XPEHH_sk_jp | 5.9 | 8.4 | ||||
| solcap_snp_c1_14442 | 4 | Soltu.DM.04G021160 | Phosphotyrosine protein phosphatases superfamily protein | XPEHH_sk_us | 4.8 | 5.8 |
| XPEHH_sk_jp | 3.8 | 3.8 | ||||
| solcap_snp_c1_16534 | 4 | Soltu.DM.04G021190 | C2H2 and C2HC zinc fingers superfamily protein | XPEHH_sk_us, | 4.4 | 5.0 |
| XPEHH_sk_jp | 3.6 | 3.6 | ||||
| solcap_snp_c2_39856 | 4 | Soltu.DM.04G021220 | Ubiquitin-specific protease | XPEHH_sk_us | 3.5 | 3.3 |
| XPEHH_sk_jp | 3.5 | 3.4 | ||||
| solcap_snp_c1_4271 | 9 | Soltu.DM.09G006270 | Phosphatidic acid phosphatase (PAP2) family protein | XPEHH_sk_us | 3.7 | 3.7 |
| XPEHH_sk_jp | 3.4 | 3.1 | ||||
| solcap_snp_c2_13242 | 9 | Soltu.DM.09G006310 | IQ-domain | XPEHH_sk_us | 3.9 | 4.0 |
| XPEHH_sk_jp | 3.5 | 3.3 | ||||
|
solcap_snp_c1_4248, solcap_snp_c2_13194 |
9 | Soltu.DM.09G006540 | Leucine-rich repeat protein kinase family protein | XPEHH_sk_us | 3.7 | 3.6 |
| XPEHH_sk_jp | 3.3 | 3.0 | ||||
| solcap_snp_c1_4076 | 9 | Soltu.DM.09G018820 | GroES-like zinc-binding dehydrogenase family protein | iHS_sk | 4.2 | 4.6 |
| XPEHH_sk_us | 3.2 | 2.9 |