Table 2. Genomic regions with significant evidence (FDR corrected, selected versus unselected populations) for recent positive selection in brown Hanwoo based on the Rsb statistic.
| Candidate regions (Chr, Mb) | Significant SNPs (P-value) | Genes in: region* | Trait associations | QTL information | |
|---|---|---|---|---|---|
| chr1 | 9–10.5 | Hapmap38887-BTA-22281 (0.038) | APP | meat tenderness, obesity [23–25] | weaning weight-maternal milk |
| GABPA | obesity [25] | ||||
| chr1 | 85–86.5 | BTB-01702174 (0.047) | - | - | marbling score, Longissimus muscle area, |
| chr2 | 102.5–104 | ARS-BFGL-NGS-3990 (0.006), ARS-BFGL-NGS-107381 (0.034), Hapmap34329-BES11_Contig247_1378 (0.014), ARS-BFGL-NGS-67961 (0.01) | ACADL | fatty acids oxidation [70] | - |
| MYL1 | skeletal muscle differentiation [71] | ||||
| chr4 | 47–48.5 | BTB-01351245 (0.049), BTB-01351221 (0.001), ARS-BFGL-NGS-38285 (0.0003), ARS-BFGL-NGS-108242 (0.004) | RELN | neural development [33] | body weight, body energy content, body length, length of productive life |
| chr5 | 32.5–34 | ARS-USMARC-635 (0.041) | WNT1 | coat color, melanocyte expansion [31] | body weight (slaughter, birth), Average daily gain, Subcutaneous fat increase |
| FAIM2 | obesity [72] | ||||
| chr5 | 54.5–56 | BFGL-NGS-111500 (0.002), Hapmap42656-BTA-73551 (0.00008), BTA-73549-no-rs (0.0000001), BFGL-NGS-111906 (0.006) | AVPR1A | mammalian social behaviour [34] | body weight (slaughter, birth), body size, height |
| chr5 | 61–62.5 | Hapmap34521-BES10_Contig695_990 (0.041), Hapmap34864-BES11_Contig325_836 (0.02), ARS-BFGL-NGS-44271 (0.016) | CD63 | body weight, pre-weaning average daily gain | |
| MYL6A | |||||
| MYL6B | skeletal muscle generation [73] | ||||
| chr6 | 10–11.5 | Hapmap42479-BTA-22862 (0.015) BTA-88441-no-rs (0.033) | NDST4 | fatness traits [74] | body weight(birth, weaning, slaughter), Average daily gain |
| chr8 | 28.5–30.5 | BTB-01271445 (0.049) | SH3GL2 | lipid binding and diabetis [75] | average daily gain, residual feed intake, body weight |
| chr11 | 75.5–77 | Hapmap35883-POMC_121F2-SNP1 (0.0002), ARS-BFGL-NGS-39507 (0.013) | POMC | obesity and coat color [32] | body weight (mature, weaning) |
| chr13 | 45.5–47 | BFGL-NGS-116062 (0.039), BFGL-NGS-116977 (0.02) | ADRB2 | body mass index and adipogenesis [76] | feed conversion ratio |
| chr14 | 41.5–43 | ARS-BFGL-NGS-59210 (0.022), BTB-01709715 (0.043) | FABP4 | intramuscular fat [77] | average daily gain, body weight(birth) |
| FABP5 | |||||
| chr15 | 12.5–14.5 | Hapmap35322-BES8_Contig457_1759 (0.028), ARS-BFGL-NGS-17747 (0.047) | MTMR2 | mammary gland metabolism [28] | body weight(birth, yearling), semen volume |
| CWC15 | reproduction [29] | ||||
| chr18 | 25.5–27 | UA-IFASA-4931 (0.049), ARS-BFGL-BAC-34198 (0.045) | - | - | resigual feed intake, body weight (weaning) |
| chr19 | 15–16.5 | UA-IFASA-8305 (0.028) | ACCN1 | QTL for reproduction [30] | calf size, body weight (mature, yearling), residual feed intake |
| chr29 | 44.5–47 | CAPN1_1 (0.02), BTA-66033-no-rs (0.034), ARS-BFGL-NGS-74975 (0.002), ARS-BFGL-NGS-20927 (0.049), ARS-BFGL-NGS-34609 (0.049) | CAPN1 | carcass trait and meat tenderness [78, 79] | body capacity, Tenderness score, Shear force, resudial feed intake |
*APP, Amyloid Beta (A4) Precursor Protein; GABPA, GA-Binding Protein alpha; ACADL, Acyl-CoA dehydrogenase, long chain; MYL1, Myosin, Light Chain 1; RELN, Reelin; WNT1, Wingless-Type MMTV Integration Site Family, Member 1; FAIM2, Fas Apoptotic Inhibitory Molecule 2; AVPR1A, Arginine Vasopressin Receptor 1A; CD63, CD63 Molecule; MYL6A, Myosin Light Polypeptide 6 alpha; MYL6B, Myosin Light Polypeptide 6 beta; NDST4, N-Deacetylase/N-Sulfotransferase (Heparan Glucosaminyl) 4; SH3GL2, SH3-Domain GRB2-Like 2; POMC, Proopiomelanocortin; ADRB2, Adrenoceptor Beta 2; FABP4, Fatty Acid Binding Protein 4; FABP5, Fatty Acid Binding Protein 5; MTMR2, Myotubularin Related Protein 2; CWC15, CWC15 Spliceosome-Associated Protein; ACCN1, Amiloride-sensitive Cation Channel 1; CAPN1, Calpain 1