TABLE 3.
Significant SNPs and related genes for four feed efficiency traits.
| Traita | Methodb | SNP name | Chromosome | Position (bp) | Genec | Distanced | Gene function |
| FCR | a&b | WU_10.2_13_3842462 | 13 | 3,655,526 | PLCL2 | -150,373 | Lipid catabolic process |
| a | ASGA0062927 | 14 | 40,507,969 | SIRT4 | +204,081 | Negative regulation of insulin secretion | |
| PLA2G1B | +185,650 | Lipid metabolic process | |||||
| a | ASGA0062929 | 14 | 40,548,521 | PLA2G1B | +226,202 | Lipid metabolic process | |
| a | ALGA0097485 | 18 | 23,538,749 | SPAM1 | -51,203 | Carbohydrate metabolic process | |
| HYAL4 | -85,477 | ||||||
| ENSSSCG00000016602 | -88,233 | ||||||
| ADG | a&b | ASGA0100941 | 2 | 147,068,762 | PRELID2 | -40,819 | Phospholipid transport process |
| a&b | WU_10.2_2_153522747 | 2 | 147,112,980 | PRELID2 | Within | Phospholipid transport process | |
| a&b | WU_10.2_3_329436 | 3 | 537,968 | GPER1 | -174,192 | Positive regulation of insulin secretion; negative regulation of lipid biosynthetic process | |
| ADFI | a | ASGA0005581 | 1 | 203,367,107 | ACER2 | -19,714 | Lipid metabolic process |
| b | ALGA0019602 | 3 | 68,298,863 | HK2 | +67,248 | Glucose metabolic process; glycolytic process | |
| a&b | ALGA0065251 | 12 | 14,839,808 | TEX2 | Within | Lipid transport process | |
| ICAM2 | -42115 | Insulin metabolic process | |||||
| RFI | b | ALGA0019602 | 3 | 68,298,863 | HK2 | +67,248 | Glucose metabolic process; glycolytic process |
| b | WU_10.2_11_4727497 | 11 | 50,92,611 | PDX1 | -211,028 | Glucose metabolic process; insulin secretion | |
| a&b | ALGA0060467 | 11 | 53,79,554 | PDX1 | +68,711 | Glucose metabolic process; insulin secretion |
aFCR, Feed conversion ratio; ADG, Average daily gain; ADFI, Average daily feed intake; RFI, Residual feed intake. ba, linear model GWAS (LM-GWAS); b, single-step GWAS (ssGWAS). cPLCL2, Phospholipase C Like 2; SIRT4, Sirtuin 4; PLA2G1B, Phospholipase A2 Group IB; SPAM1, Sperm Adhesion Molecule 1; HYAL4, Hyaluronidase 4; PRELID2, PRELI Domain Containing 2; GPER1, G Protein-coupled Estrogen Receptor 1; ACER2, Alkaline Ceramidase 2; HK2, Hexokinase 2; TEX2, Testis Expressed 2; ICAM2, Hexokinase 2; PDX1, Pancreatic and Duodenal Homeobox 1. d+/-: The SNP located in the upstream/downstream region of the nearest gene.