TABLE 4.
Number of individuals and SNPs used for GWAS after quality control for different datasets (61K genotypes of CBs, 50K genotypes of PBs, and Combined dataset).
| CB | PB | Combined dataset | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Trait | 61K | N | Imputed WGS | 50K | N | Imputed WGS | 61K + 50K | N | Imputed WGS |
| FCOLA | 44,098 | 941 a | 7,376,594 | 35,775 | 873 a | 10,094,644 | 29,349 | 1,844 | 10,331,074 |
| FCOLB | 44,068 | 953 | 7,376,594 | 35,799 | 885 a | 10,090,482 | 29,349 | 1,844 | 10,331,074 |
| FCOLL | 44,068 | 953 | 7,377,298 | 35,782 | 879 a | 10,096,911 | 29,349 | 1,844 | 10,331,074 |
| QFCOLA | 44,070 | 953 | 7,376,594 | 35,801 | 882 a | 10,095,407 | 29,349 | 1,844 | 10,331,074 |
| QFCOLB | 44,068 | 953 | 7,376,594 | 35,809 | 885 a | 10,097,161 | 29,349 | 1,844 | 10,331,074 |
| QFCOLL | 44,068 | 953 | 7,376,594 | 35,809 | 881 a | 10,097,982 | 29,349 | 1,844 | 10,331,074 |
| FMCOLA | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| FMCOLB | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| FMCOLL | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| TMCOLA | 44,103 | 950 | 7,377,387 | - | - | - | - | - | - |
| TMCOLB | 44,103 | 950 | 7,377,387 | - | - | - | - | - | - |
| TMCOLL | 44,103 | 950 | 7,377,387 | - | - | - | - | - | - |
| GMCOLA | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| GMCOLB | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| GMCOLL | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| ICOLA | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,416 | 29,349 | 1,844 | 10,331,074 |
| ICOLB | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| ICOLL | 44,070 | 953 | 7,376,594 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
| Min | 44,068 | 950 | 7,376,594 | 35,775 | 891 | 10,090,482 | 29,349 | 1,844 | 10,331,074 |
| Max | 44,103 | 954 | 7,377,387 | 35,809 | 891 | 10,099,578 | 29,349 | 1,844 | 10,331,074 |
a
The total number of PBs, with both phenotypes and genotypes were 891. However, for these traits, there were extreme phenotypic records which were removed in the analyses to check if the GWAS, results would improve. Due to little changes in GWAS, results for PBs, those removed individuals were added to the analyses of combined CBs, and PBs. CB, crossbred; PB, purebred; WGS, whole-genome sequence; N, number of animals.