Table 2.
Summary of significant SNPs and nearest genes detected at false discovery rate of 5% for body weight and antibody response to Newcastle disease in indigenous chicken in Rwanda.
| Traits | SNP ID | CHR | SNP position (bp) | GWAS value of p | Allele | Candidate gene | Distance (bp) | Biological function |
|---|---|---|---|---|---|---|---|---|
| BW | rs740980181 | 8 | 5,672,840 | 1E−10 | A | PBX1 | Within | Positive regulation of cell proliferation and negative regulation of neuron differentiation |
| rs13792572 | 11 | 10,145,725 | 7.6E−09 | G | GPATCH1 | 7,341D | mRNA processing | |
| rs314702374 | 19 | 8,356,215 | 8E−08 | G | MPHOSPH6 | 22,019U | Maturation of 5.8S rRNA | |
| rs14123335 | 11 | 15,831,341 | 8.4E−07 | C | MRM1 | 54U | Enzyme-directed rRNA 2'-O-methylation | |
| IR | rs314787954 | 1 | 137,692,275 | 4E−10 | C | CDC16 | Within | Protein K11-linked ubiquitination |
| rs13623466 | 1 | 129,958,897 | 6.42E−08 | T | ZBED1 | 7,631U | Regulation of transcription from RNA polymerase II promoter | |
| rs13910430 | 1 | 101,256,943 | 1E−07 | T | MX1 | 29,169U | Innate immune response, organelle fission, and defense response to the virus | |
| rs737507850 | 1 | 50,383,558 | 1.55E−07 | C | GRAP2 | 44,310U | Leukocyte-specific protein-tyrosine kinase signaling, innate and adaptive immune response |
CHR, chromosome; BW, body weight; IR, immune response to Newcastle disease; SNP, Single nucleotide polymorphism; PBX1, pre-B-cell leukaemia homeobox 1; GPATCH1, G-patch domain containing 1; MPHOSPH6, M-phase phosphoprotein 6; MRM1, mitochondrial rRNA methyltransferase 1; CDC16, cell division cycle 16; ZBED1, zinc finger, BED-type containing 1; MX1, myxovirus (influenza virus) resistance 1; GRAP2, GRB2 related adaptor protein 2; superscript letters U and D indicate that the SNP is located upstream and downstream of the nearest gene, respectively.