Table 4 Number of outlier SNPs detected (q-value ≤ 0.05) by BayeScan and their respective candidate genes within 5 kb up- or downstream
From: Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs
Pairwise comparison of lines | Number of outlier SNPs | Candidate genes | General term GO BP |
|---|---|---|---|
CNF–TN | 93 | CDC6, CIB4, CLEC1A, CLEC7A, ENSSSCG00000000959, ENSSSCG00000007221, ENSSSCG00000008799, ENSSSCG00000012012, ENSSSCG00000020566, ENSSSCG00000025389, ENSSSCG00000027643, ENSSSCG00000027841, ENSSSCG00000028250, GALM, GDE1, LAPTM5, LRRK2, RAB39A, SLC35F2, TCN1 | Cell cell signaling/immune, cell communication, cell cycle, intracellular transport, metabolic process, skeletal muscle function and regeneration, system process, transmembrane transport |
DL–TN | 53 | ABRACL, BECN1, CCDC6, ENSSSCG00000010218, GARS, KIAA0513, MINDY4, NOL10, REPS1, SPNS2, SPNS3, UST, WNK4 | (Cell) development/differentiation, cell communication, cellular processes, gene expression, intracellular transport, metabolic process |
DN–TN | 46 | CACNG3, CD48, CFAP45, DDX42, ENSSSCG00000024706, ENSSSCG00000026756, ENSSSCG00000027460, GLO1, GOT1, KSR1, PKHD1L1, ssc-mir-4331, TSPAN11 | Cell communication, cellular processes, immune, intracellular transport, metabolic process |
FL–TN | 18 | EHBP1L1, KCNK7, MPP7, VAT1L, ZNF354C | Intracellular transport, metabolic process |
FZ–TN | 21 | FZD2, IL17REL, PLEKHM1, WDR92 | Cellular process, developmental processes, intracellular transport |
SB–TN | 7 | – |  |