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. 2019 Nov 26;98(1):skz360. doi: 10.1093/jas/skz360

Table 4.

Summary of the windows within the three chromosomes and three genomic regions that explained the higher genomic variance for carcass quality traits in purebred pigs with a list of annotated genes in the proximity of each window1

Trait Windows Chr σ 2, % Start, Mb Stop, Mb Genes SNP σ 2 PB, % σ 2 CB, % P-value
Back fat 3 13 1.51 47.6 48.6 SLC25A26, LRIG1, ENSSSCG00000020125, KBTBD8 rs80885388 0.022 0.000019 5.66 × 10–6
3 13 1.41 198.2 199.1 RUNX1, CLIC6, ENSSSCG00000025700, ENSSSCG00000012052 rs81229953 0.020 0.00074 6.88 × 10–6
4 18 1.35 26.9 27.5 KIAA1549, ATP6V0A4, ENSSSCG00000035963, ENSSSCG00000018723, SVOPL, TRIM24 rs81468050 0.0017 0.0012 8.68 × 10–6
Loin depth 15 16 4.02 32.4 35.4 ENSSSCG00000016901, ENSSSCG00000016902, ENSSSCG00000016903, GPX8, MIR449A, MIR449B, MCIDAS, CCNO, DHX29, MTREX, ENSSSCG00000031138, ENSSSCG00000037130, PLPP1, SLC38A9, DDX4, ENSSSCG00000032013, IL31RA, IL6ST rs81479214 0.043 0.0070 3.76 × 10–6
1 2 3.34 0.006 0.466 ENSSSCG00000014554, ODF3, BET1L, RIC8A, SIRT3, PSMD13, ENSSSCG00000014554, NLRP6, PGGHG, IFITM5, ENSSSCG00000014565, ENSSSCG00000038912, ENSSSCG00000032436, ENSSSCG00000032591, ENSSSCG00000038005, B4GALNT4, PKP3, ANO9, ENSSSCG00000024389, PTDSS2, RNH1, HRAS, LRRC56, LMNTD2, RASSF7, ENSSSCG00000024389, PHRF1, IRF7, CDHR5, ENSSSCG00000040951, DRD4, DEAF1, ENSSSCG00000012849, EPS8L2, ENSSSCG00000012847 rs343026684 0.072 0.018 7.39 × 10–6
4 16 3.18 33.5 33.7 IL31RA, IL6ST ANKRD55, ENSSSCG00000038692, ENSSSCG00000036369, NDUFS4, ENSSSCG00000034649, ARL15, ENSSSCG00000016892 rs80986934 0.044 0.0064 3.72 × 10–6
ADG 8 1 2.26 10.2 10.9 rs80916931 0.031 0.0013 5.59 × 10–6
4 16 2.26 5.8 6.3 MYO10, ENSSSCG00000034022, ENSSSCG00000021807 rs81344589 0.039 0.00085 6.98 × 10–6
4 18 1.45 18.8 18.9 UBE2H, ENSSSCG00000040437, ENSSSCG00000018417, ENSSSCG00000018762, ENSSSCG00000018739, NRF1, SMKR1, STRIP2, AHCYL2, ENSSSCG00000019583, SMO, ENSSSCG00000019904 rs81472316 0.034 0.00012 5.81 × 10–6

1SNP = marker with largest variance within windows.

2Genetic variance of the marker with largest impact within window for purebred (σ2PB) and crossbred (σ2CB), expressed as percentage of total genetic variance, respectively.