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. 2021 Jun 6;52(4):440–450. doi: 10.1111/age.13095

Table 1.

Top genome regions associated with the number of teats in Italian Large White and Italian Landrace pigs. Results are stratified by population and chromosome.

Genome scan1 SSC2 Pos3 Marker4 Min/Maj5 MAF6 β 7 P 8 QTLs9 Genes10
Italian Large White
Haplotype‐based 7 97435001 CHR7_B973 H/N 0.426 0.188 1.61 × 10−15 NNF, TVN, VN ENTPD5, FAM161B, VRTN, ABCD4, ALDH6A1, SYNDIG1L, VSX2, BBOF1, COQ6, LIN52, ZNF410
Single‐marker 7 97652632 MARC0038565 A/G 0.482 −0.163 2.65 × 10−12 TVN VRTN , SYNDI1GL
Single‐marker 10 47751164 M1GA0014145 A/G 0.477 −0.135 2.83 × 10−8 – FRMD4A
Haplotype‐based 10 48035001 CHR10_B479 H/N 0.367 −0.129 1.56 × 10−8 LTN FRMD4A , PRPF18, BEND7
Single‐marker 12 24723142 MARC0031045 G/A 0.358 0.117 1.03 × 10−6 THVN SKAP1, HOXB1
Italian Landrace
Haplotype‐based 3 120600001 CHR3_B1205 H/N 0.014 −1.048 8.40 × 10−8 THVN RAD51AP2, FAM49A
Haplotype‐based 6 113000001 CHR6_B1129 H/N 0.062 −0.466 1.95 × 10−7 – CDH2
Haplotype‐based 8 4500001 CHR8_B44 H/N 0.011 −1.142 9.30 × 10−9 NFN C8H4orf50, JAKMIP1, WFS1, LOC102165510, PPP2R2C
Haplotype‐based 11 18900001 CHR11_B188 H/N 0.034 −0.529 1.55 × 10−7 – FNDC3A, CYSLTR2, RCBTB2
Haplotype‐based 13 189100001 CHR13_B1890 H/N 0.016 −0.957 5.43 × 10−9 MI ATP5J, GABPA, JAM2, MRPL39
Haplotype‐based 14 132300001 CHR14_B1322 H/N 0.014 −0.953 1.73 × 10−7 – C14H10orf120, LOC100620521, AWN, LOC100519221, FAM24B, SPMI, DMBT1, PSP‐II, AQN‐1, HTRA1, PSP‐I
Haplotype‐based 14 114800001 CHR14_B1147 H/N 0.051 −0.547 1.79 × 10−7 – COL17A1, SH3PXD2A, STN1, SLK
Single‐marker 14 23582019 WU_10.2_14_25047530 A/G 0.078 −0.445 3.18 × 10−7 – SFSWAP
Haplotype‐based 15 134400001 CHR15_B1343 H/N 0.030 −0.951 8.08 × 10−16 BW, BL, LW, TNBA, LS

TRPM8, SPP2

Close to ARL4C

Haplotype‐based 15 19300001 CHR15_B192 H/N 0.013 −0.877 6.29 × 10−8 – NCKAP5
Haplotype‐based 16 57400001 CHR16_B573 H/N 0.024 −0.806 6.15 × 10−8 – TENM2
Haplotype‐based 16 68700001 CHR16_B686 H/N 0.017 −0.993 5.08 × 10−9 – SAP30L, HAND1, GALNT10
1

Genome scans performed within each pig population. SNPs and Haplotypes indicate which DNA markers have been used to carry out the genome scans.

2

Sus scrofa chromosome.

3

Position, in bp, on the Sus scrofa reference genome (v.11.1).

4

DNA marker identifier reported in the chip panels. For haplotypes, the haploblock identifier (chromosome specific) is reported.

5

Minor/Major alleles. Haplotypes have been treated as bi‐allelic variants (H = haplotype allele and N = other N alleles).

6

Minor allele frequency.

7

Regression coefficient. A positive value indicates that the no. of teats increases with the increasing of the number of copies of the minor allele. A negative value indicates that the no. of teats decreases with the increasing of the number of copies of the minor allele.

8

P at the Wald test (GEMMA).

9

QTLs related to reproductive traits overlapping the association peaks. Short names for QTL are: BL, body length; BW, body width; LS, litter size; LTN, left teat number; LWT, litter weight; MI, maternal infanticide; NFN, non‐functional nipples; NNF, number of non‐viable foetuses; THVN, thoracolumbar vertebra number; TNBA, total number of born alive; TVN, thoracic vertebra number; VN, vertebra number.

10

Genes overlapping the haplotype or closed to a SNP. The candidate genes are reported in bold.