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. 2022 Apr 20;12(9):1057. doi: 10.3390/ani12091057

Table 2.

Significant SNPs and Indels of GLM GWAS for teat number-related traits.

SNP Trait SSC Position Effect p-Value QTLs * Annotation Gene (Distance from the Gene in bp)
chr9:130956708 LTN 9 130956708 0.64 3.85 × 10−8 intronic PACC1(within), NENF(within)
rs345573243 RTN 18 47399908 0.62 1.60 × 10−8 24,290, 7470 intronic OSBPL3(within)
rs703282466 MAXAP 3 106788730 0.45 2.29 × 10−8 5224, 8797, 8798, 4250, 4256 intergenic LTBP1(63796), ENSSSCG00000050704(9889)
chr15:137183045 TNUM 15 137183045 −0.79 7.02 × 10−8 223,293 intronic MLPH(within)
rs345573243 TNUM 18 47399908 0.96 6.25 × 10−8 24,290, 7470 intronic OSBPL3(within)
rs1108940033 ADIFF 1 45796983 0.61 2.19 × 10−8 intergenic PHF3(500583),ENSSSCG00000049526(273685)
rs321204530 ADIFF 1 177056841 0.59 1.44 × 10−8 5223, 5255, 822, 845, 1250 intronic MDGA2(within)
rs318957512 ADIFF 2 97849348 0.50 5.79 × 10−8 intronic ADGRV1(within)
rs326371568 ADIFF 2 123586226 0.62 3.87 × 10−10 4255 intergenic FAM170A(119517),PRR16(613282)
rs342451777 ADIFF 2 127224122 0.57 8.31 × 10−9 4255 intergenic ENSSSCG00000042143(13463),ENSSSCG00000040936(55836)
rs325963999 ADIFF 3 19301837 0.66 9.15 × 10−9 5224, 7455, 7472 intronic KATNIP(within)
rs326276043 ADIFF 6 34051848 0.55 6.98 × 10−8 24,289 intergenic ENSSSCG00000050973(273191),CYLD(8093)
rs338649298 ADIFF 8 129552162 0.59 2.22 × 10−9 intergenic SNCA(163855),ENSSSCG00000043431(95940)
rs321470648 ADIFF 9 10769337 0.45 5.38 × 10−8 intergenic ENSSSCG00000046278(36887),ENSSSCG00000045225(26362)
rs1109963100 ADIFF 10 2911179 0.80 3.37 × 10−10 intergenic ENSSSCG00000042899(210778),BRINP3(52348)
rs339887165 ADIFF 13 12135388 0.68 1.46 × 10−8 7479 intergenic ENSSSCG00000044771(16544),ENSSSCG00000051554(31818)
chr13:39266305 ADIFF 13 39266305 0.72 1.88 × 10−8 7479 intronic DNAH12(within)
rs701874475 ADIFF 13 134665423 −0.51 2.19 × 10−8 7479 intergenic LMLN(8675),ENSSSCG00000050583(21280)
rs338558804 ADIFF 13 179683904 −0.45 3.49 × 10−8 intergenic ENSSSCG00000038062(120975),NRIP1(140958)
rs343864506 ADIFF 13 187708682 −0.54 3.72 × 10−8 intergenic ENSSSCG00000047308(444803),ENSSSCG00000050420(500018)
rs334271954 ADIFF 14 62959726 0.52 5.70 × 10−8 intergenic FAM13C(33877),SLC16A9(66937)
rs1109225784 ADIFF 15 12581324 0.64 1.96 × 10−9 intergenic U6(133156),U6(186459)
rs326978910 ADIFF 15 84015934 0.38 3.38 × 10−8 7468 intronic OSBPL6(within)
rs334746473 ADIFF 15 97200323 0.75 4.23 × 10−10 7468 intergenic ENSSSCG00000046205(186079),U2(688281)
rs322863105 ADIFF 17 7610979 −0.88 6.01 × 10−11 intergenic ENSSSCG00000045345(132678),ENSSSCG00000047202(438984)
chr17:8221026 ADIFF 17 8221026 0.79 1.47 × 10−9 intergenic U6(19092),FAT1(227734)
rs330045817 ADIFF 17 8536301 −0.71 3.76 × 10−10 ncRNA_intronic FAT1(within)
rs324534432 ADIFF 17 13364668 0.79 1.47 × 10−9 intergenic PSD3(100469),ENSSSCG00000046441(3798)
Indel
chr6:7472906 LTN 6 7472906 −0.41 1.06 × 10−6 24,289 intronic CDYL2(within)
rs695882779 LTN 9 3690507 0.39 9.84 × 10−7 ncRNA_intronic ENSSSCG00000049604(within)
chr9:119650540 LTN 9 119650540 −0.30 3.62 × 10−7 intergenic ENSSSCG00000044083(337170),ENSSSCG00000050832(4698)
rs792699200 LTN 9 130899869 0.51 4.41 × 10−7 intronic PACC1(within)
chr12:44292044 LTN 12 44292044 −0.37 9.55 × 10−7 5227, 5261, 6472, 6479, 595, 2929 intronic NOS2(within)
chr13:194617904 LTN 13 194617904 −0.31 1.30 × 10−6 intergenic KRTAP11-1(111382),ENSSSCG00000047315(5813)
rs709659410 RTN 5 17969771 0.42 5.28 × 10−7 2927 intergenic KRT73(2682),KRT2(14544)
chr6:9186279 RTN 6 9186279 0.89 2.28 × 10−7 24,289 intronic WWOX(within)
rs790747253 RTN 15 100810568 −0.61 1.28 × 10−6 7468 intronic PGAP1(within)
chr18:48316684 RTN 18 48316684 0.41 7.00 × 10−8 24,290, 7470 intronic STK31(within)
chr3:98429885 MAXAP 3 98429885 0.50 2.93 × 10−7 5224, 8797, 8798 intergenic ENSSSCG00000045166(59604),ENSSSCG00000046007(449247)
rs793312568 MAXAP 3 106792080 0.43 8.28 × 10−8 5224, 8797, 8798, 4250, 4256 intergenic LTBP1(67153),ENSSSCG00000050704(6530)
chr6:9186279 MAXAP 6 9186279 0.82 1.59 × 10−6 24,289 intronic WWOX(within)
chr6:30642639 MAXAP 6 30642639 0.43 1.31 × 10−6 24,289 intergenic ENSSSCG00000047270(70049),ENSSSCG00000041426(189382)
chr9:131996847 MAXAP 9 131996847 −0.49 1.46 × 10−6 intronic ENSSSCG00000040650(within)
chr14:12750600 MAXAP 14 12750600 0.43 1.31 × 10−6 intronic HMBOX1(within)
rs790747253 MAXAP 15 100810568 −0.60 1.17 × 10−6 7468 intronic PGAP1(within)
rs711984029 MAXAP 17 13041965 −0.47 1.68 × 10−6 intronic PSD3(within)
rs793312568 TNUM 3 106792080 0.63 1.41 × 10−6 5224, 8797, 8798, 4250, 4256 intergenic LTBP1(67153),ENSSSCG00000050704(6530)
chr5:75592729 TNUM 5 75592729 0.98 8.38 × 10−7 intronic NELL2(within)
rs792699200 TNUM 9 130899869 1.00 9.67 × 10−7 intronic PACC1(within)
chr18:48316684 TNUM 18 48316684 0.62 4.01 × 10−7 24,290, 7470 intronic STK31(within)
chr1:44096236 LR 1 44096236 0.69 1.25 × 10−7 intergenic ENSSSCG00000042072(159101),ENSSSCG00000045405(51729)
chr1:44973455 ADIFF 1 44973455 0.70 1.96 × 10−7 intronic ZUP1(within),RSPH4A(within)
chr1:46840905 ADIFF 1 46840905 0.71 5.46 × 10−8 intergenic ENSSSCG00000050391(123491),U6(392319)
chr1:65957275 ADIFF 1 65957275 0.43 1.14 × 10−7 intergenic FBXL4(21578),FAXC(274880)
chr1:77875820 ADIFF 1 77875820 0.42 8.57 × 10−8 intergenic FYN(65243),U6(107381)
chr1:118273285 ADIFF 1 118273285 −0.64 1.96 × 10−9 5223, 6481, 5255 intergenic ENSSSCG00000049391(9019),ENSSSCG00000045826(5556)
rs1113667849 ADIFF 2 123584099 0.55 8.50 × 10−7 4255 intergenic FAM170A(117391),PRR16(615405)
chr3:54080763 ADIFF 3 54080763 0.44 1.70 × 10−6 5224, 7455, 7472, 6465 intergenic LONRF2(99093),REV1(54761)
chr3:122749868 ADIFF 3 122749868 0.76 1.91 × 10−7 intergenic LRATD1(17941),ENSSSCG00000045589(179131)
chr6:9702570 ADIFF 6 9702570 0.61 3.15 × 10−7 24,289 intronic WWOX(within)
chr6:29725029 ADIFF 6 29725029 −0.41 1.54 × 10−7 24,289 intergenic ENSSSCG00000034192(132519),CES5A(117783)
chr7:48226837 ADIFF 7 48226837 0.67 1.74 × 10−6 5257 intronic RASGRF1(within)
chr8:3878010 ADIFF 8 3878010 −0.48 4.61 × 10−7 7477 intronic ENSSSCG00000027349(within)
chr8:131927486 ADIFF 8 131927486 0.68 1.46 × 10−8 intergenic AFF1(2666),ENSSSCG00000032190(41799)
chr13:134712100 ADIFF 13 134712100 −0.50 2.83 × 10−7 7479 intergenic ENSSSCG00000050583(20384),OSBPL11(6327)
chr13:188309252 ADIFF 13 188309252 0.35 4.51 × 10−7 intergenic ENSSSCG00000050420(95234),ENSSSCG00000043493(500979)
chr13:191714830 ADIFF 13 191714830 0.76 1.91 × 10−7 intergenic ENSSSCG00000051384(248028),ENSSSCG00000048685(53357)
chr15:12585471 ADIFF 15 12585471 0.67 1.74 × 10−6 intergenic U6(137304),U6(182308)
chr15:84277014 ADIFF 15 84277014 0.53 6.57 × 10−9 7468 intergenic ENSSSCG00000036052(46519),ENSSSCG00000038561(122000)
rs792656057 ADIFF 16 69550278 −0.60 8.69 × 10−7 5228 intronic GRIA1(within)
rs793561441 ADIFF 17 5622328 −0.33 9.14 × 10−8 intronic PCM1(within)
rs700363122 ADIFF 17 8173767 0.60 1.13 × 10−8 intergenic ENSSSCG00000047202(116838),U6(28063)
rs789477433 ADIFF 18 25541841 0.43 8.35 × 10−7 24,290 intergenic ENSSSCG00000048651(270433),FAM3C(27695)

* QTL number in PigQTL database. Effect means additive effect. LTN: the number of teats on the left side; RTN: the number of teats on the right side; TNUM: the total number of teats (TNUM = LTN + RTN); MAXAP: the maximum number of teats in LTN and RTN (MAXAP); L-R: the difference between the two sides (L-R = LTN − RTN); ADIFF: the absolute difference between left and right teat number (ADIFF = |LTN − RTN|).