TABLE 4.
Most significant SNPs detected with FST analysis and the associated genes.
| Population | SNP | Chr | Position | Genes | Function |
| ALN and WAT | rs81355030 | 1 | 84,376,735 | RPL18 | Acute heat stress (Newton et al., 2012) |
| rs81367521 | 2 | 150,546,025 | IL17B | Embryonic development, tissue regeneration and inflammation (Bie et al., 2017) | |
| rs81285672 | 12 | 23,638,629 | ARHGAP23 | Inflammatory response (Liu, 2015) | |
| DUR and | rs81353971 | 1 | 49,024,494 | ADGRB3 | Growth traits (Emrani et al., 2017) |
| WAT | rs81353988 | 1 | 49,350,539 | ADGRB3 | |
| rs81353991 | 1 | 49,392,902 | ADGRB3 | ||
| rs81297001 | 1 | 49,458,254 | ADGRB3 | ||
| rs81333295 | 1 | 49,592,586 | ADGRB3 | ||
| rs80946298 | 13 | 33,531,504 | DOCK3 | Induces axonal growth (Kimura et al., 2016) | |
| rs81444796 | 13 | 33,481,604 | DOCK3 | ||
| rs81478683 | 13 | 34,024,632 | IQCF3 | Conjunctival UV to auto fluorescence (Yazar et al., 2015) | |
| rs81478482 | 13 | 34,117,528 | ACY1 | Amino acid and heat shock protein (Martínez-Montemayor et al., 2008) | |
| rs81454214 | 15 | 107,134,695 | CD28 | Endometrial gene expression (Gu et al., 2014) | |
| KOL and WAT | rs81341610 | 3 | 4,508,681 | LOC102160627 | Uncharacterized |
| rs80993200 | 4 | 234,605 | ARHGAP39 | Milk production related and mastitis resistance (Wang et al., 2015) | |
| rs80851822 | 5 | 13,913,761 | POLR3B | Residual feed intake (Gondret et al., 2017) | |
| rs80873063 | 5 | 13,940,475 | TCP11L2 | Regulated in small atretic follicles for healthy follicles (Hatzirodos et al., 2014a) | |
| rs80999600 | 5 | 66,998,856 | TSPAN9 | ADG (Fontanesi et al., 2014) | |
| rs80929588 | 5 | 67,092,749 | TSPAN9 | ||
| rs80883075 | 5 | 67,132,255 | TEAD4 | Regulation in organ size control and cell proliferation (Frankenberg et al., 2016) | |
| rs81385003 | 5 | 67,297,728 | ITFG2 | Disease resistance (Moioli et al., 2016) | |
| rs81285672 | 12 | 23,638,629 | ARHGAP23 | Inflammatory response (Liu, 2015) | |
| rs81325261 | 12 | 44,771,203 | FOXN1 | Regulation of hair follicle development (Song et al., 2017) | |
| rs80801871 | 13 | 33,170,033 | DOCK3 | Induces axonal growth (Kimura et al., 2016) | |
| rs80802886 | 13 | 33,202,454 | DOCK3 | ||
| rs81444784 | 13 | 33,306,071 | DOCK3 | ||
| rs81444796 | 13 | 33,481,604 | DOCK3 | ||
| rs80946298 | 13 | 33,531,504 | DOCK3 | ||
| rs81478683 | 13 | 34,024,632 | IQCF3 | Conjuctival UV to auto fluorescence (Yazar et al., 2015) | |
| rs335091311 | 15 | 148,461 | STAM2 | Residual feed intake (Gondret et al., 2017) | |
| rs80852223 | 15 | 77,232,829 | TLK1 | Decrease expression in the endometrium (Gray et al., 2006) | |
| rs80999734 | 15 | 77,318,065 | TLK1 | ||
| rs81453662 | 15 | 78,190,260 | DLX1 | Muscling and meat availability (Li et al., 2010) | |
| LWT and WAT | rs81349766 | 1 | 182,224,202 | GPR137C | Litter size (Sosa-Madrid et al., 2018) |
| rs81296498 | 1 | 182,722,677 | DDHD1 | Lipid metabolism (Parker Gaddis et al., 2018) | |
| rs81349773 | 1 | 182,756,343 | DDHD1 | ||
| rs332395415 | 1 | 246,195,557 | ABCA1 | Mediates the transport of excess cholesterol (Schwartz et al., 2000) | |
| rs321979518 | 1 | 246,199,966 | ABCA1 | ||
| rs81383185 | 5 | 21,606,108 | RNF41 | Lipid rafts in immune signalling (McGraw and List, 2017) | |
| rs80820161 | 5 | 21,745,636 | STAT2 | Milk production (Salehi et al., 2015) | |
| rs80894897 | 5 | 21,727,701 | PAN2 | Fat yield (Suchocki et al., 2016) | |
| rs80940129 | 5 | 21,970,939 | BAZ2A | Nutrition related (Cornelis and Hu, 2013) | |
| rs325229936 | 5 | 22,338,939 | MYO1A | Coat color and pigmentation (Gutiérrez-Gil et al., 2007) | |
| rs81285672 | 12 | 23,6386,29 | ARHGAP23 | Inflammatory response (Liu, 2015) | |
| rs80854565 | 14 | 89,185,576 | ARHGAP22 | Fertility (Browett et al., 2018) | |
| rs80833618 | 14 | 89,227,581 | ARHGAP22 | ||
| rs80957034 | 14 | 89,255,703 | ARHGAP22 | ||
| rs80962102 | 14 | 89,309,115 | ARHGAP22 | ||
| SAL and WAT | rs81395957 | 6 | 51,328,753 | NECTIN2 | Cell recognition and adhesion (Wang et al., 2010) |
| rs81395929 | 6 | 51,427,663 | CLPTM1 | Marbling score (Lim et al., 2013) | |
| WIN and WAT | rs81381252 | 4 | 65,339 | ZNF609 | Fertility (Hatzirodos et al., 2014b) |
| rs81285672 | 12 | 23,638,629 | ARHGAP23 | Inflammatory response (Liu, 2015) | |
| rs81325261 | 12 | 44,771,203 | FOXN1 | Regulation of hair follicle development (Song et al., 2017) | |
| rs331955329 | 13 | 66,004,327 | MTMR14 | Reduced with age accelerates skeletal muscle aging (Romero-Suarez et al., 2010) | |
| rs80971430 | 13 | 66,026,240 | BRPF1 | Intramuscular fatty acid (Puig-Oliveras et al., 2016) | |
| rs80945527 | 13 | 66,104,857 | ARPC4 | Mastitis resistance (Grossi et al., 2014) | |
| rs80885182 | 13 | 66,270,725 | FANCD2 | Muscle weight (Lionikas et al., 2010) | |
| rs45430493 | 13 | 66,515,894 | SEC13 | Muscle weight (Lionikas et al., 2012) | |
| rs81248260 | 13 | 66,583,753 | ATPB2 | Heat stress on reproductive performance (Dash et al., 2016) | |
| rs81446451 | 13 | 66,668,301 | ATPB2 | ||
| rs81446497 | 13 | 66,691,206 | ATPB2 | ||
| rs81446475 | 13 | 66,725,741 | ATPB2 | ||
| rs81446484 | 13 | 66,777,686 | ATPB2 | ||
| rs81478601 | 13 | 66,795,578 | ATPB2 | ||
| IND and DUR | rs80866460 | 4 | 106,698,421 | PTPN22 | Immune response (Lamsyah et al., 2009) |
| rs81413279 | 9 | 79,010,742 | NXPH1 | DMI (Olivieri et al., 2016) | |
| rs81413279 | 9 | 79,010,742 | ABCB5 | Immune function (Lee et al., 2017) | |
| rs81306790 | 6 | 89,661,963 | PHC2 | Mastitis (Chen et al., 2015) | |
| rs80854994 | 4 | 106,719,032 | PTPN22 | Immune response (Lamsyah et al., 2009) | |
| rs80854994 | 4 | 106,719,032 | BCL2L15 | Mastitis (Chen et al., 2015) | |
| Villages and DUR | rs81282695 | 6 | 94,442,844 | POU3F1 | Neurobehavioral functioning (Eusebi et al., 2018) |
| rs81282695 | 6 | 94442844 | FHL3 | Carcass traits (Zuo et al., 2004, 2007) | |
| Villages and KOL | rs81430450 | 11 | 24,063,007 | DNAJC15 | Feeding efficiency (Reyer et al., 2017a) |
| rs81430450 | 11 | 24,063,007 | EPSTI1 | Fertility traits (Gaddis et al., 2016), fat deposition (Zhang et al., 2018) | |
| SAL&LWT and IND | rs81232179 | 8 | 51,070,662 | FSTL5 | Meat quality (Ryu and Lee, 2016); skeletal muscle (Novianti et al., 2010) |
| rs45431508 | 8 | 69,912,174 | CXCL8 | Pig disease (Wang et al., 2019) | |
| rs81400554 | 8 | 55,181,102 | CEP135 | Intramuscular fat (Hamill et al., 2012); milk production (Rui et al., 2013) | |
| rs81400554 | 8 | 55,181,102 | EXOC1 | Marbling score (Wu et al., 2016) | |
| rs81400740 | 8 | 63,119,376 | EPHA5 | Feed efficiency (Reyer et al., 2017b) | |
| rs81400500 | 8 | 52,213,568 | NPY5R | Feed efficiency and fat deposition (Chen et al., 2018) | |
| rs81400500 | 8 | 52,213,568 | NPY1R | Feed efficiency and fat deposition (Chen et al., 2018) | |
| rs81302014 | 8 | 69,950,857 | RASSF6 | Body conformation (Fang and Pausch, 2019) | |
| rs80904678 | 11 | 15,274,089 | FOXO1 | Meat quality and carcass traits (Ropka-Molik et al., 2018) | |
| rs81400500 | 8 | 52,213,568 | SLC7A11 | Feed efficiency (Vigors et al., 2016) | |
| rs81300083 | 9 | 78,940,661 | NXPH1 | DMI (Olivieri et al., 2016) | |
| IND and VIT | rs81350922 | 1 | 257,096,974 | ASTN2 | Carcass weight in cattle (Júnior et al., 2016) |
| rs80970078 | 14 | 43,524,181 | MYO18B | Meat quality and carcass traits (Ropka-Molik et al., 2018) | |
| DRGA0006738 | 6 | 117,857,953 | NOL4 | Fatness (Li et al., 2011) | |
| rs80860919 | 1 | 64,018,444 | GPR63 | Fertility traits (Moran et al., 2017) | |
| rs80921694 | 13 | 73,023,057 | PLXNA1 | Meat quality (Martínez-Montes et al., 2016) | |
| rs81327396 | 12 | 53,063,765 | DNAH2 | Intramuscular fat (Luo et al., 2012); carcass weight (Kang et al., 2013) | |
| Villages and WBO | rs81244815 | 2 | 50,167,007 | SWAP70 | Disease resistance (Ma et al., 2011; Zhang et al., 2018) |
| rs81244815 | 2 | 50,167,007 | SBF2 | Fertility (Zhang et al., 2014); immune function (Ibeagha-Awemu et al., 2016) | |
| rs81401075 | 8 | 73,841,435 | FRAS1 | Sow reproductive traits (Fischer et al., 2015), feed efficiency (Messad et al., 2019) | |
| rs81401075 | 8 | 73,841,435 | NPY2R | Obesity (Siddiq et al., 2007; Hunt et al., 2011) | |
| Villages and VIT | INRA0003181 | 1 | 95,198,598 | SLC14A2 | Conformation traits (Le et al., 2017) |
| rs81332040 | 6 | 45,777,816 | ZNF382 | Conformation traits (Le et al., 2017) | |
| INRA0045852 | 14 | 10,3086,988 | HECTD2 | Fat and meat quality traits (Piórkowska et al., 2018) | |
| rs80980839 | 4 | 93,722,493 | RHBG | Ammonia transporter (Xiang et al., 2016) | |
| rs80971176 | 5 | 49,876,132 | SOX5 | Ear morphology (Edea et al., 2017) | |
| WBO and DUR | rs80837120 | 1 | 565,627 | TCTE3 | Involved in spermatogenesis (Du et al., 2016) |
| rs81389959 | 6 | 88,334,239 | PTP4A2 | Reproductive traits (Verardo et al., 2016); intramuscular fat (Martínez-Montes et al., 2016) | |
| rs81390106 | 6 | 88,751,010 | TMEM39B | Intramuscular Fat (Cesar et al., 2018) | |
| rs81390106 | 6 | 88,751,010 | TXLNA | Meat quality (Ropka-Molik et al., 2018) | |
| rs81390106 | 6 | 88,751,010 | HDAC1 | Altitude (Ban et al., 2015) | |
| rs81390106 | 6 | 88,751,010 | MARCKSL1 | Feed intake (Lindholm-Perry et al., 2016) | |
| rs81317489 | 6 | 89,640,457 | ZSCAN20 | Scrotal circumference (Sweett et al., 2018) | |
| rs81317489 | 6 | 89,640,457 | CSMD2 | Meat pH trait (Dong et al., 2014); Body weight (Yoshida et al., 2017) | |
| rs80894853 | 9 | 78,663,586 | NXPH1 | DMI (Olivieri et al., 2016) | |
| rs81389936 | 6 | 88,264,983 | COL16A1 | Carcass and meat quality traits (Choi et al., 2012) | |
| rs80790807 | 4 | 106,750,789 | PTPN22 | Immune response (Lamsyah et al., 2009) | |
| rs80790807 | 4 | 106,750,789 | BCL2L15 | Mastitis (Chen et al., 2015) | |
| rs80911350 | 14 | 11,345,116 | SCARA3 | Meat quality traits (Tizioto et al., 2015) | |
| rs80911350 | 14 | 11,345,116 | CLU | Fertility (Kumar et al., 2015), intramuscular fat (de Jager et al., 2013) | |
| rs343528814 | 13 | 36,608,977 | CACNA2D3 | Reproductive traits (Smith et al., 2019); body width in gilts and sows (Rothschild, 2010), body weight traits (Borowska et al., 2017), altitude (Zhang et al., 2014) | |
| rs81478390 | 13 | 53,707,241 | RYBP | Body conformation traits - body weight, body length, body height, and chest circumference (Zhou et al., 2016) | |
| rs81330369 | 9 | 7,449,894 | FCHSD2 | Milk production traits (Kemper et al., 2015) | |
| rs80975991 | 7 | 33,481,446 | ZFAND3 | Growth and carcass quality traits (Li and Kim, 2015) | |
| rs80855522 | 4 | 11,0552,282 | GNAI3 | Heat tolerance (Berihulay et al., 2019) | |
| rs80988392 | 1 | 213,780,848 | PTPRD | Meat quality (Raschetti et al., 2013) | |