Genome-wide detection of allele frequency change and quantitative trait loci for respiratory disease and immune-related traits in Landrace pigs selected for Mycoplasmal pneumonia of swine resistance

Yoshinobu Uemoto1†*, Kasumi Ichinoseki1†, Toshimi Matsumoto2, Nozomi Oka3, Hironori Takamori3, Hiroshi Kadowaki3, Chihiro Kojima-Shibata3, Eisaku Suzuki3, Toshihiro Okamura4, Hisashi Aso1, Haruki Kitazawa1, Masahiro Satoh1, Hirohide Uenishi2, Keiichi Suzuki1

1Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan. 2Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan 3Miyagi Prefecture Animal Industry Experiment Station, Osaki, Miyagi 989-6445, Japan 4Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki 305-0901, Japan

†These authors have contributed equally to this work and share first authorship. *Correspondence author

Supplementary table Table S2. The SNPs above the 99.9-threshold and the 99.99-threshold based on changes in allele frequency from the first generation (G1) to the fifth generation (G5). Table S2. The SNPs above the 99.9-threshold and the 99.99-threshold based on changes in allele frequency from the first generation (G1) to the fifth generation (G5). refSNP A1 A1 Allele frequency Gene symbol within SSC1 Position(bp)varidation ID Allele G1 G5 Difference Threshold2 the SNP ±200 kbp region 1 134,689,650 rs80851548 A 0.40 0.74 0.34 * C15orf41 1 134,737,012 rs80887335 C 0.40 0.74 0.34 * C15orf41 1 134,796,155 rs80940400 G 0.41 0.74 0.34 * - 1 135,274,728 rs80954520 C 0.41 0.74 0.33 * - 1 185,207,182 rs80922893 C 0.36 0.71 0.35 * - 1 185,245,368 rs80788631 G 0.36 0.71 0.35 * - 1 185,277,656 rs80953151 G 0.35 0.71 0.36 * - 1 185,750,637 rs80899215 G 0.48 0.81 0.33 * PELI2,TMEM260 FAM102A,NAIF1,SLC25A25,PTGES2,LCN2,CIZ1,DNM1,TRUB2,COQ4,S 1 268,632,812 rs80949782 G 0.12 0.39 0.28 * LC27A4,URM1 2 24,006,981 rs81356248 A 0.29 0.62 0.33 * - 2 27,012,537 rs81356557 A 0.26 0.61 0.35 * NAT10,CAPRIN1,LMO2,FBXO3 2 149,487,361 rs81245577 A 0.16 0.49 0.32 * SPINK5,SPINK14,SPINK6,SPINK7,FBXO38 3 14,568,693 rs81374336 A 0.02 0.22 0.20 * AUTS2 3 20,674,588 rs81378802 A 0.24 0.61 0.37 * - 3 20,715,185 rs81378883 G 0.41 0.76 0.36 * - 3 21,939,479 rs81379052 A 0.36 0.73 0.37 * CACNG3,PRKCB 3 21,997,882 rs81379040 G 0.36 0.73 0.37 * CACNG3,PRKCB 3 22,103,750 rs81379027 G 0.36 0.73 0.37 * CACNG3,PRKCB 3 22,153,127 rs81379035 C 0.16 0.49 0.33 * CACNG3,PRKCB 3 22,162,029 rs81379065 A 0.32 0.71 0.38 * PRKCB 3 22,688,720 rs81332536 A 0.41 0.81 0.39 ** ERN2,PLK1,DCTN5,PALB2,UBFD1,EARS2,GGA2,COG7,SCNN1B 3 22,718,923 rs81311562 G 0.49 0.81 0.33 * ERN2,PLK1,DCTN5,PALB2,UBFD1,EARS2,GGA2,COG7,SCNN1B 3 22,735,931 rs81309807 A 0.41 0.81 0.39 ** ERN2,PLK1,DCTN5,PALB2,UBFD1,EARS2,GGA2,COG7,SCNN1B 3 22,771,925 rs81314488 A 0.41 0.81 0.39 ** DCTN5,PALB2,UBFD1,EARS2,GGA2,COG7,SCNN1B 3 22,883,110 rs81478328 G 0.43 0.77 0.34 * EARS2,GGA2,COG7,SCNN1B,SCNN1G,USP31 3 22,905,875 rs81306471 A 0.43 0.77 0.34 * GGA2,COG7,SCNN1B,SCNN1G,USP31 3 22,975,393 rs81319066 C 0.43 0.77 0.34 * COG7,SCNN1B,SCNN1G,USP31 3 23,446,125 rs81475137 A 0.44 0.78 0.35 * HS3ST2,OTOA 3 23,519,366 rs81238947 A 0.38 0.77 0.39 ** HS3ST2,OTOA,METTL9,IGSF6 3 23,568,329 rs81324887 G 0.38 0.77 0.39 ** OTOA,METTL9,IGSF6 3 23,582,844 rs81340946 A 0.38 0.77 0.39 ** OTOA,METTL9,IGSF6 3 23,600,496 rs81317979 A 0.38 0.77 0.39 ** OTOA,METTL9,IGSF6 3 23,755,924 rs81314080 A 0.38 0.77 0.39 ** OTOA,METTL9,IGSF6,POLR3E,EEF2K 3 23,814,459 rs81344425 G 0.42 0.77 0.35 * OTOA,METTL9,IGSF6,POLR3E,EEF2K,SDR42E2 3 23,887,869 rs81313849 G 0.35 0.68 0.33 * METTL9,POLR3E,EEF2K,SDR42E2,VWA3A 3 23,896,817 rs81308074 A 0.35 0.68 0.33 * METTL9,POLR3E,EEF2K,SDR42E2,VWA3A 3 23,900,614 rs323881880 A 0.35 0.68 0.33 * METTL9,POLR3E,EEF2K,SDR42E2,VWA3A 3 31,632,749 rs81334381 A 0.29 0.60 0.32 * TXNDC11,SNN,LITAF,RMI2 3 31,667,242 rs81326123 A 0.29 0.60 0.32 * LITAF,RMI2,PRM1,PRM2,PRM3 3 31,675,282 rs81282787 A 0.29 0.60 0.32 * LITAF,RMI2,PRM1,PRM2,PRM3,TNP2 4 4,670,929 rs80943277 A 0.02 0.20 0.18 * FAM135B 4 14,919,602 rs81381260 A 0.02 0.22 0.20 * ZNF572,MTSS1,NDUFB9,TATDN1 4 15,064,780 rs80865899 G 0.02 0.22 0.20 * MTSS1,NDUFB9,TATDN1,RNF139,TMEM65 4 108,299,808 rs81380162 G 0.46 0.79 0.33 * KCND3 4 118,595,949 rs80895835 C 0.42 0.76 0.34 * PALMD,PLPPR4 4 118,670,792 rs80862408 G 0.40 0.74 0.35 * PLPPR4 4 118,717,350 rs80793780 G 0.44 0.77 0.33 * PLPPR4 5 4,100,366 rs81384129 A 0.35 0.68 0.34 * FBLN1,RIBC2,SMC1B,FAM118A,UPK3A,KIAA0930,NUP50,PHF21B 5 34,798,544 rs80814026 A 0.23 0.56 0.32 * KCNMB4,PTPRB,PTPRR GABARAPL1,TMEM52B,OLR1,CLEC7A,CLEC1A,CLEC12B,CLEC1B,CL 5 61,870,042 rs81384583 G 0.38 0.71 0.34 * EC12A,KLRF1,CLEC2B 5 86,749,072 rs81386110 G 0.45 0.81 0.35 * NEDD1,CFAP54 6 36,102,300 rs81323853 A 0.15 0.44 0.29 * - 6 41,876,933 rs81476543 G 0.25 0.63 0.38 * - 6 41,959,933 rs81475836 A 0.25 0.63 0.38 * - 6 41,972,632 rs81268422 A 0.28 0.69 0.41 ** - 6 41,985,717 rs81335479 A 0.25 0.63 0.38 * - 6 42,233,884 rs81342345 A 0.29 0.62 0.33 * ZNF507,DPY19L3,ANKRD27 6 42,951,646 rs81395636 A 0.17 0.46 0.30 * CEP89,FAAP24,RHPN2,GPATCH1,WDR88,LRP3,SLC7A10,CEBPA 6 82,839,805 rs81217723 G 0.02 0.20 0.18 * SYF2,RSRP1,TMEM50A,RHCE,MACO1,LDLRAP1 6 82,861,312 rs81333116 G 0.02 0.20 0.18 * SYF2,RSRP1,TMEM50A,RHCE,MACO1,LDLRAP1 6 83,013,095 rs81337608 A 0.02 0.20 0.18 * SYF2,RSRP1,TMEM50A,RHCE,MACO1,LDLRAP1,MAN1C1 6 83,142,163 rs81332505 A 0.02 0.20 0.18 * MACO1,LDLRAP1,MAN1C1,MTFR1L,AUNIP,PAQR7 6 101,875,211 rs81335192 A 0.15 0.45 0.30 * ZBTB14,AKAIN1 6 102,318,246 rs81390413 A 0.25 0.57 0.32 * - 6 104,183,387 rs81270901 G 0.32 0.69 0.37 * SMCHD1,NDC80,METTL4 6 105,346,250 rs81224470 G 0.29 0.65 0.36 * ADCYAP1,YES1 6 108,923,455 rs81390642 A 0.35 0.71 0.36 * LAMA3,TTC39C,CABYR,OSBPL1A 6 169,165,178 rs81326952 G 0.48 0.81 0.34 * FOXJ3,GUCA2A,GUCA2B BTN2A2,BTN1A1,HMGN4,ABT1,ZNF322,HIST1H2BJ,HIST1H2AG,PRSS 7 21,166,373 rs80810275 C 0.19 0.51 0.33 * 16 7 36,980,974 rs80937268 A 0.35 0.68 0.33 * FOXP4,MDFI,TFEB,PGC,FRS3,USP49,MED20,BYSL,CCND3,TAF8 ZNF219,TMEM253,ARHGEF40,RNASE13,TPPP2,NDRG2,SLC39A2,MET 7 78,221,461 rs81347360 A 0.39 0.72 0.33 * TL17,RNASE1,EDDM3B,ANG,OR6S1,RNASE12,RNASE10 7 78,784,489 rs330336224 A 0.36 0.69 0.33 * TTC5,OR11H4,OR11H7,OR11H6 7 78,864,968 rs80819852 A 0.36 0.69 0.33 * - 7 78,954,513 rs80971150 G 0.39 0.72 0.33 * - 7 99,552,539 rs80962632 A 0.01 0.18 0.16 * GPATCH2L,ESRRB 7 99,594,303 rs80940634 G 0.01 0.18 0.16 * ESRRB 7 99,616,164 rs80816481 A 0.01 0.18 0.16 * ESRRB 7 99,705,755 rs80992373 C 0.01 0.18 0.17 * ESRRB 7 100,036,339 rs80988413 A 0.01 0.18 0.17 * VASH1,ANGEL1,LRRC74A,IRF2BPL,CIPC,ZDHHC22 7 100,048,503 rs81396110 A 0.01 0.18 0.17 * VASH1,ANGEL1,LRRC74A,IRF2BPL,CIPC,ZDHHC22 9 44,022,899 rs81410351 A 0.37 0.71 0.34 * BUD13,APOA5,APOA4,APOC3,APOA1 9 44,054,340 rs81410360 A 0.37 0.71 0.34 * BUD13,APOA5,APOA4,APOC3,APOA1,SIK3 10 5,280,923 rs81332343 G 0.21 0.53 0.32 * - 10 5,298,516 rs81234159 C 0.21 0.53 0.32 * - 10 8,179,249 rs81343027 G 0.41 0.76 0.34 * SPATA17,RRP15,TGFB2 10 23,079,365 rs81422238 A 0.40 0.74 0.33 * ZNF281,KIF14,DDX59,CAMSAP2 10 26,718,377 rs81318461 G 0.32 0.65 0.33 * PTCH1,FANCC 12 14,839,808 rs81440432 A 0.32 0.66 0.34 * PECAM1,TEX2,ERN1,ICAM2,SCN4A 12 34,687,264 rs81434436 C 0.39 0.73 0.35 * EPX,MKS1,LPO,MPO,TSPOAP1,SUPT4H1,HSF5,MTMR4,SEPT4,TEX14 12 34,743,152 rs81285844 G 0.45 0.81 0.36 * LPO,MPO,TSPOAP1,SUPT4H1,HSF5,MTMR4,SEPT4,TEX14 12 40,335,964 rs81343740 A 0.30 0.65 0.34 * LIG3,CCT6B,TMEM132E 13 13,244,196 rs81478253 A 0.13 0.42 0.28 * LRRC3B 14 22,915,179 rs80846859 G 0.28 0.60 0.32 * GOLGA3,ANKLE2,PGAM5,POLE,P2RX2 15 15,522,770 rs81456646 A 0.48 0.91 0.43 ** CXCR4 15 15,576,911 rs324687449 G 0.13 0.40 0.27 * CXCR4 15 16,756,610 rs80809384 A 0.44 0.07 0.37 * ZRANB3,RAB3GAP1,MAP3K19 15 17,253,368 rs81255351 G 0.45 0.08 0.37 * ACMSD,TMEM163 15 24,738,182 rs81451940 G 0.29 0.63 0.33 * MARCO,C1QL2,STEAP3,C2orf76,DBI 15 63,351,517 rs81234787 C 0.10 0.36 0.27 * NR4A2 16 605,799 rs81307390 A 0.20 0.50 0.30 * CTNND2 17 53,587,582 rs80798999 A 0.21 0.51 0.30 * ZFP64 18 34,954,478 rs81468839 G 0.27 0.66 0.38 ** - 18 35,083,247 rs81334712 C 0.27 0.66 0.38 ** - 18 35,117,455 rs81244769 G 0.27 0.66 0.38 ** - 18 36,533,064 rs81316316 G 0.28 0.62 0.34 * DNAJB9,THAP5,GPR141 18 37,501,757 rs81469054 A 0.23 0.62 0.39 ** ELMO1,AOAH,ANLN 18 37,555,793 rs81469072 G 0.26 0.63 0.37 * AOAH,ANLN,KIAA0895 18 37,609,289 rs81469097 G 0.29 0.62 0.33 * AOAH,ANLN,KIAA0895 18 41,089,501 rs81226421 G 0.15 0.49 0.34 * PDE1C 18 44,625,702 rs81346985 G 0.37 0.72 0.35 * JAZF1,TAX1BP1 1SSC: Sus Scrofa chromosome. 2**: The SNPs above 99.99-threshold, *:The SNPs above 99.9-threshold.