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Table 8 The gene-tissue pairs significantly associated with economically important traits from cGTEx (for ROH)

From: Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Traits Gene-tissue pairs
Milk yield FAM135B-Uterus
Protein yield FAM228B-Liver、CFAP410-Liver
Protein percentage FAM228B-Liver、CHTF8-Liver、GTF3A-Liver
Fat percent MINDY4-Hypothalamus、VAPB-Macrophage
Productive lift ALDH6A1-Liver、RPS6KA4-Uterus、INMT-Liver、MINDY4-Hypothalamus、GGCT-Milk_cell
Somatic cell score ITGB2-Muscle、NCEH1-Blood、ABCD4-Blood
mastitis TARS3-Adipose、USP12-Intramuscular_fat
Sire stillbirth VPS35L-Liver、EIF4E2-Intramuscular_fat、PDE6D-Mammary
Sire conception rate NOD1-Adipose
Sire calving ease VPS35L-Liver、SLC31A1-Liver、FUCA1-Blood
Heifer conception rate COQ2-Adipose、FAM228B-Liver、TP53I3-Adipose、FKBP1B-Oviduct、LIN54-Lung
Age at first calving UNC13B-Blood、ALDH6A1-Liver、PPP1R42-Intramuscular_fat、VPS35L-Liver、PRG4-Liver、UBE2G2-Intramuscular_fat
Days to first breeding after calving KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、GTF3A-Embryo、PRPF4B-Embryo、SNRPA1-Adipose
Daughter stillbirth UNC13B-Blood、VPS35L-Liver、ATAD2B-Skin_fibroblast、CELF4-Ileum、LRRC3-Liver、SYNDIG1L-Adipose
Cow conception rate KCTD18-Adipose、FAM228B-Liver、TTC22-Blood、SRM-Mammary、PFKL-Intramuscular_fat
Daughter pregnancy rate KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、FAM228B-Liver、SRM-Mammary
Daughter calving ease FAM228B-Liver、PPP1R42-Intramuscular_fat、RAB22A-Milk_cell
Under depth ALDH6A1-Liver
Udder cleft KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、UNC13B-Blood、COQ2-Adipose、ALDH6A1-Liver、CHRND-Intramuscular_fat、TP53I3-Adipose、IQCK-Adipose、MACROD1-Liver、MOCS1-Adipose、PNRC2-Blood、HPSE-Blood、CRHR2-Jejunum、GARS1-Embryo
Teat length UNC13B-Blood、EXOSC10-Mammary
strength COQ2-Adipose、GTF3A-Embryo、PPP1R42-Intramuscular_fat、TTC22-Blood、ADIPOR2-Hypothalamus、FAM228A-Hypothalamus、UBXN2A-Blood、CSPP1-Blood、MOCS1-Adipose、WNT11-Macrophage
stature STOML2-Mammary、GTF3A-Embryo、ADIPOR2-Hypothalamus、FAM228A-Hypothalamus、UBXN2A-Blood、IQCK-Adipose、ATAD2B-Skin_fibroblast、UTP25-Adipose、ALG2-Adipose、LIN52-Liver
Rump width COQ2-Adipose、PPP1R42-Intramuscular_fat、TTC22-Blood、ADIPOR2-Hypothalamus、FAM228A-Hypothalamus、UBXN2A-Blood、CSPP1-Blood、MOCS1-Adipose、PNRC2-Blood、SGK3-Adipose、WNT11-Macrophage
Rump angle FAM228B-Liver、GTF3A-Embryo、ISCA2-Lung、MACROD1-Liver
Retained placenta UNC13B-Blood、VPS35L-Liver、SLC31A1-Liver、SRM-Mammary、WNT11-Macrophage、SSTR2-Blood、FMNL2-Blood
Rear udder height KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、UNC13B-Blood、COQ2-Adipose、CHRND-Intramuscular_fat、SGK3-Adipose
Rear teat placemen KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、UNC13B-Blood、FAM228B-Liver、ALDH6A1-Liver、CHRND-Intramuscular_fat、ISCA2-Lung、PNRC2-Blood
Rear legs side view STOML2-Mammary、ISCA2-Lung、MACROD1-Liver、SLC31A1-Liver、PROX2-Liver、RAB22A-Milk_cell、GK5-Liver
Rear legs rear view UNC13B-Blood、STOML2-Mammary、TP53I3-Adipose、IFNLR1-Blood、IL22RA1-Rumen
Net merit RPS6KA4-Uterus、TTC4-Blood
metritis KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、CHTF8-Liver、INMT-Liver
ketosis KCTD18-Adipose、SPATS2L-Blood、TTC22-Blood、CHTF8-Liver、RPS6KA4-Uterus、TMOD2-Mammary、TRMT112-Lymph_node
hypocalcemia KCTD18-Adipose、NCEH1-Blood、SSTR2-Blood、UTP25-Adipose、VAPB-Macrophage、AOX2-Mammary、ORC2-Liver
Front teat placement KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、CHRND-Intramuscular_fat、ISCA2-Lung、TSPEAR-Oviduct
Fore udder attachment KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、IQCK-Adipose
Feet and legs COQ2-Adipose、STOML2-Mammary、TP53I3-Adipose、HPSE-Blood、IFNLR1-Blood、IL22RA1-Rumen
Displaced abomasum PRG4-Liver
Dairy form ALDH6A1-Liver、STOML2-Mammary、CHRND-Intramuscular_fat、CFAP410-Liver、ITGB2-Muscle、PROX2-Liver
Cow livability STOML2-Mammary、PFKL-Intramuscular_fat、BSND-Uterus、FERMT3-Salivary_gland、HAS3-Blood
Body depth KCTD18-Adipose、COQ2-Adipose、ALDH6A1-Liver、PPP1R42-Intramuscular_fat、TTC22-Blood、ADIPOR2-Hypothalamus、FAM228A-Hypothalamus、UBXN2A-Blood、CSPP1-Blood、SGK3-Adipose
Foot angle SPATS2L-Blood、AOX1-Adipose、STOML2-Mammary、GTF3A-Embryo、NPEPL1-Macrophage、PLS1-Liver
Overall conformation score KCTD18-Adipose、SPATS2L-Blood、AOX1-Adipose、UNC13B-Blood、COQ2-Adipose、KLHL29-Mammary