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

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