Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Phenotypes
2.2. iWGS and Genomic Quality Control
2.3. Association Analyses, Statistical Models, and Significance Testing
2.4. Functional Genomic Analyses
3. Results
3.1. GWAS
3.1.1. GWAS for Milk Yield, Fat Yield, and Fat Percentage
3.1.2. GWAS for Protein Yield, Protein Percentage, and Lactation Persistency
3.2. Commonly Identified Genes for Two or More Traits
3.3. Functional Analyses of Candidate Genes
4. Discussion
4.1. Candidate Genes for Lactation Persistency
4.2. Candidate Genes for Milk Yield
4.3. Candidate Genes for Fat Yield
4.4. Candidate Genes for Fat Percentage
4.5. Candidate Genes for Protein Yield
4.6. Candidate Genes for Protein Percentage
4.7. Common Genes Identified in GO Terms
4.8. Potential Implications and Limitations
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Traits | Sample Size | dEBVs | Reliability | ||||
---|---|---|---|---|---|---|---|
Mean | Min | Max | SD | Mean | SD | ||
MILK | 8264 | −1507.99 | −58,315.8 | 89,084.9 | 13,218.18 | 63.3 | 9.5 |
FAT | 8262 | −57.62 | −3416.98 | 5254.22 | 893.60 | 64.7 | 9.9 |
PROT | 8263 | −55.87 | −2124.84 | 2479.37 | 526.11 | 60.2 | 8.9 |
FAT% | 8262 | 0.27 | −37.47 | 40.01 | 9.61 | 64.7 | 9.9 |
PROT% | 8263 | 0.11 | −17.91 | 17.96 | 4.86 | 60.2 | 8.9 |
LP | 3447 | 95.68 | −810.60 | 1008.61 | 486.37 | 36.7 | 6.8 |
TRAIT | N 1 | Chr 2 | Position (bp) | p-Value | Genes (Within ±100 Kb) | QTL 3 | QTL_Type 4 |
---|---|---|---|---|---|---|---|
MILK | 8 | 1 | 141,861,836 | 2.69 × 10−6 | ENSBTAG00000050235, ENSBTAG00000045771, ENSBTAG00000046015 | 1 | Meat/Carcass |
MILK | 2 | 2 | 80,496,336 | 9.86 × 10−6 | CAVIN2 | 0 | - |
MILK | 6 | 3 | 26,833,328 | 2.52 × 10−6 | CD58, ATP1A1 | 3 | Reproduction |
MILK | 16 | 4 | 116,598,211 | 2.28 × 10−5 | DPP6 | 4 | Milk |
MILK | 871 | 5 | 93,545,576 | 3.62 × 10−12 | MGST1, SLC15A5 | 357 | Milk |
MILK | 579 | 6 | 86,348,368 | 2.27 × 10−10 | MOB1B, DCK, SLC4A4 | 69 | Milk |
MILK | 28 | 7 | 5,452,360 | 7.17 × 10−6 | B3GNT3, FCHO1, MAP1S, UNC13A, COLGALT1 | 10 | Reproduction |
MILK | 24 | 8 | 36,048,320 | 1.30 × 10−7 | bta-mir-2285bg, PTPRD | 1 | Meat/Carcass |
MILK | 91 | 9 | 61,950,514 | 1.39 × 10−7 | SPACA1 | 0 | - |
MILK | 20 | 10 | 87,491,769 | 5.67 × 10−8 | GPATCH2L | 1 | Reproduction |
MILK | 769 | 11 | 103,587,292 | 5.24 × 10−8 | NACC2, TMEM250, LHX3 | 4 | Milk |
MILK | 1 | 12 | 72,628,679 | 1.02 × 10−5 | ENSBTAG00000023309 | 0 | - |
MILK | 37 | 13 | 6,976,693 | 2.95 × 10−10 | ISM1, TASP1 | 15 | Exterior |
MILK | 5564 | 14 | 465,742 | 5.98 × 10−196 | ARHGAP39, bta-mir-2308, C14H8orf82, LRRC24, LRRC14, RECQL4, MFSD3, GPT, PPP1R16A, FOXH1, KIFC2, CYHR1, TONSL, VPS28, ENSBTAG00000053637, SLC39A4, CPSF1, ADCK5 | 765 | Milk |
MILK | 1012 | 15 | 54,030,861 | 2.13 × 10−9 | POLD3, CHRDL2, RNF169, U6, ENSBTAG00000054207, ENSBTAG00000042319 | 3 | Milk |
MILK | 308 | 16 | 64,637,424 | 9.60 × 10−9 | SMG7, NCF2, ARPC5, APOBEC4 | 1 | Health |
MILK | 35 | 18 | 56,457,916 | 5.07 × 10−6 | IZUMO2, ENSBTAG00000053322, MYH14, KCNC3, NAPSA, ENSBTAG00000048283, NR1H2, POLD1 | 37 | Milk |
MILK | 132 | 19 | 8,625,414 | 1.77 × 10−6 | CCDC182, ENSBTAG00000045351, ENSBTAG00000051336, MRPS23, CUEDC1 | 15 | Reproduction |
MILK | 1867 | 20 | 31,609,872 | 3.36 × 10−32 | NIM1K, ENSBTAG00000042376, ZNF131, ENSBTAG00000054352, ENSBTAG00000052195, ENSBTAG00000051111 | 27 | Milk |
MILK | 27 | 21 | 33,151,073 | 6.13 × 10−6 | ENSBTAG00000051111, ODF3L1, CSPG4, SNX33 | 2 | Health |
MILK | 6 | 22 | 21,859,149 | 4.59 × 10−6 | bta-mir-2285am, U6, SUMF1 | 0 | - |
MILK | 436 | 23 | 12,589,558 | 6.37 × 10−8 | GLO1, DNAH8 | 0 | - |
MILK | 6 | 24 | 21,019,665 | 7.60 × 10−6 | MOCOS, ELP2, SLC39A6, RPRD1A | 0 | - |
MILK | 40 | 28 | 18,592,444 | 1.03 × 10−6 | ZNF365 | 5 | Milk |
MILK | 16 | 29 | 9,512,241 | 6.55 × 10−6 | PICALM | 9 | Milk |
FAT | 30 | 1 | 126,143,578 | 8.14 × 10−8 | ENSBTAG00000038111, PCOLCE2 | 3 | Reproduction |
FAT | 46 | 2 | 67,353,179 | 3.19 × 10−6 | DPP10, ENSBTAG00000050341, | 0 | - |
FAT | 15 | 4 | 28,468,986 | 5.19 × 10−8 | POLR1F, ENSBTAG00000050341, TMEM196 | 0 | - |
FAT | 1580 | 5 | 93,627,511 | 8.00 × 10−26 | SLC15A5 | 167 | Milk |
FAT | 31 | 6 | 36,205,216 | 1.00 × 10−7 | HERC3, PIGY, HERC5 | 202 | Milk |
FAT | 18 | 7 | 21,215,200 | 5.74 × 10−6 | GADD45B, LMNB2, TIMM13, TMPRSS9, SPPL2B, LSM7, LINGO3, PEAK3, OAZ1 | 23 | Reproduction |
FAT | 8 | 8 | 42,176,903 | 6.89 × 10−6 | ENSBTAG00000051041 | 7 | Milk |
FAT | 26 | 10 | 86,711,416 | 4.16 × 10−6 | JDP2, bta-mir-10162, BATF, FLVCR2 | 3 | Health |
FAT | 1275 | 11 | 95,801,995 | 2.86 × 10−9 | NR6A1, bta-mir-181a-2, bta-mir-181b-2, OLFML2A, U6, WDR38, RPL35, ARPC5L, GOLGA1 | 1 | Production |
FAT | 12 | 12 | 69,122,129 | 1.67 × 10−5 | ENSBTAG00000051519, 5S_rRNA, TGDS, GPR180, U2, SOX21 | 1 | Exterior |
FAT | 322 | 13 | 54,614,993 | 1.43 × 10−7 | DIDO1, TCFL5, COL9A3, OGFR, MRGBP, NTSR1, SLCO4A1, ENSBTAG00000051754, ENSBTAG00000051012 | 3 | Milk |
FAT | 4490 | 14 | 465,742 | 2.08 × 10−183 | ARHGAP39, bta-mir-2308, C14H8orf82, LRRC24, LRRC14, RECQL4, MFSD3, GPT, PPP1R16A, FOXH1, KIFC2, CYHR1, TONSL, VPS28, ENSBTAG00000053637, SLC39A4, CPSF1, ADCK5 | 765 | Milk |
FAT | 181 | 15 | 74,165,872 | 1.09 × 10−9 | ACCSL, ACCS, EXT2 | 6 | Reproduction |
FAT | 260 | 16 | 61,287,081 | 9.53 × 10−9 | CEP350, QSOX1 | 0 | - |
FAT | 12 | 18 | 60,972,942 | 2.06 × 10−5 | bta-mir-371, NLRP12, MGC157082, ENSBTAG00000014953 | 50 | Milk |
FAT | 35 | 19 | 34,952,167 | 1.85 × 10−6 | NT5M, COPS3, FLCN, PLD6, MPRIP | 7 | Production |
FAT | 18 | 22 | 27,251,453 | 4.27 × 10−6 | CNTN3 | 3 | Health |
FAT | 13 | 23 | 11,102,541 | 3.20 × 10−6 | ENSBTAG00000048838, PIM1, ENSBTAG00000045936, TMEM217, TBC1D22B | 0 | - |
FAT | 639 | 26 | 21,354,112 | 1.07 × 10−9 | PKD2L1, SCD, bta-mir-12016, WNT8B, SEC31B, NDUFB8, HIF1AN | 296 | Milk |
FAT | 6 | 28 | 34,969,442 | 7.51 × 10−6 | ZMIZ1, PPIF, ZCCHC24 | 2 | Production |
FAT | 20 | 29 | 49,353,940 | 1.30 × 10−6 | TSPAN32, ASCL2, TH, INS, IGF2 | 8 | Milk |
FAT% | 8 | 1 | 1,025,407 | 1.89 × 10−5 | RCAN1, KCNE1, ENSBTAG00000026259, ENSBTAG00000051226, FAM243A, SMIM11A, KCNE2 | 6 | Milk |
FAT% | 47 | 2 | 128,607,054 | 8.79 × 10−7 | STPG1, GRHL3, U6 | 2 | Milk |
FAT% | 29 | 4 | 106,456,105 | 6.10 × 10−6 | ENSBTAG00000049510, ENSBTAG00000048380, ENSBTAG00000053286, OR6V1, ENSBTAG00000052365, PIP, ENSBTAG00000050494 | 0 | - |
FAT% | 2070 | 5 | 93,627,511 | 3.55 × 10−34 | SLC15A5 | 167 | Milk |
FAT% | 41 | 6 | 36,205,216 | 5.31 × 10−12 | HERC3, PIGY, HERC5 | 202 | Milk |
FAT% | 19 | 7 | 21,215,200 | 2.60 × 10−5 | GADD45B, LMNB2, TIMM13, TMPRSS9, SPPL2B, LSM7, LINGO3, PEAK3, OAZ1 | 23 | Reproduction |
FAT% | 11 | 8 | 88,461,261 | 8.40 × 10−8 | GADD45G | 10 | Reproduction |
FAT% | 20 | 9 | 61,950,514 | 9.91 × 10−7 | SPACA1 | 0 | - |
FAT% | 3 | 10 | 77,587,306 | 4.17 × 10−6 | FUT8 | 4 | Meat/Carcass |
FAT% | 2365 | 11 | 105,500,024 | 6.21 × 10−6 | COL5A1, FCN1, ENSBTAG00000054425, OLFM1, ENSBTAG00000052600 | 15 | Milk |
FAT% | 6 | 12 | 70,194,006 | 2.47 × 10−6 | ENSBTAG00000047383 | 0 | - |
FAT% | 161 | 13 | 47,813,637 | 3.64 × 10−7 | GPCPD1, ENSBTAG00000054005, ENSBTAG00000051557 | 7 | Milk |
FAT% | 6274 | 14 | 465,742 | 2.82 × 10−317 | ARHGAP39, bta-mir-2308, C14H8orf82, LRRC24, LRRC14, RECQL4, MFSD3, GPT, PPP1R16A, FOXH1, KIFC2, CYHR1, TONSL, VPS28, ENSBTAG00000053637, SLC39A4, CPSF1, ADCK5 | 765 | Milk |
FAT% | 789 | 15 | 51,993,618 | 9.14 × 10−9 | CLPB, PDE2A, ENSBTAG00000050827 | 2 | Production |
FAT% | 714 | 16 | 61,059,994 | 7.32 × 10−10 | FAM163A, TOR1AIP2, TOR1AIP1, U6 | 11 | Reproduction |
FAT% | 33 | 17 | 65,230,489 | 1.97 × 10−6 | KIAA1671, 7SK, ENSBTAG00000053952, CRYBB3, CRYBB2 | 18 | Reproduction |
FAT% | 215 | 19 | 35,457,767 | 2.41 × 10−7 | KCNJ12, UTP18, MBTD1 | 0 | - |
FAT% | 1293 | 20 | 29,991,518 | 2.95 × 10−23 | ENSBTAG00000054476, MRPS30 | 179 | Milk |
FAT% | 6 | 25 | 11,488,475 | 4.73 × 10−6 | CPPED1 | 0 | - |
FAT% | 8 | 26 | 51,156,653 | 5.45 × 10−6 | INPP5A, ENSBTAG00000051139, BNIP3, ENSBTAG00000050527 | 2 | Reproduction |
FAT% | 3 | 27 | 36,400,257 | 1.07 × 10−5 | 5S_rRNA, GOLGA7, GINS4 | 27 | Milk |
FAT% | 13 | 28 | 26,978,779 | 1.00 × 10−5 | ADAMTS14, TBATA, SGPL1, ENSBTAG00000054819, PCBD1 | 18 | Milk |
TRAIT | N 1 | Chr 2 | Position (bp) | p-Value | Genes (Within ±100 Kb) | QTL 3 | QTL_Type 4 |
---|---|---|---|---|---|---|---|
PROT | 236 | 1 | 117,208,394 | 1.39 × 10−7 | CLRN1 | 1 | Reproduction |
PROT | 12 | 2 | 1,465,207 | 8.33 × 10−6 | AMER3 | 3 | Reproduction |
PROT | 16 | 3 | 42,939,326 | 8.31 × 10−8 | CDC14A, ENSBTAG00000054319, ENSBTAG00000015759, RTCA | 0 | - |
PROT | 61 | 4 | 106,606,419 | 8.84 × 10−6 | ENSBTAG00000050494, TAS2R39, TAS2R40, GSTK1, TMEM139, CASP2, CLCN1 | 0 | - |
PROT | 72 | 5 | 91,526,305 | 5.46 × 10−6 | PIK3C2G, ENSBTAG00000046178 | 23 | Milk |
PROT | 65 | 6 | 86,795,218 | 4.49 × 10−7 | SLC4A4 | 278 | Milk |
PROT | 6 | 7 | 93,911,428 | 1.49 × 10−5 | KIAA0825, SLF1 | 0 | - |
PROT | 30 | 8 | 948,000 | 6.96 × 10−7 | PALLD, 5S_rRNA | 16 | Production |
PROT | 21 | 10 | 10,774,713 | 1.37 × 10−6 | CMYA5, SNORA72, ENSBTAG00000049054 | 0 | - |
PROT | 121 | 11 | 77,730,244 | 1.57 × 10−7 | TDRD15 | 4 | Production |
PROT | 8 | 12 | 77,353,297 | 8.04 × 10−6 | TMTC4, ENSBTAG00000053717 | 0 | - |
PROT | 489 | 13 | 33,556,356 | 2.02 × 10−9 | ARHGAP12 | 5 | Reproduction |
PROT | 1541 | 14 | 827,938 | 3.24 × 10−22 | MAF1, ENSBTAG00000051469, SHARPIN, CYC1, GPAA1, EXOSC4, OPLAH, ENSBTAG00000015040, SPATC1, GRINA, PARP10, PLEC, bta-mir-2309 | 670 | Milk |
PROT | 32 | 15 | 41,254,106 | 5.23 × 10−7 | GALNT18 | 1 | Milk |
PROT | 22 | 17 | 65,001,641 | 5.01 × 10−6 | ENSBTAG00000054184, PIWIL3, SGSM1, TMEM211 | 3 | Reproduction |
PROT | 48 | 18 | 36,657,423 | 1.48 × 10−6 | CYB5B, ENSBTAG00000052086, NFAT5 | 0 | - |
PROT | 37 | 19 | 42,052,275 | 6.05 × 10−6 | JUP, P3H4, FKBP10, NT5C3B, KLHL10, KLHL11, ACLY, ENSBTAG00000050335, TTC25, CNP, DNAJC7 | 2 | Milk |
PROT | 7 | 21 | 10,379,606 | 2.70 × 10−6 | ENSBTAG00000049351 | 8 | Reproduction |
PROT | 30 | 22 | 23,112,217 | 3.53 × 10−6 | CRBN, TRNT1, IL5RA | 4 | Milk |
PROT | 628 | 23 | 5,551,604 | 3.67 × 10−7 | FAM83B | 2 | Milk |
PROT | 31 | 24 | 21,507,281 | 1.32 × 10−6 | GALNT1, INO80C | 0 | - |
PROT | 9 | 25 | 10,257,579 | 5.43 × 10−6 | ENSBTAG00000050716, ENSBTAG00000050363, LITAF | 2 | Milk |
PROT | 8 | 26 | 15,946,065 | 5.94 × 10−6 | PLCE1, NOC3L, U6, TBC1D12, ENSBTAG00000051299, ENSBTAG00000049089, HELLS, 7SK | 13 | Milk |
PROT | 15 | 28 | 1,284,944 | 1.04 × 10−6 | RAB4A, CCSAP, ENSBTAG00000048654, ENSBTAG00000050985 | 7 | Milk |
PROT% | 56 | 1 | 142,907,564 | 3.41 × 10−6 | SLC37A1, PDE9A | 98 | Milk |
PROT% | 106 | 3 | 9,965,020 | 5.49 × 10−10 | FCRL6, DUSP23, CRP | 9 | Milk |
PROT% | 39 | 4 | 9,165,220 | 3.80 × 10−6 | ENSBTAG00000052341, MTERF1 | 0 | - |
PROT% | 828 | 5 | 93,655,680 | 1.81 × 10−12 | SLC15A5 | 172 | Milk |
PROT% | 696 | 6 | 36,205,216 | 1.28 × 10−18 | HERC3, PIGY, HERC5 | 202 | Production |
PROT% | 6 | 7 | 104,076,138 | 1.10 × 10−5 | U6 | 0 | - |
PROT% | 16 | 8 | 1,868,612 | 2.86 × 10−6 | MFAP3L, ENSBTAG00000051098, AADAT | 6 | Reproduction |
PROT% | 61 | 9 | 26,103,917 | 4.56 × 10−8 | TPD52L1, RNF217 | 0 | - |
PROT% | 36 | 10 | 40,647,347 | 2.08 × 10−6 | ENSBTAG00000034580 | 3 | Reproduction |
PROT% | 1309 | 11 | 63,476,482 | 1.52 × 10−10 | SLC1A4, CEP68, RAB1A | 26 | Milk |
PROT% | 5 | 12 | 76,184,908 | 2.08 × 10−5 | UBAC2, GPR18, GPR183, ENSBTAG00000038268 | 4 | Milk |
PROT% | 100 | 13 | 46,366,498 | 2.96 × 10−7 | ADARB2, ENSBTAG00000054346, WDR37, IDI1, GTPBP4, U6, LARP4B, ENSBTAG00000051962 | 15 | Milk |
PROT% | 5949 | 14 | 465,742 | 2.75 × 10−122 | ARHGAP39, bta-mir-2308, C14H8orf82, LRRC24, LRRC14, RECQL4, MFSD3, GPT, PPP1R16A, FOXH1, KIFC2, CYHR1, TONSL, VPS28, ENSBTAG00000053637, SLC39A4, CPSF1, ADCK5 | 765 | Milk |
PROT% | 2221 | 15 | 51,232,796 | 1.85 × 10−13 | STIM1, RHOG, PGAP2, NUP98 | 14 | Health |
PROT% | 749 | 16 | 60,724,655 | 2.34 × 10−9 | SOAT1, AXDND1, NPHS2, TDRD5 | 4 | Milk |
PROT% | 997 | 19 | 35,457,767 | 4.58 × 10−9 | KCNJ12, UTP18, MBTD1 | 0 | - |
PROT% | 2201 | 20 | 31,391,058 | 5.47 × 10−45 | PAIP1, ENSBTAG00000049623, C20H5orf34, TMEM267, CCL28, HMGCS1, ENSBTAG00000048672, NIM1K | 72 | Milk |
PROT% | 40 | 22 | 54,244,267 | 3.21 × 10−6 | CLEC3B, EXOSC7, ZDHHC3, TMEM42, GHRL, SEC13 | 3 | Milk |
PROT% | 554 | 23 | 47,176,195 | 8.66 × 10−10 | SLC35B3 | 0 | - |
PROT% | 25 | 24 | 56,331,031 | 3.77 × 10−6 | WDR7 | 0 | - |
PROT% | 5 | 25 | 14,923,140 | 2.20 × 10−6 | ENSBTAG00000051040 | 6 | Milk |
PROT% | 281 | 26 | 23,088,324 | 2.56 × 10−8 | GBF1, NFKB2, PSD, FBXL15, CUEDC2, bta-mir-146b, MFSD13A, ACTR1A, SUFU | 40 | Milk |
PROT% | 26 | 28 | 35,624,139 | 1.40 × 10−5 | ENSBTAG00000048082, SFTPD, MBL1, SFTPA1, ENSBTAG00000052322, MAT1A, DYDC1 | 2 | Health |
PROT% | 686 | 29 | 40,803,159 | 4.78 x10−10 | ASRGL1, ENSBTAG00000042287, SCGB1A1, AHNAK | 19 | Milk |
LP | 2 | 4 | 19,848,832 | 1.74 × 10−6 | THSD7A | 2 | Milk |
LP | 23 | 6 | 104,139,800 | 6.86 × 10−6 | STK32B, 5S_rRNA, CYTL1 | 8 | Milk |
LP | 3 | 7 | 2,852,946 | 9.20 × 10−6 | ENSBTAG00000051744, ENSBTAG00000052719, ENSBTAG00000049190 | 1 | Milk |
LP | 3 | 8 | 59,108,254 | 1.81 × 10−6 | ENSBTAG00000042498, ENSBTAG00000049991, FAM205C | 0 | - |
LP | 2 | 9 | 11,532,901 | 2.65 × 10−5 | RIMS1 | 1 | Reproduction |
LP | 5 | 12 | 68,955,769 | 1.48 × 10−5 | ENSBTAG00000054671, ENSBTAG00000051263, DCT, ENSBTAG00000051519, 5S_rRNA | 8 | Milk |
LP | 0 | 14 | 10,086,164 | 9.93 × 10−6 | - | 17 | Milk |
LP | 2 | 15 | 17,222,016 | 1.88 × 10−5 | ELMOD1, SLN | 3 | Reproduction |
LP | 0 | 17 | 35,605,687 | 1.69 × 10−5 | - | 0 | - |
LP | 26 | 18 | 54,117,753 | 8.56 × 10−7 | ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1 | 4 | Production |
LP | 25 | 19 | 36,768,672 | 5.36 × 10−6 | DLX4, ENSBTAG00000045805, U6, ENSBTAG00000053450, ENSBTAG00000049677, KAT7, ENSBTAG00000052793 | 20 | Milk |
LP | 4 | 21 | 31,125,876 | 2.14 × 10−5 | UBE2Q2, ENSBTAG00000048528, FBXO22, ENSBTAG00000043187 | 0 | - |
LP | 3 | 22 | 48,814,749 | 1.19 × 10−6 | POC1A, DUSP7 | 4 | Milk |
LP | 16 | 23 | 15,502,651 | 1.39 × 10−5 | FOXP4, MDFI, TFEB, PGC, FRS3, ENSBTAG00000038916, TOMM6 | 3 | Milk |
LP | 15 | 26 | 51,053,430 | 5.16 × 10−6 | INPP5A, ENSBTAG00000054967 | 0 | - |
LP | 2 | 27 | 35,948,511 | 3.46 × 10−5 | ZMAT4 | 1 | Meat/Carcass |
LP | 2 | 28 | 34,869,857 | 5.28 × 10−7 | ZMIZ1, PPIF | 5 | Milk |
LP | 1 | 29 | 22,382,652 | 2.17 × 10−5 | SLC17A6 | 0 | - |
Trait | GO | Term | p-Value | Genes |
---|---|---|---|---|
MILK | GO:0004890 | GABA-A receptor activity | 2.4 × 10−4 | GABRA2, GABRG1, GABRA4, GABRB1, and GABRD |
MILK | GO:0006749 | Glutathione metabolic process | 6.7 × 10−4 | OPLAH, ALDH5A1, CLIC5, GSTA2, GSTA3, GSTA4, GSTK1, and MGST1 |
MILK | GO:0005230 | Extracellular ligand-gated ion channel activity | 7.9 × 10−4 | GABRA2, GABRG1, GABRA4, GABRB1, and GABRD |
MILK | GO:1903496 | Response to 11-deoxycorticosterone | 1.4 × 10−3 | CSN1S1, CSN1S2, CSN2, and CSN3 |
MILK | GO:0007605 | sensory perception of sound | 3.2 × 10−3 | BARHL1, EYA4, FBXO11, NIPBL, USH1G, CLIC5, CHD7, COL2A1, DCDC2, MYH14, SNAI2, SLC1A3, and TUB |
MILK | GO:0005513 | Detection of calcium ion | 7.0 × 10−3 | CALM2, CALM3, KCNMB4, and STIM1 |
MILK | GO:0043950 | Positive regulation of cAMP-mediated signaling | 7.0 × 10−3 | CXCL10, CXCL11, CXCL9, and PTGIR |
MILK | GO:0003273 | Cell migration involved in endocardial cushion formation | 8.3 × 10−3 | DCHS1, NOTCH1, and SNAI2 |
MILK | GO:0071479 | Cellular response to ionizing radiation | 9.4 × 10−3 | FBXO4, RAD1, CLOCK, EEF1D, SPIDR, and SNAI2 |
MILK | GO:0004364 | Glutathione transferase activity | 1.0 × 10−3 | CLIC5, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, and MGST1 |
FAT | GO:0015125 | Bile acid transmembrane transporter activity | 4.1 × 10−4 | SLCO1A2, SLCO1B3, SLCO1C1, and SLCO2B1 |
FAT | GO:0055089 | Fatty acid homeostasis | 5.4 × 10−4 | POLD1, DGAT1, GOT1, GPAM, and INS |
FAT | GO:0030154 | Cell differentiation | 6.1 × 10−4 | DHCR7, EHF, ETV6, EYA3, HCK, SPIB, CREBL2, EXT2, GADD45B, GADD45G, MGP, NR5A1, PPDPF, PRRC2B, PTK2, PTK6, RGS19, SCX, SFRP5, STYK1, SNAPC4, SRMS, TRAPPC9, and TTF1 |
FAT | GO:0007275 | Multicellular organism development | 2.4 × 10−3 | ALX4, DDX1, EYA3, SUFU, TNFRSF1A, TNFRSF6B, GADD45B, GADD45G, LBH, LTBR, PPDPF, PLCZ1, SFRP5, STRBP, SPRED2, TPI1, TRIM5,4 and ZFAT |
FAT | GO:0000978 | RNA polymerase II core promoter proximal region sequence-specific DNA binding | 2.7 × 10−3 | AEBP2, EHF, ETV6, FEZF2, FOSL2, JDP2, MAFA, MXD1, MEIS1, NACC2, SOX18, TLX1, ASCL2, BHLHE41, BATF, CHD7, FOXJ2, GMEB2, HSF1, HHEX, NR1H2, NR6A1, OTX1, TP73, and ZGPAT |
FAT | GO:0042127 | Regulation of cell proliferation | 4.3 × 10−3 | DHCR7, HCK, NDRG1, NKX2-3, SRC, TNFRSF1A, TNFRSF6B, APOBEC1, GUCY2C, HHEX, LTBR, PTGS1, PTK2, PTK6, STYK1, and SRMS |
FAT | GO:0016509 | Long-chain-3-hydroxyacyl-CoA dehydrogenase activity | 6.5 × 10−3 | HADHA, HADHB, and HSD17B12 |
FAT | GO:0036094 | Small molecule binding | 7.2 × 10−3 | LCN2, LCN9, PAEP, and RBP4 |
FAT | GO:0001671 | ATPase activator activity | 9.9 × 10−3 | AHSA2, ATP1B3, TOR1AIP1, and TOR1AIP2 |
FAT% | GO:0005149 | Interleukin-1 receptor binding | 8.5 × 10−8 | IL1A, IL1B, IL1F10, IL1RN, IL36RN, IL36A, IL36B, IL36G, and IL37 |
FAT% | GO:0007585 | Respiratory gaseous exchange | 7.6 × 10−4 | PBX3, TLX3, CHST11, FUT8, GRIN1, SFTPB, and SFTPD |
FAT% | GO:0015125 | Bile acid transmembrane transporter activity | 9.1 × 10−4 | SLCO1A2, SLCO1B3, SLCO1C1, and SLCO2B1 |
FAT% | GO:0015459 | Potassium channel regulator activity | 3.6 × 10−3 | DPP6, LRRC26, KCNMB4, KCNIP4, KCNE1, KCNE2, and KCNE3 |
FAT% | GO:0005031 | Tumor necrosis factor-activated receptor activity | 5.1 × 10−3 | RELT, TNFRSF1A, TNFRSF1B, TNFRSF8, LTBR, and NGFR |
Trait | GO | Term | p-Value | Genes |
---|---|---|---|---|
PROT | GO:0008289 | Lipid binding | 1.7 × 10−5 | BPIFA1, BPIFA3, BPIFA2A, BPIFA2B, BPIFA2C, BPIFB1, BPIFB2, BPIFB3, BPIFB4, BPIFB6, ACBD7, and PLTP |
PROT | GO:0016998 | Cell wall macromolecule catabolic process | 6.9 × 10−5 | LYSB, LYZ1, LYZ3, LYZ2, and LYZ |
PROT | GO:0003796 | Lysozyme activity | 8.0 × 10−5 | LYSB, LYZ1, LYZ3, LYZ2, and LYZ |
PROT | GO:0042742 | Defense response to bacterium | 1.2 × 10−4 | DEFB122, DEFB122A, CSN1S2, DEFB116, DEFB119, DEFB123, DEFB124, DEFB119, HSTN, LYZ1, and NOD2 |
PROT | GO:0019835 | Cytolysis | 1.7 × 10−4 | LYSB, LYZ1, LYZ3, LYZ2, and LYZ |
PROT | GO:1903496 | Response to 11-deoxycorticosterone | 2.4 × 10−4 | CSN1S1, CSN1S2, CSN2, and CSN3 |
PROT | GO:0050829 | Defense response to Gram-negative bacterium | 8.5 × 10−4 | BPI, LYSB, LYZ1, LYZ3, LYZ2, and LYZ |
PROT | GO:0045087 | Innate immune response | 2.7 × 10−3 | BPIFA1, BPIFB1, BPIFB3, CYLD, HCK, DEFB122, DEFB122A, DEFB116, DEFB119, DEFB123, DEFB124, NOD2, TRIM10, TRIM15, and TRIM31 |
PROT | GO:0032570 | Response to progesterone | 3.4 × 10−3 | CSN1S1, CSN1S2, CSN2, and CSN3 |
PROT | GO:0032355 | Response to estradiol | 3.4 × 10−3 | CSN1S1, CSN1S2, CSN2, and CSN3 |
PROT | GO:0007586 | Digestion | 6.4 × 10−3 | LYZ1, LYZ3, LYZ2, and UCN3 |
PROT | GO:0045028 | G-protein coupled purinergic nucleotide receptor activity | 6.4 × 10−3 | GPR171, GPR87, P2RY12, and P2RY14 |
PROT | GO:0050830 | Defense response to Gram-positive bacterium | 9.2 × 10−3 | H2B, LYSB, LYZ1, LYZ3, LYZ2, and LYZ |
PROT% | GO:0005149 | Interleukin-1 receptor binding | 9.0 × 10−8 | IL1A, IL1RN, IL36A, IL36B, IL37, IL1B, IL36G, IL36RN, IRAK4, and IL1F10 |
PROT% | GO:1903496 | Response to 11-deoxycorticosterone | 3.5 × 10−4 | CSN1S2, CSN3, LALBA, CSN1S1, and CSN2 |
PROT% | GO:1903494 | Response to dehydroepiandrosterone | 3.5 × 10−4 | CSN1S2, CSN3, LALBA, CSN1S1, and CSN2 |
PROT% | GO:0005452 | Inorganic anion exchanger activity | 3.8 × 10−4 | SLC22A12, SLC4A8, SLC22A6, SLC22A8, SLC4A4, SLC22A10, SLC4A5, SLC22A9, and SLC22A11 |
PROT% | GO:0032355 | Response to estradiol | 2.0 × 10−3 | STAT3, CSN1S2, CSN3, LALBA, CSN1S1, and CSN2 |
PROT% | GO:0015347 | Sodium-independent organic anion transmembrane transporter activity | 2.2 × 10−3 | SLC22A12, SLC22A6, SLCO4A1, SLCO2B1, SLC22A8, SLC22A10, SLC22A9, and SLC22A11 |
PROT% | GO:0046983 | Protein dimerization activity | 2.6 × 10−3 | TFAP2A, PPP3CA, STAT5B, HEY1, MYC, ID2, TCF23, STAT3, ANO4, and E2F6 |
PROT% | GO:0043252 | Sodium-independent organic anion transport | 3.0 × 10−3 | SLC22A12, SLC22A6, SLCO4A1, SLCO2B1, SLC22A8, SLC22A10, SLC22A9, and SLC22A11 |
PROT% | GO:0043153 | Entrainment of circadian clock by photoperiod | 3.3 × 10−3 | PPP1CB, PER1, RBM4, ID2, CRY1, RBM4B, and TP53 |
PROT% | GO:0007595 | Lactation | 3.9 × 10−3 | STAT5A, STAT5B, VDR, NEURL1, ATP2B2, CSN3, CSN2, and PRLR |
PROT% | GO:0007259 | JAK-STAT cascade | 4.8 × 10−3 | STAT5A, STAT5B, CTR9, IL31RA, PRLR, and SOCS5 |
PROT% | GO:0030282 | Bone mineralization | 5.1 × 10−3 | KLF10, CLEC3B, WNT11, PKDCC, RSPO2, FBXL15, IFITM5, and LGR4 |
PROT% | GO:0048013 | Ephrin receptor signaling pathway | 6.2 × 10−3 | EPHB6, EFNA1, EFNA3, EFNB3, NCK2, EFNA4, and PTK2 |
PROT% | GO:0010628 | Positive regulation of gene expression | 6.4 × 10−3 | CRP, SEC16B, OSR2, RAMP2, PRKAA1, ODAM, ROCK2, RBM4B, SCX, SERPINB9, LRRC32, WNT11, FGF8, FABP4, ID2, KIT, RPS3, DROSHA, STAP1, KRAS, APOB, IL7R, ZBTB7B, and ZPR1 |
PROT% | GO:0008380 | RNA splicing | 6.5 × 10−3 | RBFOX2, MTERF3, PRPF4B, MAGOHB, JMJD6, RBM4, RBMXL2, PUF60, C1QBP, SRSF2, LUC7L3, PABPC1, SRSF7, and ZPR1 |
PROT% | GO:0005344 | Oxygen transporter activity | 6.9 × 10−3 | MB, HBE2, HBE1, HBE4, HBB, and CYGB |
PROT% | GO:0006397 | mRNA processing | 7.1 × 10−3 | RNASEL, RBFOX2, DDX1, PRPF4B, HNRNPLL, MAGOHB, JMJD6, RBM4, RBMXL2, ALKBH5, PUF60, C1QBP, SRSF2, PABPC1, AURKAIP1, SRSF7, and ZPR1 |
PROT% | GO:0048704 | Embryonic skeletal system morphogenesis | 7.8 × 10−3 | OSR2, COL11A1, PCGF2, HOXB4, HOXB3, HOXB2, HOXB1, HOXB7, and DSCAML1 |
LP | GO:0030334 | Regulation of cell migration | 1.3 × 10−1 | ABI3 and LDB2 |
LP | GO:1903955 | Positive regulation of protein targeting to mitochondrion | 1.5 × 10−1 | ELMOD1 and SAE1 |
LP | GO:0004867 | Serine-type endopeptidase inhibitor activity | 1.9 × 10−1 | SERPINB6 and SERPINB9 |
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Pedrosa, V.B.; Schenkel, F.S.; Chen, S.-Y.; Oliveira, H.R.; Casey, T.M.; Melka, M.G.; Brito, L.F. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes 2021, 12, 1830. https://doi.org/10.3390/genes12111830
Pedrosa VB, Schenkel FS, Chen S-Y, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes. 2021; 12(11):1830. https://doi.org/10.3390/genes12111830
Chicago/Turabian StylePedrosa, Victor B., Flavio S. Schenkel, Shi-Yi Chen, Hinayah R. Oliveira, Theresa M. Casey, Melkaye G. Melka, and Luiz F. Brito. 2021. "Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data" Genes 12, no. 11: 1830. https://doi.org/10.3390/genes12111830