Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Phenotypes
2.2. Sampling and Genotyping
2.3. Quality Control (QC)
2.4. Association Analysis
3. Results
3.1. Descriptive Statistics
3.2. Quality Control
3.3. Principal Component Analysis
3.4. Significant SNPs Associated with SCS
3.5. Linkage Disequilibrium (LD) Blocks of the Significant SNPs
4. Discussion
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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Breed | Trait | N | Mean | SD | Min | Max | h2 | VP | VA |
---|---|---|---|---|---|---|---|---|---|
RS | LSCS1 | 11,081 | 2.81 | 1.72 | −1.64 | 8.84 | 0.08 | 2.9916 | 0.2564 |
LSCS2 | 7479 | 3.06 | 1.89 | −2.06 | 8.82 | 0.10 | 3.4975 | 0.3686 | |
LSCS3 | 5735 | 3.27 | 1.88 | −2.06 | 8.83 | 0.11 | 3.5347 | 0.3966 | |
RB | LSCS1 | 3462 | 4.53 | 1.92 | −0.84 | 8.82 | 0.03 | 2.7739 | 0.0857 |
LSCS2 | 3072 | 4.51 | 1.86 | −1.36 | 8.84 | 0.07 | 2.9304 | 0.2067 | |
LSCS3 | 2501 | 4.62 | 1.87 | −1.64 | 8.82 | 0.06 | 3.0061 | 0.2048 |
Parity 1 | Informative SNP 2 | SNP rsID | Chr:Position 3 | A1 | A2 | SNP Effect 4 | –log10 (p) | Nearest Gene 5 | Distance (bp) |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
AX-115117070 | NA | 13:78383148 | G | A | −4.74 × 10−8 | 4.28 | NA | NA | |
AX-117085597 | rs137805472 | 1:95119031 | C | T | 5.34 × 10−8 | 4.07 | NA | NA | |
L2 | |||||||||
AX-106721594 | NA | 1:71370844 | T | C | 3.07 × 10−8 | 4.87 | ZDHHC19 | 25909 | |
AX-106755404 | NA | 23:17013312 | A | G | 2.21 × 10−8 | 4.61 | NA | NA | |
AX-106740205 | rs109232438 | 9:71884731 | C | T | 5.01 × 10−8 | 4.32 | NA | NA | |
AX-171465786 | rs110140732 | 17:3030264 | G | A | 9.27 × 10−8 | 4.28 | NA | NA | |
AX-117088706 | rs43209122 | 16:70728849 | A | G | −2.50 × 10−8 | 4.23 | NA | NA | |
AX-106761299 | NA | 8:25435054 | C | T | −1.70 × 10−8 | 4.23 | NA | NA | |
L3 | |||||||||
AX-106761943 | rs110749552 | 6:37526622 | G | A | 5.47 × 10−8 | 6.37 | HERC3 | within | |
AX-106728871 | rs29021886 | 14:17674401 | C | A | −1.20 × 10−8 | 4.62 | NA | NA | |
AX-124381671 | NA | 4:79254806 | A | G | 1.20 × 10−8 | 4.6 | NA | NA | |
AX-106740778 | rs42627158 | 8:81747455 | C | T | −7.00 × 10−8 | 4.36 | DAPK1 | 459784 | |
AX-115112140 | NA | 15:5927942 | A | G | 3.73 × 10−8 | 4.19 | MMP7 | 462217 | |
AX-185121504 | rs209378984 | 6:70369168 | A | G | 5.97 × 10−8 | 4.11 | NA | NA | |
AX-115108867 | NA | 14:41169239 | A | G | 6.76 × 10−9 | 4 | NA | NA |
Parity 1 | Informative SNP 2 | SNP rsID | Chr:Position 3 | A1 | A2 | SNP Effect 4 | –log10 (p) | Nearest Gene 5 | Distance (bp) |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
AX-106741653 | NA | 7:8272794 | C | A | 6.14 × 10−9 | 5.37 | AKAP8 | 514640 | |
AX-115114947 | NA | 7:8276425 | G | A | 6.14 × 10−9 | 5.37 | AKAP8 | 511009 | |
AX-106739297 | rs108991944 | 11:37261133 | A | C | 1.54 × 10−9 | 4.41 | CLHC1 | 526855 | |
AX-124375018 | rs42894728 | 6:20276795 | G | A | 7.39 × 10−9 | 4.33 | NA | NA | |
AX-171466608 | rs42228650 | 7:27601185 | G | A | 5.65 × 10−10 | 4.29 | MEGF10 | 219169 | |
AX-106727011 | NA | 13:76008898 | G | A | −3.96 × 10−9 | 4.24 | NA | NA | |
AX-117090125 | rs110642171 | 6:39688028 | A | G | −2.65 × 10−9 | 4.19 | NA | NA | |
AX-117084655 | rs109189476 | 2:88162563 | C | T | 6.31 × 10−10 | 4.14 | SATB2 | 86169 | |
AX-106731475 | NA | 8:75798051 | T | C | 2.67 × 10−9 | 4.14 | NA | NA | |
AX-124381310 | NA | 24:34453446 | A | G | −1.98 × 10−9 | 4.08 | GATA6 | 96211 | |
L2 | |||||||||
AX-124381305 | rs43358795 | 3:97560648 | A | G | −3 × 10−10 | 5.38 | SPATA6 | 809734 | |
AX-169513997 | rs133252983 | 13:77447650 | G | T | 5.07 × 10−9 | 4.61 | NA | NA | |
AX-117080179 | rs110709131 | 2:46155190 | G | A | 3.47 × 10−9 | 4.56 | NA | NA | |
AX-117083483 | rs133489631 | 2:46126141 | T | C | 3.47 × 10−9 | 4.56 | NA | NA | |
AX-124350324 | rs42797639 | 9:20734430 | C | T | −9.3 × 10−10 | 4.19 | NA | NA | |
AX-124377880 | rs41981703 | 21:40381539 | A | C | 1.02 × 10−8 | 4.15 | NA | NA | |
AX-106735825 | rs43585636 | 9:14745626 | C | A | 3.02 × 10−9 | 4.09 | COL12A1 | 123884 | |
AX-117085949 | rs43585209 | 9:14767890 | A | G | 3.02 × 10−9 | 4.09 | COL12A1 | 101620 | |
AX-106726354 | NA | 5:94517415 | A | G | 5.58 × 10−9 | 4.08 | EPS8 | 156339 | |
L3 | |||||||||
AX-115109333 | NA | 22:26294371 | A | G | 6.59 × 10−9 | 5.17 | NA | NA | |
AX-124375014 | rs110955314 | 29:19740081 | C | A | −1.57 × 10−8 | 4.38 | LUZP2 | 519687 | |
AX-106753982 | NA | 21:23675656 | A | G | −6.09 × 10−9 | 4.35 | RAMAC | 30303 | |
AX-106735391 | rs110359025 | 19:16700029 | C | T | −7.19 × 10−9 | 4.21 | NA | NA | |
AX-106735614 | rs43256975 | 1:108154057 | A | G | −3.37 × 10−9 | 4.1 | IL12A | 131225 | |
AX-115115579 | rs110825674 | 19:50547082 | T | C | −9.06 × 10−9 | 4.06 | NA | NA | |
AX-106730586 | rs109619272 | 20:22823334 | A | G | 4.48 × 10−9 | 4.03 | ANKRD55 | 184056 |
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Ilie, D.E.; Mizeranschi, A.E.; Mihali, C.V.; Neamț, R.I.; Goilean, G.V.; Georgescu, O.I.; Zaharie, D.; Carabaș, M.; Huțu, I. Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle. Genes 2021, 12, 1495. https://doi.org/10.3390/genes12101495
Ilie DE, Mizeranschi AE, Mihali CV, Neamț RI, Goilean GV, Georgescu OI, Zaharie D, Carabaș M, Huțu I. Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle. Genes. 2021; 12(10):1495. https://doi.org/10.3390/genes12101495
Chicago/Turabian StyleIlie, Daniela Elena, Alexandru Eugeniu Mizeranschi, Ciprian Valentin Mihali, Radu Ionel Neamț, George Vlad Goilean, Ovidiu Ionuț Georgescu, Daniela Zaharie, Mihai Carabaș, and Ioan Huțu. 2021. "Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle" Genes 12, no. 10: 1495. https://doi.org/10.3390/genes12101495
APA StyleIlie, D. E., Mizeranschi, A. E., Mihali, C. V., Neamț, R. I., Goilean, G. V., Georgescu, O. I., Zaharie, D., Carabaș, M., & Huțu, I. (2021). Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle. Genes, 12(10), 1495. https://doi.org/10.3390/genes12101495