Genome-Wide Association Study of Milk Composition in Karachai Goats
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and Phenotypic Measurements
2.2. Genotyping and Quality Control of Data
2.3. Genome-Wide Association Studies and Gene Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | Abbreviated Name | Min | Max | Mean | Std. Dev | Cv, % |
---|---|---|---|---|---|---|
TS and MSNF, % | TS | 7.44 | 24.59 | 14.58 | 0.18 | 19.31 |
MSNF | 5.32 | 15.63 | 9.44 | 0.09 | 12.63 | |
Protein and β-casein, % | PT | 3.07 | 10.53 | 4.45 | 0.07 | 25.47 |
PC | 3.22 | 11.03 | 4.67 | 0.07 | 26.22 | |
Cas. β | 2.10 | 9.27 | 3.62 | 0.06 | 23.85 | |
Fat, % FA, TFA, g/100 g | Fat | 2.37 | 10.13 | 5.68 | 0.12 | 31.70 |
SFA | 1.36 | 8.85 | 3.92 | 0.19 | 32.73 | |
MUFA | 0.487 | 3.412 | 0.337 | 0.077 | 45.2 | |
PUFA | 0.042 | 0.520 | 0.228 | 0.009 | 31.5 | |
LCFA | 0.073 | 4.675 | 1.889 | 0.114 | 47.2 | |
MCFA | 0.011 | 4.689 | 2.223 | 0.111 | 38.9 | |
SCFA | 0.008 | 2.390 | 1.127 | 0.061 | 42.1 | |
C14:0 | 0.150 | 1.368 | 0.593 | 0.032 | 41.8 | |
C16:0 | 0.305 | 3.138 | 1.348 | 0.076 | 43.8 | |
C18:1 | 0.016 | 3.604 | 1.462 | 0.085 | 45.5 | |
TFA | 0.001 | 0.493 | 0.185 | 0.013 | 53.8 | |
Lactose, % | Lactose | 0.430 | 4.940 | 4.02 | 0.05 | 17.15 |
Metabolites, mmol/L, mg × 100 mL−1 * | Acetone | −0.51 | 1.62 | 0.035 | 0.01 | 334.13 |
BHB | −0.40 | 2.36 | 0.038 | 0.01 | 397.22 | |
Urea | 15.70 | 103.7 | 71.06 | 0.95 | 19.38 | |
Technological properties of milk, −1 × 10−3 °C ** | FPD | 483.0 | 612.0 | 546.25 | 1.40 | 2.24 |
pH | 5.02 | 6.82 | 6.39 | 0.02 | 4.18 |
Trait | Genome-Wide Threshold | Suggestive Threshold | ||
---|---|---|---|---|
Number | Chr | Number | Chr | |
TS | 5 | 2, 3, 8, 10, 25 | 18 | 1, 2, 3, 4, 6, 8, 12, 13, 16, 23, 25 |
MSNF | 2 | 2, 21 | 15 | 2, 7, 8, 9, 11, 14, 21, 24, 27 |
PT | 3 | 2, 8 | 13 | 1, 2, 8, 13, 21, 24, 26, 27, 28 |
PC | 6 | 1, 2, 8, 24 | 13 | 1, 2, 8, 13, 21, 23, 26, 27, 28 |
Cas. β | 2 | 2 | 16 | 8, 13, 20, 21, 24, 26, 27, 28 |
Fat | 2 | 8, 25 | 14 | 2, 3, 4, 5, 6, 12, 13, 16, 21, 25 |
SFA | 3 | 2, 3, 8 | 13 | 4, 5, 6, 13, 15, 16, 21, 23, 25 |
MUFA | - | 13 | 1, 2, 3, 8, 9, 13, 16, 21, 25 | |
PUFA | - | 12 | 3, 4, 8, 10, 16, 18, 19, 23, 25 | |
LCFA | 3 | 8, 16, 25 | 9 | 1, 2, 3, 4, 8, 9, 10, 21, 29 |
MCFA | 4 | 2, 3, 10, 25 | 6 | 13, 15, 16, 18, 21, 23 |
SCFA | 4 | 2, 3, 8, 25 | 4 | 3, 6, 23, 25 |
C14:0 | 3 | 2, 3, 8 | 6 | 5, 16, 18, 23, 25, 27 |
C16:0 | 3 | 2, 3, 25 | 9 | 5, 6, 15, 18, 21, 23 |
C18:1 | 3 | 8, 16, 25 | 11 | 2, 3, 4, 9, 10, 13, 21, 25 |
TFA | 1 | 25 | 4 | 3, 8, 18 |
Lactose | 6 | 1, 6, 8, | 6 | 2, 6, 11, 17, 18, 21 |
Acetone | 4 | 3, 7, 9, 27 | 17 | 2, 4, 5, 6, 7, 10, 17, 27 |
BHB | 1 | 2 | 6 | 2, 3, 4, 6 |
Urea | 3 | 2, 3 | 5 | 8, 10, 15, 18, 19, 27 |
FPD | 2 | 1 | 16 | 1, 2, 3, 4, 11, 13, 15, 24 |
pH | 4 | 1, 8 | 12 | 1, 3, 13, 17, 21 |
Traits | № Chr | № SNP | SNP | Gene/Position |
---|---|---|---|---|
PC | 8 | 18 | snp10589-scaffold1376-259452573806016…73406016 | DPYSL273547764…73663711 |
ADRA1A73747397…73862840 | ||||
PC, Cas. β | 8 | 20 | snp43681-scaffold585-225552578696104…78296104 | AGTPBP178600749…78791306 |
PC, Cas. β | 8 | 22 | snp997-scaffold1026-37855670884382…70484382 | NKX3-170600953…70606837 |
NKX2-670639383…70643794 | ||||
STC170791218…70806076 | ||||
PC, Cas. β | 13 | 27 | snp5221-scaffold1180-23624036057527…35657527 | ODAD235971967…36143096 |
PT | 16 | 32 | snp8683-scaffold131-458964254997494…54597494 | TNN54831011…54903426 |
PC | 23 | 36 | snp48737-scaffold692-15831445730320…45330320 | BAG245658115…45668381 |
Cas. β | 26 | 39 | snp18573-scaffold1878-33788114293322…13893322 | PDZD814290884…14368219 |
PC, Cas. β | 26 | 41 | snp47577-scaffold67-335155417989628…17589628 | CASP717808414…17850585 |
NRAP32471325…32547298 | ||||
HABP217935249…17970574 | ||||
Cas. β | 27 | 43 | snp55772-scaffold864-401298820994598…20594598 | MFHAS120648690…20757838 |
Traits | № Chr | № SNP | SNP | Gene/Position |
---|---|---|---|---|
MUFA | 1 | 1 | snp27412-scaffold292-177570141251692…140851692 | MX2141193475…141232778 |
SFA, MCFA, SCFA, C14, C16 | 2 | 3 | snp18646-scaffold1882-539299111252769…110852769 | METTL8111185392…111270066 |
PUFA, LCFA, C18:1 | 4 | 14 | snp1935-scaffold1053-15283962946300…2546300 | INSIG12747017…2757803 |
EN22659430…2666542 | ||||
PAXIP12922811…2963751 | ||||
PUFA, TFA | 8 | 21 | snp47195-scaffold66-184191947980184…47580184 | CEMIP247675207…47756816 |
Fat | 8 | 23 | snp34748-scaffold412-87171991227795…90827795 | BAAT90845022…90861305 |
PLPPR190695441…90835782 | ||||
PUFA, C14 | 8 | 24 | snp28090-scaffold300-391314639951214…39551214 | SLC1A39770036…39845247 |
LCFA, C18:1 | 10 | 25 | snp1441-scaffold104-78028525686826…25286826 | FUT825310706…25629694 |
PUFA, MCFA | 10 | 26 | snp24669-scaffold251-162591356289166…55889166 | TPM1 |
LACTB | ||||
SFA, MUFA, C18:1 | 13 | 28 | snp8522-scaffold1308-172901075567491…75167491 | EYA275025156…75283017 |
PUFA | 16 | 29 | snp18361-scaffold186-25173468574935…68174935 | PROX168179003…68234777 |
SFA, MCFA, C14 | 16 | 30 | snp50562-scaffold727-52483637486538… 37086538 | FMO237286455…37330116 |
FMO137336303…37376884 | ||||
MUFA, LCFA, C18:1 | 16 | 31 | snp3754-scaffold112-397350463571269…63171269 | NCF263224955…63263716 |
Fat | 16 | 32 | snp8683-scaffold131-458964254997494…54597494 | TNN54831011…54903426 |
SFA, MCFA, PUFA, SCFA, C14, C16 | 23 | 35 | snp10273-scaffold1368-27018347104785…6704785 | PHACTR16556030…7073500 |
SFA, MUFA, PUFA, MCFA, LCFA, SCFA, C16, C18:1, C14, TFA | 25 | 37, 38 | snp16907-scaffold1766-5824892027754…1627754 snp16908-scaffold1766-6161402061790…1661790 | ECI11672290…1685556 |
PGP1649864…1652731 | ||||
ABCA31701870…1743075 | ||||
AMDHD21915270…1921956 | ||||
PDPK11932902…1996678 | ||||
SCFA | 26 | 40 | snp41130-scaffold532-172787030209081…29809081 | SEMA4G29853719…29867663 |
Traits | № Chr | № SNP | SNP | Gene/Position |
---|---|---|---|---|
BHB, Acetone | 2 | 4 | snp9402-scaffold1341-2132092114722555…114322555 | ATF2114518050…114597771 |
Urea | 2 | 7 | snp25937-scaffold2682-105434814121…414121 | NECAP2486514…500217 |
BHB | 2 | 9 | snp2511-scaffold1071-12995715102755…14702755 | HPCA14931533…14940116 |
FNDC514907902…14915966 | ||||
Acetone | 3 | 11 | snp22179-scaffold219-7717428377011…7977011 | NEU28043799…8057992 |
GIGYF28226338…8358229 | ||||
INPP5D7877943…8015888 | ||||
4 | 15 | snp38614-scaffold49-1209913110877395… 110477395 | CDK6110413189…110678573 | |
5 | 16 | snp47348-scaffold666-5289997220952… 96820952 | ETV696570433…96857059 | |
17 | snp12158-scaffold1450-249468107408739…107008739 | CACNA1C107328368…107719644 | ||
Urea | 18 | 33 | snp18289-scaffold1857-30866756470790…56070790 | SULT2B156239547…56275810 |
GRIN2D56117047…56151568 | ||||
SPHK256292056…56299987 | ||||
NTN556321271…56326460 | ||||
IZUMO156393899…56396881 | ||||
FUT156399123…56402123 | ||||
Acetone | 27 | 42 | snp51881-scaffold762-23493194343759…3943759 | THRB3763978…4201001 |
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Selionova, M.; Trukhachev, V.; Aibazov, M.; Sermyagin, A.; Belous, A.; Gladkikh, M.; Zinovieva, N. Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals 2024, 14, 327. https://doi.org/10.3390/ani14020327
Selionova M, Trukhachev V, Aibazov M, Sermyagin A, Belous A, Gladkikh M, Zinovieva N. Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals. 2024; 14(2):327. https://doi.org/10.3390/ani14020327
Chicago/Turabian StyleSelionova, Marina, Vladimir Trukhachev, Magomet Aibazov, Alexander Sermyagin, Anna Belous, Marianna Gladkikh, and Natalia Zinovieva. 2024. "Genome-Wide Association Study of Milk Composition in Karachai Goats" Animals 14, no. 2: 327. https://doi.org/10.3390/ani14020327
APA StyleSelionova, M., Trukhachev, V., Aibazov, M., Sermyagin, A., Belous, A., Gladkikh, M., & Zinovieva, N. (2024). Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals, 14(2), 327. https://doi.org/10.3390/ani14020327