Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Population and Phenotypic Data
2.2. SNPs Identification and Genotyping
2.3. Estimation of linkage disequilibrium (LD)
2.4. Association Analyses
2.5. Protein Structure and Function Prediction
2.6. Predication of Transcription Factors Binding Sites (TFBSs)
2.7. Gene Expressions Assay of LIPK and LIPJ
3. Results
3.1. SNPs Identification
3.2. Associations between SNPs/Haplotype Blocks and Milk FAs
3.3. Linkage disequilibrium among the SNPs of LIPK, LIPJ and SCD Genes
3.4. rs42774527 Caused the Changes of the LIPK Protein Structure and Function
3.5. Transcription Factors Binding Sites (TFBSs) Changed by rs110322221 and rs211373799
3.6. Expressions of LIPK and LIPJ Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of interest
Ethics Approval
References
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Gene | SNP Name | Location | Position | GenBank no. | Significant Milk FAs | p-Interval | Allele | TFBS | Amino | Changes of Protein Secondary Structure | SIFT | PROVEAN | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
(UMD 3.1) | Acid | Alpha Helix | Extended Strand | Beta Turn | Random Coil | ||||||||||
LIPK | g.10428101G>A | 5′ UTR | Chr26: 10428101 | rs110322221 | C6:0, C8:0, C10:0, C14:0, C20:0, SFA, SFA/UFA, total index | <1.00 × 10−4~4.88 × 10−2 | G | ||||||||
A | FAC1 | ||||||||||||||
g.10449831C>A | Exon-11 | Chr26: 10449831 | rs42774527 | C6:0, C8:0, C10:0, C14:0, C17:0, C17:1, C18:1cis-9, C20:0, C17index, total index | <1.00 × 10−4~3.76 × 10−2 | C | Thr | 34.09% | 19.95% | 6.06% | 39.90% | 0.04 | -3.315 | ||
A | Lys | 33.08% | 19.44% | 6.31% | 41.16% | ||||||||||
LIPJ | g.10214117A>C | 5′ flanking region | Chr26: 10214117 | rs41606812 | C17:0, C17:1, C20:0 | <1.00 × 10−4~2.55 × 10−2 | A | ||||||||
C | |||||||||||||||
g.10217380C>A | 5′ UTR | Chr26: 10217380 | rs211373799 | C6:0, C8:0, C10:0, C14:0, C17:1, C20:0 | <1.00 × 10−4~3.41 × 10−2 | C | AIRE | ||||||||
MTBF | |||||||||||||||
A | FAST1 | ||||||||||||||
g.10247997T>C | 3′ UTR | Chr26: 10247997 | rs42107056 | C6:0, C8:0, C14:0, C17:1, C14index, C16index, SFA, total index | 1.30 × 10−3~2.15 × 10−2 | T | |||||||||
C | |||||||||||||||
g.10250098C>T | 3′ flanking region | Chr26: 10250098 | rs42107122 | C6:0, C14:0, C14index, C16index, SFA, UFA, total index | 3.00 × 10−4~4.36 × 10−2 | C | |||||||||
T | |||||||||||||||
g.10250120A>G | 3′ flanking region | Chr26: 10250120 | ss158213049726 | C6:0, C10:0, C14:0, C17:1, C18:1cis-9, C14index, C16index, SFA, UFA, total index | <1.00 × 10−4~3.37 × 10−2 | A | |||||||||
G | |||||||||||||||
g.10251075G>T | 3′ flanking region | Chr26: 10251075 | rs209219656 | C6:0, C14:0, C17:1, C20:0, C14index, C16index | 1.00 × 10−3~3.68 × 10−2 | G | |||||||||
T | |||||||||||||||
g.10251111T>C | 3′ flanking region | Chr26: 10251111 | rs42107114 | C6:0, C8:0, C10:0, C17:1, C20:0, C14index, total index | <1.00 × 10−4~4.22 × 10−2 | T | |||||||||
C |
Haplotype Combination (No.) | C6:0 (%) | C8:0 (%) | C10:0 (%) | C11:0 (%) | C12:0 (%) | C13:0 (%) | C14:0 (%) | C14:1 (%) | C15:0 (%) | C16:0 (%) | C16:1 (%) | C17:0 (%) |
---|---|---|---|---|---|---|---|---|---|---|---|---|
H1H1 (236–250) | 0.4915 ± 0.0138 A | 0.9582 ± 0.0120 Aa | 2.8777 ± 0.0356 Aa | 0.0607 ± 0.0028 | 3.0778 ± 0.0464 | 0.1002 ± 0.0035 | 10.3703 ± 0.0785 | 0.6266 ± 0.0209 | 0.9980 ± 0.0143 | 34.8257 ± 0.2024 | 1.2791 ± 0.0283 | 0.5652 ± 0.0036 |
H1H2 (196–215) | 0.5079 ± 0.0143 A | 0.9214 ± 0.0126 Ab | 2.8373 ± 0.0368 A | 0.0607 ± 0.0029 | 3.0641 ± 0.0478 | 0.1020 ± 0.0036 | 10.2305 ± 0.0814 | 0.6608 ± 0.0219 | 0.9895 ± 0.0150 | 34.5606 ± 0.2108 | 1.3468 ± 0.0295 | 0.5725 ± 0.0038 |
H1H3 (134–147) | 0.4066 ± 0.0163 B | 0.8758 ± 0.0139B | 2.6856 ± 0.0408 B | 0.0536 ± 0.0032 | 2.9704 ± 0.0526 | 0.0971 ± 0.0042 | 10.3702 ± 0.0897 | 0.6668 ± 0.0249 | 1.0024 ± 0.0170 | 34.9864 ± 0.2406 | 1.3309 ± 0.0333 | 0.5729 ± 0.0043 |
H1H4 (84–91) | 0.4642 ± 0.0186 AB | 0.9134 ± 0.0159 ABb | 2.7806 ± 0.0463 | 0.0593 ± 0.0038 | 2.9892 ± 0.0611 | 0.0981 ± 0.0050 | 10.3107 ± 0.1029 | 0.6756 ± 0.0291 | 0.9988 ± 0.0200 | 34.7553 ± 0.2768 | 1.3364 ± 0.0384 | 0.5688 ± 0.0050 |
H2H2 (94–99) | 0.5145 ± 0.0180 ACa | 0.9540 ± 0.0154 A | 2.7562 ± 0.0451 ABb | 0.0590 ± 0.0037 | 3.0134 ± 0.0584 | 0.0978 ± 0.0049 | 10.2163 ± 0.0996 | 0.6841 ± 0.0285 | 0.9919 ± 0.0192 | 34.7388 ± 0.2684 | 1.3455 ± 0.0376 | 0.5670 ± 0.0049 |
H2H3 (52–56) | 0.5886 ± 0.0215 Cb | 0.9553 ± 0.0182A | 2.7167 ± 0.0526 ABb | 0.0551 ± 0.0044 | 2.9365 ± 0.0691 | 0.1012 ± 0.0059 | 10.1683 ± 0.1181 | 0.6606 ± 0.0340 | 0.9837 ± 0.0236 | 34.8336 ± 0.3231 | 1.3490 ± 0.0443 | 0.5638 ± 0.0059 |
p | <1.00 × 10−4 ** | <1.00 × 10−4 ** | <1.00 × 10−4 ** | 2.50 × 10−1 | 8.57 × 10−2 | 9.06 × 10−1 | 1.74 × 10−1 | 2.91 × 10−1 | 9.65 × 10−1 | 6.11 × 10−1 | 1.75 × 10−1 | 2.64 × 10−1 |
Haplotype combination (No.) | C17:1 (%) | C18:0 (%) | C18:1cis-9 (%) | C18index (%) | C20:0 (%) | C14index (%) | C16index (%) | C17index (%) | SFA (%) | UFA (%) | SFA/UFA (%) | Total index (%) |
H1H1 (212–250) | 0.1877 ± 0.0028A | 14.0724 ± 0.1029 | 19.0132 ± 0.1380 | 57.1817 ± 0.3145 | 0.1671 ± 0.0020a | 5.7655 ± 0.1594 Aa | 3.5534 ± 0.0726 | 24.5170 ± 0.2489a | 68.2270 ± 0.1876 | 30.1878 ± 0.1709 | 2.3037 ± 0.0250 | 27.2671 ± 0.1630a |
H1H2 (174–215) | 0.1955 ± 0.0029a | 14.0472 ± 0.1081 | 19.1074 ± 0.1447 | 57.2138 ± 0.3281 | 0.1737 ± 0.0021 Ab | 6.1702 ± 0.1694 | 3.7593 ± 0.0752 | 25.3334 ± 0.2578 b | 68.0475 ± 0.1961 | 30.3502 ± 0.1793 | 2.2650 ± 0.0260 | 27.5520 ± 0.1695 |
H1H3 (119–148) | 0.1944 ± 0.0033 | 14.0278 ± 0.1234 | 18.9345 ± 0.1647 | 56.9697 ± 0.3745 | 0.1696 ± 0.0024 | 6.1980 ± 0.1838 | 3.6901 ± 0.0849 | 24.8310 ± 0.2861 | 68.0476 ± 0.2240 | 30.3144 ± 0.2052 | 2.2995 ± 0.0298 | 27.2367 ± 0.1857 a |
H1H4 (79–91) | 0.1960 ± 0.0039 | 14.1424 ± 0.1452 | 19.4779 ± 0.1965 | 57.8644 ± 0.4411 | 0.1619 ± 0.0028 B | 6.3962 ± 0.2167 b | 3.7332 ± 0.0982 | 25.1307 ± 0.3321 | 67.5861 ± 0.2651 | 30.7677 ± 0.2399 | 2.2465 ± 0.0350 | 27.9861 ± 0.2200 b |
H2H2 (86–99) | 0.2014 ± 0.0037 B | 13.8249 ± 0.1418 | 19.3393 ± 0.1880 | 57.8175 ± 0.4261 | 0.1680 ± 0.0027 | 6.5399 ± 0.2096 | 3.7366 ± 0.0958 | 25.2834 ± 0.3248 | 67.5006 ± 0.2558 | 30.8790 ± 0.2348 | 2.2421 ± 0.0337 | 27.9063 ± 0.2131 b |
H2H3 (41–56) | 0.1822 ± 0.0045 Ab | 13.9019 ± 0.1738 | 19.0366 ± 0.2300 | 57.2853 ± 0.5135 | 0.1605 ± 0.0035 B | 6.1413 ± 0.2510 B | 3.7223 ± 0.1123 | 24.1729 ± 0.3870 a | 67.9823 ± 0.3101 | 30.4244 ± 0.2834 | 2.2738 ± 0.0414 | 27.5623 ± 0.2559 |
p | 2.00 × 10−4 ** | 4.92 × 10−1 | 1.05 × 10−1 | 3.13 × 10−1 | <1.00 × 10−4 ** | 1.90 × 10−3 ** | 7.34 × 10−2 | 2.40 × 10−3 ** | 5.06 × 10−2 | 3.98 × 10−2 * | 3.32 × 10−1 | 9.00 × 10−4 ** |
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Shi, L.; Han, B.; Liu, L.; Lv, X.; Ma, Z.; Li, C.; Xu, L.; Li, Y.; Zhao, F.; Yang, Y.; et al. Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle. Genes 2019, 10, 86. https://doi.org/10.3390/genes10020086
Shi L, Han B, Liu L, Lv X, Ma Z, Li C, Xu L, Li Y, Zhao F, Yang Y, et al. Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle. Genes. 2019; 10(2):86. https://doi.org/10.3390/genes10020086
Chicago/Turabian StyleShi, Lijun, Bo Han, Lin Liu, Xiaoqing Lv, Zhu Ma, Cong Li, Lingna Xu, Yanhua Li, Feng Zhao, Yuze Yang, and et al. 2019. "Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle" Genes 10, no. 2: 86. https://doi.org/10.3390/genes10020086
APA StyleShi, L., Han, B., Liu, L., Lv, X., Ma, Z., Li, C., Xu, L., Li, Y., Zhao, F., Yang, Y., & Sun, D. (2019). Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle. Genes, 10(2), 86. https://doi.org/10.3390/genes10020086