Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Genotype and Quality Control
2.2. Statistical Analysis
2.3. Significance Test
2.4. Population Stratification Analysis
2.5. Screening and Annotation of the Candidate Genes
2.6. Enrichment Analysis of the Candidate Genes
2.7. Software and the Database Website Used in This Study
3. Results
3.1. Population Stratification
3.2. Genome-Wide Association Study
3.3. Significant SNPs and the Candidate Genes
3.4. Enrichment Analysis of the Candidate Genes
4. Discussion
4.1. Genome-Wide Association Study
4.1.1. Candidate Genes Associated with the HCR
4.1.2. Candidate Genes Associated with the CCR
4.1.3. Candidate Genes Associated with the DPR
4.2. Candidate-Gene Enrichment Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait | Number | Average | Maximum | Minimum | Variance | Standard Deviation |
---|---|---|---|---|---|---|
HCR | 637 | 0.81 | 4.1 | −2.4 | 1.30 | 1.14 |
CCR | 637 | 0.62 | 4.9 | −3.1 | 1.69 | 1.30 |
DPR | 637 | 0.00031 | 3.4 | −3.2 | 1.27 | 1.13 |
Before Quality Control | After Quality Control | ||||
---|---|---|---|---|---|
Chromosome | Length (Mb) | SNPs Count | Density (kb/snp) | SNPs Count | Density (kb/snp) |
1 | 158.3 | 5556 | 35.1 | 4693 | 29.6 |
2 | 137.1 | 4688 | 34.2 | 3917 | 28.6 |
3 | 121.4 | 4508 | 37.1 | 3749 | 30.9 |
4 | 120.8 | 4049 | 33.5 | 3390 | 28.1 |
5 | 121.2 | 4523 | 37.3 | 3734 | 30.8 |
6 | 119.5 | 4364 | 36.5 | 3617 | 30.3 |
7 | 112.6 | 3903 | 34.7 | 3232 | 28.7 |
8 | 113.4 | 3805 | 33.6 | 3289 | 29.0 |
9 | 105.7 | 3695 | 35.0 | 3181 | 30.1 |
10 | 104.3 | 3626 | 34.8 | 3116 | 29.9 |
11 | 107.3 | 3801 | 35.4 | 3216 | 30.0 |
12 | 91.2 | 3044 | 33.4 | 2563 | 28.1 |
13 | 84.2 | 3064 | 36.4 | 2617 | 31.1 |
14 | 84.6 | 3045 | 36.0 | 2561 | 30.3 |
15 | 85.3 | 3119 | 36.6 | 2674 | 31.3 |
16 | 81.7 | 2826 | 34.6 | 2338 | 28.6 |
17 | 75.2 | 2668 | 35.5 | 2286 | 30.4 |
18 | 66.0 | 2605 | 39.5 | 2197 | 33.3 |
19 | 64.1 | 2726 | 42.5 | 2226 | 34.7 |
20 | 72.0 | 2737 | 38.0 | 2253 | 31.3 |
21 | 71.6 | 2573 | 35.9 | 2167 | 30.3 |
22 | 61.4 | 2201 | 35.8 | 1878 | 30.6 |
23 | 52.5 | 2110 | 40.2 | 1774 | 33.4 |
24 | 62.7 | 2259 | 36.0 | 1934 | 30.8 |
25 | 42.9 | 1726 | 40.2 | 1443 | 33.6 |
26 | 51.7 | 1823 | 35.3 | 1551 | 30.0 |
27 | 45.4 | 1699 | 37.4 | 1488 | 32.8 |
28 | 46.3 | 1735 | 37.5 | 1506 | 32.5 |
29 | 51.5 | 1871 | 36.3 | 1570 | 30.5 |
Character | SNP | Chromosome | Site (bp) | p Value | The Gene Region | Distance (bp) |
---|---|---|---|---|---|---|
HCR | BovineHD0200029628 | 2 | 102,699,078 | 9.18 × 10−3 | VWC2L | 81,620 |
BovineHD0200022967 | 2 | 79,537,846 | 3.11 × 10−5 | STAT1 | 21,534 | |
BTA-37416-no-rs | 6 | 23,807,252 | 8.69 × 10−4 | PPP3CA | 36,965 | |
BovineHD28000743 | 28 | 41,387,894 | 7.36 × 10−5 | LDB3 | 2984 | |
BovineHD2800005891 | 28 | 22,263,728 | 6.23 × 10−5 | CTNNA3 | 10,962 | |
CCR | LGB_X14710_5174 | 11 | 103,259,143 | 7.68 × 10−3 | PAEP | 1719 |
BovineHD1100000394 | 11 | 1,230,012 | 3.72 × 10−4 | ACOXL | 6654 | |
BovineHD4100008487 | 11 | 2,827,428 | 2.86 × 10−4 | EPAS1 | 73,158 | |
BovineHD1700011952 | 17 | 42,103,930 | 4.12 × 10−4 | GLRB | 6465 | |
BovineHD2600004843 | 26 | 18,941,126 | 4.61 × 10−5 | MARVELD1 | 68,791 | |
DPR | ARS-USMARC-666 | 5 | 25,527,614 | 1.51 × 10−6 | PDE1B | 11,893 |
BovineHD0500025349 | 5 | 88,911,724 | 6.17 × 10−4 | SLCO1A2 | 22,340 | |
BovineHD0700016212 | 7 | 54,281,313 | 6.66 × 10−4 | ARHGAP26 | 3543 | |
Hapmap58695-rs29019899 | 10 | 51,673,875 | 1.95 × 10−5 | ADAM10 | 5385 | |
BovineHD1500013531 | 15 | 46,637,606 | 1.29 × 10−5 | APBB1 | 11,182 | |
UFL-rs41859871 | 18 | 4,419,224 | 1.94 × 10−5 | MON1B | 3866 | |
COQ9_rs109301586 | 18 | 25,446,323 | 4.27 × 10−4 | COQ9 | 2139 | |
ARS-BFGL-NGS-115062 | 21 | 67,739,884 | 8.39 × 10−3 | CDC42BPB | 18,754 | |
ARS-BFGL-NGS-115980 | 26 | 20,196,747 | 1.74 × 10−5 | HPSE2 | 61,344 | |
BovineHD2600004843 | 26 | 18,941,126 | 4.61 × 10−5 | MARVELD1 | 68,791 |
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Liu, J.; Xu, L.; Ding, X.; Ma, Y. Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle. Genes 2024, 15, 12. https://doi.org/10.3390/genes15010012
Liu J, Xu L, Ding X, Ma Y. Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle. Genes. 2024; 15(1):12. https://doi.org/10.3390/genes15010012
Chicago/Turabian StyleLiu, Jiashuang, Lingyang Xu, Xiangbin Ding, and Yi Ma. 2024. "Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle" Genes 15, no. 1: 12. https://doi.org/10.3390/genes15010012
APA StyleLiu, J., Xu, L., Ding, X., & Ma, Y. (2024). Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle. Genes, 15(1), 12. https://doi.org/10.3390/genes15010012