Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle
<p>Boxplots of genome based inbreeding coefficients with F<sub>IS</sub>, F<sub>ROH</sub>, F<sub>ROH>4</sub>, F<sub>ROH>8</sub>, F<sub>ROH>16</sub> and F<sub>ROH>32</sub> for German Browns.</p> "> Figure 2
<p>Cumulative F<sub>ROH</sub> by birth years.</p> "> Figure 3
<p>Number of ROH (<b>A</b>) and total length of ROH (<b>B</b>) by US Brown Swiss classes.</p> "> Figure 4
<p>Cumulative distribution of F<sub>ROH</sub> by US Brown Swiss classes.</p> "> Figure 5
<p>Cumulative F<sub>ROH</sub> by survival traits.</p> "> Figure 6
<p>Effective population size (N<sub>e</sub>) and increase in inbreeding (ΔF) in German Brown cows for 20 generations (<b>A</b>) and 20–500 (<b>B</b>) generations ago based on linkage disequilibrium between consecutive SNPs.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Detection of Runs of Homozygosity
2.3. Inbreeding and Effective Population Size
2.4. Statistical Analysis
2.5. ROH Islands, Consensus ROH and Gene Ontology Enrichment
3. Results
3.1. Descriptive Statistics for ROH and Inbreeding for All Animals
3.2. ROH and Inbreeding by US Brown Swiss Classes
3.3. ROH and Genomic Inbreeding by Survival Classes
3.4. Consensus ROH and ROH Islands
3.5. Effective Population Size
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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ROH Items | Mean | SD | Min | Max |
---|---|---|---|---|
Average number of ROH | 35.996 | 7.498 | 1 | 63 |
Average ROH length (Mb) | 8.323 | 1.181 | 3.793 | 15.112 |
Combined length of ROH (Mb) | 301.070 | 80.500 | 3.794 | 755.517 |
Inbreeding Coefficients | Mean | SD | Median | Mode | 95% CI | 75% CI |
---|---|---|---|---|---|---|
FPED | 0.040 | 0.020 | 0.038 | 0.000 | 0.010–0.072 | 0.027–0.049 |
Fa_Bal | 0.111 | 0.043 | 0.116 | 0.000 | 0.031–0.174 | 0.084–0.140 |
Ahc | 0.123 | 0.050 | 0.128 | 0.000 | 0.032–0.200 | 0.091–0.158 |
Fa_Kal | 0.014 | 0.008 | 0.013 | 0.000 | 0.001–0.027 | 0.008–0.019 |
FNew | 0.028 | 0.014 | 0.026 | 0.000 | 0.001–0.051 | 0.019–0.034 |
FIS | −0.001 | 0.044 | −0.001 | −0.020 | −0.070–0.064 | −0.025–0.024 |
FROH | 0.122 | 0.032 | 0.120 | 0.090 | 0.072–0.174 | 0.101–0.141 |
FROH>4 | 0.113 | 0.032 | 0.113 | 0.110 | 0.065–0.165 | 0.091–0.132 |
FROH>8 | 0.074 | 0.028 | 0.071 | 0.000 | 0.034–0.122 | 0.055–0.090 |
FROH>16 | 0.031 | 0.022 | 0.027 | 0.000 | 0.007–0.071 | 0.016–0.043 |
FROH>32 | 0.006 | 0.012 | 0.000 | 0.000 | 0.000–0.030 | 0.000–0.013 |
Fa_Bal | Ahc | Fa_Kal | FNew | FIS | FROH | FROH>4 | FROH>8 | FROH>16 | FROH>32 | BS | |
---|---|---|---|---|---|---|---|---|---|---|---|
FPED | 0.498 | 0.490 | 0.832 | 0.964 | 0.571 | 0.572 | 0.567 | 0.546 | 0.490 | 0.383 | 0.153 *** |
Fa_Bal | 0.998 | 0.803 | 0.308 | 0.467 | 0.395 | 0.377 | 0.285 | 0.166 | 0.084 | 0.111 *** | |
Ahc | 0.801 | 0.297 | 0.464 | 0.393 | 0.376 | 0.284 | 0.164 | 0.085 | 0.099 *** | ||
Fa_Kal | 0.672 | 0.559 | 0.535 | 0.525 | 0.466 | 0.378 | 0.265 | 0.150 *** | |||
FNew | 0.516 | 0.533 | 0.531 | 0.530 | 0.492 | 0.396 | 0.143 *** | ||||
FIS | 0.925 | 0.926 | 0.851 | 0.684 | 0.469 | 0.070 *** | |||||
FROH | 0.993 | 0.936 | 0.770 | 0.519 | 0.070 *** | ||||||
FROH>4 | 0.945 | 0.780 | 0.526 | 0.064 ** | |||||||
FROH>8 | 0.838 | 0.565 | 0.049 * | ||||||||
FROH>16 | 0.681 | 0.006 ns | |||||||||
FROH>32 | −0.027 ns |
ROH Parameters | BS <60% | BS 60–69% | BS 70–79% | BS 80–89% | BS 90–99% | |||||
---|---|---|---|---|---|---|---|---|---|---|
(n = 70) | (n = 228) | (n = 407) | (n = 967) | (n = 636) | ||||||
Average number of ROH | 33.800 | ±0.863 a | 36.439 | ±0.478 bc | 35.074 | ±0.358 a | 36.070 | ±0.232 c | 37.280 | ±0.286 d |
Average ROH length (Mb) | 8.13 | ±0.14 ab | 8.30 | ±0.08 ab | 8.36 | ±0.06 ab | 8.39 | ±0.04 a | 8.24 | ±0.05 b |
Combined ROH length (Mb) | 278.86 | ±9.363 a | 304.040 | ±5.188 bc | 294.432 | ±3.883 ab | 303.823 | ±251.911 c | 307.774 | ±3.106 c |
BS <60% | BS 60–69% | BS 70–79% | BS 80–89% | BS 90–99% | |
---|---|---|---|---|---|
(n = 70) | (n = 228) | (n = 407) | (n = 967) | (n = 636) | |
FIS | −0.0141 a | 0.0003 bc | −0.0041 ab | −0.0019 c | 0.0018 c |
FROH | 0.113 a | 0.123 bc | 0.119 ab | 0.123 c | 0.124 c |
FROH>4 | 0.104 a | 0.114 bc | 0.110 ab | 0.114 cb | 0.115 c |
FROH>8 | 0.068 a | 0.074 ab | 0.072 ab | 0.075 b | 0.075 b |
FROH>16 | 0.028 a | 0.032 a | 0.031 a | 0.033 a | 0.031 a |
FROH>32 | 0.006 ab | 0.007 ab | 0.006 ab | 0.007 a | 0.005 b |
Surv1 | Surv3 | Surv5 | Surv7 | Surv9 | SE | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Homozygosity Item | No | Yes | No | Yes | No | Yes | No | Yes | No | Yes | |
(n = 434) | (n = 1804) | (n = 977) | (n = 791) | (n = 1115) | (n = 329) | (n = 1154) | (n = 273) | (n = 1183) | (n = 243) | ||
Average number of ROH | 37.968 | 34.281 *** | 37.427 | 30.978 *** | 37.166 | 29.032 *** | 36.842 | 29.242 *** | 36.595 | 29.542 *** | 0.202–0.454 |
Average ROH length (Mb) | 8.413 | 8.268 | 8.354 | 8.221 | 8.354 | 8.162 * | 8.352 | 8.141 * | 8.360 | 8.075 *** | 0.034–0.075 |
FIS | 0.011 | −0.009 *** | 0.008 | −0.026 *** | 0.006 | −0.033 *** | 0.004 | −0.031 *** | 0.002 | −0.029 *** | 0.001–0.003 |
FROH | 0.129 | 0.115 *** | 0.127 | 0.103 *** | 0.126 | 0.096 *** | 0.125 | 0.097 *** | 0.124 | 0.097 *** | 0.001–0.002 |
FROH>4 | 0.120 | 0.107 *** | 0.117 | 0.096 *** | 0.117 | 0.090 *** | 0.115 | 0.090 *** | 0.115 | 0.090 *** | 0.001–0.002 |
FROH>8 | 0.079 | 0.070 *** | 0.077 | 0.062 *** | 0.077 | 0.058 *** | 0.076 | 0.058 *** | 0.075 | 0.058 *** | 0.001–0.002 |
FROH>16 | 0.034 | 0.029 ** | 0.033 | 0.026 *** | 0.033 | 0.024 *** | 0.033 | 0.024 *** | 0.032 | 0.023 *** | 0.001–0.002 |
FROH>32 | 0.007 | 0.005 * | 0.007 | 0.004 *** | 0.007 | 0.004 *** | 0.007 | 0.003 *** | 0.007 | 0.003 *** | 0.000–0.002 |
Classification | BTA | SNPs | Start | End |
---|---|---|---|---|
All | 5 | 78 | 74891674 | 78859007 |
6 | 18 | 49731100 | 50316384 | |
6 | 281 | 73932138 | 91492398 | |
16 | 127 | 21496181 | 29716390 | |
BS <60% | 5 | 116 | 74891674 | 80425933 |
6 | 27 | 49731100 | 50746128 | |
6 | 239 | 73932138 | 90169101 | |
16 | 5 | 25226450 | 25877452 | |
BS 60–69% | 5 | 112 | 12308274 | 24373750 |
5 | 89 | 74891674 | 78895966 | |
6 | 17 | 49731100 | 50291712 | |
6 | 222 | 77603159 | 90169101 | |
16 | 119 | 21859732 | 29716390 | |
BS 70–79% | 5 | 117 | 74162338 | 80235852 |
6 | 17 | 49731100 | 50291712 | |
6 | 233 | 76817878 | 90169101 | |
16 | 115 | 22445908 | 29760720 | |
BS 80–89% | 5 | 52 | 74945315 | 76888810 |
6 | 27 | 49731100 | 50746128 | |
6 | 299 | 73932138 | 91629835 | |
16 | 99 | 21859732 | 28688202 | |
BS 90–99% | 5 | 103 | 72264476 | 76888810 |
6 | 41 | 49094600 | 50746128 | |
6 | 220 | 73932138 | 90169101 | |
16 | 166 | 21138669 | 30904995 | |
Surv1 | 5 | 53 | 74891674 | 76888810 |
6 | 18 | 49731100 | 50316384 | |
6 | 233 | 73932138 | 90169101 | |
16 | 127 | 21496181 | 29716390 | |
Surv3 | 5 | 51 | 74945315 | 76888810 |
6 | 17 | 49731100 | 50291712 | |
6 | 115 | 82855050 | 90169101 | |
16 | 66 | 24020699 | 28259305 | |
Surv5 | 5 | 47 | 75174437 | 76888810 |
6 | 46 | 85633295 | 88134986 | |
Surv7 | 5 | 47 | 75174437 | 76888810 |
6 | 33 | 86378938 | 88134986 | |
Surv9 | 5 | 49 | 75086818 | 76888810 |
6 | 46 | 85633295 | 88134986 |
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Wirth, A.; Duda, J.; Emmerling, R.; Götz, K.-U.; Birkenmaier, F.; Distl, O. Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle. Genes 2024, 15, 1051. https://doi.org/10.3390/genes15081051
Wirth A, Duda J, Emmerling R, Götz K-U, Birkenmaier F, Distl O. Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle. Genes. 2024; 15(8):1051. https://doi.org/10.3390/genes15081051
Chicago/Turabian StyleWirth, Anna, Jürgen Duda, Reiner Emmerling, Kay-Uwe Götz, Franz Birkenmaier, and Ottmar Distl. 2024. "Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle" Genes 15, no. 8: 1051. https://doi.org/10.3390/genes15081051