Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Overview
2.2. Traits
2.3. Genotypes
2.4. Definition of the Prenatal Environment
2.5. Data Quality Control
2.6. Multiple-Trait Reaction Norm Model
2.7. Single-Step Genomic-Wide Association Study (ssGWAS)
2.8. Reaction Norms
3. Results
3.1. Effect of Gestational Environment on the Phenotypic Scale
3.2. Covariance Components and Genetic Parameters
3.3. Heritability Estimates
3.4. Intra-Trait Genetic Correlations
3.5. Inter-Trait Genetic Correlations
3.6. ssGWAS
3.7. Reaction Norms
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement:
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Item | Experimental Data | ||||
---|---|---|---|---|---|
BW (kg) | W120 (kg) | W210 (kg) | SC (cm) | DFC (days) | |
Animals in the pedigree, n | 10,350 | 9614 | 9573 | – | 2969 |
Sires in the pedigree, n | 384 | 384 | 384 | – | 341 |
Dams in the pedigree, n | 2540 | 2470 | 2469 | – | 1452 |
Phenotypic records, n | 9816 | 9078 | 9003 | – | 2222 |
Sires with progeny record, n | 370 | 370 | 370 | – | 306 |
Dams with progeny record, n | 2519 | 2446 | 2447 | – | 1289 |
Genotyped sires with progeny record, n | 116 | 116 | 116 | – | 70 |
Genotyped dams with progeny record, n | 370 | 365 | 366 | – | 158 |
Progeny records from genotyped sire, n | 3328 | 3077 | 3058 | – | 572 |
Progeny records from genotyped dams, n | 1299 | 1199 | 1194 | – | 199 |
Genotyped animals with phenotypic records, n | 1516 | 1503 | 1502 | – | 258 |
Average of the trait | 28.92 | 122.91 | 188.99 | – | 347.80 |
Standard deviation of the trait | 5.43 | 19.94 | 31.02 | – | 35.81 |
Company data | |||||
Animals in the pedigree, n | 356,730 | – | 216,707 | 120,619 | 25,072 |
Sires in the pedigree, n | 3060 | – | 2476 | 2022 | 1318 |
Dams in the pedigree, n | 133,863 | – | 99,553 | 67,291 | 35,950 |
Phenotypic records, n | 287,705 | – | 146,020 | 52,259 | 22,405 |
Sires with progeny record, n | 2342 | – | 1817 | 1418 | 765 |
Dams with progeny record, n | 95,820 | – | 65,379 | 33,588 | 17,391 |
Average of the trait | 31.87 | – | 188.65 | 27.62 | 340.47 |
Standard deviation of the trait | 3.96 | – | 27.53 | 3.28 | 27.22 |
Trait | Parameter | Experimental Data | Company Data | ||||
---|---|---|---|---|---|---|---|
Mean | SD | HPD95% | Mean | SD | HPD95% | ||
W120 | 107.633 | 12.570 | 83.951 to 133.148 | – | – | – | |
87.426 | 13.384 | 62.855 to 115.186 | – | – | – | ||
53.373 | 5.747 | 42.060 to 64.750 | – | – | – | ||
0.166 | 0.019 | 0.129 to 0.202 | – | – | – | ||
110.854 | 4.826 | 101.550 to 120.200 | – | – | – | ||
0.177 | 0.094 | −0.016 to 0.353 | – | – | – | ||
0.215 | 0.129 | −0.051 to 0.460 | – | – | – | ||
0.164 | 0.045 | 0.083 to 0.260 | – | – | – | ||
0.170 | 0.044 | 0.099 to 0.267 | – | – | – | ||
W210 | 286.698 | 30.428 | 230.108 to 349.021 | 98.198 | 5.570 | 87.560 to 109.307 | |
210.659 | 30.545 | 153.761 to 273.906 | 38.787 | 3.560 | 32.170 to 46.338 | ||
120.340 | 12.948 | 95.290 to 146.20 | 57.233 | 1.877 | 53.550 to 60.990 | ||
0.163 | 0.018 | 0.127 to 0.200 | 0.150 | 0.005 | 0.140 to 0.160 | ||
232.043 | 11.000 | 210.500 to 253.750 | 189.93 | 2.575 | 184.900 to 194.800 | ||
−0.063 | 0.087 | −0.235 to 0.103 | 0.607 | 0.045 | 0.526 to 0.708 | ||
0.198 | 0.128 | −0.064 to 0.441 | 0.392 | 0.085 | 0.219 to 0.546 | ||
0.190 | 0.045 | 0.108 to 0.287 | 0.112 | 0.021 | 0.073 to 0.157 | ||
0.159 | 0.038 | 0.095 to 0.243 | 0.120 | 0.026 | 0.072 to 0.174 | ||
SC | – | – | – | 38.837 | 1.485 | 35.978 to 41.789 | |
– | – | – | 3.612 | 0.911 | 3.434 to 3.790 | ||
– | – | – | 0.313 | 0.057 | 0.201 to 0.419 | ||
– | – | – | 0.029 | 0.006 | 0.019 to 0.042 | ||
DFC | 62.612 | 15.708 | 35.954 to 96.952 | 16.832 | 3.742 | 10.873 to 25.451 | |
222.314 | 9.133 | 204.400 to 240.700 | 239.606 | 3.124 | 233.100 to 245.400 | ||
−0.073 | 0.188 | −0.422 to 0.311 | 0.550 | 0.130 | 0.286 to 0.754 | ||
0.651 | 0.230 | 0.309 to 1.195 | 0.484 | 0.210 | 0.181 to 0.990 |
Experimental Data (EXP) | ||||
---|---|---|---|---|
W120 (direct effects: below diagonal, maternal above) | ||||
GE | −2.5 | −1.0 | +1.0 | +2.5 |
−2.5 | 1 | 0.901 (0.03) | 0.622 (0.08) | 0.343 (0.11) |
−1.0 | 0.909 (0.02) | 1 | 0.899 (0.03) | 0.713 (0.06) |
+1.0 | 0.639 (0.08) | 0.900 (0.03) | 1 | 0.947 (0.01) |
+2.5 | 0.357 (0.12) | 0.710 (0.07) | 0.946 (0.01) | 1 |
W210 (direct effects: below diagonal, maternal above) | ||||
−2.5 | 1 | 0.908 (0.02) | 0.645 (0.07) | 0.371 (0.10) |
−1.0 | 0.929 (0.01) | 1 | 0.904 (0.02) | 0.722 (0.06) |
+1.0 | 0.646 (0.07) | 0.882 (0.03) | 1 | 0.948 (0.01) |
+2.5 | 0.284 (0.11) | 0.617 (0.07) | 0.914 (0.02) | 1 |
DFC (above) | ||||
−2.5 | 1 | 0.885 (0.04) | 0.241 (0.17) | −0.294 (0.16) |
−1.0 | – | 1 | 0.657 (0.10) | 0.172 (0.17) |
+1.0 | – | – | 1 | 0.849 (0.05) |
+2.5 | – | – | – | 1 |
Company data (COM) | ||||
W210 (direct effects: below diagonal, maternal above) | ||||
−2.5 | 1 | 0.957 (0.01) | 0.869 (0.03) | 0.640 (0.06) |
−1.0 | 0.959 (0.01) | 1 | 0.975 (0.01) | 0.834 (0.03) |
+1.0 | 0.885 (0.03) | 0.889 (0.02) | 1 | 0.936 (0.01) |
+2.5 | 0.722 (0.06) | 0.885 (0.03) | 0.961 (0.01) | 1 |
SC (below), DFC (above) | ||||
−2.5 | 1 | 0.818 (0.07) | 0.502 (0.18) | 0.102 (0.25) |
−1.0 | 0.991 (0.00) | 1 | 0.904 (0.05) | 0.640 (0.14) |
+1.0 | 0.969 (0.01) | 0.994 (0.00) | 1 | 0.904 (0.04) |
+2.5 | 0.892 (0.02) | 0.945 (0.01) | 0.976 (0.01) | 1 |
Trait | BTA | Position (bp) | Var (%) | Candidate Genes | QTL |
---|---|---|---|---|---|
W120 (direct) | 25 | 40,619,157–41,019,157 | 1.26 | GNA12, AMZ1, BRAT1, bta-mir-11980, IQCE, TTYH3, LFNG, bta-mir-12029, GRIFIN, CHST12, bta-mir-12019, EIF3B, SNX8, NUDT1, MRM2, MAD1L1 | Residual feed intake, conception rate, milking speed, average daily gain |
15 | 45,597,833–45,997,833 | 1.23 | RBMXL2, NLRP14, ZNF214, ZNF215, OR2D3, OR2D2, OR10A4, OR10A5, U6, OR10A5L, OR10A5G, OR6A2, OR6B18, OR6B17, OR2D4 | Milk-fat yield, body weight gain | |
10 | 52,283,853–52,683,853 | 0.95 | ALDH1A2, U6, POLR2M, MYZAP | Carcass weight, milk butyric acid content, milking speed, marbling score, m. paratuberculosis susceptibility, shear force, milk kappa-casein percentage, omega-6 to omega-3 fatty acid ratio, age at puberty | |
W120 (maternal) | 7 | 21,907,628–22,307,628 | 0.99 | IRF1, SLC22A5, SLC22A4, bta-mir-2457, PDLIM4, P4HA2, bta-mir-12040 | Milking speed, m. paratuberculosis susceptibility, calving ease (maternal), daughter pregnancy rate, stillbirth (maternal), udder attachment, net merit, length of productive life, somatic cell score, stillbirth, udder depth |
2 | 54,729,312–55,129,312 | 0.73 | - | milk palmitoleic acid content, inseminations per conception, bovine respiratory disease susceptibility | |
8 | 52,728,463–53,128,463 | 0.64 | PRUNE2, FOXB2 | Residual feed intake, twinning, milk unglycosylated kappa-casein percentage, milk kappa-casein percentage, bovine tuberculosis susceptibility, milk protein yield | |
W210 (direct) | 25 | 40,6191,57–41,019,157 | 0.94 | GNA12, AMZ1, BRAT1, bta-mir-11980, IQCE, TTYH3, LFNG, bta-mir-12029, GRIFIN, CHST12, bta-mir-12019, EIF3B, SNX8, NUDT1, MRM2, MAD1L1 | Residual feed intake, conception rate, milking speed, average daily gain |
21 | 14,794,265–15,194,265 | 0.71 | SLCO3A1 | Bovine tuberculosis susceptibility, age at first calving, kidney, pelvic, heart fat percentage, milk tridecylic acid content, somatic cell score | |
15 | 45,597,833–45,997,833 | 0.64 | RBMXL2, NLRP14, ZNF214, ZNF215, OR2D3, OR2D2, OR10A4, OR10A5, U6, OR10A5L, OR10A5G, OR6A2, OR6B18, OR6B17, OR2D4 | Milk-fat yield, body weight gain | |
W210 (maternal) | 8 | 52,728,463–53,128,463 | 0.94 | PRUNE2, FOXB2 | Residual feed intake, twinning, milk unglycosylated kappa-casein percentage, milk kappa-casein percentage, bovine tuberculosis susceptibility, milk protein yield |
11 | 94,730,926–95,130,926 | 0.75 | DENND1A, LHX2 | cheese protein recovery, number of embryos, milk beta-lactoglobulin percentage, anti-müllerian hormone level, non-return rate | |
29 | 15,282,330–15,682,330 | 0.68 | - | milk kappa-casein percentage, milk glycosylated kappa-casein percentage, milk unglycosylated kappa-casein percentage, somatic cell score | |
DFC | 10 | 66,575,785–66,975,785 | 1.32 | CDKN3, CNIH1 | Milking speed, bovine tuberculosis susceptibility, milk protein yield, body depth, PTA type, udder attachment, udder height, rump width, somatic cell score, stature, strength, udder depth |
7 | 29,486,606–29,886,606 | 0.86 | - | Clinical mastitis, body weight (birth), milk protein yield, body capacity, daughter pregnancy rate, stillbirth (maternal), udder attachment, length of productive life, somatic cell score, stillbirth, udder depth | |
2 | 89,254,217–89,654,217 | 0.80 | AOX4, AOX2, BZW1, CLK1, PPIL3, NIF3L1, ORC2, FAM126B, U6 | Conception rate, intramuscular fat, milk-fat yield |
Trait | BTA | Position (bp) | Var (%) | Genes | QTL |
---|---|---|---|---|---|
W120 (direct) | 22 | 17,317,952–17,717,952 | 1.77 | SRGAP3, RAD18 | Milk tridecylic acid content, body weight (yearling), lean-meat yield, white spotting |
9 | 89,328,896–89,728,896 | 0.82 | 7SK, MYCT1, VIP | muscle magnesium content, muscle phosphorus content, teat placement—front, teat placement—rear, teat length, udder cleft | |
26 | 40,536,474–40,936,474 | 0.74 | PLPP4, WDR11 | milk-fat yield, stature, milk c14 index, milk myristoleic acid content, milk yield, milk protein yield | |
W120 (maternal) | 2 | 89,254,217–89,654,217 | 1.96 | AOX4, AOX2, BZW1, CLK1, PPIL3, NIF3L1, ORC2, FAM126B, U6 | Conception rate, intramuscular fat, milk-fat yield |
10 | 5,768,117–6,168,117 | 0.85 | - | body weight (yearling), body weight gain, udder depth, conception rate | |
23 | 22,140,708–22,540,708 | 0.81 | MMUT, CENPQ, GLYATL3, C23H6orf141, U6, RHAG, CRISP2, CRISP3, 7SK, CRISP1 | milk protein percentage, milk glycosylated kappa-casein percentage, milk iron content, length of productive life, daughter pregnancy rate, stillbirth (maternal), calving ease, somatic cell score | |
W210 (direct) | 29 | 6,736,030–7,136,030 | 0.71 | GRM5 | Shear force |
7 | 36,882,466–37,282,466 | 0.68 | - | Milk alpha-s1-casein percentage, milking speed, intramuscular fat | |
15 | 54,575,598–54,975,598 | 0.63 | RPS3, SNORD15, KLHL35, GDPD5, SERPINH1, MAP6, MOGAT2 | Milk-fat yield, first service conception, inseminations per conception, 305-day milk yield, milk rennet coagulation time, bovine respiratory disease susceptibility, conception rate | |
W210 (maternal) | 29 | 6,736,030–7,136,030 | 0.89 | GRM5 | Shear force |
5 | 50,640,891–51,040,891 | 0.69 | PPM1H, MON2 | Milk-fat yield, milk yield, inhibin level, insulin-like growth factor 1 level, intramuscular fat | |
24 | 1,244,237–1,644,237 | 0.53 | - | Body weight (yearling) | |
DFC | 11 | 76,492,925–76,892,925 | 1.09 | - | Body weight (yearling), milk alpha-lactalbumin percentage, lean-meat yield |
2 | 111,967,207–112,367,207 | 1.04 | WDFY1, U6, MRPL44, SERPINE2 | Metabolic body weight, fecal larva count, first service conception, heat tolerance, fertilization rate, conception rate, milk protein percentage, milk-fat yield | |
1 | 149,053,882–149,453,882 | 0.84 | HLCS, RIPPLY3, U6, PIGP, TTC3 | Conception rate, somatic cell score, teat length, length of productive life |
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Santana, M.L.; Bignardi, A.B.; Pereira, R.J.; Oliveira Junior, G.A.; Freitas, A.P.; Carvalheiro, R.; Eler, J.P.; Ferraz, J.B.S.; Cyrillo, J.N.S.G.; Mercadante, M.E.Z. Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions. Animals 2023, 13, 2321. https://doi.org/10.3390/ani13142321
Santana ML, Bignardi AB, Pereira RJ, Oliveira Junior GA, Freitas AP, Carvalheiro R, Eler JP, Ferraz JBS, Cyrillo JNSG, Mercadante MEZ. Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions. Animals. 2023; 13(14):2321. https://doi.org/10.3390/ani13142321
Chicago/Turabian StyleSantana, Mário L., Annaiza B. Bignardi, Rodrigo J. Pereira, Gerson A. Oliveira Junior, Anielly P. Freitas, Roberto Carvalheiro, Joanir P. Eler, José B. S. Ferraz, Joslaine N. S. G. Cyrillo, and Maria E. Z. Mercadante. 2023. "Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions" Animals 13, no. 14: 2321. https://doi.org/10.3390/ani13142321
APA StyleSantana, M. L., Bignardi, A. B., Pereira, R. J., Oliveira Junior, G. A., Freitas, A. P., Carvalheiro, R., Eler, J. P., Ferraz, J. B. S., Cyrillo, J. N. S. G., & Mercadante, M. E. Z. (2023). Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions. Animals, 13(14), 2321. https://doi.org/10.3390/ani13142321