ImmuneDEX: updated genomic estimates of genetic parameters and breeding values for Australian Angus cattle

Reverter, Antônio; Hine, Brad C.; Porto-Neto, Laércio R.; Li, Yutao; Duff, Christian J.; Dominik, Sonja; Ingham, Aaron

doi:10.1071/an21054

Cited by 3 publications

(4 citation statements)

References 12 publications

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“…of 0.025, and ranged from −0.112 to 0.657. These values are very similar to the ones reported by Reverter et al (2021a) using a population of 3715 Angus steers and heifers that were progeny of ASBP sires. Also, the similarity in the variance of diagonal and off-diagonal elements indicates that both a sufficiently large number of SNPs was used to estimate relationships and the presence of a single-breed population (Simeone et al 2011).…”

Section: Genotypes Genomic Relationships and Genetic Parameterssupporting

confidence: 88%

On the value of adding commercial data into the reference population of the Angus SteerSELECT genomic tool

et al. 2023

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Context Angus SteerSELECT is a genomic tool designed to provide genomic estimated breeding values (GEBV) for nine traits related to growth, feedlot performance, carcase characteristics and immune competence. At present, GEBV for carcase characteristics are based on a reference population of 3766 Australian Angus steers. Aims We aimed to investigate the potential benefit of incorporating commercial data into the existing reference population of the Angus SteerSELECT. To this aim, we employ a population of 2124 genotyped commercial Angus steers with carcase performance data from four commercial feedlot operators. Methods The benefit of incorporating the commercial data (COMM) into the reference (REFE) population was assessed in terms of quality and integrity of the COMM data and meta-data to model the phenotypes adequately. We computed bias, dispersion, and accuracy of GEBV for carcase weight (CWT) and marbling (MARB) before and after including the COMM data, in whole or in partial, into the REFE population. Key results The genomic estimate of the Angus content in the COMM population averaged 96.9% and ranged from 32.87% to 100%. For CWT, the estimates of heritability were 0.419 ± 0.026 and 0.368 ± 0.038 for the REFE and COMM populations respectively, and with a genetic correlation of 0.756 ± 0.068. For MARB, the same three parameter estimates were 0.357 ± 0.027, 0.340 ± 0.038 and 0.879 ± 0.073 respectively. The ACC of CWT GEBV increased significantly (P < 0.0001) from 0.475 when the COMM population was not part of the REFE to 0.546 (or 15%) when a random 50% of the COMM population was included in the REFE. Similarly significant increases in ACC were observed for MARB GEBV (0.470–0.521 or 11%). Conclusions The strong genomic relationship between the REFE and the COMM populations, coupled with the significant increases in GEBV accuracies, demonstrated the potential benefits of including the COMM population into the reference population of a future improved version of the Angus SteerSELECT genomic tool. Implications Commercial feedlot operators finishing animals with a strong Angus breed component will benefit from having their data represented in the reference population of the Angus SteerSELECT genomic tool.

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Section: Genotypes Genomic Relationships and Genetic Parameterssupporting

confidence: 88%

On the value of adding commercial data into the reference population of the Angus SteerSELECT genomic tool

et al. 2023

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“…3 are the ACC T for the 129 XB cattle with low Angus content. Across the 20 accuracy estimates obtained from five traits and four validation datasets, the correlation between ACC T and ACC LR was 0.922, an estimate higher than the 0.73 reported by Alexandre et al (2021) across 49 estimates, and the 0.831 reported by Reverter et al (2021) across 15 estimates and both studies with feedlot and carcase traits in Angus cattle.…”

Section: Genomic Predictions and Cross-validation Resultsmentioning

confidence: 66%

“…Finally, the genomic relationships among all individuals were processed following the network-based Pedigromics pipeline (Reverter et al 2019) by establishing network connections after considering genomic relationships ≥0.125 corresponding to the equivalent of a great-grandparent to great-grand offspring relationship.…”

Section: Genotypes and Genomic Relationshipsmentioning

confidence: 99%

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Wagyu Feeder Check: A genomic-based tool to identify performance differences of Australian Wagyu and Wagyu crossed cattle

Reverter,

Li,

Alexandre

et al. 2023

Anim. Prod. Sci.

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Context Wagyu Feeder Check is a genomic-based tool designed to provide genomic estimated breeding values (GEBV) for five feedlot growth and carcase traits. At present, Wagyu Feeder Check is based on a reference population of 8316 genotyped and phenotyped Australian fullblood (FB; N = 2120) Wagyu and Wagyu-crossed (XB; N = 6196) cattle, principally Wagyu × Angus F1 animals. Aims We provide technical details behind the development of the Wagyu Feeder Check and validate the ability of its GEBV to predict differences in performance of Wagyu cattle in daily weight gain at feedlot, carcase weight, carcase eye muscle area, carcase marbling score and carcase rump fat at the P8 site. Methods Data supplied from eight commercial supply chains across Australia was used to generate GEBV using mixed-model equations that incorporated a genomic relationship matrix build with 82 504 autosomal markers. The bias, dispersion, and accuracy of the GEBV were evaluated using a four-way cross-validation scheme where, in each turn, the phenotypes from a random 1549 (or 25%) XB cattle were set as missing. Key results The genomic estimate of the Wagyu content in the FB and XB population averaged 99.12% and 59.55%, respectively, and with most of the non-Wagyu content associated with Angus. The estimates of heritability (± s.e.) were 0.497 ± 0.016, 0.474 ± 0.004, 0.347 ± 0.014, 0.429 ± 0.003 and 0.422 ± 0.003 for daily weight gain at feedlot, carcase weight, eye muscle area, marbling and rump fat, respectively. Averaged across the four XB validation populations, the accuracy of GEBV was 0.624, 0.634, 0.385, 0.620, and 0.526 for the same set of traits. Conclusions Genomic predictions generated by Wagyu Feeder Check can predict differences in feedlot and carcase performance of Australian Wagyu cattle. Given the large content of Angus in the XB population, further research is required to determine the predictive ability of GEBV in Wagyu × Bos indicus and Wagyu × dairy animals. Implications Commercial feedlot operators finishing animals with a strong Wagyu breed component will benefit from using Wagyu Feeder Check for decision making.

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Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds

Gouveia,

Ribeiro,

Fortes

et al. 2023

Genet Sel Evol

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Background Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. Results Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. Conclusions Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.

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ImmuneDEX: updated genomic estimates of genetic parameters and breeding values for Australian Angus cattle

Cited by 3 publications

References 12 publications

On the value of adding commercial data into the reference population of the Angus SteerSELECT genomic tool

On the value of adding commercial data into the reference population of the Angus SteerSELECT genomic tool

Wagyu Feeder Check: A genomic-based tool to identify performance differences of Australian Wagyu and Wagyu crossed cattle

Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds

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