Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population

Estimated breeding values for the selection of more profitable sheep for the sheep meat and wool industries are currently based on pedigree and phenotypic records. With the advent of a medium-density DNA marker array, which genotypes ~50 000 ovine single nucleotide polymorphisms, a third source of information has become available. The aim of this paper was to determine whether this genomic information can be used to predict estimated breeding values for wool and meat traits. The effects of all single nucleotide polymorphism markers in a multi-breed sheep reference population of 7180 individuals with phenotypic records were estimated to derive prediction equations for genomic estimated breeding values (GEBV) for greasy fleece weight, fibre diameter, staple strength, breech wrinkle score, weight at ultrasound scanning, scanned eye muscle depth and scanned fat depth. Five hundred and forty industry sires with very accurate Australian sheep breeding values were used as a validation population and the accuracies of GEBV were assessed according to correlations between GEBV and Australian sheep breeding values . The accuracies of GEBV ranged from 0.15 to 0.79 for wool traits in Merino sheep and from –0.07 to 0.57 for meat traits in all breeds studied. Merino industry sires tended to have more accurate GEBV than terminal and maternal breeds because the reference population consisted mainly of Merino haplotypes. The lower accuracy for terminal and maternal breeds suggests that the density of genetic markers used was not high enough for accurate across-breed prediction of marker effects. Our results indicate that an increase in the size of the reference population will increase the accuracy of GEBV.

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Genomic prediction of weight and wool traits in a multi-breed sheep population

Animal Production Science ◽

10.1071/an13129 ◽

2014 ◽

Vol 54 (5) ◽

pp. 544 ◽

Cited By ~ 4

Author(s):

N. Moghaddar ◽

A. A. Swan ◽

J. H. J. van der Werf

Keyword(s):

Genomic Prediction ◽

Pearson Correlation ◽

Reference Population ◽

Breeding Value ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Sheep Population ◽

Australian Sheep ◽

Estimated Breeding Value ◽

Breed Sheep

The objective of this study was to predict the accuracy of genomic prediction for 26 traits, including weight, muscle, fat, and wool quantity and quality traits, in Australian sheep based on a large, multi-breed reference population. The reference population consisted of two research flocks, with the main breeds being Merino, Border Leicester (BL), Poll Dorset (PD), and White Suffolk (WS). The genomic estimated breeding value (GEBV) was based on GBLUP (genomic best linear unbiased prediction), applying a genomic relationship matrix calculated from the 50K Ovine SNP chip marker genotypes. The accuracy of GEBV was evaluated as the Pearson correlation coefficient between GEBV and accurate estimated breeding value based on progeny records in a set of genotyped industry animals. The accuracies of weight traits were relatively low to moderate in PD and WS breeds (0.11–0.27) and moderate to relatively high in BL and Merino (0.25–0.63). The accuracy of muscle and fat traits was moderate to relatively high across all breeds (between 0.21 and 0.55). The accuracy of GEBV of yearling and adult wool traits in Merino was, on average, high (0.33–0.75). The results showed the accuracy of genomic prediction depends on trait heritability and the effective size of the reference population, whereas the observed GEBV accuracies were more related to the breed proportions in the multi-breed reference population. No extra gain in within-breed GEBV accuracy was observed based on across breed information. More investigations are required to determine the precise effect of across-breed information on within-breed genomic prediction.

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Using Australian Sheep Breeding Values to increase lean meat yield percentage

Animal Production Science ◽

10.1071/an10144 ◽

2010 ◽

Vol 50 (12) ◽

pp. 1098 ◽

Cited By ~ 30

Author(s):

G. E. Gardner ◽

A. Williams ◽

J. Siddell ◽

A. J. Ball ◽

S. Mortimer ◽

...

Keyword(s):

Carcass Composition ◽

Production Traits ◽

Eye Muscle ◽

Meat Yield ◽

Sheep Breeding ◽

Breeding Values ◽

Lean Meat ◽

Target Weight ◽

Australian Sheep ◽

The Impact

This study describes the impact of Australian Sheep Breeding Values (ASBV) for post-weaning weight (PWWT), C-site fatness (PFAT) and eye muscle depth (PEMD) on lamb carcasses within the Australian Sheep Industry CRC Information Nucleus Flock. These results are taken from the 2007 drop progeny, consisting of ~2000 lambs slaughtered at a target weight of 21.5 kg. These lambs were the progeny of sires selected to ensure genetic diversity across various production traits. As expected, the PWWT ASBV increased weight at slaughter, and hot standard carcass weight. Dressing percentage was markedly improved by increasing PEMD ASBV, thus prime lamb producers will be maintaining an animal of similar weight on farm, but delivering a markedly larger carcass at slaughter. Lean meat yield % (LMY%) was highest in the progeny of sires with low PFAT ASBV, which decreased whole carcass fatness and increased muscularity. PWWT ASBV affected carcass composition but had little impact on LMY%, as the decreased fatness was largely offset by increased bone, with relatively little change in muscle content. Lastly, PEMD ASBV had little impact on whole carcass LMY%, but did appear to cause some level of muscle redistribution to the higher value loin cuts, in turn increasing the value of the carcass lean.

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Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

BMC Genetics ◽

10.1186/s12863-017-0476-8 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 22

Author(s):

Luiz F. Brito ◽

Shannon M. Clarke ◽

John C. McEwan ◽

Stephen P. Miller ◽

Natalie K. Pickering ◽

...

Keyword(s):

Meat Quality ◽

Quality Traits ◽

Sheep Population ◽

Genomic Breeding ◽

Breeding Values ◽

Snp Chip ◽

Meat Quality Traits ◽

Breed Sheep

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Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait

Heredity ◽

10.1038/s41437-020-0339-3 ◽

2020 ◽

Vol 126 (1) ◽

pp. 206-217

Author(s):

Xiang Ma ◽

Ole F. Christensen ◽

Hongding Gao ◽

Ruihua Huang ◽

Bjarne Nielsen ◽

...

Keyword(s):

Egg Production ◽

Quantitative Traits ◽

Group Structure ◽

Genetic Evaluation ◽

Genomic Information ◽

Bivariate Model ◽

Breeding Values ◽

Lower Accuracy ◽

Small Group Size ◽

Estimated Breeding Values

AbstractRecords on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.

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Indices of cellular development in muscles of lambs are influenced by sire estimated breeding values and pastoral nutritional system

Australian Journal of Agricultural Research ◽

10.1071/ar05205 ◽

2006 ◽

Vol 57 (6) ◽

pp. 651 ◽

Cited By ~ 3

Author(s):

P. L. Greenwood ◽

G. E. Gardner ◽

R. S. Hegarty

Keyword(s):

Muscle Growth ◽

Genetic Selection ◽

Inverse Association ◽

Semitendinosus Muscle ◽

Eye Muscle ◽

Weaning Weight ◽

Breeding Values ◽

Sire Group ◽

Selection For ◽

Estimated Breeding Values

This study examined influences of sire (n = 9) estimated breeding values (EBVs), sire-group (Muscle, Growth, and Control), and nutrition (low and high quality and availability pasture) from birth to slaughter at ~8 months of age on indices of muscle cellularity and transcriptional and translational capacity in 56 castrate lambs. Effects of nutritional systems to 8 months of age were greater, overall, than those due to EBVs or sire-group. Amount of DNA increased with increasing EBV for post-weaning eye muscle depth (PEMD or Muscle EBV) in longissimus but not in semimembranosus and semitendinosus muscles, while Muscle EBV also had an inverse association with concentration of DNA. Protein to DNA and RNA to DNA were related positively to Muscle EBV, the associations being strongest for the semitendinosus muscle. Post-weaning weight (PWWT or Growth) EBV correlated positively with the RNA to DNA ratio and, among high but not low nutrition lambs, was inversely related to concentration of muscle DNA, whereas post-weaning fat depth (PFAT or Fat) EBV was correlated positively with RNA concentration. Overall, the magnitude of effects of sire-group was less than for sire EBVs, presumably due to differing selection pressures for muscling, fatness, and growth. High nutrition lambs had more protein to DNA than low nutrition lambs in the longissimus and semitendinosus muscles, but not in the semimembranosus muscle. In low compared with high nutrition lambs, concentration of DNA was greater in the longissimus and semitendinosus muscles. Total amount of DNA was reduced by more in low compared with high nutrition in the longissimus and semimembranosus than in the semitendinosus, and amount of protein was reduced by more in low compared with high nutrition in the longissimus than in the other two muscles. We conclude that genetic selection for eye muscle depth in sheep has differing effects on cellular characteristics of the longissimus, semimembranosus, and semitendinosus muscles, and has greater effects on muscle cellular characteristics than genetic selection for post-weaning weight or fat depth.

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Performance of steer progeny of sires differing in genetic potential for fatness and meat yield following postweaning growth at different rates. 2. Carcass traits

Animal Production Science ◽

10.1071/ea08267 ◽

2009 ◽

Vol 49 (6) ◽

pp. 525 ◽

Cited By ~ 9

Author(s):

W. A. McKiernan ◽

J. F. Wilkins ◽

J. Irwin ◽

B. Orchard ◽

S. A. Barwick

Keyword(s):

Production Systems ◽

Carcass Traits ◽

Quality Traits ◽

Muscle Area ◽

Eye Muscle ◽

Meat Yield ◽

Breeding Values ◽

Genetic Potential ◽

Estimated Breeding Values ◽

Selection Of

The steer progeny of sires genetically diverse for fatness and meat yield were grown at different rates from weaning to feedlot entry and effects on growth, carcass and meat-quality traits were examined. The present paper, the second of a series, reports the effects of genetic and growth treatments on carcass traits. A total of 43 sires, within three ‘carcass class’ categories, defined as high potential for meat yield, marbling or both traits, was used. Where available, estimated breeding values for the carcass traits of retail beef yield (RBY%) and intramuscular fat (IMF%) were used in selection of the sires, which were drawn from Angus, Charolais, Limousin, Black Wagyu and Red Wagyu breeds, to provide a range of carcass sire types across the three carcass classes. Steer progeny of Hereford dams were grown at either conventional (slow: ~0.5 kg/day) or accelerated (fast: ~0.7 kg/day) rates from weaning to feedlot entry weight, with group means of ~400 kg. Accelerated and conventionally grown groups from successive calvings were managed to enter the feedlot at similar mean feedlot entry weights at the same time for the 100-day finish under identical conditions. Faster-backgrounded groups had greater fat levels in the carcass than did slower-backgrounded groups. Dressing percentages and fat colour were unaffected by growth treatment, whereas differences in ossification score and meat colour were explained by age at slaughter. There were significant effects of sire type for virtually all carcass traits measured in the progeny. Differences in hot standard carcass weight showed a clear advantage to European types, with variable outcomes for the Angus and Wagyu progeny. Sire selection by estimated breeding values (within the Angus breed) for yield and/or fat traits resulted in expected differences in the progeny for those traits. There were large differences in both meat yield and fatness among the types of greatest divergence in genetic potential for those traits, with the Black Wagyu and the Angus IMF clearly superior for IMF%, and the European types for RBY%. The Angus IMF progeny performed as well as that of the Black Wagyu for all fatness traits. Differences in RBY% among types were generally reflected by similar differences in eye muscle area. Results here provide guidelines for selecting sire types to target carcass traits for specific markets. The absence of interactions between growth and genetic treatments ensures that consistent responses can be expected across varying management and production systems.

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Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus)

Genetics and Molecular Biology ◽

10.1590/s1415-47572007000600005 ◽

2007 ◽

Vol 30 (4) ◽

pp. 1058-1063 ◽

Cited By ~ 4

Author(s):

Fernando Henrique Biase ◽

Flávio Vieira Meirelles ◽

Ricardo Gunski ◽

Pedro Alejandro Vozzi ◽

Luiz A.F. Bezerra ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mitochondrial Dna ◽

Bos Indicus ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Values ◽

Estimated Breeding Values ◽

Nelore Cattle

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Contribution of domestic production records, Interbull estimated breeding values, and single nucleotide polymorphism genetic markers to the single-step genomic evaluation of milk production

Journal of Dairy Science ◽

10.3168/jds.2012-6157 ◽

2013 ◽

Vol 96 (3) ◽

pp. 1865-1873 ◽

Cited By ~ 17

Author(s):

J. Přibyl ◽

P. Madsen ◽

J. Bauer ◽

J. Přibylová ◽

M. Šimečková ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Markers ◽

Milk Production ◽

Single Step ◽

Nucleotide Polymorphism ◽

Genomic Evaluation ◽

Single Nucleotide ◽

Breeding Values ◽

Domestic Production ◽

Estimated Breeding Values

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Genetic relationships between internal parasite resistance and production traits in Merino sheep

Animal Production Science ◽

10.1071/an15469 ◽

2017 ◽

Vol 57 (2) ◽

pp. 209 ◽

Cited By ~ 14

Author(s):

D. J. Brown ◽

N. M. Fogarty

Keyword(s):

Genetic Parameters ◽

Genetic Correlations ◽

Production Traits ◽

Parasite Resistance ◽

Breeding Programs ◽

Sheep Breeding ◽

Breeding Values ◽

Merino Sheep ◽

Internal Parasite ◽

Australian Sheep

Breeding Merino sheep that are resistant to internal parasites alleviates the high costs associated with treatment of worm infestation and loss of production, as well as mitigating the development of anthelmintic resistance among the major worm species. Faecal worm egg count ((cube root transformation), wec) can be used in sheep as a measure of internal parasite resistance. Accurate estimates of genetic parameters for wec are required for calculation of Australian Sheep Breeding Values and inclusion of worm resistance in sheep breeding programs. This study provides updated estimates of heritability for wec and its genetic correlations with production traits. Data were analysed from a wide range of Australian and New Zealand Merino sheep in the MERINOSELECT database, which included 141 flocks with 801 flock years and up to 217 137 animals with wec recorded in at least one of four ages (W = weaning, P = post weaning, Y = yearling, H = hogget). The heritability estimates ranged from 0.16 ± 0.01 for Ywec to 0.29 ± 0.01 for Wwec, with generally high genetic correlations between the ages. Bivariate analyses estimated genetic correlations between wec at the various ages and growth, carcass quality, reproduction and wool production traits at various ages. These genetic correlations were generally small or close to zero, albeit with some significantly different from zero. The moderate heritability for wec (0.2–0.3) and its high phenotypic variation (coefficient of variation >30%) shows that relatively rapid selection response for worm resistance could be achieved. Inclusion of wec in sheep breeding programs to increase worm resistance would be expected to have little if any impact on other important production traits. These genetic parameters have been incorporated into MERINOSELECT by Sheep Genetics to provide Australian Sheep Breeding Values for wec and appropriate indices for wool and meat production. There is evidence that genotype × environment interactions may be important in some environments by reducing the accuracy of Australian Sheep Breeding Values for wec. Hence it may be prudent for breeders to implement strategies that manage the risk of any impact of genotype × environment on their breeding program.

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