Comparison between multiple-trait and random regression models for genetic evaluation of weight traits in Australian meat sheep

Random regression (RR) models are recommended as an alternative to multiple-trait (MT) models for better capturing the variance-covariance structure over a trajectory and hence more accurate genetic evaluation of traits that are repeatedly measured and genetically change gradually over time. However, a limited number of studies have been done to empirically compare RR over a MT model to determine how much extra benefit could be achieved from one method over another. We compared the prediction accuracy of RR and MT models for growth traits of Australian meat sheep measured from 60 to 525 d, using 102,579 weight records from 24,872 animals. Variance components and estimated breeding values (EBVs) estimated at specific ages were compared and validated with forward prediction. The accuracy of EBVs obtained from the MT model was 0.58, 0.51, 0.54, and 0.56 for weaning, postweaning, yearling, and hogget weight stages, respectively. RR model produced accuracy estimates of 0.56, 0.51, 0.54, and 0.54 for equivalent weight stages. Regression of adjusted phenotype on EBVs was very similar between the MT and the RR models (P > 0.05). Although the RR model did not significantly increase the accuracy of predicting future progeny performance, there are other benefits of the model such as no limit to the number of records per animal, estimation of EBVs for early and late growth, no need for age correction. Therefore, RR can be considered a more flexible method for the genetic evaluation of Australian sheep for early and late growth, and no need for age correction.

Model definition for genetic evaluation of purebred and crossbred lambs including heterosis

Crossbreeding is a common practice among commercial sheep producers to improve animal performance. However, genetic evaluation of U.S. sheep is performed within breed type (terminal sire, semi-prolific, and western range). While incorporating crossbred records may improve assessment of purebreds, it requires accounting for heterotic and breed effects in the evaluation. The objectives of this study were to: 1) describe the development of a paternal composite (PC) line, 2) determine the effect of direct and maternal heterosis on growth traits of crossbred lambs, 3) estimate (co)variance components for direct and maternal additive, and uncorrelated maternal environmental, effects, and 4) provide an interpretation of the estimates of random effects of genetic groups, and to use those solutions to compare the genetic merit of founding breed subpopulations. Data included purebred and crossbred records on birth weight (BN; n = 14,536), pre-weaning weight measured at 39 or 84 d (WN; n = 9,362) depending on year, weaning weight measured at 123 d (WW; n = 9,297), and post-weaning weight measured at 252 d (PW; n = 1,614). Mean (SD) body weights were 5.3 (1.1), 16.8 (3.9) and 28.0 (7.6), 39.1 (7.2), and 54.2 (8.7) kg for BN, WN (at the two ages), WW, and PW, respectively. In designed experiments, the Siremax, Suffolk, Texel, Polypay, Columbia, Rambouillet, and Targhee breeds were compared within the same environment. Estimates of heterotic effects and covariance components were obtained using a multiple trait animal model. Genetic effects based on founders' breeds were significant and included in the model. Percent estimates of direct heterosis were 2.89 ± 0.61, 2.60 ± 0.65, 4.24 ± 0.56, and 6.09 ± 0.86, and estimates of maternal heterosis were 1.92 ± 0.87, 4.64 ± 0.80, 3.95 ± 0.66, and 4.04 ± 0.91, for BN, WN, WW, and PW, respectively. Correspondingly, direct heritability estimates were 0.17 ± 0.02, 0.13 ± 0.02, 0.17 ± 0.02, and 0.46 ± 0.04 for BN, WN, WW, and PW. Additive maternal effects accounted for trivial variation in PW. For BN, WN, and WW, respectively, maternal heritability estimates were 0.16 ± 0.02, 0.10 ± 0.02, and 0.07 ± 0.01. Uncorrelated maternal environmental effects accounted for little variation in any trait. Direct and maternal heterosis had considerable impact on growth traits, emphasizing the value of crossbreeding and the need to account for heterosis, in addition to breed effects, if crossbred lamb information is included in genetic evaluation.

Genetic parameter estimates for gastrointestinal nematode parasite resistance and maternal efficiency indicator traits in Santa Inês breed

Infection with Haemonchus contortus is the most economically important gastrointestinal nematode parasitosis and the most important cause of mortality in sheep production. The aim of this study was to estimate variance components of gastrointestinal parasite resistance traits, maternal efficiency (ME) and ewe adult weight (AW) in Santa Inês breed in tropical conditions. The phenotypic records were collected from 700 animals, belonging to four flocks located south-east and north-east in Brazil. The evaluated traits were as follows: degree of anaemia assessed using the FAMACHA chart (FMC), haematocrit (HCT), white blood cell (WBC), red blood cell (RBC), haemoglobin (HGB), platelets (PLT), faecal egg count (EPG_log ), ME, metabolic maternal efficiency (MME), AW and metabolic ewe adult weight (MAW). From the 700 animals, 576 (82% of the evaluated population) were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.). Markers with unknown genomic position, located on sex chromosomes, monomorphic, with minor allele frequency <0.05, call rate <90% and with excess heterozygosity were excluded. The variance components were estimated using a single-trait animal model with ssGBLUP procedure. The correlation between the parasite's resistance indicators and the ME suggested that selecting animals with both higher adult weight and ME will also favour the selection of animals with better resistance to gastrointestinal nematodes parasites, specially H. contortus. Therefore, since there are few or no studies with Santa Inês breed in this area, it is important to study those traits to better manage selection programs.

Genetic parameter estimates for fecal egg counts and their relationship with growth in Avikalin and Malpura sheep

Breeding for resistance against nematodes has become the need of the hour due to emergence of anthelmintic resistant strains of major pathogenic nematodes of economic importance and rising demand for chemical residue free food by consumers. ICAR-Central Sheep and Wool Research Institute Avikanagar (Rajasthan) has developed Haemonchus contortus resistant lines of sheep in Avikalin and Malpura breeds by harvesting benefits of over-dispersion in fecal egg counts (FEC) through executing a breeding program since year 2004. Aim of the present study was to assess the genetic parameters for nematode resistance in these lines and also to develop suitable criteria for selection targeting resistance as well as growth improvement in these two lines. The data on 1240 Avikalin and 2172 Malpura sheep generated over 13 years (2004-16) for FEC along with deep pedigree and growth records for live weight at 6 (6WT) and 12 month were used for study. Data were analyzed using Average Information Restricted Maximum Likelihood (AIREML) approach. Results revealed moderate heritability (h2) for pre-drench log transformed fecal egg count (LFEC) in Avikalin (0.21±0.06) and Malpura (0.18±0.04) sheep. The post-drench h2 for LFEC was low in Avikalin (0.04±0.03) and Malpura (0.11±0.03) sheep. Effective selection program can be carried out for further improving the resistance against H. contortus in both the breeds using pre-drench LFEC estimates. The genetic correlation between the pre-drench LFEC and growth traits was not in the desired direction. Existence of substantial genotype × environment (G×E) interaction was seen in Malpura sheep, where major shift in ranks of sheep based on pre-drench LFEC as that of post-drench LFEC was observed owing to genetic correlation of 0.65±0.15. The G×E was absent in Avikalin sheep. Unreliable genetic correlation between growth and LFEC does not warrant a multi trait selection index development and its utilization in breeding program. The independent selection for LFEC followed by corrected 6WT can precisely help in achieving the goal of improving growth in nematode resistant sheep.

Genetic parameters for wool traits, live weight, and ultrasound carcass traits in Merino sheep

Genetic correlations between 29 wool production and quality traits and live weight and ultrasound fat depth (FAT) and eye muscle depth (EMD) traits were estimated from the Information Nucleus (IN). The IN comprised 8 genetically linked flocks managed across a range of Australian sheep production environments. The data were from a maximum of 9,135 progeny born over 5 yr from 184 Merino sires and 4,614 Merino dams. The wool traits included records for yearling and adult fleece weight, fiber diameter (FD), staple length (SL), fiber diameter CV (FDCV), scoured color, and visual scores for breech and body wrinkle. We found high heritability for the major yearling wool production traits and some wool quality traits, whereas other wool quality traits, wool color, and visual traits were moderately heritable. The estimates of heritability for live weight generally increased with age as maternal effects declined. Estimates of heritability for the ultrasound traits were also higher when measured at yearling age rather than at postweaning age. The genetic correlations for fleece weight with live weights were positive (favorable) and moderate (approximately 0.5 ± 0.1), whereas those with FD were approximately 0.3 (unfavorable). The other wool traits had lower genetic correlations with the live weights. The genetic correlations for FAT and EMD with FD and SL were positive and low, with FDCV low to moderate negative, but variable with wool weight and negligible for the other wool traits. The genetic correlations for FAT and EMD with postweaning weight were positive and high (0.61 ± 0.18 to 0.75 ± 0.14) but were generally moderate with weights at other ages. Selection for increased live weight will result in a moderate correlated increase in wool weight as well as favorable reductions in breech cover and wrinkle, along with some unfavorable increases in FD and wool yellowness but little impact on other wool traits. The ultrasound meat traits, FAT and EMD, were highly positively genetically correlated (0.8), and selection to increase them would result in a small unfavorable correlated increase in FD, moderately favorable reductions in breech cover and wrinkle, but equivocal or negligible changes in other wool traits. The estimated parameters provide the basis for calculation of more accurate Australian Sheep Breeding Values and selection indexes that combine wool and meat objectives in Merino breeding programs.

Increased genetic gains in multi-trait sheep indices using female reproductive technologies combined with optimal contribution selection and genomic breeding values

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro fertilisation and embryo transfer (JIVET) can produce multiple offspring per mating in sheep and cattle. In breeding programs this allows for higher female selection intensity and, in the case of JIVET, a reduction in generation interval, resulting in higher rates of genetic gain. Low selection accuracy of young females entering JIVET has often dissuaded producers from using this technology. However, genomic selection (GS) could increase selection accuracy of candidates at a younger age to help increase rates of genetic gain. This increase might vary for different traits in multiple trait breeding programs depending on genetic parameters and the practicality of recording, particularly for hard to measure traits. This study used both stochastic (animals) and deterministic (GS) simulation to evaluate the effect of reproductive technologies on the genetic gain for various traits in sheep breeding programs, both with and without GS. Optimal contribution selection was used to manage inbreeding and to optimally assign reproductive technologies to individual selection candidates. Two Australian sheep industry indexes were used – a terminal sire index that focussed on growth and carcass traits (the ‘Lamb 2020’ index) and a Merino index that focuses on wool traits, bodyweight, and reproduction (MP+). We observed that breeding programs using artificial insemination or natural mating (AI/N) + MOET, compared with AI/N alone, yielded an extra 39% and 27% genetic gain for terminal and Merino indexes without GS, respectively. However, the addition of JIVET to AI/N + MOET without GS only yielded an extra 1% genetic gain for terminal index and no extra gain in the Merino index. When GS was used in breeding programs, we observed AI/N + MOET + JIVET outperformed AI/N + MOET by 21% and 33% for terminal and Merino indexes, respectively. The implementation of GS increased genetic gain where reproductive technologies were used by 9–34% in Lamb 2020 and 37–98% in MP+. Individual trait response to selection varied in each breeding program. The combination of GS and reproductive technologies allowed for greater genetic gain in both indexes especially for hard to measure traits, but had limited effect on the traits that already had a large amount of early age records.