Number Of Sires Research Articles

Molecular Evaluation of the Mating Dynamics of Snow Crab (Chionoecetes opilio) in the Eastern Bering Sea

ABSTRACTSnow crab (Chionoecetes opilio) in the eastern Bering Sea (EBS) supports a valuable crab fishery that harvests large males. To better understand the potential impact of the presence of snow‐Tanner hybrids (C. opilio × C. bairdi) on snow crab mating dynamics, the maternal lineage of hybrids was evaluated using single nucleotide polymorphisms (SNPs). Contrary to results from a previous study that indicated hybrids result only from crosses between Tanner crab (C. bairdi) males and snow crab females, results from this study showed hybrids result from bidirectional parental crosses. SNP and microsatellite markers were used to evaluate the species and number of males detected as mates in female sperm reserves acquired during mating and as sires among embryos in brooded clutches. The incidence of interspecies mating between female snow crab and Tanner crab or hybrid males was low (2%), suggesting interspecies mating is not currently a pressing fishery management concern. Most females had stored sperm from either a single mate (59%) or two mates (32%), which reflects fewer mates than observed for other snow crab populations. Few females were observed with either no stored sperm (5%) or sperm from three to four mates (4%). Single (82%) or dual (18%) paternity was found among embryos in brooded clutches. Sperm from some mates appeared to be fully utilized for fertilization of the brooded clutch for 35% of females. In contrast to findings for other snow crab populations, no significant differences were detected in the numbers of mates or sires between primiparous and multiparous females. The low extent of polyandry observed may suggest that female snow crab in the EBS have limited mating opportunities, potentially leading to insufficient sperm reserves to fertilize subsequent clutches without remating.

How much multiple paternity should we expect? A study of birds and contrast with mammals.

Parentage analyses via molecular markers have revealed multiple paternity within the broods of polytocous species, reshaping our understanding of animal behavior, ecology, and evolution. In a meta-analysis of multiple paternity in bird and mammal species, we conducted a literature search and found 138 bird and 64 mammal populations with microsatellite DNA paternity results. Bird populations averaged 19.5% multiple paternity and mammals more than twice that level (46.1%). We used a Bayesian approach to construct a null model for how multiple paternity should behave at random among species, under the assumption that all mated males have equal likelihood of siring success, given mean brood size and mean number of sires. We compared the differences between the null model and the actual probabilities of multiple paternity. While a few bird populations fell close to the null model, most did not, averaging 34.0-percentage points below null model predictions; mammals had an average probability of multiple paternity 13.6-percentage points below the null model. Differences between bird and mammal species were also subjected to comparative phylogenetic analyses that generally confirmed our analyses that did not adjust for estimated historical relationships. Birds exhibited extremely low probabilities of multiple paternity, not only compared to mammals but also relative to other major animal taxa. The generally low probability of multiple paternity in birds might be produced by a variety of factors, including behaviors that reflect sexual selection (extreme mate guarding or unifocal female choice) and sperm competition (e.g., precedence effects favoring fertilization by early or late matings).

59. Comparing pedigree and genomic relationships to control inbreeding in optimum-contribution selection restricting the number of sires in pigs

59. Comparing pedigree and genomic relationships to control inbreeding in optimum-contribution selection restricting the number of sires in pigs

Genetic characteristics of the herd of KP "Rybkovskoe" by alleles of the EAB-locus of blood groups

The analysis of the genetic structure of the herd to the marker alleles of the EAB locus - blood groups was according. The EAB-allele G2Y2E/1Q/according to the results of the study with a high frequency of 11.9 – 15.7%, in the herd, whereas its frequency is 18% for the breed was found. In the period 2011-2015 sixteen main alleles of the EAB-locus of blood groups with a total frequency of 0.802 in the herd were found. In 2016-2020, the main EAB-alleles were 12 and the frequency of their occurrence was equal 0,752. The number of four main alleles of the Red-and-White Holstein breed Y1A/1, O2A/2J/2K/O/, I1Y2E/3G/G//, B1O1 decreased from 0,213 to 0,102. With the highest frequency, totaling 40.6% marker EAB - alleles G2T2Y2A/1B/D/G/I/Q/Y/B// (0.052), E/3G/G// (0,070), B1I1Q (0,053), O1I/Q/ (0,080), B2G2O1Y2D/E/2G// (0,056), b (0.095) in KP "Rybkovskoe" are found. In the breed, these alleles occur with a frequency of 29.8%. There are no significant differences between the breed and the herd in the frequency of EAB alleles. The difference did not exceed 2.4 – 2.7%. From a genetic standpoint, the animals of the herd and the breed are close. The index of genetic similarity between them is 0.95. The level of homozygosity was 6.2% in the herd in the period 2016-2020, but its increase over the past five years was 1,2%, indicating a decrease in the genetic diversity of animals. The number of producer sires used by the pedigree farm decreased to 14 and the total diversity of their alleles decreased to 15. Comparative analysis showed that the difference in productivity of the daughters of bulls with alternative EAB-alleles was from 7 to 710 kg of milk, 0.01 – 0.19% fat and 0.02 – 0.09% protein for the first lactation in favor of one or another marker allele from the producer. By the highest lactation, the differences in milk yield are 55 – 1034 kg of milk, in fat content – 0.01 – 0.22%, protein – 0.02 – 0.14%.

Impact of kinship matrices on genetic gain and inbreeding with optimum contribution selection in a genomic dairy cattle breeding program

BackgroundGenomic selection has increased genetic gain in dairy cattle, but in some cases it has resulted in higher inbreeding rates. Therefore, there is need for research on efficient management of inbreeding in genomically-selected dairy cattle populations, especially for local breeds with a small population size. Optimum contribution selection (OCS) minimizes the increase in average kinship while it maximizes genetic gain. However, there is no consensus on how to construct the kinship matrix used for OCS and whether it should be based on pedigree or genomic information. VanRaden’s method 1 (VR1) is a genomic relationship matrix in which centered genotype scores are scaled with the sum of 2p(1-p) where p is the reference allele frequency at each locus, and VanRaden’s method 2 (VR2) scales each locus with 2p(1-p), thereby giving greater weight to loci with a low minor allele frequency. We compared the effects of nine kinship matrices on genetic gain, kinship, inbreeding, genetic diversity, and minor allele frequency when applying OCS in a simulated small dairy cattle population. We used VR1 and VR2, each using base animals, all genotyped animals, and the current generation of animals to compute reference allele frequencies. We also set the reference allele frequencies to 0.5 for VR1 and the pedigree-based relationship matrix. We constrained OCS to select a fixed number of sires per generation for all scenarios. Efficiency of the different matrices were compared by calculating the rate of genetic gain for a given rate of increase in average kinship.ResultsWe found that: (i) genomic relationships were more efficient than pedigree-based relationships at managing inbreeding, (ii) reference allele frequencies computed from base animals were more efficient compared to reference allele frequencies computed from recent animals, and (iii) VR1 was slightly more efficient than VR2, but the difference was not statistically significant.ConclusionsUsing genomic relationships for OCS realizes more genetic gain for a given amount of kinship and inbreeding than using pedigree relationships when the number of sires is fixed. For a small genomic dairy cattle breeding program, we recommend that the implementation of OCS uses VR1 with reference allele frequencies estimated either from base animals or old genotyped animals.

STATISTICAL ANALYSIS OF THE FEATURES OF THE BREEDING BASE OF CATTLE OF THE VOLYN BEEF BREED

STATISTICAL ANALYSIS OF THE FEATURES OF THE BREEDING BASE OF CATTLE OF THE VOLYN BEEF BREED

Productivity of cows depending on the type of mating and genotype of sires

At breeding enterprises, the number of sires of Holstein breed homozygous for the genotype of the ЕАВ-locus is increasing, and there is a tendency for inbreeding coefficients to increase in populations of this breed. The dairy productivity of fi rst-calf heifers obtained from heterozygous and homozygous sires, as well as the change in indicators per generation with intra-line mating and line crosses were studied. It was found that in terms of the total yield of milk fat and protein for 305 days of lactation in the line Wes Back Ideal 1013415, the fi rst-calf heifers obtained from intra-line mating and line crossing exceeded the cows their mothers by 21,4 kg, and in the whole group of fi rst-calf heifers of homozygous sires this indicator was 51,0 kg higher against the average of fi rst-calf heifers of heterozygous sires. At the same time, for the cow-mothers of these groups, the corresponding diff erence was negative: –31,6 and –64,7 kg. Similar data were revealed for another main line Refl ection Sovereign 198998. When mating heterozygous sires according to the variants of line crosses, the milk yield was 227 kg higher (p < 0,05), but the mass fat fraction in milk decreased by 0,06 – 0,08 abs.% (p < 0,01). However, the levels of manifestation of traits among fi rst-calf heifers in comparison with cow-mothers with intra-line mating increased by groups of homozygous sires in milk yield by 32,5 %, mass fat fraction by 17,6 % and mass protein fraction by 25,0 %. The correlation coefficients «mother – daughter» for milk yield, mass fat fraction and mass protein fraction were relatively higher in the group of homozygous sires, whose heritability coeffi cient in one of the farms for milk yield was higher by 0,495, mass fat fraction by 0,305; mass protein fraction by –0,110, and in the other, respectively, by 0,026; 0,161; 0,121. The conclusion is made about a higher prepotency of heterozygous sires with improving mating.

46 Pedigree tracing to determine origins of the Palomino Horse Breeders of America stock-type horse

Registration numbers for the Palomino Horse Breeders of America (PHBA) have risen over the years due in part to new registration guidelines. In fact, PHBA has recently changed registration guidelines allowing registration of any horse with a palomino body color including those with unknown pedigrees. While this trend promotes registry growth, pedigree tracing can assist in documenting breed origins. Pedigree tracing is particularly valuable for color registries as the study of coat color patterns is a relatively new science plagued with misunderstandings due to pedigrees with inaccurate color designations. The objective of this study was to develop a better understanding of the historical origins of today's PHBA stock-type horse through pedigree tracing. 800 horses were randomly sampled from published entries from 10 years of the PHBA World Show. Only 460 of the 800 samples were utilized for this study due to the lack of verified documentation of extended pedigrees that included documented coat colors taken from the All-Breed Database. A complete record was defined as having an uninterrupted generation to generation inheritance pattern of a cream dilution gene influenced coat color from the sampled individual that directly traces back to the earliest existing recorded relative. Results indicate that a small number of foundation sires (Table 1) are responsible for the modern PHBA stock-type horse. The majority of horses within the Hall of Fame have pedigrees that trace back to only one of the sires identified in this study. Two of the identified sires have conflictsconcerning color designation and can be only identified as obligate cream gene carriers. While this study assists in documenting the origins of the breed, as PHBA continues to grow, additional genetic testing to accurately identify the cream gene within the horses registered may further support the goals of a color registry that is based upon horses with a cream phenotype.

Search for additional variability in the herd of Holstein cows

Relevance. When breeding a large herd of the Holstein breed, the improvement of traits in the selection system is reflected, the integral basis (part of the basis) of which was belonging to the line. Against the background of a reduction in the number of lines, the selection of a limited number of sires related to each other into the herd, and the breeding of daughters from them by various types of rebounds, an increase in milk yield and mass fraction of protein (MPF) over three generations is reflected.Methods. The indices of the genetic value of sires in the population were evaluated according to the author's method, while taking into account the indicators of mothers and peers of the same herd. Comparison of the levels of variability of milk productivity traits in terms of standard deviations (±s) in breeding groups.Results. The relative increase in milk yield per generation for the highest lactations was 8.9–15.4% (P < 0.001), and MDL – 1.3–3.2% (P < 0.01). A comparison was made of groups of peer-daughters obtained by targeted selection of homo- and heterozygous fathers according to genetic markers of controlled EAB loci. Another aspect was the high standard deviation of milk yields in the group of daughters of homozygous fathers by 19% against the group of heterozygous, and among the crossed offspring – by 8.6% against intraline. It is assumed that this happened due to the introduction of new and rare alleles with sires into the herd.

Critérios de parada para programa de melhoramento genético para seleção de acasalamentos em gado de corte

Abstract The objective of this work was to propose a new stopping criterion to shorten the computing time of the PampaPlus genetic improvement software, while maximizing the genetic qualification index (GQI) of the progeny, controlling inbreeding, and avoiding unintended culling. Data from two beef-cattle herds integrating PampaPlus were used. Five mating scenarios were built using different numbers of sires (9 to 37) and dams (142 to 568). The analyzed algorithm inputs were: expected progeny differences, pedigree information, maximum inbreeding, maximum and minimum number of matches for each sire, and penalty weights for poor performance. The analyzed response variables were computing time and the GQI of the progenies. Three stopping criteria were used: original stopping criterion fixed at 1,000 iterations; saturation stopping criterion (SSC), based on GQI variance; and Bhandari’s stopping criterion (BSC), which includes the generation interval parameter. SSC and BSC reduced processing time in 24.43-53.64% and in 14.32-50.87%, respectively. BSC reaches solution in less time, without losses in GQI quality. BSC is generalizable and effective to reduce the processing time of mating recommendations.

Comparative evaluation of the breeding value of Holstein bulls-producers

Modern dairy cattle breeding efficiency is largely determined by the strategy of choosing a producer for herd reproduction, which determines the growth rate of herd productivity for the next 3 to 5 years. According to the results of 2022, there are 20 organisations in the Sverdlovsk region with milk production per feed cow of more than 9 thousand kg, including 10 farms with milk production of more than 10 thousand kg. The best farm in the region, APC “Kilachevsky”, produced an average of 12829 kg of milk for each of 3000 cows. Two record-breaking cows were milked there, each of which yielded more than 21 tonnes of milk for a standard lactation. Thirty-four breeding bulls were included in the study. As a result of their evaluation, it was found that in bulls whose genomic breeding value for milk yield exceeded 1000 kg of milk 80.0% of producers were actual improvers for this trait, and in bulls with low genomic breeding value for milk yield (0-99 kg) only 25.0% of producers were actual improvers. Bulls with a negative breeding value for milk production in 66.6 percent of cases turned out to be actual improvers. In terms of protein content in milk, the dependence is similar, the higher the genomic value of the sire according to MDB, the more bulls actually have a positive effect on the protein-milk content of daughters (Tables 3,4). However, the number of sires that confirmed genomic breeding value for protein-milk yield is much less than for milk yield. For milk yield, 17 sires out of 34 (50.0%) received confirmation of breeding value, and for protein-milk yield only 11 (32.0%).

Genetic diversity, asexual reproduction and conservation of the edible fruit tree Spondias purpurea L. (Anacardiaceae) in the Costa Rican tropical dry forest.

The term circa situm has been used to describe different conservation strategies within agricultural landscapes. Circa situm conserves planted or remnant species in farmlands, where natural vegetation has been modified through anthropogenic intervention. It has been proposed that trees planted or retained under circa situm conditions may contribute to maintaining genetic diversity, however information on the role of this strategy in preserving genetic diversity is scarce. The aim of this study was to determine the levels of genetic diversity and structure, and mating patterns in planted and unmanaged stands of the tropical fruit tree Spondias purpurea L. in north western Costa Rica. In three localities, we used seven polymorphic microsatellite loci and genotyped 201 adults and 648 seeds from planted and wild stands. We found no differences in genetic diversity among planted and wild stands. Genetic structure analysis revealed that gene flow occurs among planted and wild stands within localities. Clones were present and their diversity and evenness were both high and similar between planted and wild stands. The number of pollen donors per progeny array was low (Nep = 1.01) which resulted in high levels of correlated paternity (rp = 0.9). Asexual seeds were found in 4.6% of the progeny arrays, which had multilocus genotypes that were identical to the maternal trees. Our results show that although planted stands under circa situm conditions can maintain similar levels of genetic diversity than wild stands, the low number of sires and asexual seed formation could threaten the long term persistence of populations.

Seasonal variation in cuckoldry rates in the socially monogamous cichlid fish Variabilichromis moorii

Mating patterns in animal populations can respond to environmental conditions and consequently vary across time. To examine this variation in nature, studies must include temporal replicates from the same population. Here, we report temporal variation in genetic parentage in the socially monogamous cichlid Variabilichromis moorii from Lake Tanganyika, using samples of broods and their brood-tending parents that were collected across five field trips from the same study population. The sampled broods were either spawned during the dry season (three field trips) or during the rainy season (two trips). In all seasons, we detected substantial rates of extra-pair paternity, which were ascribed to cuckoldry by bachelor males. Paternity shares of brood-tending males were consistently higher, and the numbers of sires per brood were consistently lower, in broods that were spawned in the dry seasons compared to broods from the rainy seasons. In contrast, the strength of size-assortative pairing in our V. moorii population did not vary temporally. Seasonal fluctuations in environmental conditions, such as water turbidity, are proposed as a mechanism behind variable cuckolder pressure. Our data demonstrate the utility of long-term monitoring to improve our understanding of animal mating patterns.

How many fathers? Study design implications when inferring multiple paternity in crocodilians.

Up to 10 males were reported to sire clutches of crocodilian eggs but review of the underlying study designs raised questions of potential upward bias of inferred sire numbers. To test this premise, different scenarios were explored using a published dataset of 16 known single‐sire saltwater crocodile pairs and their offspring which were originally confirmed using a 11 loci microsatellite panel in CERVUS. Varying the number of microsatellites, omitting one or both parental genotypes and using different parentage analysis techniques revealed that total allele number, rather than number of loci, determined inferred sire accuracy in two opposing ways. Using the single‐locus minimum method and GERUD, which both require prior knowledge of family groupings (i.e., nests), fewer alleles (and loci) accurately inferred only one father. In contrast, CERVUS and COLONY required all 11 loci (65 alleles) and both parental genotypes to (a) assign correct family groups and (b) infer the correct sire number, except in one family where two sires were equally assigned based on their number of homozygous loci. When less genotype information was provided, CERVUS and COLONY inferred up to six and seven sires, respectively. Given this data is from confirmed single‐sire matings, and yet up to seven sires could be inferred, the significance of inappropriate study design is clearly demonstrated. Consideration should be carefully given to genotype data, particularly those collected specifically for population diversity studies, which are also used to infer multiple paternity because the underlying data collection assumptions are not equivalent between the two outcomes.

Genetic Evaluation of Body Weight and Body Measurements in Madura Cattle at Weaning Age

Body weight and body measurements at weaning age are important traits representing growth in beef cattle. This research was conducted at the Technical Unit of Madura Cattle and Forage for Animal Feed, Pamekasan, Madura, Indonesia. Eighty-six data points of performance of Madura cattle at weaning age, born in 2014-2019 were used to evaluate the performance and estimate the heritability for weaning weight (WW) and body measurement (chest girth (CG), body length (BL) and wither height (WH)) at weaning age. Weaning age was corrected to 205 days. Estimation of variance components was performed using restricted maximum likelihood applying genetic models of Genstat version 18. The mean of WW, CG, BL and WH for female were 83.82 +17.91 kg; 100.87 +7.80 cm; 87.66 +8.96 cm; and 93.04 +5.49 cm, respectively. The mean of WW, CG, BL and WH for male were 81.02 +20.52 kg; 100.12 +9.82 cm; 85.94 +9.54 cm; and 92.69 +7.46 cm, respectively. There were significant difference for WW, CG, BL and WH between year of calf birth. The number of sires used each year varied between 1 to 7 sires. The heritability values for WW, CG, BL and WH were 0.60, 0.43, 0.48 and 0.44, respectively.
 Keywords: body length, chest girth, heritability, weaning weight, wither height

Multiple paternity in the Asp viper

AbstractMany male reptiles maximize their reproductive success by mating with multiple females. This behaviour has often been observed in female reptiles as well, although one mating would usually be sufficient to fertilize the available female eggs. Using 13 microsatellite markers, multiple paternity (MP) was confirmed for the first time in the asp viper (Vipera aspis) in 47% of the tested clutches, with only up to two different fathers. Phenotypic characteristics (length, weight) of the mother did not influence the number of sires, and the number of young did not differ between litters with one or two sires. Males that sired offspring were larger than males that did not successfully reproduce. Excluding an exceptionally long‐distance movement (2464 m), the distance between fathers and mothers was limited (127 m ± 162). Although males exhibit notable combat behaviour during the breeding season, there was no sexual size dimorphism in the study population.

Multiple paternity in superfetatious live-bearing fishes.

Superfetation, the ability to carry several overlapping broods at different developmental stages, has evolved independently multiple times within the live-bearing fish family Poeciliidae. Even though superfetation is widespread among poeciliids, its evolutionary advantages remain unclear. Theory predicts that superfetation should increase polyandry by increasing the probability that temporally overlapping broods are fertilized by different fathers. Here, we test this key prediction in two poeciliid species that each carry two temporally overlapping broods: Poeciliopsis retropinna and P. turrubarensis. We collected 25 females per species from freshwater streams in South-Eastern Costa Rica and assessed multiple paternity by genotyping all their embryos (420 embryos for P. retropinna; 788 embryos for P. turrubarensis) using existing and newly developed microsatellite markers. We observed a high frequency of unique sires in the simultaneous, temporally overlapping broods in P. retropinna (in 56% of the pregnant females) and P. turrubarensis (79%). We found that the mean number of sires within females was higher than the number of sires within the separate broods (2.92sires within mothers vs. 2.36 within separate broods in P. retropinna; and 3.40 vs 2.56 in P. turrubarensis). We further observed that there were significant differences in the proportion of offspring sired by each male in 42% of pregnant female P. retropinna and 65% of female P. turrubarensis; however, this significance applied to only 9% and 46% of the individual broods in P. retropinna and P. turrubarensis, respectively, suggesting that the unequal reproductive success of sires (i.e. reproductive skew) mostly originated from differences in paternal contribution between, rather than within broods. Together, these findings tentatively suggest that superfetation may promote polyandry and reproductive skew in live-bearing fishes.

Genomic Prediction of Complex Traits in Animal Breeding with Long Breeding History, the Dairy Cattle Case.

In accordance with the infinitesimal model for quantitative traits, a very large number of genes affect nearly all economic traits. In only two cases has the causative polymorphism been determined for genes affecting economic traits in dairy cattle. Most current methods for genomic evaluation are based on the "two-step" method. Genetic evaluations are computed by the individual animal model, and functions of the evaluations of progeny-tested sires are the dependent variable for estimation of marker effects. With the adoption of genomic evaluation in 2008, annual rates of genetic gain in the US increased from ∼50-100% for yield traits and from threefold to fourfold for lowly heritable traits, including female fertility, herd-life and somatic cell concentration. Gradual elimination of the progeny test scheme has led to a reduction in the number of sires with daughter records and less genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and "environmentally friendly" production. Genetic variance for economic traits is maintained by increase in frequency of rare alleles, new mutations, and changes in selection goals and management.

Genetic parameters for methane emissions in Australian sheep measured in portable accumulation chambers in grazing and controlled environments

Context Genotype by environment interaction or sire re-ranking between measurements of methane emission in different environments or from using different measurement protocols can affect the efficiency of selection strategies to abate methane emission. Aim This study tested the hypothesis that measurements of methane emission from grazing sheep under field conditions, where the feed intake is unknown, are genetically correlated to measurements in a controlled environment where feed intake is known. Methods Data on emission of methane and carbon dioxide and uptake of oxygen were measured using portable accumulation chambers from 499 animals in a controlled environment in New South Wales and 1382 animals in a grazing environment in Western Australia were analysed. Genetic linkage between both environments was provided by 140 sires with progeny in both environments. Multi-variate animal models were used to estimate genetic parameters for the three gas traits corrected for liveweight. Genetic groups were fitted in the models to account for breed differences. Genetic correlations between the field and controlled environments for the three traits were estimated using bivariate models. Key results Animals in the controlled environment had higher methane emission compared to the animals in the field environment (37.0 ± s.d 9.3 and 35.3 ± s.d 9.4 for two protocols vs 12.9 ± s.d 5.1 and 14.6 ± s.d 4.8 mL/min for lambs and ewes (±s.d); P < 0.05) but carbon dioxide emission and oxygen uptake did not significantly differ. The heritability estimates for methane emission, carbon dioxide emission and oxygen uptake were 0.15, 0.06 and 0.11 for the controlled environment and 0.17, 0.27 and 0.35 for the field environment. The repeatability for the traits in the controlled environment ranged from 0.51 to 0.59 and from 0.24 to 0.38 in the field environment. Genetic correlations were high (0.85–0.99) but with high standard errors. Conclusion Methane emission phenotypes measured using portable accumulation chambers in grazing sheep can be used in genetic evaluation to estimate breeding values for genetic improvement of emission related traits. The combined measurement protocol-environment did not lead to re-ranking of sires. Implication These results suggest that both phenotypes could be used in selection for reduced methane emission in grazing sheep. However, this needs to be consolidated using a larger number of animals and sires with larger progeny groups in different environments.

Estimation of macro- and micro-genetic environmental sensitivity in unbalanced datasets

Genotype-by-environment interaction is caused by variation in genetic environmental sensitivity (GES), which can be subdivided into macro- and micro-GES. Macro-GES is genetic sensitivity to macro-environments (definable environments often shared by groups of animals), while micro-GES is genetic sensitivity to micro-environments (individual environments). A combined reaction norm and double hierarchical generalised linear model (RN-DHGLM) allows for simultaneous estimation of base genetic, macro- and micro-GES effects. The accuracy of variance components estimated using a RN-DHGLM has been explicitly studied for balanced data and recommendation of a data size with a minimum of 100 sires with at least 100 offspring each have been made. In the current study, the data size (numbers of sires and progeny) and structure requirements of the RN-DHGLM were investigated for two types of unbalanced datasets. Both datasets had a variable number of offspring per sire, but one dataset also had a variable number of offspring within macro-environments. The accuracy and bias of the estimated macro- and micro-GES effects and the estimated breeding values (EBVs) obtained using the RN-DHGLM depended on the data size. Reasonably accurate and unbiased estimates were obtained with data containing 500 sires with 20 offspring or 100 sires with 50 offspring, regardless of the data structure. Variable progeny group sizes, alone or in combination with an unequal number of offspring within macro-environments, had little impact on the dispersion of the EBVs or the bias and accuracy of variance component estimation, but resulted in lower accuracies of the EBVs. Compared to genetic correlations of zero, a genetic correlation of 0.5 between base genetic, macro- and micro-GES components resulted in a slight decrease in the percentage of replicates that converged out of 100 replicates, but had no effect on the dispersion and accuracy of variance component estimation or the dispersion of the EBVs. The results show that it is possible to apply the RN-DHGLM to unbalanced datasets to obtain estimates of variance due to macro- and micro-GES. Furthermore, the levels of accuracy and bias of variance estimates when analysing macro- and micro-GES simultaneously are determined by average family size, with limited impact from variability in family size and/or cohort size. This creates opportunities for the use of field data from populations with unbalanced data structures when estimating macro- and micro-GES.