Peer Berg

Genetic variation for growth rate, feed conversion efficiency, and disease resistance exists within a farmed population of rainbow trout

Abstract The objective of this study was to test that additive genetic (co)variation for survival, growth rate, feed conversion efficiency, and resistance to viral haemorrhagic septicaemia (VHS) exists within a farmed population of rainbow trout. Thirty sires and 30 dams were mated by a partly factorial mating design. Each sire was mated to two dams, and each dam was mated to two sires, producing 50 viable full-sib families (29 sires, 25 dams). The fish from these families were reared for a 215-day growout period, and were assessed for survival between days 52 and 215, growth rate (i.e., body weight on days 52, 76, 96, 123, 157, 185, and 215, and body length on days 52 and 215); feed conversion efficiency between days 52–215, 52–76, 77–96, 97–123, 124–157, 158–185, and 186–215, and VHS resistance. REML estimates of additive genetic variation for the body weights, body lengths, and feed conversion efficiencies were obtained by fitting univariate linear (reduced) animal models. Additive genetic variation for VHS resistance was estimated by fitting a Weibull, sire–dam frailty model to time until death of fish challenged with VHS. Genetic correlations were estimated among the body weights, body length, and feed conversion efficiencies that expressed additive genetic variation, while genetic correlations between VHS resistance and the body weights, body length, and feed conversion efficiencies were approximated as product–moment correlations among predicted breeding values of the sires and dams. Additive genetic variation was found to be very low for survival, body weight on days 52 and 76, body length on day 52, and feed conversion efficiency between days 185 and 215. However, additive genetic variation was detected for body weight on days 96, 123, 157, 185, and 215 [coefficient of additive genetic variation (CV)=8.4–28.4%, heritability (h2)=0.35 for body weight on day 215], body length on day 215 (CV=6.9%, h2=0.53), feed conversion efficiency between days 52–215, 52–76, 77–96, 97–123, 124–157, and 158–185 (CV=4.0–13.9%), and VHS resistance (additive genetic variance for log-frailty=0.24, h2 on the logarithmic-time scale=0.13). Genetic correlations among the body weights, body length, and feed conversion efficiencies that expressed additive genetic variation were generally favourable and moderate-to-very strong (0.55–0.99), though there were unfavourable correlations (−0.01 to −0.33) between the predicted breeding values for VHS resistance and the predicted breeding values for the body weights, body length, and feed conversion efficiencies. These results demonstrate that additive genetic (co)variation for growth rate, feed conversion efficiency, and VHS resistance does exist within the farmed population of rainbow trout, and indicates that selective breeding for these traits can be successful.

Neonatal piglet traits of importance for survival in crates and indoor pens

The primary aim of the present study was to investigate whether the same piglet traits contributed to the same causes of neonatal piglet mortality in crates (CT) and pens (PN). Gilts originating from 2 distinct genetic groups that differed in breeding value for piglet survival rate at d 5 (SR5) were used. These were distributed to farrow in either PN or CT as follows: high-SR5 and CT (n = 30); low-SR5 and CT (n = 27); high-SR5 and PN (n = 22); and low-SR5 and PN (n = 24). Data on individual piglets were collected at birth, including interbirth interval; birth order; birth weight; rectal temperature at birth, 2 h after birth, and 24 h after birth; cordal plasma lactate; and latency to first suckle. Based on autopsy, causes of mortality were divided into stillborn, bitten to death, starvation, crushed, disease, and other causes. Potential risk factors of dying were estimated using a GLM with a logit link function. No significant effect (NS) of housing was observed on the odds of a piglet being stillborn (F(1,73) = 0.1, NS), being crushed (F(1,53) = 1.4, NS), or dying of starvation (F(1,53) = 0.3, NS). No significant differences were observed between the 2 genetic groups for any category of mortality. Piglet traits for pre- and postnatal survival were the same for CT and PN. The odds of being stillborn were increased in piglets born late in the birth order (F(1,1061) = 33.5, P < 0.0001), after a long interbirth interval (F(1,1061) = 19.2, P < 0.0001), and with a lighter birth weight (F(1,1061) = 9.2, P = 0.003). The lighter the birth weight of the piglets, the greater were the odds of being crushed (F(1,1050) = 18, P < 0.0001) and dying of starvation (F(1,1050) = 19, P < 0.0001). The lower the rectal temperature 2 h after birth, the greater were the odds of being crushed (F(1,1050) = 4.6, P = 0.03), starving (F(1,1050) = 16.6, P < 0.0001), or dying of diseases (F(1,1050) = 4.9, P = 0.03). Increased cordal plasma lactate increased the odds of dying from starvation (F(1,1050) = 18, P < 0.0001). In both CT and PN, the birth weight, body temperature 2 h after birth, and birth process were important traits related to crushing, starvation, and disease. Neither housing nor breeding value influenced mortality or traits of importance for the inborn viability of piglets. The results emphasize that the microclimate in the PN for newborn piglets and its heat-preserving properties are more important for survival than whether the sow is crated or penned.

Genetic variation for resistance to clinical and subclinical diseases exists in growing pigs

The objective of this study was to test that genetic variation for resistance to clinical and subclinical diseases exists in growing pigs. A total of 13 551 male growing pigs were assessed for resistance to five categories of clinical and subclinical disease: (i) any clinical or subclinical disease, (ii) lameness, (iii) respiratory diseases, (iv) diarrhoea, and (v) other diseases (i.e. any clinical or subclinical disease with the exception of (ii), (iii), and (iv)). Additive genetic variation for resistance to each disease category was estimated by fitting a Weibull, sire-dam frailty model to time until the pigs were first diagnosed with a disease from that category. Genetic correlations among the resistances to each disease category were approximated as product-moment correlations among predicted breeding values of the sires. Additive genetic variation was detected for resistance to (i) any clinical or subclinical disease (additive genetic variance for log-frailty (± s.e. ) = 0·18 ± 0·05, heritability on the logarithmic-time scale = 0·10), (ii) lameness (0·29 ± 0·11, 0·16), (iii) respiratory diseases (0·24 ± 0·16, 0·12), (iv) diarrhoea (0·30 ± 0·27, 0·16), and (v) the other diseases (0·34 ± 0·15, 0·19) and there were generally positive and low-to-moderate correlations among the predicted breeding values (–0·03 to + 0·65). These results demonstrate that additive genetic variation for resistance to clinical and subclinical diseases does exist in growing pigs, and suggests that selective breeding for resistance could be

Hygiene-related and feed-related hoof diseases show different patterns of genetic correlations to clinical mastitis and female fertility

Hoof diseases are a problem in many dairy herds. To study one aspect of the problem, genetic correlations between 4 hoof diseases, protein yield, clinical mastitis, number of inseminations, and days from calving to first insemination were estimated in first-parity Swedish Red cows using trivariate linear animal models. Occurrence of dermatitis, heel horn erosion, sole hemorrhage, and sole ulcer were reported by hoof trimmers. The data set contained about 314,000 animals with records on at least one of the traits; among these, about 64,000 animals had records on hoof diseases. Heritabilities were low for all hoof diseases (0.03 to 0.05). The hoof diseases fell into 2 groups: (1) dermatitis and heel horn erosion (i.e., diseases related to hygiene) and (2) sole hemorrhage and sole ulcer (i.e., diseases related to feeding). The genetic correlations between traits within the 2 groups were high (0.87 and 0.73, respectively), whereas the genetic correlations between traits in different groups were low (≤0.23). These results indicate that the 2 groups of hoof diseases are partly influenced by the same genes. All genetic correlations between hoof diseases and protein yield were low to moderate and unfavorable. Moderate and favorable genetic correlations were found between the feed-related hoof diseases and clinical mastitis (0.35 and 0.32), whereas the genetic correlations between the hygiene-related hoof diseases and clinical mastitis were low and not significantly different from zero. The genetic correlations between the hygiene-related hoof diseases and number of inseminations were low to moderate and favorable (0.32 and 0.22), and the genetic correlations between the feed-related hoof diseases and number of inseminations were low and not significantly different from zero. A moderate genetic correlation was found between sole ulcer and days from calving to first insemination (0.33), whereas the genetic correlations between days from calving to first insemination and sole hemorrhage and the hygiene-related hoof diseases were low and not significantly different from zero. In general, the 2 groups of hoof diseases showed different patterns of genetic correlations to the other functional traits, but both were unfavorably correlated to protein yield. A simulation study showed that inclusion of hoof diseases in the selection index will not only reduce the genetic decline in resistance to hoof diseases but also be favorable for other functional traits and improve overall genetic merit.

Genomic selection strategies in dairy cattle: Strong positive interaction between use of genotypic information and intensive use of young bulls on genetic gain

We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔG(AG) ), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii) a positive interaction exists between the use of genotypic information and a short generation interval on ΔG(AG) and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔG(AG) if genotypic information about the breeding goal trait is known. We examined four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔG(AG) , greater contributions of the functional trait to ΔG(AG) and lower ΔF than the two breeding schemes without genomic selection. Thus, the use of genotypic information may lead to more sustainable breeding schemes. In addition, a short generation interval increases the effect of using genotypic information on ΔG(AG) . Hence, a breeding scheme with genomic selection and with intensive use of young bulls (a turbo scheme) seems to offer the greatest potential. The third hypothesis was disproved as inclusion of genomically enhanced breeding values (GEBV) for an indicator trait in the selection index increased ΔG(AG) in the turbo scheme. Moreover, it increased the contribution of the functional trait to ΔG(AG) , and it decreased ΔF. Thus, indicator traits may still be profitable to use even when GEBV for the breeding goal traits are available.

The value of cows in reference populations for genomic selection of new functional traits

Today, almost all reference populations consist of progeny tested bulls. However, older progeny tested bulls do not have reliable estimated breeding values (EBV) for new traits. Thus, to be able to select for these new traits, it is necessary to build a reference population. We used a deterministic prediction model to test the hypothesis that the value of cows in reference populations depends on the availability of phenotypic records. To test the hypothesis, we investigated different strategies of building a reference population for a new functional trait over a 10-year period. The trait was either recorded on a large scale (30 000 cows per year) or on a small scale (2000 cows per year). For large-scale recording, we compared four scenarios where the reference population consisted of 30 sires; 30 sires and 170 test bulls; 30 sires and 2000 cows; or 30 sires, 2000 cows and 170 test bulls in the first year with measurements of the new functional trait. In addition to varying the make-up of the reference population, we also varied the heritability of the trait (h2 = 0.05 v. 0.15). The results showed that a reference population of test bulls, cows and sires results in the highest accuracy of the direct genomic values (DGV) for a new functional trait, regardless of its heritability. For small-scale recording, we compared two scenarios where the reference population consisted of the 2000 cows with phenotypic records or the 30 sires of these cows in the first year with measurements of the new functional trait. The results showed that a reference population of cows results in the highest accuracy of the DGV whether the heritability is 0.05 or 0.15, because variation is lost when phenotypic data on cows are summarized in EBV of their sires. The main conclusions from this study are: (i) the fewer phenotypic records, the larger effect of including cows in the reference population; (ii) for small-scale recording, the accuracy of the DGV will continue to increase for several years, whereas the increases in the accuracy of the DGV quickly decrease with large-scale recording; (iii) it is possible to achieve accuracies of the DGV that enable selection for new functional traits recorded on a large scale within 3 years from commencement of recording; and (iv) a higher heritability benefits a reference population of cows more than a reference population of bulls.

Marker-assisted selection can reduce true as well as pedigree-estimated inbreeding

This study investigated whether selection using genotype information reduced the rate and level of true inbreeding, that is, identity by descent, at a selectively neutral locus as well as a locus under selection compared with traditional BLUP selection. In addition, the founder representation at these loci and the within-family selection at the nonneutral locus were studied. The study was carried out using stochastic simulation of a population resembling the breeding nucleus of a dairy cattle population for 25 yr. Each year, 10 proven bulls were selected across herds along with 100 dams from within each of 40 herds. Selection was performed using BLUP, marker-assisted, or gene-assisted selection for a trait with low heritability (h2 = 0.04) only expressed in females, mimicking a health trait. The simulated genome consisted of 2 chromosomes. One biallelic quantitative trait loci (QTL) with an initial frequency of the favorable allele of 0.1, and initially explaining 25% of the genetic variance as well as 4 markers were simulated in linkage disequilibrium, all positioned at chromosome 1. Chromosome 2 was selectively neutral, and consisted of a single neutral locus. The results showed that in addition to reducing pedigree-estimated inbreeding, the incorporation of genotype information in the selection criteria also reduced the level and rate of true inbreeding. In general, true inbreeding in the QTL was greater than pedigree-estimated inbreeding with respect to both the level and rate of inbreeding, as expected. Also as expected, true and pedigree-estimated inbreeding in the neutral locus were the same. Furthermore, after 25 yr, or approximately 5 generations, the pedigree-estimated level of inbreeding was reduced by 11 and 24% compared with BLUP in gene- and marker-assisted selection, respectively, and the level of true inbreeding in the QTL was reduced by 22 and 13%, respectively. The difference between selection scenarios was found to be caused by a larger number of founders being represented at the QTL when using genotype information in the selection criteria. This in turn was caused by an increased selection of individuals sharing the favorable QTL allele rather than individuals sharing genes on average, which was shown by a higher Mendelian selection differential in the QTL. Hence, even though the selection pressure was increased at the QTL, more variation was retained. The results suggest that marker-assisted selection is a useful selection strategy.

Genetic contributions and their optimization

Genetic contributions were first formalized in 1958 by James and McBride (Journal of Genetics, 56, 55-62) and have since been shown to provide a unifying framework for theories of gain and inbreeding. As such they have underpinned the development of methods that provide the most effective combination of maximizing gain whilst managing inbreeding and loss of genetic variation. It is shown how this optimum contribution technology can be developed from theory and adapted to provide practical selection protocols for a wide variety of situations including overlapping generations and multistage selection. The natural development of the theory to incorporate genomic selection and genomic control of inbreeding is also shown.

Late reproductive senescence in a rabbit line hyper selected for reproductive longevity, and its association with body reserves

The aim of the present study was to investigate differences in reproductive and body traits during successive parities between two genetic lines. The LP line was constituted by means of selection of animals having an extremely high number of parities (at least 25) and an average reproductive performance compared to the V line selected for litter size at weaning during 31 generations. The two lines were found to have an equal reproductive performance in the first three parities, but the LP line had higher reproductive performance from the fourth parturition onwards. The low reproductive performance after the third parity in the V line was suggested to be caused by constrained environmental conditions in the test station. A line by parity interaction was also observed for body weight, since body weight declined going from the third to the fourth parity in the LP line but not the V line. Thus, it was concluded that hyper selection for reproductive longevity and average prolificacy successfully delayed reproductive senescence, and that this newly founded line showed less environmental sensitivity, which might have been mediated by a higher body reserve.

Hsp72 is present in plasma from Holstein-Friesian dairy cattle, and the concentration level is repeatable across days and age classes

Abstract Although heat shock proteins (Hsps) are primarily considered as being intracellular, this study identified the presence of Hsp72 in plasma from female Holstein-Friesian dairy cattle. Plasma samples were collected from the same animals at different ages and on different days after calving and accordingly divided into 5 age classes. The age classes were calves less than 235 days of age, young heifers between 235 and 305 days of age, older heifers between 305 and 560 days of age, cows early in lactation, and cows later in lactation. For a subsample of animals within each age class, replicate plasma samples were collected from 1 to 7 days apart to test whether the Hsp72 concentration levels are repeatable on this shorter timescale. Hsp72 was observed in plasma samples from animals of all 5 age classes. For animals with blood samples taken a few days apart, the repeatability (within age class) of the Hsp72 concentration was 0.52 ± 0.06. Age and days from calving significantly affected the Hsp72 concentration level. The highest Hsp72 level was observed in older heifers (305–560 days of age). The repeatability of Hsp72 concentrations across age classes within animal was 0.22 ± 0.06. High environmental sensitivity and negative genetic associations between production and health traits in this high-producing breed have been documented earlier. Hsp72 is believed to be strictly stress inducible, and the finding of Hsp72 in plasma indicates that even apparently healthy individuals may experience extrinsic or intrinsic stress (or both).