A major gene for host response to porcine reproductive and respiratory syndrome is not unfavorably associated with overall performance under nonchallenging conditions in commercial pig lines

A QTL for host response to porcine reproductive and respiratory syndrome (PRRS) was identified in a previous study. The SNP WUR10000125 (WUR) is used as a tag SNP for this QTL. The favorable (B) allele at this SNP is in low frequency in commercial populations, possibly because this allele is unfavorably associated with an important trait under nonchallenging conditions and, therefore, may have been selected against. Therefore, objectives of this study were to estimate the effect of WUR on traits under selection in commercial lines under nonchallenging conditions and to estimate the effect of WUR genotype of parents on performance of crossbred progeny in a commercial-like environment. Data were collected on 4 purebred lines: a Landrace dam line (D1), a Large White dam line (D2), a synthetic sire line (S1), and a Pietrain sire line (S2). Traits analyzed included total number born, number stillborn, farrowing survival, lactation survival, litter mortality, daily feed intake (DFI), backfat, average test daily gain (TGR), average lifetime daily gain (LGR), and Topigs Norsvin selection index (TSI) value, indicative of overall economic value. Deregressed EBV were calculated for each trait (except TSI) and analyzed within line. In the S1 line, AB and BB pigs had significantly lower TGR (P = 0.002) and LGR (P = 0.001) than AA pigs but also lower DFI (P = 0.004). Conversely, AB and BB pigs had significantly higher DFI (P < 0.001) and AB pigs had significantly higher TGR (P = 0.03) than AA pigs in the S2 line. The effect of WUR on TSI was not significant for any line (P ≥ 0.15). Analyses of phenotypic records collected on crossbred progeny of S1 sires and D1 × D2 F₁ females showed no significant effect of parent WUR genotype on DFI, backfat, TGR, or LGR (P ≥ 0.07). In conclusion, the effect of WUR was nonsignificant for most traits but the magnitude and direction of the effect differed by trait and by line. The favorable allele for host response to PRRS was associated with greater DFI and a tendency for greater TGR in the S2 line, but the opposite direction of effect was detected for the S1 line. Regardless of the effect on individual traits, no significant effect of WUR on TSI was detected for any line. Therefore, selecting for the B allele is expected to result in progeny with increased resistance to PRRS without compromising overall economic value under normal, nonchallenging conditions.

Genetic variation for farrowing rate in pigs in response to change in photoperiod and ambient temperature

Seasonal infertility is often observed as anestrus and a lower conception rate resulting in a reduced farrowing rate (FR) during late summer and early autumn. This is often regarded as an effect of heat stress; however, we observed a reduction in the FR of sows even after correcting for ambient temperature in our data. Therefore, we added change in photoperiod in the analysis of FR considering its effect on sow fertility. Change in photoperiod was modeled using the cosine of the day of first insemination within a year. On an average, the FR decreased by 2% during early autumn with decreasing daily photoperiod compared with early summer with almost no change in daily photoperiod. It declined 0.2% per degree Celsius of ambient temperature above 19.2°C. This result is a step forward in disentangling the 2 environmental components responsible for seasonal infertility. Our next aim was to estimate the magnitude of genetic variation in FR in response to change in photoperiod and ambient temperature to explore opportunities for selecting pigs to have a constant FR throughout the year. We used reaction norm models to estimate additive genetic variation in response to change in photoperiod and ambient temperature. The results revealed a larger genetic variation at stressful environments when daily photoperiod decreased and ambient temperatures increased above 19.2°C compared with neutral environments. Genetic correlations between stressful environments and nonstressful environments ranged from 0.90 (±0.03) to 0.46 (±0.13) depending on the severity of the stress, indicating changes in expression of FR depending on the environment. The genetic correlation between responses of pigs to changes in photoperiod and to those in ambient temperature were positive, indicating that pigs tolerant to decreasing daily photoperiod are also tolerant to high ambient temperatures. Therefore, selection for tolerance to decreasing daily photoperiod should also increase tolerance to high ambient temperatures or vice versa.

Estimation of genetic parameters and breeding values across challenged environments to select for robust pigs

Robustness is an important issue in the pig production industry. Since pigs from international breeding organizations have to withstand a variety of environmental challenges, selection of pigs with the inherent ability to sustain their productivity in diverse environments may be an economically feasible approach in the livestock industry. The objective of this study was to estimate genetic parameters and breeding values across different levels of environmental challenge load. The challenge load (CL) was estimated as the reduction in reproductive performance during different weeks of a year using 925,711 farrowing records from farms distributed worldwide. A wide range of levels of challenge, from favorable to unfavorable environments, was observed among farms with high CL values being associated with confirmed situations of unfavorable environment. Genetic parameters and breeding values were estimated in high- and low-challenge environments using a bivariate analysis, as well as across increasing levels of challenge with a random regression model using Legendre polynomials. Although heritability estimates of number of pigs born alive were slightly higher in environments with extreme CL than in those with intermediate levels of CL, the heritabilities of number of piglet losses increased progressively as CL increased. Genetic correlations among environments with different levels of CL suggest that selection in environments with extremes of low or high CL would result in low response to selection. Therefore, selection programs of breeding organizations that are commonly conducted under favorable environments could have low response to selection in commercial farms that have unfavorable environmental conditions. Sows that had experienced high levels of challenge at least once during their productive life were ranked according to their EBV. The selection of pigs using EBV ignoring environmental challenges or on the basis of records from only favorable environments resulted in a sharp decline in productivity as the level of challenge increased. In contrast, selection using the random regression approach resulted in limited change in productivity with increasing levels of challenge. Hence, we demonstrate that the use of a quantitative measure of environmental CL and a random regression approach can be comprehensively combined for genetic selection of pigs with enhanced ability to maintain high productivity in harsh environments.

Sire evaluation for total number born in pigs using a genomic reaction norms approach

In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBV) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits, such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential for choosing the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season, HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree ( A: ) and genomic ( G: ) relationship matrices were considered. The genetic parameters (variance components, h(2) and genetic correlations) were very similar when estimated using the A: and G: relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G: matrix analysis, SNP by environment interactions were observed. For some SNP, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBV for "juvenile" boars varying from 0.14 to 0.44 across different HYS levels, while the accuracy of the standard genomic prediction model, without reaction norms, varied from 0.09 to 0.28. These results show that it is important and feasible to consider G×E interactions in evaluations of sires using genomic prediction models and that genomic information can increase the accuracy of selection across environments.

Genetic relationship between boar taint compounds, human nose scores, and reproduction traits in pigs

A reduction in boar taint, an unpleasant odor arising in pork from some intact males, is desirable if routine castration of piglets needs to be stopped. Commercial slaughter pigs are typically crosses between sire lines mainly selected for finishing traits and dam lines mainly selected for reproduction traits. Previous studies suggest the possibility of reducing boar taint in sire lines due to favorable genetic correlations between boar taint and finishing traits. However, there are indications of unfavorable genetic associations between boar taint and female reproduction traits, but a lack of genetic correlation estimates remain a major roadblock in reducing boar taint in dam lines. This study was conducted to estimate genetic correlations between boar taint traits and female reproduction traits, investigate differences in these genetic relationships among sire and dam lines, and evaluate possible consequences of selection against boar taint in dam lines. The data consisted of 32,549 reproduction records from a Landrace dam line, 23,874 records from a Yorkshire dam line, and 3,745 records from a Pietrain sire line. Androstenone, skatole, and indole were measured on 1,896 carcasses, and human nose scores were recorded on 7,742 carcass samples. In general, the level of boar taint was significantly greater (P < 0.05) in the two dam lines than in the sire line. A majority of genetic correlations of boar taint compounds with reproduction traits were either low or nonsignificant, except for those of skatole and indole, with age at first insemination in dam lines that were -0.32 and -0.46, respectively. Genetic correlations also differed (P < 0.05) between sire and dam lines. The consequences of selection against boar taint in dam lines were evaluated, using selection indexes based on reproduction traits only, boar taint traits only, and both boar taint and reproduction traits. Selection on an index of only reproduction traits increased the number of carcasses with boar taint from 4 to 7.3% in 5 generations. Selection on a combined index reduced carcasses with boar taint from 4 to <0.1% in 19 generations at the cost of a 10% less economic gain in reproduction traits. In markets for intact males, overall economic gain is 78% greater than with selection for reproduction only. Breeding programs for boar taint in commercial production should include boar taint in breeding goals of dam lines as the levels of boar taint and the risk of a further increase are greater.

Methods for evaluating genotype-environment interactions illustrated by laying hens

SUMMARY

The relative efficiency of several methods of studying genotype-environment interactions has been illustrated, considering some performance traits in laying hens as a model. The comparison involved methods of classifying, detecting the existence, and estimating the magnitude of genotype-environment interactions. The environments consisted of warm (32 °C) and temperate (20 °C) climatic conditions. Classification and qualitative description of interactions is useful when very few genotypes and environments are involved. The illustration with an example suggested that a classification based on comparison of relative magnitudes of average genotypic, environmental and interaction effects would be most meaningful. The interactions carry greater significance if they exceed the average genotypic effects. A factorial analysis of variance followed by an F-test can be useful in detecting the existence of interactions, but statistical significance should not be overemphasized for biological relevance. Invariably, the magnitude of interactions must be estimated to derive useful conclusions. The seven methods of estimating this correlation mainly involved principles of intraclass correlation, rank correlation and product-moment correlation. An analysis of data revealed that the intraclass correlation methods, in general, yielded higher estimates compared to the rest of the methods. Among them, the formula given by Dickerson (1962) was found more appropriate in mixed-model analysis with unbalanced data, while the method given by Yamada (1962) resulted in negative estimates when the interaction variance was large. The least reliable among the methods were estimations directly utilizing the mean squares from factorial analysis of variance as suggested by Robertson (1959). Rank correlations were similar for phenotypic as well as genetic rankings and also coincided to some extent with the correlation among the breeding values, revealing distinct changes in ranks of genotypes in those traits where the interactions were larger. Product-moment correlations between the breeding values of sires in the two environments should be the most reliable and suitable for predicting selection response when the sires are selected in one environment and their progeny is required to perform under different conditions. However, their expectations were lower than 1, depending upon the genetic foundation of the traits and effective progeny size. ZUSAMMENFASSUNG: Verschiedene Methoden der Untersuchung von Genotyp-Umwelt-Interaktionen hinsichtlich ihrer relativen Effizienz wurden verglichen. Dieser Vergleich erfolgte modellhaft an Leistungsmerkmalen von Legehennen. Die angewandten Methoden beinhalten solche des Nachweises, der Klassifizierung und der Schätzung des Ausmaßes von Genotyp-Umwelt-Interaktionen. An Umweltbedingungen wurden warme (32°) und gemäßigte (20°C) Stalltemperaturen einbezogen. Die Klassifizierung und qualitative Beschreibung von Interaktionen ist immer dann besonders geeignet, wenn nur sehr wenige Genotypen und Umwelten berücksichtigt werden müssen. Die Beispielsberechnungen ergaben, daß eine Klassifizierung aufgrund eines Vergleiches des relativen Ausmaßes der Durchschnittseffekte von Genotypen, Umwelten und der Interaktionseffekte am sinnvollsten ist. Die Interaktionen zeigten immer dann stärkere Ausprägung, wenn sie die Durchschnittseffekte der Genotypen übertrafen. Eine faktorielle Varianzanalyse ist in Verbindung mit einem F-Test geeignet, das Auftreten von Interaktionen nachzuweisen. Von der statistischen Signifikanz kann jedoch nicht direkt auf biologische Relevanz geschlossen werden. Um züchterische Konsequenzen ziehen zu können, muß das Ausmaß von Interaktionen geschätzt werden. Es wurden sieben Schätzmethoden auf der Basis der Berechnung von Intraklasskorrelationen, Rangkorrelationen und Produkt-Moment-Korrelationen angewandt. Mit den Intraklasskorrelationsmethoden wurden allgemein die höchsten Schätzwerte ermittelt. Dabei erwies sich die Formel von Dickerson (1962) als geeigneter für Analysen im gemischten Modell mit unbalanzierten Daten, während die Methode von Yamada (1962) immer dann zu negativen Schätzwerten führte, wenn die Interaktionsvarianz hoch war. Am wenigsten zuverlässig waren die Schätzwerte nach Robertson (1959), die direkt aus den Durchschnittsquadraten der faktoriellen Varianzanalyse ermittelt wurden. Bezüglich der Rangkorrelationen ergaben sich ähnliche Ergebnisse nach phänotypischer und genetischer Rangierung und eine annähernde Übereinstimmung mit den Korrelationen zwischen den Zuchtwerten. Es traten in all jenen Merkmalen deutliche Rangverschiebungen auf, für die höhere Interaktionen erwartet wurden. Produkt-Moment-Korrelationen zwischen den Zuchtwerten der Väter in den beiden Umwelten ergaben die zuverlässigsten Schätzwerte und ermöglichten die besten Voraussagen des Selektionserfolges für den Fall, daß die Väter in einer Umwelt selektiert werden, während ihre Nachkommen unter anderen Bedingungen produzieren müssen. Die Erwartungswerte dieser Korrelationen können jedoch kleiner als 1 sein und hängen sowohl von der genetischen Fundierung der Merkmale als auch von der Anzahl geprüfter Nachkommen ab.

A human nose scoring system for boar taint and its relationship with androstenone and skatole

A system for sensory evaluation of boar taint was used to evaluate boar taint in fat samples from 6574 entire males. The term "human nose scoring" has been used to describe this system. The samples from each boar were heated with a hot iron and three panelists assigned scores of 0 to 4. The reproducibility of HNS ranged from 0.19 to 0.32 reflecting natural variation in the ability of human beings to detect different odors. The correlations of HNS with androstenone ranged from 0.22 to 0.52, while those with skatole ranged from 0.31 to 0.89, suggesting that skatole is a better predictor of boar taint. Considering (1) the relationship of HNS with the boar taint compounds, (2) the ability of HNS to capture variation not accounted for by the boar taint compounds, (3) low estimation costs and (4) low time requirements, HNS can be used in large scale evaluations of boar taint.

Genetic parameters for androstenone, skatole, indole, and human nose scores as measures of boar taint and their relationship with finishing traits

The purpose of this study was to evaluate measures of boar (Sus scrofa) taint as potential selection criteria to reduce boar taint so that castration of piglets will become unnecessary. Therefore, genetic parameters of boar taint measures and their genetic correlations with finishing traits were estimated. In particular, the usefulness of a human panel assessing boar taint (human nose score) was compared with chemical assessment of boar taint compounds, androstenone, skatole, and indole. Heritability estimates for androstenone, skatole, and indole were 0.54, 0.41, and 0.33, respectively. The heritability for the human nose score using multiple panelists was 0.12, and ranged from 0.12 to 0.19 for individual panelists. Genetic correlations between scores of panelists were generally high up to unity. The genetic correlations between human nose scores and the boar taint compounds ranged from 0.64 to 0.999. The boar taint compounds and human nose scores had low or favorable genetic correlations with finishing traits. Selection index estimates indicated that the effectiveness of a breeding program based on human nose scores can be comparable to a breeding program based on the boar taint compounds themselves. Human nose scores can thus be used as a cheap and fast alternative for the costly determination of boar taint compounds, needed in breeding pigs without boar taint.

Studies on the genotoxicity of endosulfan in different tissues of fresh water fish Mystus vittatus using the comet assay

Endosulfan, a widely used organochlorine pesticide, is readily bio-accumulative in fishes and can be indirectly harmful to human populations. Limited efforts have been made to study long-term genotoxic effects of endosulfan in different tissues of fish using gentoxicity biomarkers. Therefore, the current investigation was undertaken to detect single-cell DNA strand breaks induced by endosulfan in the fresh water teleost fish Mystus vittatus using the comet assay. The LC(50) value of technical grade endosulfan was first determined for the fish species in a semistatic system, and on the basis of the LC(50) value, the sublethal and nonlethal concentrations were determined. The DNA damage was measured in gill, kidney, and erythrocytes as the percentage of DNA in comet tails of fish specimens exposed to the sublethal and nonlethal concentrations of endosulfan. In general, significant effects (p < 0.01) from both concentration and time of exposure were observed in exposed fishes. It was found that all the tissues at all concentrations exhibited the highest DNA damage on day 1, after which there was a nonlinear decline in the percentage of tail DNA. The comparison of DNA damage among the tissues at different concentrations could not show the sensitivity of particular tissue to endosulfan. The current study explored the utility of the comet assay for in vivo laboratory studies using fish species to screen the genotoxic potential of chemical agents.

Simplifications of marker-assisted genetic evaluation and accounting for non-additive interaction effects

Abstract. A computing simplification was applied to marker-assisted genetic evaluation of quantitative traits including additive and non-additive effects of QTL as well as residual polygenic effects. Different situations including QTL and the residual polygenic effect estimated as a sum or separately, and with or without non-additive effects integrated in models were evaluated. The computing simplification was used in combinations with different models and parameterizations. An example data was adopted to illustrate the simplified computing strategy and was compared with the computing method of direct inversion. Identical results were obtained from both computing strategies. The main advantage of the simplification is that it does not require inversion of non-additive relationship matrices and relationship matrices of QTL, and the number of random effects in mixed model equations is the same as any animal model with only additive effects.

Genetic distinctness of African, Asian and South American local chickens

The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upgMa analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed.

Characterization of a species-specific repetitive DNA from a highly endangered wild animal, Rhinoceros unicornis, and assessment of genetic polymorphism by microsatellite associated sequence amplification (MASA)

We have cloned and sequenced a 906bp EcoRI repeat DNA fraction from Rhinoceros unicornis genome. The contig pSS(R)2 is AT rich with 340 A (37.53%), 187 C (20.64%), 173 G (19.09%) and 206 T (22.74%). The sequence contains MALT box, NF-E1, Poly-A signal, lariat consensus sequences, TATA box, translational initiation sequences and several stop codons. Translation of the contig showed seven different types of protein motifs, among which, EGF-like domain cysteine pattern signatures and Bowman-Birk serine protease inhibitor family signatures were prominent. The presence of eukaryotic transcriptional elements, protein signatures and analysis of subset sequences in the 5' region from 1 to 165nt indicating coding potential (test code value=0.97) suggest possible regulatory and/or functional role(s) of these sequences in the rhino genome. Translation of the complementary strand from 906 to 706nt and 190 to 2nt showed proteins of more than 7kDa rich in non-polar residues. This suggests that pSS(R)2 is either a part of, or adjacent to, a functional gene. The contig contains mostly non-consecutive simple repeat units from 2 to 17nt with varying frequencies, of which four base motifs were found to be predominant. Zoo-blot hybridization revealed that pSS(R)2 sequences are unique to R. unicornis genome because they do not cross-hybridize, even with the genomic DNA of South African black rhino Diceros bicornis. Southern blot analysis of R. unicornis genomic DNA with pSS(R)2 and other synthetic oligo probes revealed a high level of genetic homogeneity, which was also substantiated by microsatellite associated sequence amplification (MASA). Owing to its uniqueness, the pSS(R)2 probe has a potential application in the area of conservation biology for unequivocal identification of horn or other body tissues of R. unicornis. The evolutionary aspect of this repeat fraction in the context of comparative genome analysis is discussed.

Genotype by environment interactions in laying hens based on relationship between breeding values of sires in temperate and tropical environments

This study was conducted to evaluate the significance of genotype by environment (G x E) interactions for tropical poultry breeding. Three environmental conditions were considered: controlled normal-temperature (20 +/- 2 C, CN) and controlled high-temperature (32 C, CH) housing in Germany as well as natural open tropical housing in Malaysia (22 to 34 C, TO). Eighty-four sires were considered as genotypes. Their 5,352 progeny were tested simultaneously over three environments. For each sire, its part breeding value (BV) was estimated within each environment for each performance trait. Correlations between these BV for a pair of environments were used to estimate the magnitude of G x E interactions and the degree of relationship between them to demonstrate their implications on breeding strategies. Differences between observed and expected genetic correlations of BV for body weight, egg weight, egg number, egg mass, feed intake, and production efficiency as a fraction of the expected correlation were 5.1, 4.0, 36.7, 36.5, 17.7, and 31.6%, respectively, suggesting greater significance of G x E interactions for reproduction and production efficiency. The relationships between BV over the three environments were linear for most of the traits studied, but the coefficients of determination were dependent upon the magnitude of interactions involved. Relative efficiencies of indirect selection in CN or CH for performance in TO were also very low.