An approximate method for optimum independent culling level selection for n stages of selection with explicit solutions

Summary An approximate method with explicit solutions to apply independent culling levels for multiple traits in n-stages of selection was developed. An approximate solution was found for sequentially selected traits. Two assumptions were necessary. The first was to assume that subsequent selection would not appreciably change the mean of traits already selected, and the second was to approximate the variance of a correlated trait in a selected population with an upward biased projection. The procedure was shown to give near optimal results regardless of selection intensity or genetic correlations if phenotypic correlations among traits were low. The procedure gave poor results only for certain sequences of selection when phenotypic correlations were high. However, in those cases good results were obtained using a different sequence of selection. With high correlations, the procedure is recommended only after comparing solutions and expected genetic gain for all sequences of selection. If the expected aggregate gain for the sequence of selection desired is less than that of another order, culling points associated with the optimal ordering must be determined. Genetic gain from use of culling points is independent of order of selection. The procedure is recommended for use with computer programs that attempt to find optimal culling points to reduce computational time and to check results.Journal Paper No. 12448 of the Purdue University Agricultural Experiment Station     

Multistage Selection for Genetic Gain by Orthogonal Transformation

An exact transformed culling method for any number of traits or stages of selection with explicit solution for multistage selection is described in this paper. This procedure does not need numerical integration and is suitable for obtaining either desired genetic gains for a variable proportion selected or optimum aggregate breeding value for a fixed total proportion selected. The procedure has similar properties to multistage selection index and, as such, genetic gains from use of the procedure may exceed ordinary independent culling level selection. The relative efficiencies of transformed to conventional independent culling ranged from 87% to over 300%. These results suggest that for most situations one can chose a multistage selection scheme, either conventional or transformed culling, which will have an efficiency close to that of selection index. After considering cost savings associated with multistage selection, there are many situations in which economic returns from use of independent culling, either conventional or transformed, will exceed that of selection index.     

Selection index updating

Summary When traits become evident at different ages or there are large differences in the costs of measuring various traits, selection by independent culling levels may give a higher aggregate economic return than index selection because not all traits need to be measured on all individuals. The problems with optimum independent culling selection is that general solutions are not possible and numerical integration is needed for specific cases. Recently, Xu and Muir (1991) developed a new independent culling level procedure by use of orthogonal transformation of the original characters. With their procedure, explicit solutions for optimum truncation points are possible without numerical integration. As such, the procedure is proficient for any number of stages, and generalized theoretical comparisons of alternative breeding strategies are possible. However, their procedure was limited to the case where selection is for one character at each stage. In this paper, our previous results are extended to the general case of multi-stage index selection, called selection index updating. This procedure is called selection index updating because as traits become available in latter stages, each subsequent index contains all of the traits available up to that stage.The procedure is to develop sequential indices for each stage such that correlations among indices at different stages are zero. Optimum culling points are obtained for the updating procedure by using Xu and Muir's (1991) iterative equations. Due to the property of orthogonality of the updated indices, aggregate gain can be partitioned into gains due to various stages of selection. Partitioning of aggregate economic gain is useful to breeders who desire to adjust individual trait selection intensity based on facilities available at that stage. Methods are discussed to modify the procedure to obtain maximum aggregate economic return per unit of cost associated with obtaining measures on each trait. An application of multi-stage selection is demonstrated using a set of data for Rhode Island Red layer type chickens. A second example demonstrates the use of multi-stage selection optimized with respect to aggregate economic gain and costs associated with obtaining measurements.Journal Paper No. 12813 of the Purdue University Agricultural Experiment Station     

Reproductive fitness and artificial selection in animal breeding: culling on fitness prevents a decline in reproductive fitness in lines of Drosophila melanogaster selected for increased inebriation time

Summary The maintenance of reproductive fitness in lines subjected to artificial selection is one of the major problems in animal breeding. The decline in reproductive performance has neither been predictable from heritabilities and genetic correlations, nor have conventional selection indices been adequate to avoid the problem. Gowe (1983) has suggested that the heritabilities of reproductive traits are non-linear, with heritabilities being higher on the lower fitness side. Consequently, he has predicted that culling on reproductive fitness in artificial selection lines will be effective in preventing the usual declines in fitness. An experimental evaluation of Gowe's prediction has been carried out by comparing fitnesses of replicated lines of three treatments: selection for increased inebriation time without culling on fitness (HO), selection for inebriation time with culling of 20% (4/20) of selected females on reproductive fitness (HS), and unselected controls (C). Response to selection for inebriation time in the two selection treatments was similar. After 25 generations, the competitive index, a measure of reproductive fitness, was significantly lower in the HO treatment than the HS treatment, while the HS treatment did not differ from the control lines or the base population. These results demonstrate for the first time that culling on reproductive fitness in selection lines can be used to prevent the usual decline in reproductive performance.     

Some population genetic models combining artificial and natural selection pressures in the presence of assortative mating

Summary We have attempted quantitatively through a series of assortative mating models to gain insight into the interaction between the usually antagonistic tendencies of artificial and natural selection pressures. We summarize some of the robust conclusions. In cases where natural selection is expressed only through the phenotype and acts in the opposite direction to the culling incline, then fixation of the dominant or recessive type can be achieved and which occurs depends critically on the initial composition of the population and the magnitude of the degree of culling compared to the selection coefficients.With traits determined at two loci in the case that the double heterozygote is the desired kind, the effect of selfing can only be overcome by very strong artificial selection pressures (high culling order). The degree of culling to achieve its objective can be relaxed with weakening of linkage. The relevant comparison is r ₂ + (1 – r)₂ < (1 – c)indicating the precise extent of culling needed, to prevent fixation. The relationships are more complex when natural selection forces are also involved (see Model IV).Supported in part by NIH Grant USPHS 10452-09.     

A proposal to improve the efficiency of index selection by “rounding”

Summary This paper describes a rounding procedure to improve the efficiency of index selection. The procedure involves performing canonical variate analysis on the phenotypic and genotypic variances of a group of traits estimated from a progeny test experiment. The eigenvectors corresponding to the significant eigenvalues are used to transform the original traits into a set of independent variables. The selection index is then constructed based on the new set of variables. The efficiency of the new index is expected to be improved by rounding off the variables associated with the insignificant eigenvalues.     

Associations between the breeding values of Holstein-Friesian bulls and longevity and culling reasons of their daughters

Taking into account functional traits in the breeding practice should lead to a longer productive life of cows. However, despite the increased contribution of these traits in bull selection indices, their daughters are frequently culled as early as the 2nd or 3rd lactation. The problem is whether and to what extent the genetic potential of animals is realized in the production practice. Therefore, the purpose of this study was to determine the associations between the breeding value (BV) of bulls and their daughters for cow longevity and culling reasons in the Holstein-Friesian cattle population in Poland. Data for 532 062 cows culled in 2012, 2015, and 2018 were analyzed. A majority of 5 045 cow sires originated from Poland, Germany, France, the Netherlands, and the United States. The highest variation in the contribution of culling reasons was for the cows culled at the age of 2–4 years. The contribution of the culling reasons, analyzed in relation to the cow culling age, remained similar and the only exception was culling because of old age, for which a significant increase was observed only for the culling age of at least 9 years (13.8%), which was reached by only 7.3% of the cows. The sires were characterized by generally high BV for conformation and reproductive traits. However, they had, at most, the average genetic potential for functional longevity. There were a number of beneficial associations found between the BV of bulls and the distribution of culling reasons in their daughters. For example, it concerns relations between the somatic cell score in milk and culling due to udder diseases and low milk yield, between the interval from calving to first insemination and low milk yield, between the protein yield and old age, or between the BV for certain conformation traits (size, udder) and cow culling due to age. In these cases, as the BV increased for a given trait, the contribution of the corresponding cow culling reason tended to decrease. Our study showed that it seems reasonable to consider Holstein-Friesian cows aged at least 9 years at culling to be long-living animals. This is primarily evidenced by the rapid increase in the culling due to old age in relation to younger cows. Nowadays the above age limit can be suggested as a criterion of longevity for Holstein-Friesian cows but the criterion should be updated to the relation genotype-environment-economy that tends to change over time.     

Predicting observed and latent responses to BLUP selection involving logistic variates

Multivariate BLUPs can be derived when data are a mixture of continuous traits and observed discrete traits controlled by logistic latent traits. Algorithms were developed for predicting discrete responses to BLUP selection, and latent responses when the selection process included additional culling on scores. These algorithms were Taylor expansions using well-known expressions such as the probabilities and the two first moments of the truncated multinormal distribution, after appropriate re-parametrizations. They were compared to very accurate quadrature integrations. The test examples were suggested by a situation found in chickens where selection can involve body weight and leg deformity described by two logistic latent variates. Quadratic Taylor expansions generally provided a good accuracy. Therefore, they could be recommended when quadrature methods are too demanding, e.g., for complex breeding schemes.     

Genetic improvement of production while maintaining fitness

Selection for production tends to decrease fitness, in particular, major components such as reproductive performance. Under an infinitesimal genetic model restricted index selection can maintain reproductive performance while improving production. However, reproductive traits are thought to be controlled by a finite number of recessive alleles at low frequency. Culling for low reproduction may weed out the negative homozygous genotypes for reproduction in any generation, thus controlling the frequencies of alleles negative for reproduction. Restricted index selection, culling for low reproduction and a new method called empirical restricted index selection were compared for their efficiency in improving production while maintaining reproduction. Empirical restricted index selection selects animals that have on average the highest estimated breeding values for production and on average the same estimated breeding values for reproduction as the base population. An infinitesimal genetic model and models with a finite number of loci for reproduction with rare deleterious recessive alleles, which have additive, dominant or no pleiotropic effects on production, were considered. When reproduction was controlled by a finite number of loci with rare recessive alleles, restricted index selection could not maintain reproduction. The culling of 20% of the animals on reproduction maintained reproduction with all genetic models, except for the model where loci for reproduction had additive effects on production. Empirical restricted selection maintained reproduction with all models and yielded higher production responses than culling on reproduction, except when there were dominant pleiotropic effects on production.     

Variation in male sexual behavior

Relaxation of natural selection on sexual performance traits in male ruminants has increased phenotypic variation in these heritable traits. Thus, males with sub-standard sexual performance continue to reproduce. This has created a "dud" phenomenon that is costly to animal agriculture. Identification and culling of these lesser performers at an early age and identification of high performing males are critical management goals that must be addressed, and for which greater research priority is needed.     

The use of canonical analysis for selection within a population of spring barley

A selection method is described involving the application of canonical analysis to data for a number of measured traits in a composite population of spring barley grown in two seasons. Lines were selected which fell within the Euclidean space defined by the range, for a number of standard cultivars, on each significant canonical variate. Alternatively, limits were fixed for an acceptable range for each trait and transformed to canonical variates. Lines were selected which fell nearest to the centroid of this acceptable space. The method might be used as an alternative to the selection index method where difficulty is often encountered in assigning appropriate economic weightings to the traits measured.     

Optimising two-stage independent culling selection in tree and animal breeding

Summary Theory is given for a simple practical method of predicting gain from two-stage independent culling, where stage 1 of selection is for individual performance and stage 2 is for either progeny performance only, or an index combining individual and progeny performance. Expected gain is determined as a direct function of heritabilities, genetic correlations, selection intensities and progeny-testing capacity. Results show the effect these parameters can have on proportions selected at each stage and, if multiple selection criteria are used, traits selected for first. Methods are discussed in the context of tree and animal breeding, with an example taken from forestry.     

Viability selection on early body mass and the effect of female body size on fecundity: a study on the leaf-eared mouse <Emphasis Type="Italic">Phyllotis darwini</Emphasis>

Viability selection and fecundity of size-related traits has been demonstrated to be strong in vertebrates. In small mammals, both offspring and adult size are important for viability and fecundity, respectively. We studied the role of early phenotypic selection on size attributes and female fecundity in the leaf-eared mouse (Phyllotis darwini). Our results support that larger females produce more offspring, and since the likelihood of attaining adulthood is similar for different sizes of the females, those larger females also produce more offspring that attain sexual maturity. From the offspring perspective, larger pups at birth have significantly more probability of attaining sexual maturity. However, weaning mass and growth rate did not show any differential survival. Our study suggests that early selection could be important and could prevent further episodes of selection by early culling of the distribution of sizes, and that “effective” fecundity is strongly dependent on the size of the female.     

Converting multi-trait breeding objectives into operative selection indexes to ensure genetic gains in low-input sheep and goat breeding programmes

Small ruminant breeding programmes in low-input production systems are best organised at the community level. Participant farmers have to agree on goal traits and their relative importance. When BLUP breeding values of goal traits are not available in time, appropriate selection indexes can be used to aid visual selection. Taking Ethiopian Abergelle goat and Bonga sheep community-based breeding programmes (CBBPs) as an example, breeding objective functions were defined and selection indexes were constructed and evaluated. Breeding goals for Abergelle goats included early sale weight, survival and milk production. Breeding goals for Bonga included the number of offspring born, sale weight and survival. Economic weights of objective traits can be used in several ways depending on measured traits and the reliability of their genetic parameters. Selection indexes included combinations of objective traits measured on candidates and their dams and situations when Abergelle communities prefer to restrict genetic changes in number of offspring born or adult weight and when Bonga communities prefer to restrict changes in adult weight. Genetic and economic gains were evaluated as well as sensitivity to feed cost assumptions and to repeated dam records. After independent culling on preponderant traits such as coat colour and horn/tail type, sires in Abergelle goat community breeding programmes should be selected on indexes including at least own early live weight and their dams average milk production records. Sires for Bonga sheep programmes should be selected on own early live weight and desirably also on their dam’s number of offspring born. Sensitivity to feed cost assumptions was negligible but repeated measurements of dam records improved index accuracies considerably. Restricting genetic changes in number of offspring born or adult weight is not recommended.     

Phenotypic and genetic consequences of size selection at the larval stage in the Pacific oyster (Crassostrea gigas)

The life histories of oysters in the genus Crassostrea, like those of most marine bivalves, are typified by high fecundity and low survival in nature. Rearing conditions in hatcheries however ensure optimized density, diet, and temperature. Hatcheries are becoming increasingly important for the production of juveniles in aquaculture, and their culture practices often include culling of slow growing larvae to reduce and synchronize the time taken to reach settlement. Because previous studies have found substantial genetic variation for early life developmental traits in Crassostrea gigas, these culling practices are likely to cause highly different selective pressures in hatcheries from those in the natural environment. We studied the phenotypic and genetic impact of such culling practices in a factorial cross between 10 males and 3 females subjected to progressive culling of the smallest 50% of larvae, compared with a non-culled control. Measurements were made on larval growth, survival, time taken to attain pediveliger stage and settlement success. Culling had a larger effect on the variance of these larval traits than on their means. The larvae in culled cultures were approximately 10% larger than those in controls, whereas the coefficient of variation was reduced by 30-40%. Culling also reduced the mean time to settlement by 12% and its variance by 55%. Using a multiplexed set of microsatellite markers to trace parentage, we also estimated the variance in reproductive success in a controlled experiment to quantify the consequences of intensive hatchery rearing practices. We also focused on changes in effective population size and genetic structure over time (and developmental stages). Our results show a loss of genetic diversity following removal of the smallest larvae by culling, as well as temporally varying genetic structure of the larval population. This supports the existence of genetic variability in early life developmental traits in C. gigas. Culling in hatcheries, like size-related selective pressures in the wild, are likely to have a significant genetic impact, through their effects on the timing of settlement.     

Correlated responses on litter size traits and survival traits after two-stage selection for ovulation rate and litter size in rabbits

Farmer profit depends on the number of slaughter rabbits. The improvement of litter size (LS) at birth by two-stage selection for ovulation rate (OR) and LS could modify survival rate from birth to slaughter. This study was aiming to estimate direct and correlated response on LS traits and peri- and postnatal survival traits in the OR_LS rabbit line selected first only for OR (first period) and then for OR and LS using independent culling levels (second period). The studied traits were OR, LS measured as number of total born, number of kits born alive (NBA) and dead (NBD), and number of kits at weaning (NW) and young rabbits at slaughter (NS). Prenatal survival (LS/OR) and survival at birth (NBA/LS), at weaning (NW/NBA) and at slaughter (NS/NW) were also studied. Data were analysed using Bayesian inference methods. Heritability for LS traits were low, 0.07 for NBA, NW and NS. Survival traits had low values of heritability 0.07, 0.03 and 0.03 for NBA/LS, NW/NBA and NS/NW, respectively. After six generations of selection by OR (first period), a small increase in NBD and a slight decrease in NBA/LS were found. However, no correlated responses on NW/NBA and NS/NW were observed. After 11 generations of two-stage selection for OR and LS (second period), correlated responses on NBA, NW and NS were 0.12, 0.12 and 0.11 kits per generation, respectively, whereas no substantial modifications on NBA/LS, NW/NBA and NS/NW were found. In conclusion, two-stage selection improves the number of young rabbits at slaughter without modifying survival from birth to slaughter.     

Genetic Variance and Correlation after Selection for Two Traits by Index, Independent Culling Levels and Extreme Selection

Three two-trait selection methods were analyzed for their effects on genetic variance and correlation by multivariate methods, two-locus methods and computer simulation. The two-trait selection methods studied were independent culling levels (ICL), index (IND) and extreme (EXT) selection. The effects of the selection methods on genetic variance and correlation were partitioned into permanent effects due to changes in gene frequencies and temporary effects due to nonrandom association of alleles at different loci. Multivariate methods were used to predict temporary effects from a single generation of selection by each method and from several generations of index selection. Two-locus theory was used to determine the stability and rank of temporary effects on genetic correlation for all three methods. Predictions were compared to computer simulation results. When selection increased the means of both traits, EXT had the lowest (closest to -1.0) genetic correlation and highest variances, while ICL tended to have the highest (closest to 1.0) genetic correlation. When selection increased the mean of one trait and decreased the mean of the other, EXT had the highest genetic variances and correlation, while ICL had the lowest genetic variances and correlation.     

A canonical correlation analysis of the association between carcass and ham traits in pigs used to produce dry-cured ham

The association between carcass and ham traits in a pig population used to produce dry-cured ham was studied using canonical correlation analysis. The carcass traits examined were hot carcass weight (HCW), backfat thickness (BT) and loin depth (LD), and the ham traits studied were gross ham weight (GHW), trimmed ham weight (THW), ham inner layer fat thickness (HIFT), ham outer layer fat thickness (HOFT), pH (pH) and the Göfo value. Carcass and ham traits are not independent. The canonical correlations (r) between the carcass and ham traits at 130 kg were 0.77, 0.24 and 0.20 for the first, second and third canonical pair, respectively, and were all significant (p < 0.01) by the Wilks test. The corresponding canonical correlations between the three canonical variate pairs for the carcass and ham traits at 160 kg were 0.88, 0.42 and 0.14, respectively (p < 0.05 for all, except the third). The correlations between the traits and their canonical variate showed an association among HCW, GHW and THW, and between BT and HOFT. These results indicate that carcass traits should be used to cull pigs that are not suitable for dry-cured ham production.     

Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12

Reproductive performance is a critical trait in dairy cattle. Poor reproductive performance leads to prolonged calving intervals, higher culling rates and extra expenses related to multiple inseminations, veterinary treatments and replacements. Genetic gain for improved reproduction through traditional selection is often slow because of low heritability and negative correlations with production traits. Detection of DNA markers associated with improved reproductive performance through genome-wide association studies could lead to genetic gain that is more balanced between fertility and production. Norwegian Red cattle are well suited for such studies, as very large numbers of detailed reproduction records are available. We conducted a genome-wide association study for non-return rate, fertility treatments and retained placenta using almost 1 million records on these traits and 17 343 genome-wide single-nucleotide polymorphisms. Genotyping costs were minimized by genotyping the sires of the cows recorded and by using daughter averages as phenotypes. The genotyped sires were assigned to either a discovery or a validation population. Associations were only considered to be validated if they were significant in both groups. Strong associations were found and validated on chromosomes 1, 5, 8, 9, 11 and 12. Several of these were highly supported by findings in other studies. The most important result was an association for non-return rate in heifers in a region of BTA12 where several associations for milk production traits have previously been found. Subsequent fine-mapping verified the presence of a quantitative trait loci (QTL) having opposing effects on non-return rate and milk production at 18 Mb. The other reproduction QTL did not have pleiotropic effects on milk production, and these are therefore of considerable interest for use in marker-assisted selection.     

Simultaneous selection for grain yield and protein percentage in backcross populations fromAvena sterilis ×A. sativa matings by using the independent culling levels procedure

Summary The method of independent culling levels was applied for simultaneous improvement in grain yield, protein percentage, and protein yield in a population of oat lines from the BC₀–BC₅ of the interspecific matingAvena sativa ×A. sterilis. Grain yield and protein percentage were subjected to selection with various combination of culling levels to give samples with 2% of the lines from the original population. — Intense selection for grain yield resulted in samples with high grain and protein yields but low protein percentage. Intense selection for protein percentage resulted in samples with high protein percentage but low grain and protein yields. The sample selected for protein yield only showed no significant difference from the recurrent parent for any trait. The recommended regime for improving protein percentage and grain and protein yields simultaneously was one that initially saved approximately 25–50% of the original population on the basis of protein percentage, and then provided intense selection for grain yield on the lines that remained. At least three backcrosses were necessary to obtain lines with high protein percentage and acceptable agronomic traits.Journal Paper No. J-11439 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, IA 50011. Project No. 2447