Optimum breeding strategies using genomic and phenotypic selection for the simultaneous improvement of two traits

Key message A breeding strategy combining genomic with one-stage phenotypic selection maximizes annual selection gain for net merit. Choice of the selection index strongly affects the selection gain expected in individual traits. Abstract Selection indices using genomic information have been proposed in crop-specific scenarios. Routine use of genomic selection (GS) for simultaneous improvement of multiple traits requires information about the impact of the available economic and logistic resources and genetic properties (variances, trait correlations, and prediction accuracies) of the breeding population on the expected selection gain. We extended the R package “selectiongain” from single trait to index selection to optimize and compare breeding strategies for simultaneous improvement of two traits. We focused on the expected annual selection gain (ΔGa) for traits differing in their genetic correlation, economic weights, variance components, and prediction accuracies of GS. For all scenarios considered, breeding strategy GSrapid (one-stage GS followed by one-stage phenotypic selection) achieved higher ΔGa than classical two-stage phenotypic selection, regardless of the index chosen to combine the two traits and the prediction accuracy of GS. The Smith–Hazel or base index delivered higher ΔGa for net merit and individual traits compared to selection by independent culling levels, whereas the restricted index led to lower ΔGa in net merit and divergent results for selection gain of individual traits. The differences among the indices depended strongly on the correlation of traits, their variance components, and economic weights, underpinning the importance of choosing the selection indices according to the goal of the breeding program. We demonstrate our theoretical derivations and extensions of the R package “selectiongain” with an example from hybrid wheat by designing indices to simultaneously improve grain yield and grain protein content or sedimentation volume.

Estimation of the economic efficiency of Lacaune sheep farms, based on theoretical bio-economic models

The aim of the present study was to develop theoretical bio-economic models of Lacaune sheep farms and establish their economic efficiency. Based on three main criteria, 15 options were considered and analyzed. Data were processed using the program EWSH2 as a part of ECOWEIGHT Package for calculating economic weights in livestock. Revenues from sales, variable costs, gross margin and profitability before and after subsidies and per ewe were calculated. It was found that raising sheep of the high productive Lacaune breed could generate profit and provide profitability for the studied models of farms, regardless of the level of selection, type of production system, flock size and even the amount of subsidies. Nucleus farms reported the largest gross margin, followed by the basic and commercial farms. Profitability without subsidies showed the highest values for the nucleus flocks of 1000 ewes – 24.24% when adopting semi-intensive production system and 23.14% for the intensive one. With the addition of subsidies, nucleus and basic farms of 1000 ewes were considered the most profitable with 40% and 37.37%, as for both options the semi-intensive conditions were preferable. A tendency for the values of the studied indicators to grow with the increase in the number of ewes in the flocks was observed, as only for the variable costs it was reversed. Due to the lack of studies on economic efficiency of Lacaune sheep farms in Bulgaria, an additional detailed research, based on real data, is advisable to be conducted.

Determination of relative economic weights of growth and egg production traits in Nigerian indigenous chicken

The relative economic weight (REW) of a trait is the additional gain/loss from a unit change in the trait relative to other traits in an individual. They are used to calculate aggregate economic values for purposes of genetic improvement in animals. The present study was designed to evaluate the bio-economic variables of growth and 16 weeks egg production parameters: egg number (EN16) egg weight (EWT16) body weight at first egg (BWTFE), body weight at 16 week of lay (BWTE16), cost of feed, and revenue from eggs and chicken carcass, 16 feed conversion ratio (FCR ), and body weight gain (BWG16) in the Nigerian indigenous chicken, and to determine the economic weights (EW) and REW of EN16, EWT16 and BWTE16 for G0, G1, and G2 generations. A total of 250 pullets (20 week old, point of lay) from a population of heavy body weight local chickens were used for the study. The birds were housed individually in cages, fed optimally on layers mash (G and G : 100g/bird/day; G : 0 1 2 125g/bird/day) and given water ad libitum. Data included EN , EWT , BWTE , BWTFE, 16 16 16 and prices of feed, eggs and spent hens, FCR , and BWG . Data on EN , EWT , BWTE , 16 16 16 16 16 and BWTFE were compared across generations using ANOVAand with other variables were used to generate the EW of the traits. The EW were then standardized relative to that of BWTE . Results showed that EW and REW of EN , EWT , and BWTE were 7.47 and 3.15, 16 16 16 16 13.67 and 5.77 and -2.37 and -1.00, respectively in G ; 13.07 and 3.82, 23.69 and 6.93, and - 0 3.42 and -1.00, respectively in G ; 16.80 and 2.89, 30.75 and 5.28 and -5.82 and -1.00, 1 respectively in G generation. Thus EN and EWT enhanced while BWTE depressed the 2 16 16 16 worth of the hen as a layer. EWT was more important than EN and both were more 16 16 important than BWTE economically. Therefore, EWT and EN are the major bio-economic 16 variables of the local hen as an egg chicken.

Asymptotic Genetic Response Due to Two-Stage Genomic Index Selection Derived from Correlated or Independent Indices during Both Stages

We developed equations to predict the asymptotic response due to two-stage selection, where first-stage selection was performed by using GEBVs based solely on genotypes and second-stage selection was performed with GEBVs that combined genotypes and phenotypes. The situation that we considered involved four-path selection executed as sires to breed sons, sires to breed daughters, dams to breed sons, and dams to breed daughters. We established two procedures to predict the response. The first incorporated correlated indices during the first and second-stage selections of two-stage selection. The other procedure used independent indices during two-stage selection. The response per generation in the initial generation was greater for the correlated indices than for the independent indices. However, the asymptotic response per generation was slightly greater for the independent indices than for the correlated indices. The asymptotic response per generation was lower during two-stage selection than during single-stage selection. However, the asymptotic response per year was greater for two-stage selection than for single-stage selection. In addition, that trend was more conspicuous when the economic weight was 1:3 for the first (h2 =0.3) to second (h2 =0.05) index trait compared with economic weights of 1:1 and 3:1. However, the magnitude of the response to the aggregate genotype-relative not to single-stage selection but to absolute magnitude was greater at an economic weight of 3:1 than at those of 1:1 and 1:3. The reduction in genetic variance from the initial to an asymptotic generation was greater for a scenario where young parents selected at the first-stage accounted for 30% of all parents in two-stage selection than where they accounted for 70%. The reduction in genetic variance of the aggregate genotype over generations was smaller for independent indices than correlated indices during two-stage selection. Our new formula for predicting genetic response applies to any combination of accuracies of GEBVs and intensities of selection. Therefore, the formula presented is a general equation for predicting genetic response over generations due to two-stage genomic index selection.

The efficiency of multi-generation selection on maternal traits, with implications for reindeer

Maternally affected traits, such as juvenile growth and survival, provide resilience in mammal species, in particular for reindeer living in extreme northern habitat. The genetic variation in such traits is caused by direct and maternal genetic effects (DGE and MGE, respectively). We used Willham’s variance-component approach and extended a family index with the focal individual and its full- and half-sibs to an approximated BLUP (pseudo-BLUP) by including the parents’ estimated breeding values. Most of the deviations of the predicted responses from the simulated ones were 4.1% for DGE and 5.3% for MGE. The benefits of index and BLUP selection are high in the case of negative correlation, large full-sib family and in particular, when maternal half-sibs are available. Higher economic value for MGE than for DGE is needed, since with equal heritabilities and economic weights for the effects the maternal response is 40 to 70% of the direct one. With negative correlation, records on collateral relatives beyond sibs are possibly needed. They would support also the prediction of MGE in uniparous reindeer lacking full-sib information.

Economic weights of current and new breeding objective traits in Aberdeen Angus

Breeding values estimated for growth, calving performance, and exterior traits are currently combined into simple selection indices for bulls, cows, and heifers of the Aberdeen Angus breed. To establish a comprehensive economic index for this breed, the absolute and relative economic weights (EW) for a complex of 16 production, functional, carcass, and feed efficiency traits were calculated. The absolute EW of a trait expressed the difference in the present values of profit that will be obtained from the descendants of a bull with the average breeding value for this trait, and descendants of a bull with the breeding value one unit higher than the average one. The relative EW of a trait was defined as the standardised EW of a trait (i.e. EW per genetic standard deviation) expressed as percentage of the sum of standardised EWs of all evaluated traits. Sensitivity analysis was conducted to explore the EW of traits under variable production and economic conditions. Variability in the marketing strategy, in product prices and costs, and in trait means was considered in this analysis. Relative EW of the feed efficiency of breeding heifers and of cows reached 4%. The highest relative EW was obtained in three growth traits: weight gains of calves from birth to 120, from 120 to 210, and from 210 to 365 days of age (66% combined). The survival rate of calves until weaning and cow productive lifetime reached 11% and 8% of the total economic importance of traits, respectively. These growth and functional traits accounted for 84% (in marketing strategy involving selling breeding animals) to 90% (in populations with high growth intensity) of the total economic weight of all 16 evaluated traits. Therefore, these traits should be considered as new selection criteria when constructing a comprehensive selection index for the Czech Aberdeen Angus population in future.

Selection indexes in the simultaneous increment of yield components in topcross hybrids of green maize

The objective of this work was to define the most suitable selective strategy for the simultaneous increment of yield components of green maize, by comparing three selection indexes weighted by economic weights and by the REML/BLUP method, in the assessment of predicted genetic gains for traits of interest. An experiment with 75 topcross hybrids from partially inbred S1 lines of green maize was carried out in Jataí, in the state of Goiás, Brazil, using a randomized complete block design, with four replicates. The following yield traits were evaluated: straw ears and commercial ears, grain mass, ear length, ear diameter, and number of ear rows. The selection indexes of Smith and Hazel, Williams, and Mulamba & Mock were applied and weighted for four economic weights (1, CVg, CVg/CVe, and h2). Among the tested selection indexes, those of Williams and Mulamba & Mock are the best-fit ones for the selection of topcross hybrids of green maize, as they provide positive and more balanced selection gains for all evaluated traits. The REML/BLUP method shows better predicted genetic gains than those achieved by the three selection indexes, besides being efficient for the selection of topcross hybrids of green maize.

The work of the Konrad-Adenauer-Stiftung (KAS) in Northeast Asia

Northeast Asia contains several geopolitical hot spots, which alone or in combination, have a high risk potential for regional and global security. The rising assertiveness of the PR China, shifting economic weights, the need for a comprehensive economic transformation in an age of digitalisation and demographic shifts - these challenges shape the future of all Northeast Asian nations.The Konrad-Adenauer-Stiftung (KAS), one of the largest political foundations of Germany, takes up these challenges not only with and within the respective societies, but also by developing platforms in the region and with Europe.The article describes key issues, the target groups, and the methodological approaches taken by KAS in each of the Northeast Asian countries. It shows the diversity of the approaches, and highlights the opportunities and limits for a German political foundation in the region.

Udder and Claw-Related Health Traits in Selection of Czech Holstein Cows

The aim of the study was to investigate the impact of the implementation of new health traits into the breeding objective and selection criteria for Czech Holstein cows on the genetic selection response in the breeding objective traits. Incidence of overall claw diseases was included into the current breeding objective for cows (11 traits together). Three traits that indicated claw health (incidence of claw diseases overall and infectious and non-infectious claw diseases) and incidence of clinical mastitis were successively added to the current selection criteria in a cow selection index (a maximum of 19 traits). Selection responses in the breeding objective traits were estimated by applying the general principles of the selection index theory. The required genetic variances for the new traits, the economic weights for all breeding objective traits and the genetic correlations among the selection index traits were estimated within this study. The marginal economic weights, which were calculated for two-year-old cows by applying a bioeconomic model with implemented gene flow, were -193 and -168 € per case for clinical mastitis and overall claw disease incidence, respectively. Using the comprehensive selection index with 19 traits, the reduction in the incidence of both udder and claw diseases was calculated to be 0.004 cases per cow per year. At the same time, a more favourable genetic selection response was obtained for other functional traits, e.g., +0.020% for cow conception rate and +0.010 years for productive life of cow (which represented the profit of 67 € and 367 € per herd and per year, respectively) when compared to the current index. Based on this study, a direct selection of cows for claw and udder health is nowadays recommended to improve the health status of herds and economics in production systems.