Analysis of Alternative Pure-breeding Structures for Sheep in Smallholder and Pastoral Production Circumstances in the Tropics

The key issue in this study was to technically compare, through stochastic simulation, different breeding programmes that vary in the level of interaction between breeders and producers. The breeding structures considered were: (i) a single closed nucleus providing seed-stock to village flocks, (ii) a group of commercial flocks running a co-operative (‘ram circle’) breeding programme with no nucleus, (iii) an interactive two-tier open nucleus breeding scheme, comprising a nucleus and a commercial tier - the best males are used within the nucleus while the remainder migrate to the commercial flocks, with no female migration, and (iv) as scheme iii but with female migration between tiers. For the latter two schemes, 100% of the nucleus animals are distributed over village flocks every 3 years. The nucleus is then replaced by a new batch of selected males and females from the village flocks obtained through ‘interactive cycling screening’, based on ‘picking the best phenotype’ in the commercial flocks. Single trait selection was considered, and based on estimated breeding value, using either best linear unbiased prediction (BLUP) or the individual’s phenotype as a deviation from contemporaries in the same flock, year and season. The results showed that genetic merit increased slightly and inbreeding decreased significantly with increase in nucleus size. For instance, with BLUP selection and trait measurement on both sexes, and first record established at year 2, a nucleus size of 100 dams with 50 dams mated to each sire resulted in genetic merit of 0.118 units and an average inbreeding coefficient of 0.119 while that with 500 dams gave a response of 0.134 with an average inbreeding coefficient of 0.037. Running one closed nucleus had a 6-24% advantage over a ‘ram circle’ in terms of genetic gain. Decreasing the dam to sire ratio was a simple way to avoid inbreeding in breeding schemes of small size, with very little compromise towards genetic gain or even an increase in the longer term. Relative to a two-tier nucleus (scheme i), cyclic screening of commercial animals for use in the nucleus gave an almost optimum genetic response, while the villagers acquired superior breeding stock in return as an incentive to participate in genetic improvement. Participation of farmers offers them a sense of ownership of the breeding programme, and is likely to make it more sustainable in the long-term. This study provides insight into the advantages and disadvantages of designed breeding structures, especially the ‘interactive cyclic’ breeding schemes, which should be useful in deciding breeding programmes to adopt for sheep in developing countries in the tropics. Keywords: Sheep, Breeding Structures, Selection, Tropic

La Tomografia sismica in velocità, attenuazione e scattering e l'immagine della struttura dei vulcani.

a) A brief review of the results from travel time tomography at Mt. Vesuvius ed at Campi Flegrei. b) New approaches: (passive) attenuation and scattering tomography. c) Results obtained (passive attenuation and scattering) at Mt. Vesuvio and Campi Flegre

Sensitivity of the breeding values for growth rate and worm egg count to environmental worm burden in Australian Merino sheep

The objective of this study was to explore the sensitivity of breeding values for growth rate and worm egg count (WEC, cube root transformed) to environmental worm burden, measured as the average WEC for each contemporary group (CGWEC). Growth rate and WEC were measured on 7,818 naturally infected Merino lambs in eight flocks across Australia, linked through common use of AI sires. Through bivariate analysis, genetic correlations of 0.55 ± 0.23 and 0.30 ± 0.16 were found for growth rate and WEC between low and high CGWEC, respectively. In a second analysis, breeding values for growth rate and WEC were regressed on CGWEC with a random regression model. The heritability for growth rate varied from 0.23 to 0.16 from low to high CGWEC, and the heritability for WEC varied from 0.25 to 0.36. Results suggest that breeding values for both growth rate and WEC are sensitive to environmental worm burden. Animals expressed less genetic variation for growth rate and more genetic variation for WEC in high CGWEC than in low CGWEC. This form of genotype-by-environment interaction should therefore be considered in genetic evaluation of both growth rate and WEC, to increase the efficiency of selection for animals that are more parasite resistant and more resilient to environmental worm challenge.</p

Sensitivity of the breeding values for growth rate and worm egg count to environmental worm burden in Australian Merino sheep

The objective of this study was to explore the sensitivity of breeding values for growth rate and worm egg count (WEC, cube root transformed) to environmental worm burden, measured as the average WEC for each contemporary group (CGWEC). Growth rate and WEC were measured on 7,818 naturally infected Merino lambs in eight flocks across Australia, linked through common use of AI sires. Through bivariate analysis, genetic correlations of 0.55 ± 0.23 and 0.30 ± 0.16 were found for growth rate and WEC between low and high CGWEC, respectively. In a second analysis, breeding values for growth rate and WEC were regressed on CGWEC with a random regression model. The heritability for growth rate varied from 0.23 to 0.16 from low to high CGWEC, and the heritability for WEC varied from 0.25 to 0.36. Results suggest that breeding values for both growth rate and WEC are sensitive to environmental worm burden. Animals expressed less genetic variation for growth rate and more genetic variation for WEC in high CGWEC than in low CGWEC. This form of genotype-by-environment interaction should therefore be considered in genetic evaluation of both growth rate and WEC, to increase the efficiency of selection for animals that are more parasite resistant and more resilient to environmental worm challenge.</p

Supplemental Material for Mulder et al., 2019

This file contains additional figures

The Impact of Genomic and Traditional Selection on the Contribution of Mutational Variance to Long-Term Selection Response and Genetic Variance

De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection exploits mutational variance less than traditional selection methods such as mass selection or selection on pedigree-based breeding values, because DNM in selection candidates are not captured when the selection candidates' own phenotype is not used in genomic selection, DNM are not on SNP chips and DNM are not in linkage disequilibrium with the SNP on the chip. We tested this hypothesis with Monte Carlo simulation. From whole-genome sequence data, a subset of ∼300,000 variants was used that served as putative markers, quantitative trait loci or DNM. We simulated 20 generations with truncation selection based on breeding values from genomic best linear unbiased prediction without (GBLUP_no_OP) or with own phenotype (GBLUP_OP), pedigree-based BLUP without (BLUP_no_OP) or with own phenotype (BLUP_OP), or directly on phenotype. GBLUP_OP was the best strategy in exploiting mutational variance, while GBLUP_no_OP and BLUP_no_OP were the worst in exploiting mutational variance. The crucial element is that GBLUP_no_OP and BLUP_no_OP puts no selection pressure on DNM in selection candidates. Genetic variance decreased faster with GBLUP_no_OP and GBLUP_OP than with BLUP_no_OP, BLUP_OP or mass selection. The distribution of mutational effects, mutational variance, number of DNM per individual and nonadditivity had a large impact on mutational selection response and mutational genetic variance, but not on ranking of selection strategies. We advocate that more sustainable genomic selection strategies are required to optimize long-term selection response and to maintain genetic diversity.</p