SelAction: Software to Predict Selection Response and Rate of Inbreeding in Livestock Breeding Programs

Breeding programmes for livestock require economic weights for traits that reflect the most profitable animal in a given production system, which affect the response in each trait after selection. The profitability of sheep production systems is affected by changes in pasture growth as well as grain, meat and wool prices between seasons and across years. Annual pasture growth varies between regions within Australia's Mediterranean climate zone from low growth with long periods of drought to high growth with shorter periods of drought. Therefore, the objective of this study was to assess whether breeding objectives need to be adapted for regions, depending on how reliable the pasture growth is across years. We modelled farms with Merino sheep bred for wool and meat in 10 regions in Western Australia. Across these 10 regions, mean annual pasture growth decreased, and the CV of annual pasture growth increased as pasture growth for regions became less reliable. We calculated economic values for nine traits, optimising management across 11 years, including variation for pasture growth and wool, meat and grain prices between and within years from 2002 to 2012. These economic values were used to calculate responses to selection for each trait for the 10 regions. We identified two potential breeding objectives, one for regions with low or high reliability and the other for regions with medium reliability of pasture growth. Breeding objectives for high or low pasture growth reliability had more emphasis on live weight traits and number of lambs weaned. Breeding objectives for medium reliability of pasture growth had more emphasis on decreasing fibre diameter. Relative economic weights for fleece weight did not change across the regions. Regions with low or high pasture reliability had similar breeding objectives and response to selection, because the relationship between the economic values and CV of pasture growth were not linear for live weight traits and the number of lambs weaned. This non-linearity was caused by differences in distribution of pasture growth between regions, particularly during summer and autumn, when ewes were pregnant, with increases in energy requirements affecting the value of lambs weaned. In addition, increasing live weight increased the intake capacity of sheep, which meant that more poor quality pasture could be consumed during summer and autumn, which had more value in regions with low and high pasture reliability. We concluded that breeding values for sheep production systems should be customised depending on the reliability of pasture growth between years.

Section: Economic Valuesmentioning

confidence: 99%

“…For all traits at all ages, ewes and sires were selected based on BLUP-estimated breeding value. Selection responses were predicted with a pseudo-BLUP selection index (Rutten et al, 2002).…”

Section: Economic Valuesmentioning

confidence: 99%

Breeding objectives for sheep should be customised depending on variation in pasture growth across years

Rose

Mulder

Thompson

et al. 2015

“…Therefore, breeding schemes should only be optimised with respect to genetic gain when the rate of inbreeding is restricted simultaneously. Modern software tools for the optimisation of breeding schemes predict selection response and the rate of inbreeding resulting from breeding programs (Rutten et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Population structure of the Trakehner Horse breed

Teegen

Edel

Thaller

2009

The objective of this study was to examine the population structure of the Trakehner Horse breed. A total of 13 793 pedigree records were used for analysing the active breeding population and their ancestors dating back to 1950. Ancestors that were born before 1950 were called as base animals. The average generation interval was calculated as 10.2 years. The effective population size (N e ) was estimated by the increase in average year-wise inbreeding coefficient and average coancestry, respectively. Two methods were applied to estimate the effective population size: 1. Numerator-relationship-matrix (NRM), which did not consider missing ancestries. 2. Uncertain-parentage-matrix (UPM), which considered a probabilistic correction for unknown ancestors. There were no major differences between these two methods with respect to the rate of increase in inbreeding although the global levels using the UPM method were observed to be higher. Estimates for the inbreeding coefficients and the average coancestries varied little between both methods. The estimates of the effective population size per generation based on the rate of inbreeding ranged from 169 (NRM) to 150 (UPM) and 158 (NRM) to 144 (UPM) calculated by the average coancestry. From the early 1990s onwards, a strong increase in the rate of inbreeding was observed. This may be due to an increasing variance of the family size of sires and may be interpreted as a consequence of the growing use of artificial insemination. Analysing coancestries within and between the centrally managed regional breeding societies in Germany further revealed the Trakehner horse breed to be a genetically fragmented population with a main partition corresponding to formerly divided East and West Germany. The average rate of gene contributions (Thoroughbred (xx), Arab Horse breed (ox)) to the defined actual breeding population was calculated to be 22.3% xx-genes and 11.7% ox-genes.

“…The selection response was predicted using the software SelAction (Rutten et al, 2002). Two scenarios were analysed: (i) a conventional breeding scenario where genetic progress is determined by progress made in a conventional breeding programme.…”

Section: Methodsmentioning

confidence: 99%

Breeding replacement gilts for organic pig herds

Leenhouwers¹,

Napel

Hanenberg³

et al. 2011

In this study, breeding structures and commercial sow lines were evaluated by economic and genetic simulation studies for their suitability to provide the Dutch organic pig sector with replacement gilts. Sow and litter performance from over 2000 crossbred sows from 2006 to 2007 were collected on 11 to 14 Dutch organic pig herds, respectively, and compared with conventional herds. Results showed that organic herds had lower farrowing rates (3.6% to 7.5%), more live born piglets per litter (0.4% to 1.2%) and higher preweaning mortality rates (7% to 13%) compared to conventional herds. These results were used to simulate economic performance of various combinations of breeding structures and sow lines under organic conditions, under the assumption of absence of genotype-environment interactions. Sow and litter performance data under organic conditions (total piglets born/litter, stillborn piglets/litter, mortality until weaning, lactation length, interval weaning-oestrus and sow culling rate) and the costprice calculation for the Dutch organic pig sector were used as input for the economic simulation studies. The expected genetic progress was simulated for three potential breeding structures of the organic sector: organic breeding herds producing F1 gilts (OrgBS), a flower breeding system (FlowerBS) and a two-line rotation breeding system (RotBS). In FlowerBS, an organic purebred sow line is bred, using on-farm gilt replacement. The OrgBS with a Yorkshire 3 Landrace cross had the highest margin per sow place (h779), followed by RotBS with Yorkshire 3 Landrace cross (h706) and FlowerBS with Yorkshire sow line (h677). In case that an organic purebred sow population of 5000 sows would be available, FlowerBS gave the highest genetic progress in terms of cost price reduction (h3.72/slaughter pig per generation), followed by RotBS and OrgBS (h3.60/slaughter pig per generation). For FlowerBS, additional costs will be involved for maintaining a dedicated breeding programme. In conclusion, OrgBS using conventional genetics is economically the most viable option for the organic pig sector. However, this structure has clear disadvantages in terms of risks with regard to disease transmission and market demand. FlowerBS using a dedicated purebred organic line will only be cost-effective if sow population size is sufficiently large. RotBS might be a viable alternative, especially in combination with artificial insemination (AI) boars that are ranked according to an organic selection index. Regardless of breeding structure, the Yorkshire sow line gave the highest prolificacy and the highest economic returns on organic herds.