A fast Newton-Raphson based iterative algorithm for large scale optimal contribution selection.

Binyam S Dagnachew,Theo H E Meuwissen

doi:10.1186/s12711-016-0249-2

Abstract

BackgroundThe management of genetic variation in a breeding scheme relies very much on the control of the average relationship between selected parents. Optimum contribution selection is a method that seeks the optimum way to select for genetic improvement while controlling the rate of inbreeding.MethodsA novel iterative algorithm, Gencont2, for calculating optimum genetic contributions was developed. It was validated by comparing it with a previous program, Gencont, on three datasets that were obtained from practical breeding programs in three species (cattle, pig and sheep). The number of selection candidates was 2929, 3907 and 6875 for the pig, cattle and sheep datasets, respectively.ResultsIn most cases, both algorithms selected the same candidates and led to very similar results with respect to genetic gain for the cattle and pig datasets. In cases, where the number of animals to select varied, the contributions of the additional selected candidates ranged from 0.006 to 0.08 %. The correlations between assigned contributions were very close to 1 in all cases; however, the iterative algorithm decreased the computation time considerably by 90 to 93 % (13 to 22 times faster) compared to Gencont. For the sheep dataset, only results from the iterative algorithm are reported because Gencont could not handle a large number of selection candidates.ConclusionsThus, the new iterative algorithm provides an interesting alternative for the practical implementation of optimal contribution selection on a large scale in order to manage inbreeding and increase the sustainability of animal breeding programs.

Highlights

The management of genetic variation in a breeding scheme relies very much on the control of the average relationship between selected parents
The expected genetic gain decreased as the constraint became more stringent (Fig. 1)
These results are expected because as more severe restrictions are placed on future inbreeding, contributions from superior animals will decrease and more animals are selected in order to achieve the average relationship constraint

Summary

Introduction

The management of genetic variation in a breeding scheme relies very much on the control of the average relationship between selected parents. Optimum contribution selection is a method that seeks the optimum way to select for genetic improvement while controlling the rate of inbreeding. Advancements in genetic evaluation methods such as the use of best linear unbiased prediction (BLUP) have substantially increased response to selection in modern animal breeding programs. Selection programs are usually designed to optimize genetic gain with no or an implicit limitation on the rate of inbreeding (for example [1]). The main goal in breeding programs is to maximize genetic gain, management of inbreeding is vital for the sustainability of breeding schemes. The optimal balance between rate of inbreeding ( F) and genetic gain ( G) is a core problem in practical animal breeding. OC selection attempts to maximize genetic response for a given rate of inbreeding (i.e. as influenced by relationships among selection candidates) by considering the genetic contribution of candidates and using the numerator relationship matrix (A)

Methods

Results

Conclusion