Combined detection and introgression of QTL in outbred populations

M Hossein Yazdi,John A Woolliams,Anna K Sonesson,Theodorus He Meuwissen

doi:10.1186/1297-9686-42-16

Abstract

BackgroundDetecting a QTL is only the first step in genetic improvement programs. When a QTL with desirable characteristics is found, e.g. in a wild or unimproved population, it may be interesting to introgress the detected QTL into the commercial population. One approach to shorten the time needed for introgression is to combine both QTL identification and introgression, into a single step. This combines the strengths of fine mapping and backcrossing and paves the way for introgression of desirable but unknown QTL into recipient animal and plant lines.MethodsThe method consisting in combining QTL mapping and gene introgression has been extended from inbred to outbred populations in which QTL allele frequencies vary both in recipient and donor lines in different scenarios and for which polygenic effects are included in order to model background genes. The effectiveness of the combined QTL detection and introgression procedure was evaluated by simulation through four backcross generations.ResultsThe allele substitution effect is underestimated when the favourable QTL allele is not fixed in the donor line. This underestimation is proportional to the frequency differences of the favourable QTL allele between the lines. In most scenarios, the estimates of the QTL location are unbiased and accurate. The retained donor chromosome segment and linkage drag are similar to expected values from other published studies.ConclusionsIn general, our results show that it is possible to combine QTL detection and introgression even in outbred species. Separating QTL mapping and introgression processes is often thought to be longer and more costly. However, using a combined process saves at least one generation. With respect to the linkage drag and obligatory drag, the results of the combined detection and introgression scheme are very similar to those of traditional introgression schemes.

Highlights

Detecting a QTL is only the first step in genetic improvement programs
Positions at the chromosome's centre and ends were avoided respectively because QTL mapping methods can show a bias towards the centre of the considered segment [7] and because an end location would result in truncated likelihood peaks which are unsatisfactory for assessing the procedures proposed
Heterozygous individuals for which the favourable QTL allele originated from the donor line, Qdqr, are informative in the sense that they contribute to the accuracy of the QTL mapping as formulated

Summary

Introduction

Detecting a QTL is only the first step in genetic improvement programs. When a QTL with desirable characteristics is found, e.g. in a wild or unimproved population, it may be interesting to introgress the detected QTL into the commercial population. One approach to shorten the time needed for introgression is to combine both QTL identification and introgression, into a single step. This combines the strengths of fine mapping and backcrossing and paves the way for introgression of desirable but unknown QTL into recipient animal and plant lines. In QTL mapping designs such as those using F2 or backcross animals, the power to detect QTL is based on the assumptions that all genes affecting the trait of interest are biallelic with alternative alleles fixed in each parental inbred line and that there is no genetic variation within the line. The effectiveness of this method was investigated through computer simulation considering two outbred lines, in which QTL alleles were segregating and polygenic effects were included

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Conclusion