Abstract
BackgroundIntrogression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome segments from an exotic donor in the genetic background of an elite line. The goal of our study was to investigate the detection of favorable donor chromosome segments in introgression lines with statistical methods developed for genome-wide prediction.ResultsComputer simulations showed that genome-wide prediction employing heteroscedastic marker variances had a greater power and a lower false positive rate compared with homoscedastic marker variances when the phenotypic difference between the donor and recipient lines was controlled by few genes. The simulations helped to interpret the analyses of glycosinolate and linolenic acid content in a rapeseed introgression population and plant height in a rye introgression population. These analyses support the superiority of genome-wide prediction approaches that use heteroscedastic marker variances.ConclusionsWe conclude that genome-wide prediction methods in combination with permutation tests can be employed for analysis of introgression populations. They are particularly useful when introgression lines carry several donor segments or when the donor segments of different introgression lines are overlapping.
Highlights
Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding
For introgression population 1 (Figure 1A) and the observation vector shown in Figure 1B, the least squares estimation (LSQ), best linear unbiased prediction (BLUP), and RMLV analyses estimated effects of similar size for all donor segments (Figure 1C)
The F-tests for the LSQ analysis as well as the permutation tests for the BLUP and RMLV analyses correctly detected the effect in the center of chromosome 1 as significant and all other donor effects as not significant (Type 1 error rate: 0.01)
Summary
Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome segments from an exotic donor in the genetic background of an elite line. That is significantly better than the recipient with respect to a certain trait, contains only one single donor chromosome segment, such an analysis is able to identify this segment as affecting the trait. The lines of an introgression populations typically carry more than one donor segment [5,15] For such introgression lines, the Dunnett test is not able to identify which of the donor segments affects the trait
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