Abstract
Genomic imprinting is an epigenetic phenomenon, which plays important roles in the growth and development of animals and plants. Immortalized F2 (imF2) populations generated by random cross between recombinant inbred (RI) or doubled haploid (DH) lines have been proved to have significant advantages for mapping imprinted quantitative trait loci (iQTLs), and statistical methods for this purpose have been proposed. In this paper, we propose a special type of imF2 population (R-imF2) for iQTL mapping, which is developed by random reciprocal cross between RI/DH lines. We also propose two modified iQTL mapping methods: two-step point mapping (PM-2) and two-step composite point mapping (CPM-2). Simulation studies indicated that: (i) R-imF2 cannot improve the results of iQTL mapping, but the experimental design can probably reduce the workload of population construction; (ii) PM-2 can increase the precision of estimating the position and effects of a single iQTL; and (iii) CPM-2 can precisely map not only iQTLs, but also non-imprinted QTLs. The modified experimental design and statistical methods will facilitate and promote the study of iQTL mapping.
Highlights
Genomic imprinting is a phenomenon found in animal and plant, in which two alleles of a gene show unequal expression depending on their parental origins
The advantages of imprinted QTL (iQTL) mapping based on Immortalized F2 (imF2) populations have been demonstrated before (Wen and Wu, 2014)
reciprocal-cross imF2 (R-imF2) is a special type of imF2 population
Summary
Genomic imprinting is a phenomenon found in animal and plant, in which two alleles of a gene show unequal expression depending on their parental origins. We demonstrate by simulation studies that the modified methods can map both iQTLs and non-imprinted QTLs (niQTLs) simultaneously as well as improve the accuracies of estimation of the positions and effects of iQTLs. In addition, the modified design can potentially reduce the workload in the construction of the imF2 population. A genomic region covered by a LOD1 peak exceeding the threshold is thought to harbor an iQTL and the highest point of the peak is the most probable position of the iQTL This is a one-step method (denoted as PM-1), in which an iQTL is mapped based on its imprinting effect only. The LOD1 significance threshold used in the second step can be estimated by permutation tests, but the tests are performed only on the mapped QTLs rather than on every marker in the genome. Even for type DIB, the former was still a little
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