Abstract
Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.
Highlights
In flowering plants, double fertilization of the female gametophyte by the two sperm cells of a pollen grain produces the diploid embryo and the triploid endosperm enclosed within the maternal tissue of the integuments
MEDEA [MEA] was the first gene in plants where expression was observed to depend on the parental origin of the allele; only maternal MEA alleles operate at the MEA locus during early seed development [17]
We propose a new statistical strategy for integrating the concept of maternal-zygotic interactions into a mapping framework for the detection of imprinting QTLs
Summary
Double fertilization of the female gametophyte by the two sperm cells of a pollen grain produces the diploid embryo and the triploid endosperm enclosed within the maternal tissue of the integuments. A number of mutations were detected to be involved in integument development [7,8], and genes affecting embryo and endosperm pattern formation have been observed [9,10,11]. Some of these genes function by regulating the interactions and coordinations between different cell types within maternal-zygotic interfaces in the seed, but the relative contributions of the maternal and zygotic genomes and the nature of how these two types of genomes communicate to coordinate seed growth are poorly understood. Identification of all imprinted genes and their biological functions is far from complete, this can help to understand why parent-of-origin effects are essential for seed development and how they have evolved
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