Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca.

Yaping Liu,Yushan Qiao,Hong Zhang,Xiaotong Jing,Jinsong Xiong

doi:10.3390/genes12030380

Abstract

Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.

Highlights

By analyzing the imprinting status of candidate conserved imprinted genes based on single nucleotide polymorphisms (SNPs) site variation ratios and parent-of-origin expression patterns, we found that five genes were conserved imprinted in strawberry endosperm
Four candidate genes similar to conserved imprinted genes of A. thaliana, rice, and sorghum were obtained from F. vesca, namely, FvVIP2, FvKHDP-2, FvDRIP2, and FvBRO1
FvTAR4 genes are all expressed in the embryos of the hybrid combinations 18-86 × 10-41 and 10-41 × 18-86, and base variation ratio at the SNP site is close to the expected value of 1:1

Summary

Introduction

Genomic imprinting is a phenomenon in which paternal and maternal alleles are differentially expressed in the offspring depending on their parental origin [1]. Based on their parent-of-origin manner, imprinted genes are divided into two groups, maternally expressed genes (MEGs) and paternally expressed genes (PEGs). The endosperm and embryo of flowering plants are both derived from a double fertilization event: the egg cell (1n) and central cell (2n) fuse with two sperm cells (1n) to form the diploid embryo (2n) and the triploid endosperm (3n), composed of two maternal and one paternal genome copy, respectively [8,9,10]

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Results

Conclusion