Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense\xd7Tanacetum vulgare hybrid and allopolyploid (Asteraceae)

Xiangyu Qi,Jiafu Jiang,Aiping Song,Haibin Wang,Fadi Chen,Sumei Chen

doi:10.1038/s41438-017-0003-0

Xiangyu Qi, Jiafu Jiang + Show 4 more

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https://doi.org/10.1038/s41438-017-0003-0

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Journal: Horticulture Research	Publication Date: Feb 7, 2018
Citations: 18	License type: open-access

Affiliation: Nanjing Agricultural University

Abstract

Allopolyploid formation involves two major events: interspecific hybridization and polyploidization. A number of species in the Asteraceae family are polyploids because of frequent hybridization. The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported. In this study, we obtained allopolyploids by applying a colchicine treatment to a synthesized C. nankingense×T. vulgare hybrid. Sequence-related amplified polymorphism (SRAP), methylation-sensitive amplification polymorphism (MSAP), and high-throughput RNA sequencing (RNA-Seq) technologies were used to investigate the genomic, epigenetic, and transcriptomic alterations in both the hybrid and allopolyploids. The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments. The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization. There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent. Most differentially expressed genes (DEGs) showed down-regulation in the hybrid/allopolyploid relative to the parents. Among the non-additive genes, transgressive patterns appeared to be dominant, especially repression patterns. Maternal expression dominance was observed specifically for down-regulated genes. Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents. Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids. The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.

Highlights

Hybridization has contributed to the evolution of higher plants, and it is considered to be a potent evolutionary force driving genetic variation and functional novelty.[1,2,3] Hybridization occurs frequently in flowering plants and is considered a useful tool to aid in importing desirableQi et al Horticulture Research (2018)5:5Molecular markers, microarray data, and highthroughput RNA sequencing (RNA-Seq) have been used to study genomic and transcriptomic changes in allopolyploids[10,11,12,13,14]
The three allopolyploids were generated from a chromosomedoubled C. nankingense×T. vulgare hybrid, and they had similar phenotypes to one another
Chromosome number and phenotype analysis A series of allopolyploids were generated through colchicine treatment of a C. nankingense×T. vulgare hybrid

Summary

Introduction

Microarray data, and highthroughput RNA sequencing (RNA-Seq) have been used to study genomic and transcriptomic changes in allopolyploids[10,11,12,13,14]. To determine the adjustment of duplicated genes and genomes during the early stages of polyploidization, many studies have used artificially synthesized polyploid materials using molecular markers and RNA-Seq technologies[11,13,14,15]. Hybridization appears to be often accompanied by changes to genomic sequences, the epigenome, and the patterns of gene transcript levels[16,17,18]. Recent studies have indicated that allopolyploid formation is accompanied by extensive alterations in parental gene expression (“transcriptome shock”)[12,13,14,25], which is likely the result of interspecific hybridization rather than polyploidization[26]

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