Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice

Xuejun Bei; Muhammad Qasim Shahid; Jinwen Wu; Zhixiong Chen; Lan Wang; Xiangdong Liu

doi:10.1371/journal.pone.0214953

Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice

PLoS One. 2019 Apr 5;14(4):e0214953. doi: 10.1371/journal.pone.0214953. eCollection 2019.

Authors

Xuejun Bei^{1

2

3}, Muhammad Qasim Shahid^{1

2

3}, Jinwen Wu^{2

3}, Zhixiong Chen^{2

3}, Lan Wang^{2

3}, Xiangdong Liu^{1

2

3}

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
² Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
³ College of Agriculture, South China Agricultural University, Guangzhou, China.

Abstract

Autotetraploid rice is a useful germplasm for polyploid rice breeding, however, low seed setting is the major barrier in commercial utilization of autotetraploid rice. Our research group has developed neo-tetraploid rice lines, which have the characteristics of high fertility and heterosis when crossed with autotetraploid rice. In the present study, re-sequencing and RNA-seq were employed to detect global DNA variations and differentially expressed genes (DEGs) during meiosis stage in three neo-tetraploid rice lines compared to their parents, respectively. Here, a total of 4109881 SNPs and 640592 InDels were detected in neo-tetraploid lines compared to the reference genome, and 1805 specific presence/absence variations (PAVs) were detected in three lines. Approximately 12% and 0.5% of the total SNPs and InDels identified in three lines were located in genic regions, respectively. A total of 28 genes, harboring at least one of the large-effect SNP and/or InDel which affect the integrity of the encoded protein, were identified in the three lines. Together, 324 specific mutation genes, including 52 meiosis-related genes and 8 epigenetics-related genes were detected in neo-tetraploid rice compared to their parents. Of these 324 genes, five meiosis-related and three epigenetics-related genes displayed differential expressions during meiosis stage. Notably, 498 specific transcripts, 48 differentially expressed transposons and 245 differentially expressed ncRNAs were also detected in neo-tetraploid rice. Our results suggested that genomic structural reprogramming, DNA variations and differential expressions of some important meiosis and epigenetics related genes might be associated with high fertility in neo-tetraploid rice.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA, Plant* / genetics
DNA, Plant* / metabolism
Fertility / genetics
Gene Expression Profiling
Gene Expression Regulation, Plant*
High-Throughput Nucleotide Sequencing
Oryza* / genetics
Oryza* / metabolism
Tetraploidy*

Substances

DNA, Plant

Grants and funding

This work was supported by the NSFC to XD Liu (31571625), the Guangzhou Science and Technology Key Program to XD Liu (201707020015), the Guangdong Provincial Science and Technique Project Grant 2017A030303069 (to XD Liu), Science and Technology Innovation Program of Guangdong Higher Education of China to W L (2013KJCX0035). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.