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.
Highlights
Polyploidy plays an important role in plant evolution and could be an important source for plant breeders in future [1,2]
The distribution of DNA polymorphisms in neo-tetraploid rice/autotetraploid parents was analyzed across the twelve rice chromosomes, and the results indicated that total number of single nucleotide polymorphisms (SNPs) and insertion–deletion polymorphisms (InDels) on a chromosome were proportional to chromosome length (S8 Table and S9 Table)
The lower lane indicated the expression of reference gene in neo-tetraploid rice lines and autotetraploid parents. (B) and (C) represent differentially expressed ncRNA in neo-tetraploid rice compared to autotetraploid rice, (B): the differentially expressed ncRNA in neo-tetraploid rice lines compared to T44, (C): the differentially expressed ncRNA in neo-tetraploid rice lines compared to T45. (D) and (E) represent the differentially expressed genes in neo-tetraploid rice lines compared to autotetraploid rice. (D): the differentially expressed genes in neo-tetraploid rice lines compared to T44, (E): the differentially expressed genes in neo-tetraploid rice lines compared to T45
Summary
Polyploidy plays an important role in plant evolution and could be an important source for plant breeders in future [1,2]. Partial pollen sterility is one of the most important reasons for low fertility in autotetraploid rice, which caused by different factors, such as abnormal microtubule distribution pattern and chromosome behavior [16,17,18]. These abnormalities might be caused by the abrupt changes in the expression patterns of genes and miRNAs associated with meiosis [2, 19, 20]. Another study revealed that pollen sterility mechanism is very complex and sequence variation, differential levels of methylation and differentially expressed genes have a strong influence on the fertility of autotetraploid rice [21]. The results of this study may help to explain the molecular mechanism of high fertility in neo-tetraploid rice
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