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

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.

Comparative cytological and transcriptome analysis reveals high pollen fertility and upregulation of environmentally sensitive genic male sterility genes in neo-tetraploid rice

“…It is great demand to reveal the mechanism of its low pollen fertility and acquired the high pollen fertility tetraploid materials. After years of efforts, we successfully developed a new "autotetraploid rice lines" by selective breeding and crossing for successive generations (Guo et al 2017;Bei et al 2019; Ghaleb et al 2020). The new "autotetraploid rice" displayed high fertility (>80%) and high heterosis while crossed with other autotetraploid rice lines having low fertility (Guo et al 2017;Chen et al 2018;Bei et al 2019).…”

“…After years of efforts, we successfully developed a new "autotetraploid rice lines" by selective breeding and crossing for successive generations (Guo et al 2017;Bei et al 2019; Ghaleb et al 2020). The new "autotetraploid rice" displayed high fertility (>80%) and high heterosis while crossed with other autotetraploid rice lines having low fertility (Guo et al 2017;Chen et al 2018;Bei et al 2019). Moreover, F 2 and F 3 populations also displayed high fertility and stable morphological traits like neo-Arabidopsis (Yu et al 2009;Guo et al 2017;Bei et al 2019).…”

“…The new "autotetraploid rice" displayed high fertility (>80%) and high heterosis while crossed with other autotetraploid rice lines having low fertility (Guo et al 2017;Chen et al 2018;Bei et al 2019). Moreover, F 2 and F 3 populations also displayed high fertility and stable morphological traits like neo-Arabidopsis (Yu et al 2009;Guo et al 2017;Bei et al 2019). Notably, the new "autotetraploid rice" wasn't an allotetraploid rice; however, its chromosome behavior was nearly normal, which contributed to high fertility and harbors speci c DNA mutations that were different from autotetraploid rice (Yu et al 2020).…”

“…Neo-tetraploid rice is a created new tetraploid rice lines with normal fertility and is a key step to overcome the sterility of F 1 hybrids in tetraploid rice. Our group has reported three neo-tetraploid rice materials that could overcome the sterility of autotetraploid rice and produce high heterosis (Guo et al 2017;Chen et al 2018;Bei et al 2019). However, little is known regarding the complex regulatory mechanisms of heterosis and fertility in neotetraploid rice.…”

“…Extensive genome-wide studies using high-throughput technologies to identify SNPs and Indels have identi ed phenotypic variations and variation in gene expression and function in rice. In autotetraploid rice, very few studies have focused on the relationship between the genetic variations within the genome and pollen fertility (Guo et al 2017;Li et al 2018;Bei et al 2019).…”