Abstract
BackgroundNeo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive.ResultsTwo season’s field trials of 15 NTRs and 27 autotetraploid rice (ATR) lines revealed that the improvement of YPP (yield per plant, 4.45 g increase) were significantly associated with the increase of SS (seed setting, 29.44% increase), and yield and seed setting of NTRs improved significantly compared to parental lines. Whole genome resequencing of 13 NTR sister lines and their parents at about 48.63 depth were conducted and genome compositions were illustrated using inherited chromosomal blocks. Interestingly, 222 non-parental genes were detected between NTRs and their low fertility parental lines, which were conserved in 13 NTRs. These genes were overlapped with yield and fertility QTLs, and RNA-Seq analysis revealed that 81 of them were enriched in reproductive tissues. CRISPR/Cas9 gene knockout was conducted for 9 non-parental genes to validate their function. Knockout mutants showed on an average 25.63% and 4.88 g decrease in SS and YPP, respectively. Notably, some mutants showed interesting phenotypes, e.g., kin7l (kinesin motor gene) and kin14m (kinesin motor gene), bzr3 (BES1/BZR1 homolog) and nrfg4 (neo-tetraploid rice fertility related gene) exhibited 44.65%, 24.30%, 24.42% and 28.33% decrease in SS and 8.81 g, 4.71 g, 5.90 g, 6.22 g reduction in YPP, respectively.ConclusionComparative genomics provides insights into genome composition of neo-tetraploid rice and the genes associated with fertility and yield will play important role to reveal molecular mechanisms for the improvement of tetraploid rice.
Highlights
Neo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential
Production Assessment of Neo-Tetraploid Rice (NTR) Firstly, we evaluated yield and yield related traits in 15 neo-tetraploid rice (NTR) (Figure S1) and 27 autotetraploid rice (ATRs) lines, and the results showed that seed setting, yield per plant and grain numbers per panicle improved significantly in NTRs (Table S1a and b)
The correlation coefficient was ranged from − 0.26 to 0.82, and seed setting (SS) showed the highest correlation coefficient (0.82), which indicated that SS contributed greatly to improve the yield in NTRs (Fig. 1)
Summary
Neo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. Low fertility limited the yield performance of autotetraploid rice and its commercial utilization (Shahid et al 2010; He et al 2011; Shahid et al 2013; Wu et al 2014; Wu et al 2015; Li et al 2017; Chen et al 2018b; Li et al 2018; Ghouri et al 2019) To solve this issue, rice scientists had made unremitting efforts for many years, and bred some new autotetraploid rice lines with high fertility (Tu et al 2003; Luan et al 2007; Cai et al 2007; Guo et al 2016; Guo et al 2017). In contrast to autotetraploid and allotetraploid rice, neo-tetraploid rice (NTR) will play an important role in polyploid rice breeding because of high seed setting (> 70%), wide compatibility genes and stable fertility in generations, like neo-tetraploid Arabidopsis (Yu et al 2009; Guo and Liu 2014; Bei et al 2019; Chen et al 2019). The systematic investigation of yield improvement, and the detection of specific DNA variations of neo-tetraploid rice will be helpful to decipher the high yield mechanism and optimize the directions of tetraploid rice breeding
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