Background

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. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive.

Results

Two 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.

Conclusion

Comparative 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.

中文翻译：

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生产评估和基因组比较揭示了新四倍体水稻的高产潜力和与生育力和产量相关的新型特定等位基因。

背景

新四倍体水稻（NTR）是由不同同源四倍体水稻品系杂交和定向选育而成的新四倍体水稻种质，具有高育性和高产潜力。然而，系统的产量评估、基因组组成以及与生育力和产量相关的功能变异仍然难以捉摸。

结果

对15个NTR和27个同源四倍体水稻（ATR）品系进行两季田间试验表明，YPP（单株产量，增加4.45克）的提高与SS（结实率，增加29.44％）的增加以及产量和产量的增加显着相关。与亲本系相比，NTR 的结实率显着提高。对 13 个 NTR 姐妹系及其亲本进行了约 48.63 深度的全基因组重测序，并使用遗传染色体块说明了基因组组成。有趣的是，在 NTR 与其低育性亲本系之间检测到 222 个非亲本基因，这些基因在 13 个 NTR 中保守。这些基因与产量和育性 QTL 重叠，RNA-Seq 分析显示其中 81 个在生殖组织中富集。对9个非亲本基因进行CRISPR/Cas9基因敲除以验证其功能。敲除突变体的 SS 和 YPP 平均分别减少 25.63% 和 4.88 g。值得注意的是，一些突变体表现出有趣的表型，例如kin7l（驱动蛋白运动基因）和kin14m（驱动蛋白运动基因）、bzr3（BES1/BZR1同源物）和nrfg4（新四倍体水稻育性相关基因）表现出44.65%、24.30%、24.42 SS 减少 % 和 28.33%，YPP 分别减少 8.81 g、4.71 g、5.90 g、6.22 g。

结论

比较基因组学提供了对新四倍体水稻基因组组成的见解，与育性和产量相关的基因将在揭示四倍体水稻改良的分子机制中发挥重要作用。