Background

Neo-tetraploid rice (NTR) is a useful new germplasm that developed from the descendants of the autotetraploid rice (ATR) hybrids. NTR showed improved fertility and yield potential, and produced high yield heterosis when crossed with indica ATR for commercial utilization. However, their classification, population structure and genomic feature remain elusive.

Results

Here, high-depth genome resequencing data of 15 NTRs and 18 ATRs, together with 38 publicly available data of diploid rice accessions, were analyzed to conduct classification, population structure and haplotype analyses. Five subpopulations were detected and NTRs were clustered into one independent group that was adjacent to japonica subspecies, which maybe the reason for high heterosis when NTRs crossed with indica ATRs. Haplotype patterns of 717 key genes that associated with yield and other agronomic traits were revealed in these NTRs. Moreover, a novel specific SNP variation was detected in the first exon of HSP101, a known heat-inducible gene, which was conserved in all NTRs but absent in ATRs, 3KRG and RiceVarMap2 databases. The novel allele was named as HSP101–1, which was confirmed to be a heat response factor by qRT-PCR, and knockout of HSP101–1 significantly decreased the thermotolerance capacity of NTR. Interestingly, HSP101–1 was also specifically expressed in the anthers of NTR at pre-meiotic and meiosis stages under optimal environment without heat stress, and its loss-of-function mutant showed significant decrease in fertility of NTR.

Conclusion

The construction of first genomic variation repository and the revelation of population structure provide invaluable information for optimizing the designs of tetraploid rice breeding. The detection of specific genomic variations offered useful genomic markers and new directions to resolve high fertility mechanism of NTR.

中文翻译：

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基因组学分析揭示新四倍体水稻的独特分类、种群结构和新等位基因

 背景

新四倍体水稻（NTR）是从同源四倍体水稻（ATR）杂交后代发展而来的一种有用的新种质。 NTR 与籼稻ATR 杂交用于商业利用时，表现出提高的育性和产量潜力，并产生高产杂种优势。然而，它们的分类、种群结构和基因组特征仍然难以捉摸。

 结果

在这里，对15个NTR和18个ATR的深度基因组重测序数据以及38个二倍体水稻种质的公开数据进行了分析，以进行分类、种群结构和单倍型分析。检测到5个亚群，NTRs聚集成一个与粳稻亚种相邻的独立群体，这可能是NTRs与籼稻ATRs杂交时杂种优势较高的原因。这些 NTR 揭示了与产量和其他农艺性状相关的 717 个关键基因的单倍型模式。此外，在HSP101 的第一个外显子中检测到一种新的特异性 SNP 变异，HSP101 是一种已知的热诱导基因，该基因在所有 NTR 中都是保守的，但在 ATR、3KRG 和 RiceVarMap2 数据库中不存在。该新等位基因被命名为HSP101-1 ，通过qRT-PCR证实其是热反应因子， HSP101-1的敲除显着降低了NTR的耐热能力。有趣的是，在无热胁迫的最佳环境下， HSP101-1也在减数分裂前和减数分裂阶段的NTR花药中特异性表达，其功能丧失突变体表现出NTR育性的显着下降。

 结论

第一个基因组变异库的构建和群体结构的揭示为优化四倍体水稻育种设计提供了宝贵的信息。特定基因组变异的检测为解决NTR的高育性机制提供了有用的基因组标记和新方向。