Abstract
The ongoing deficit of fresh water resource in rice growing regions has made the selection of water-saving and drought-resistance rice (WDR) a crucial factor in developing sustainable cultivation. HuHan2B, a new japonica maintainer for WDR breeding, had the same yield potential as recurrent parent HanFengB but showed improved drought resistance in fields. We investigated the genomic content accumulation and candidate genes passed from parent to offspring using the genomic and transcriptomic approaches. The genomic constitution indicated that the genetic similarity was 84% between HuHan2B and HanFengB; additionally, 7,256 genes with specific alleles were inherited by HuHan2B from parents other than HanFengB. The differentially expressed genes (DEGs) under drought stress showed that biological function was significantly enriched for transcript regulation in HuHan2B, while the oxidation-reduction process was primarily enriched in HanFengB. Furthermore, 36 DEGs with specific inherited alleles in HuHan2B were almost involved in the regulatory network of TFs and target genes. These findings suggested that major-effect genes were congregated and transformed into offspring in manner of interacting network by breeding. Thus, exploiting the potential biological function of allelic-influencing DEGs would be of great importance for improving selection efficiency and the overall genetic gain of multiple complex traits.
Highlights
Breeding has been regarded as a reliable method for selecting excellent valuable agronomic traits for rice, and genetic materials from rice parents were convenient in studying the gene actions involved in drought stress response
We bred a new japonica maintainer HuHan2B for water-saving and drought-resistance rice (WDR) breeding, and its cytoplasmic male sterile (CMS) line Huhan 2A was hybridized with restorer line Xiangqing to breed a hybrid combination Hanyou 8, which was registered in China in 2010 and the extensive areas were increased to 12,000 hectares in 201517,18
For many transcription factor binding sites (TFBS) genes, drought response activity was reported for the induction of the adaptive processes in a drought environment. Among these genes in the network, we found that a protein synthesis related gene eRF1-1 (LOC_Os05g31020), a member of the eukaryotic release factor 1 family, was highly induced by drought stress
Summary
Breeding has been regarded as a reliable method for selecting excellent valuable agronomic traits for rice, and genetic materials from rice parents were convenient in studying the gene actions involved in drought stress response. We further detected candidate genes in combined with genomic and transcriptomic data and discovered they were congregated into the gene network to be transformed into offspring by breeding. Based on these findings, we presented a transcriptional regulation model of response to drought stress as determined by TFBS complexity. This research is essential and helpful for understanding the manner in which genetic variations of drought resistance traits are passed from parent to offspring following artificial selection by pedigree breeding
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