Panibe Jerome P, Wang Long, Lee Yi-Chen, Wang Chang-Sheng, Li Wen-Hsiung
Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan.
Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.
Bot Stud. 2022 Mar 26;63(1):9. doi: 10.1186/s40529-022-00336-x.
Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits.
Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response.
We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
台中本地1号（TN1）是引发绿色革命的首个半矮秆水稻品种。由于TN1是矮脚乌尖品种的直接后代，而矮脚乌尖是sd1半矮秆基因的来源，因此可以通过TN1来定义sd1基因。此外，TN1对稻瘟病敏感，但具有耐旱性。然而，与TN1这些特性相关的基因尚不清楚。我们的目的是鉴定和表征与这些性状相关的TN1基因。
将TN1的sd1与日本晴的sd1进行比对，我们发现了一个382 bp的缺失，其中包括一个移码突变。桑格测序验证了sd1中的这个缺失区域，我们提出了一个sd1基因模型，纠正了文献中的错误。我们还预测了TN1的稻瘟病抗性（R）基因。然后在TN1中寻找著名的抗性品种特特普（Tetep）中R基因的直系同源基因，Tetep通常用作培育新的抗稻瘟病品种的供体，如果存在这些基因，我们会寻找突变。TN1中不存在著名的R基因Pi54，这部分解释了为什么TN1比特特普更容易感染稻瘟病。我们还使用PosiGene软件扫描了TN1基因组，鉴定出11个被认为经历了正选择的基因。其中一些与抗旱性和应激反应有关。
我们重新定义了矮脚乌尖品种的直接后代TN1中sd1基因的缺失，并纠正了一些文献错误。此外，我们已经鉴定出抗稻瘟病基因和经历正选择的基因，包括表征TN1对稻瘟病易感性和非生物胁迫反应的基因。这些新发现增加了利用TN1培育新水稻品种的潜力。
