State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
Sci Rep. 2017 Sep 4;7(1):10362. doi: 10.1038/s41598-017-10617-2.
In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
在这项研究中，利用 3000 份水稻基因组重测序数据（3K RGP）分析了水稻稻瘟病抗性（R）Pid3 位点的等位基因变异。在 3K 基因组中 2621 个 Pid3 纯合等位基因的 71 个核苷酸多态性位点的基础上，共鉴定出 40 种单倍型。由于提前终止突变，大多数粳稻品种的 Pid3 等位基因是假基因，而大多数籼稻品种的 Pid3 等位基因与功能单倍型 Hap_6 相同，其具有与先前报道的 Pid3 基因相似的抗性谱。通过对中国广泛种植的品种中的 Pid3 等位基因进行测序和 CAPS 标记分析，我们验证了 Hap_6 已广泛应用于中国籼稻的育种。因此，我们建议在水稻育种中利用 Pid3 位点时，应优先将功能 Pid3 等位基因导入粳稻品种，并将非 Hap_6 单倍型的功能等位基因导入籼稻品种，以增加遗传多样性。
