Gene Identification and Validation Group, Genetic Design and Validation Unit, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.
Institute of Crop Science (ICropS), College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, Los Baños, Laguna, Philippines.
Sci Rep. 2021 Apr 26;11(1):8962. doi: 10.1038/s41598-021-88533-9.
Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a "genetic reservoir" for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
野生稻属（由 24 个物种组成，具有 11 种不同的基因组类型）的水稻近缘种对水稻（Oryza sativa）的品种改良做出了重大贡献。目前有超过 4000 份野生稻种可供利用，它们被视为进一步改良水稻的“遗传库”。DNA 标记是遗传分析和育种的重要工具。迄今为止，尚未建立野生稻种的全基因组标记集，这是有效利用野生种质资源的主要困难之一。在这里，我们通过对五个 AA 基因组物种中的四个水稻品种进行位置多重序列比对，开发了 541 个用于区分栽培种 O. sativa 和其他七个 AA 基因组物种等位基因的全基因组 InDel 标记。通过对来自八个 AA 基因组物种的 24 个（每个物种三个）的 24 个物种的 PCR-琼脂糖凝胶分析对新开发的标记进行了测试，以及两个代表品种（O. sativa subsp。indica cv。IR24 和 subsp。japonica cv。Nipponbare）。对 475 个标记进行了标记多态性验证。IR24 与每个物种（三个品种）之间的多态性标记数量从 338（与 O. rufipogon 相比）到 416（与 O. longistaminata 相比），与 Nipponbare 相比的数量从 179（与 O. glaberrima 相比）到 323（与 O. glumaepatula 相比）。这些标记集将有助于遗传研究和利用 AA 基因组野生稻种。
