Ray Soham, Bose Lotan K, Ray Joshitha, Ngangkham Umakanta, Katara Jawahar L, Samantaray Sanghamitra, Behera Lambodar, Anumalla Mahender, Singh Onkar N, Chen Meingsheng, Wing Rod A, Mohapatra Trilochan
National Rice Research Institute, Cuttack, 753006, Odisha, India.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
Mol Genet Genomics. 2016 Aug;291(4):1783-94. doi: 10.1007/s00438-016-1214-z. Epub 2016 Jun 14.
African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.
非洲野生稻短药野生稻（FF）是栽培稻亚洲栽培稻（AA）的远亲，携带着抗病虫害基因。由于缺乏可明确区分这两个物种的可交叉转移且具有多态性的分子标记，从该野生种向其驯化对应种进行分子标记辅助的外源基因渐渗受到很大阻碍。这两个物种全基因组序列（WGS）的可得性为开发可交叉转移的标记提供了独特机会。我们观察到亚洲栽培稻特异性序列标签微卫星（STMS）标记向短药野生稻的交叉转移能力较差（约0.75%）。通过利用基因组序列信息，我们开发了一组45个基于低成本PCR的共显性多态性标记（STS和CAPS）。这些标记在两个物种之间具有交叉转移性（84.78%），能够区分它们，从而可追踪外源基因组渐渗。最后，我们使用这些标记验证了一个在亚洲栽培稻背景下携带短药野生稻第1号染色体的单体异附加系（MAAL），作为概念验证。因此，在本研究中，我们鉴定出了一组能够检测从短药野生稻到亚洲栽培稻外源基因组渐渗的分子标记（包括STMS、STS和CAPS）。
