Journal
MOLECULAR GENETICS AND GENOMICS
Volume 291, Issue 4, Pages 1783-1794Publisher
SPRINGER HEIDELBERG
DOI: 10.1007/s00438-016-1214-z
Keywords
Oryza sativa; Oryza brachyantha; Whole genome sequence (WGS); Cross-transferable co-dominant molecular markers; Simple sequence repeats (SSR); Sequence tagged microsatellite (STMS); Sequence tagged sites (STS); Cleaved amplified polymorphic sequence (CAPS); Monosomic alien addition line (MAAL); Relative gene enrichment index (RGEI)
Funding
- NRRI
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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 (similar to 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.
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