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Published on: August 12, 2019
SNP Discovery for mapping alien introgressions in wheat.
Vijay K Tiwari, Shichen Wang, Sunish Sehgal
1Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA. bsgill@ksu.edu.
Researchers developed novel SNP markers from the Aegilops geniculata 5Mg chromosome arm to track alien DNA in wheat. This breakthrough aids in improving wheat by incorporating beneficial traits from wild relatives.
Area of Science:
- Plant genetics
- Crop improvement
- Genomics
Background:
- Monitoring alien DNA introgressions in crops is challenging due to limited genetic data from wild relatives.
- The tertiary gene pool of wheat offers valuable genetic diversity for stress resistance.
- Exploring the 5Mg short arm of Aegilops geniculata is key for developing molecular tools.
Purpose of the Study:
- To discover single nucleotide polymorphism (SNP) markers from the 5Mg short arm (5MgS) of Aegilops geniculata.
- To utilize these SNP markers for monitoring alien introgressions in wheat (Triticum aestivum L.).
Main Methods:
- Flow-sorting the 5MgS chromosome arm from Aegilops geniculata.
- DNA amplification and sequencing using Illumina Hiseq 2000.
- SNP discovery by comparing 5MgS sequences with wheat homoeologous group-5 assemblies.
- Validation of discovered SNPs using KASPar assay and Sanger sequencing.
Main Results:
- Discovered 2,178 unique, 5MgS-specific SNPs, with 84% validated.
- Validated SNPs successfully mapped to wheat chromosome 5Mg additions and introgressions.
- Identified specific 5MgS segments in translocation lines, including those conferring leaf and stripe rust resistance (Lr57 and Yr40).
Conclusions:
- The developed SNP discovery approach is broadly applicable for identifying species/genome-specific markers.
- A large number of SNP markers will enhance precise introgression and monitoring of alien segments in crop breeding.
- These markers will aid in mapping and cloning novel genes from wild crop relatives.
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