We demonstrate the application of agarose-based TILLING (Targeting Induced Local Lesions IN Genomes) for mapping and association studies. Using the agarose-based TILLING procedure we were able to detect SNPs in pools of 8 DNA templates and expand the window for SNP detection by analyzing large amplicons (~3 kb). Using mapping populations and pedigrees in breeding programs, we evaluated SNP polymorphism of candidate genes showing differential expression patterns during host-pathogen interaction. We applied this technique for mapping oxalate oxidase, a candidate defense gene in RILs obtained from parental rice lines Sanhuangzhan 2 (SHZ-2) (indica) and Lijiangxin-tuan-heigu (LTH) (japonica). Results suggested that mismatch detection offers a simple way to track specific genes in breeding pedigrees and segregating populations without upfront investment in sequencing.
Raghavan, C.; Liu, B.; Leach, J.E.; Nelson, R.J.; McNally, K.; Leung, H. Application of a simple SNP detection method for mapping and association studies. Presented at the Plant & Animal Genome XIV Conference, 14-18 January 2006, San Diego, CA, USA. (2006) 1 pp.