Analysis of five near-isogenic lines (NILs) differing in tolerance of P deficiency was conducted using simple sequence repeat (SSR) markers. These NILs were segregating for a major QTL on chomosome 12, called Pup1, which explains about 80% of the phenotypic variance for P-deficiency tolerance. By analysing the graphical genotypes of the NILs, a relatively small chromosomal segment containing Pup1 was identified. SSR markers that were linked to the Pup1 locus were tested in a sample of accessions in order to determine whether these markers could be useful for marker-assisted selection. The four polymorphic markers identified could be useful for monitoring Pup1 introgression in breeding programs. Band sizes varied in other accessions including other potential P-deficiency tolerance donors and elite genotypes, which might suggest that markers need to be individually selected for a particular cross.
Collard, B.C.Y.; Thomson, M.; Penarubia, M.; Lu, X.; Heuer, S.; Wissuwa, M.; Mackill, D.J.; Ismail, A.M. SSR analysis of rice near isogenic lines (NILs) for P deficiency tolerance. SABRAO Journal of Breeding and Genetics (2006) 38 (2) 131-138.