QTL mapping with near-isogenic lines in maize

A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0–15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists.