Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines.

Genome wide association studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect, and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1,270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height, and resistance to three foliar diseases and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4-0.8) was relatively high. The 896 genotyped nNILs contain 2,638 introgressions, which span the entire genome with substantial overlap within and among allele donors. Genome wide association with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize nested association mapping population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions and could readily be used for future fine mapping studies.