Genomewide association mapping of flowering time, kernel composition, and disease resistance in historical minnesota maize inbreds

Association mapping in maize (Zea mays L.) has been effective at identifying major quantitative trait loci (QTL) for less-complex traits, and historical inbreds are a potential source of useful variation. Our objectives were to (i) characterize genomewide linkage disequilibrium, (ii) assess variation for flowering time, kernel composition, and resistance to northern corn leaf blight (NCLB) (caused by Setosphaeria turcica) and Goss's wilt and blight (GWB) (caused by Clavibacter michiganensis subsp. nebraskensis), and (iii) identity major QTL for these traits in a collection of 284 historical maize inbreds mostly developed at the University of Minnesota. Linkage disequilibrium (LD) was high, decaying (r² = 0.1) in 802 kb, among 39,166 single nucleotide polymorphism (SNP) markers on the Illumina MaizeSNP50 Beadchip. The mean LD between adjacent markers was r2 = 0.38. The A321 subpopulation, to which 60% of the Minnesota inbreds belonged, had inbreds with either or both the minimum and maximum inbred mean value for all traits except protein concentration. We identified QTL for days to anthesis (eight QTL), days to silking (11 QTL), oil concentration (11 QTL), starch concentration (two QTL), NCLB (13 QTL), and GWB (nine QTL). The Minnesota inbreds were enriched for favorable QTL alleles for days to flowering and oil concentration but not for starch concentration and disease resistance. These QTL identified in historical maize inbreds may be useful in modern breeding programs.