<i>Aspergillus flavus</i> and <i>Fusarium verticilloides</i> cause contamination of maize (<i>Zea mays</i>) and concern to maize farmers because they reduce maize quantity and quality. These fungi produce mycotoxins, some of which are poisonous to both humans and animals. Over 300 mycotoxins are known but in this study aflatoxins and fumonisins produced by <i>A. flavus</i> and <i>F. verticilloides</i>, respectively, are reported due to their health concerns in Africa. Contamination of maize grain by these fungi occurs before harvest and selection of maize parental lines resistant to accumulation of aflatoxin, and fumonisin for breeding purposes is the easiest strategy to reduce consumption of maize grains contaminated by these toxins. In addition to selecting for resistant lines, breeders would prefer inbred lines with top performing agronomic traits. This study aimed at identifying possible source of resistance together with good agronomic traits among 23 maize inbred lines (13 sourced from the MAIZE Competitive Grants Initiative, International Maize and Wheat Improvement Centre and 10 from Agricultural Research Council, South Africa). The lines were planted in two blocks; <i>Aspergillus</i>, and <i>Fusarium</i>, in a randomized complete-block design for two seasons in one location in Kenya. Germination rate, days to silking, and days to anthesis were determined in each line. Inoculation of the maize ears was done at silking with three toxigenic strains of <i>A. flavus</i> for <i>Aspergillus</i> block, and <i>F. verticilloides</i> for <i>Fusarium</i> block. Aflatoxins and fumonisins concentration in the kernels was determined using Enzyme-linked immunosorbent assay (ELISA). A positive significant correlation (r = 0.9458846, P = < 9.845e-12) occurred between days to anthesis and days to silking, aflatoxins and fumonisins (r = 0.43149988, P ≤ 0.05) accumulated in the inbred lines. A negative correlation between germination and accumulated fumonisin levels (r = -0.5156961, P = 0.01178), days to pollen shed and aflatoxin (r = -0.4617732, P = 0.02654) was revealed. Apart from being good germinating lines and drought tolerant, CML 390 and CML 247 accumulated least fumonisin, and aflatoxin levels compared to the other germplasms. These two lines with consistent low aflatoxin, and fumonisin levels may, therefore be useful sources of resistance for maize breeding programs to reduce both aflatoxin and fumonisn contamination in maize. Four aflatoxin resistant lines (CB 222, CML 495 and CML 444) and one (CKL05003) fumonisin resistant line showed good agronomic traits. The lines may be suitable for breeding for resistance to aflatoxins, and fumonisins respectively in maize.
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