The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.

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Dwarfism plays a key role in adapting crops to high-input production systems by contributing to improved lodging resistance and fertilizer efficiency. In sorghum [Sorghum bicolor (L.) Moench], four dwarfing mutations have been found that profoundly reduce the stalk height. Notable among these mutations is dwarf-3 {dw3), even though the phenotype it confers is unstable. The objectives of this research were to identify and characterize a stable mutant alíele of the dw3 locus. Polymerase chain reaction (PCR) was used to amplify a region of dw3 containing the 882 bp tandem duplication that is diagnostic for the unstable alíele. Analyses of PCR fragments from dwarf sorghum accessions that lacked the duplicated region led to the identification of Tx2737 as a possible carrier of a novel mutant dw3 alíele. Sequence analysis confirmed and revealed the presence of a 6 bp deletion in exon 5 of dw3 that eliminates two highly conserved amino acids, Q1275 and R1276, from the enzyme. The frequency of this alíele in sorghum germplasm appears to be very low with only 1% of the accessions in the diversity panel exhibiting this deletion. Field trials demonstrated that this alíele of dw3 produces a stable dwarf phenotype with no height mutants found in Tx2737 and KS19. The new alíele has been coined dw3-sd2. The discovery of dw3-sd2 and a DNA marker assay to facilitate selection will provide an opportunity to replace the unstable dw3 alíele currently used in most commercial sorghum hybrids through introgression of dw3-sd2 into elite parent lines.