Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

Enviromic Assembly Increases Accuracy and Reduces Costs of the Genomic Prediction for Yield Plasticity in Maize

Quantitative genetics states that phenotypic variation is a consequence of the interaction between genetic and environmental factors. Predictive breeding is based on this statement, and because of this, ways of modeling genetic effects are still evolving. At the same time, the same refinement must be used for processing environmental information. Here, we present an “enviromic assembly approach,” which includes using ecophysiology knowledge in shaping environmental relatedness into whole-genome predictions (GP) for plant breeding (referred to as enviromic-aided genomic prediction, E-GP). We propose that the quality of an environment is defined by the core of environmental typologies and their frequencies, which describe different zones of plant adaptation. From this, we derived markers of environmental similarity cost-effectively. Combined with the traditional additive and non-additive effects, this approach may better represent the putative phenotypic variation observed across diverse growing conditions (i.e., phenotypic plasticity). Then, we designed optimized multi-environment trials coupling genetic algorithms, enviromic assembly, and genomic kinships capable of providing in-silico realization of the genotype-environment combinations that must be phenotyped in the field. As proof of concept, we highlighted two E-GP applications: (1) managing the lack of phenotypic information in training accurate GP models across diverse environments and (2) guiding an early screening for yield plasticity exerting optimized phenotyping efforts. Our approach was tested using two tropical maize sets, two types of enviromics assembly, six experimental network sizes, and two types of optimized training set across environments. We observed that E-GP outperforms benchmark GP in all scenarios, especially when considering smaller training sets. The representativeness of genotype-environment combinations is more critical than the size of multi-environment trials (METs). The conventional genomic best-unbiased prediction (GBLUP) is inefficient in predicting the quality of a yet-to-be-seen environment, while enviromic assembly enabled it by increasing the accuracy of yield plasticity predictions. Furthermore, we discussed theoretical backgrounds underlying how intrinsic envirotype-phenotype covariances within the phenotypic records can impact the accuracy of GP. The E-GP is an efficient approach to better use environmental databases to deliver climate-smart solutions, reduce field costs, and anticipate future scenarios.

Validation and Application of a Low-Cost Sorting Device for Fumonisin Reduction in Maize

Fumonisin mycotoxins are a persistent challenge to human and livestock health in tropical and sub-tropical maize cropping systems, and more efficient methods are needed to reduce their presence in food systems. We constructed a novel, low-cost device for sorting grain, the “DropSort”, and tested its effectiveness on both plastic kernel models and fumonisin-contaminated maize. Sorting plastic kernels of known size and shape enabled us to optimize the sorting performance of the DropSort. The device sorted maize into three distinct fractions as measured by bulk density and 100-kernel weight. The level of fumonisin was lower in the heaviest fractions of maize compared to the unsorted samples. Based on correlations among fumonisin and bulk characteristics of each fraction, we found that light fraction 100-kernel weight could be an inexpensive proxy for unsorted fumonisin concentration. Single kernel analysis revealed significant relationships among kernel fumonisin content and physical characteristics that could prove useful for future sorting efforts. The availability of a low-cost device (materials~USD 300) that can be used to reduce fumonisin in maize could improve food safety in resource-limited contexts in which fumonisin contamination remains a pressing challenge.

Heterosis and Heterotic Grouping among Tropical Maize Germplasm

Maize (Zea mays L.) is the most important staple cereal cultivated in sub-Saharan Africa but its productivity is considerable low due to several factors. Development and deployment of maize hybrids have been reported as one of the crucial options in achieving sustainable maize production in sub-Saharan Africa. Information on the heterotic response among available genetic materials in a breeding program is valuable before commencement of any hybrid development program. Unlike the temperate germplasm, maize tropical germplasm is characterized with wide genetic base and genetic complexities and thus, proper organization of the pools, populations, varieties and inbreds that can serve as parental materials for hybrid development through identification of a distinct heterotic groups and patterns among tropical germplasm becomes very essential. This paper reviewed past research efforts at characterizing heterotic response among tropical maize genetic materials with a view to point out merits and demerits in the methods used and future direction towards achieving sustainable hybrid cultivation and enhancing food security in the sub-region.

Introgression of Temperate Material to Improve Grain Yield in a Tropical Maize Population

The effect of introgression of the temperate maize population BUGARD on the grain yield of a low-yielding tropical maize population well appreciated for the quality of its grains, NCP80, was studied. NCP80 was crossed with BUGARD to obtain the F1. The BC1 obtained by backcrossing the F1 to NCP80 was random mated thrice. The tropical parent NCP80 and the BC1 (NBN) were evaluated in two tropical locations using a randomized complete block design with three replications. Introgression of the temperate population BUGARD into the tropical population NCP80 significantly increased grain yield. The resulting population, NBN, appeared, moreover, significantly earlier than NCP80 and not significantly different from it for resistance to rust, tropical blight and maize streak, ear height, husk cover and harvest index. NBN may, further, be improved for resistance to maize streak and grain yield by recurrent selection.