Prospects for marker assisted improvement of African tropical maize germplasm for low nitrogen tolerance

Abstract

Nitrogen (N) is one of the most yield limiting nutrients in maize. However, farmers in sub-Saharan Africa (SSA) use very little N due to low income. Nitrogen Use Efficient (NUE) varieties can provide a partial solution to the problem through efficient N uptake and utilisation. Designing an effective breeding strategy for improving any trait of interest requires knowledge of quantitative genetic parameters, genomic regions associated with the traits and the use of efficient selection methods. The objectives of this study were to 1) assess the efficiency of indirect selection for grain yield under low N stress conditions through grain yield under optimum N conditions and through secondary traits under low N conditions, 2) identify single nucleotide polymorphism (SNP) marker loci significantly associated with grain yield and secondary traits under low N and optimum conditions, 3) map and characterize the quantitative trait loci (QTL) for grain yield and some secondary traits under optimum and low N stressed conditions, and 4) evaluate the accuracy of genomic selection for improvement of grain yield and other secondary traits under optimum and low N stressed environments. Results showed that genetic variance for grain yield was highly affected by low N stress, more than secondary traits, and low correlation was observed between optimum and low N environments for grain yield. This lead to low relative efficiency of indirect selection for grain yield under low N using grain yield under optimum conditions. The efficiency of indirect selection for grain yield under low N through secondary traits under low N conditions was also low. The efficiency of selection could be enhanced through identification of genomic regions and associated markers linked with grain yield under low N. A total of 158 putative protein coding genes associated with significant SNPs, of which seven linked with four known genes, were identified through a genome-wide association study. Markers associated with the putative and known genes could be used for marker assisted selection (MAS) in NUE breeding. In addition, a total of 155 significant QTL were identified for grain yield and six secondary traits under optimum and low N stress conditions in five doubled haploid (DH) lines derived from bi-parental lines. Interestingly, for grain yield, plant height, ear height and leaf senescence, the highest number of QTL were found under low N stressed environments compared to optimum conditions, indicating the availability of QTL under low N. However, no common QTL between optimum and low N stressed conditions were identified for grain yield and anthesis silking interval. Lack of significant QTL for grain yield common across populations and between management conditions indicates that MAS cannot be an efficient method for selection of grain yield under both optimum and low N conditions. An alternative to MAS is genomic selection, which uses information from all markers. In this study, the magnitude of both genome-wide and phenotypic predictions was negatively affected by low N stress, and phenotypic prediction ability was always higher than genome-wide prediction ability for all traits under all N conditions. Low N stress had a larger effect on the prediction accuracy for grain yield than other secondary traits. In general, genomic selection that uses information from all markers is a promising method for the improvement of the selection efficiency for grain yield under low N.