Genotypes with better root development have good nutrient acquisition capacity and may yield better under limited nitrogen (N) conditions and consequently can help reduce the N fertilization rate and hence mitigate some economic and ecological problems. This study focused on the genotypic variation among diverse maize inbred lines for seedling and adult plant traits under contrasting N levels. Seventy four lines were screened under high and low N levels in a climate chamber and in the field. High phenotypic diversity was observed for seedling and adult plant traits together with moderate to high broad-sense heritability estimates. Seedling total root length and root dry weight were significantly correlated with other root traits in maize. Of the adult plant traits evaluated in the field, the anthesis-silking interval and the leaf chlorophyll contents were significantly correlated with grain yield under both low and high N levels. In one location, the seminal root length was correlated with grain yield both under low and high N levels and the root dry weight was correlated with grain yield under high N. Selection indices based on secondary root traits along with grain yield could lead to an increase in selection efficiency for grain yield under N stress condition. By identifying lines with better root development, particularly lines with longer SRL, it may be possible to select inbred lines with higher grain yield particularly under low N condition.

The aim of this study was to examine the extent of genotypic variability for root traits in a diverse set of maize inbred lines. Root traits were measured in maize lines grown up to 6, 10 and 14 days in the growth chamber on a germination paper. Combined analysis of variance revealed intermediate to high heritability values (range = 0.6-0.9) for all measured traits, indicating consistency across experiments. Euclidian distance value ranged from 1.8 to 19.6, indicating high levels of variability among the studied lines. First three principle components explained more than 80% of total genetic variation with high loadings from primary root parameters, seminal root parameters, total root length and root dry weight (DW). Root DW was significantly correlated with other root traits, indicating that direct selection based on root DW might be sufficient to improve other root traits. Some outstanding genotypes (PHT77, GEMN-0193, PHG35) with high relative growth rate at different time points were identified. These lines could be of potential use for the improvement of nutrient and water-use efficiency in maize.

Several genes involved in maize root development have been isolated. Identification of SNPs associated with root traits would enable the selection of maize lines with better root architecture that might help to improve N uptake, and consequently plant growth particularly under N deficient conditions. In the present study, an association study (AS) panel consisting of 74 maize inbred lines was screened for seedling root traits in 6, 10, and 14-day-old seedlings. Allele re-sequencing of candidate root genes Rtcl, Rth3, Rum1, and Rul1 was also carried out in the same AS panel lines. All four candidate genes displayed different levels of nucleotide diversity, haplotype diversity and linkage disequilibrium. Gene based association analyses were carried out between individual polymorphisms in candidate genes, and root traits measured in 6, 10, and 14-day-old maize seedlings. Association analyses revealed several polymorphisms within the Rtcl, Rth3, Rum1, and Rul1 genes associated with seedling root traits. Several nucleotide polymorphisms in Rtcl, Rth3, Rum1, and Rul1 were significantly (P<0.05) associated with seedling root traits in maize suggesting that all four tested genes are involved in the maize root development. Thus considerable allelic variation present in these root genes can be exploited for improving maize root characteristics.

Exploring and understanding the genetic basis of cob biomass in relation to grain yield under varying nitrogen management regimes will help breeders to develop dual-purpose maize. With rising energy demands and costs for fossil fuels, alternative energy from renewable sources such as maize cobs will become competitive. Maize cobs have beneficial characteristics for utilization as feedstock including compact tissue, high cellulose content, and low ash and nitrogen content. Nitrogen is quantitatively the most important nutrient for plant growth. However, the influence of nitrogen fertilization on maize cob production is unclear. In this study, quantitative trait loci (QTL) have been analyzed for cob morphological traits such as cob weight, volume, length, diameter and cob tissue density, and grain yield under normal and low nitrogen regimes. 213 doubled-haploid lines of the intermated B73 × Mo17 (IBM) Syn10 population have been resequenced for 8575 bins, based on SNP markers. A total of 138 QTL were found for six traits across six trials using composite interval mapping with ten cofactors and empirical comparison-wise thresholds (P = 0.001). Despite moderate to high repeatabilities across trials, few QTL were consistent across trials and overall levels of explained phenotypic variance were lower than expected some of the cob trait × trial combinations (R (2) = 7.3-43.1 %). Variation for cob traits was less affected by nitrogen conditions than by grain yield. Thus, the economics of cob usage under low nitrogen regimes is promising.

A better understanding of the genetic control of root development might allow one to develop lines with root systems with the potential to adapt to soils with limited nutrient availability. For this purpose, an association study (AS) panel consisting of 74 diverse set of inbred maize lines were screened for seedling root traits and adult plant root traits under two contrasting nitrogen (N) levels (low and high N). Allele re-sequencing of RTCL, RTH3, RUM1, and RUL1 genes related to root development was carried out for AS panel lines. Association analysis was carried out between individual polymorphisms, and both seedling and adult plant traits, while controlling for spurious associations due to population structure and kinship relations. Based on the SNPs identified in RTCL, RTH3, RUM1, and RUL1, lines within the AS panel were grouped into 16, 9, 22, and 7 haplotypes, respectively. Association analysis revealed several polymorphisms within root genes putatively associated with the variability in seedling root and adult plant traits development under contrasting N levels. The highest number of significantly associated SNPs with seedling root traits were found in RTCL (19 SNPs) followed by RUM1 (4 SNPs) and in case of RTH3 and RUL1, two and three SNPs, respectively, were significantly associated with root traits. RTCL and RTH3 were also found to be associated with grain yield. Thus considerable allelic diversity is present within the candidate genes studied and can be utilized to develop functional markers that allow identification of maize lines with improved root architecture and yield under N stress conditions.