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.

BackgroundTo safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus.ResultsIn this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73 × Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database  (iPlant, http://data.maizecode.org/maize/qtl/syn10/). Moreover, in this population combined with the IBM Syn4 RIL population, we detected 135 QTLs for flowering time and plant height traits across the two populations. Eighteen known functional genes and twenty-five candidate genes for flowering time and plant height trait were fine-mapped into a 2.21–4.96 Mb interval. Map expansion and segregation distortion were also analyzed, and evidence for inadvertent selection of early flowering time in the process of mapping population development was observed. Furthermore, an updated integrated map with 1,151,856 high-quality SNPs, 2,916 traditional markers and 6,618 bin markers was constructed. The data were deposited into the iPlant Discovery Environment (DE), which provides a fundamental resource of genetic data for the maize genetic research community.ConclusionsOur findings provide basic essential genetic data for the maize genetic research community. An updated IBM Syn10 population and a reliable, verified high-quality SNP set between Mo17 and B73 will aid in future molecular breeding efforts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2242-5) contains supplementary material, which is available to authorized users.

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.

With rising energy demand and limited resources, the need for alternative energy production is increasing. Maize cobs have an advantageous composition for the production of biofuels such as cellulosic ethanol but are currently left unused on the fields after harvest. Furthermore, cobs contain a low concentration of nitrogen (<1%). Therefore, cob harvest will not deplete soil fertility. Consequently, maize cobs are a cheap and promising source for sustainable energy production. Yet with primary focus on grain yield, no or little effort has been spent to increase cob biomass yield in addition to grain yield. Both cob and grain yield are complex inherited traits affected by the environment. Breeding of dual-purpose maize varieties with simultaneously increased cob and grain yield requires a deeper understanding of factors influencing both cob and grain development. In this article, the available knowledge on the genetics of cob formation and current and future applications of maize cob utilization are discussed to evaluate the prospects for development of dual-purpose maize varieties.

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.