The results of previous studies conducted at the University of Hohenheim and the International Center for Agricultural Research in the Dry Areas (ICARDA) indicated that the yielding ability and stability of barley (Hordeum vulgare L.) could be improved in environments with drought stress by increasing the level of heterozygosity. This would require increasing the outbreeding rate of locally adapted breeding materials. As a first step, we estimated the outcrossing rate of 12 barley landraces (Hordeum vulgare ssp. vulgare, in short H. vulgare) and 13 sympatrically occurring populations of its wild progenitor [Hordeum vulgare ssp. spontaneum (C. Koch), in short H. spontaneum] collected from semi-arid localities in Jordan during the 1999/2000 growing season. In each H. vulgare or H. spontaneum population 28-48 spikes were sampled, and up to six offspring (seeds) per spike (called a family) were used for PCR analyses. Collection sites covered high-low transects for rainfall and altitude in order to detect possible environmental effects on the outcrossing rate. Four microsatellite markers located on different chromosomes were used to genotype the samples for estimating the outcrossing rate. Low season-specific multilocus outcrossing rates (tm) were found in both cultivated and wild barley, ranging among populations from 0-1.8% with a mean of 0.34%. Outcrossing rates based on inbreeding equilibrium (te), indicating outcrossing averaged across years, were two- to threefold higher than the season-specific estimates. Under high rainfall conditions somewhat higher--though not significantly higher--outcrossing rates were observed in H. spontaneum than in H. vulgare. The season-specific outcrossing rate in H. spontaneum was positively correlated (r = 0.67, P = 0.01) with average annual precipitation and negatively correlated (r = 0.59, P = 0.05) with monthly average temperature during flowering. The results suggest that outcrossing may vary considerably among seasons and that high precipitation and cool temperatures during flowering tend to enhance outcrossing. The rather low levels of outcrossing detected indicate that increased vigour due to heterozygosity has not been a major fitness advantage in the evolution and domestication of H. spontaneum and H. vulgare, respectively. Stable seed production to secure survival under extreme heat and drought stress may have been more important. Cleistogamy may be considered as an effective mechanism to warrant pollination even in drought-stunted plants with non-extruding spikes.

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.

Background Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits. Results A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1 , HvCry2 , HvCO4 and HvPRR73 . Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate. Conclusions This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley . Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation. Electronic supplementary material The online version of this article (10.1186/s12870-019-1828-5) contains supplementary material, which is available to authorized users.

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.