A similar pattern was observed in Feldman et al. 2017, in which the authors identified QTL on chromosome 2 at 96cM, 5 at 109cM, 7 at 99cM, and 9 at 127 cM which were associated with water use efficiency using the same A10 x B100 RIL population . Though the processes of water and ion uptake are independent, there is a strong relationship between the two; ion homeostasis depends upon transpiration rate, active transport, and membrane permeability, all of which are affected by the water status of the plant. As drought and density of planting are both variables that impact the available water supply, it appears that alteration in the water status of Setaria substantially perturbs the ionome.This additionally suggests that, while the ionome can be interrogated with individual ions, a multi-elemental approach is more likely to identify regions of the genome with weak signal, or those that evince pleiotropy.Rb is a striking example of this, with 13 of its 15 QTL identified via differential analysis. Combined with this trait’s high heritability within each experiment and low repeatability across experiments, these data suggest that there is a strong genotype by treatment component in Rb content in this RIL population. This genotype by treatment effect was apparent in many elements that were assayed, with an average of 74% of the ion specific QTL identified in the differential traits. The preponderance of differential QTL was not universal,vertical farm as within treatment mapping allowed for the identification of 50% or more of the QTL found for Mo and Sr, suggesting that the homeostasis of these elements experiences a smaller degree of environmental perturbation. Several QTL identified in this study overlie genes known to be associated with the control of elemental concentration. One example is Sevir.
G251200, the ortholog of MOT2 in A. thaliana. MOT1, a MOT2 paralog, is responsible for a large fraction of the variation in Mo content in A. thaliana . Although MOT1 has an ortholog in S. viridis on chromosome 9, it was not identified by any of the QTL in this study. This finding suggests that either 1) the RIL population contains allelic diversity in MOT2 that is not present at the chromosome 9 locus or 2) the MOT2 locus in Setaria is responsible for more of the variation in Mo content in this species. Additionally Sevir.5G106900, imputed from the A. thaliana gene ESB1, underlay 10 QTL, the majority of which were identified in the PC QTL mapping. ESB1 is involved in the production of the casparian strip, with mutants in A. thaliana developing increased suberin levels and disordered casparian strips, as well as altered levels of many ions. The identification of QTL in this region in both the DN13 and DR14 experiments and for several different treatments, as well as in the first principal component for both DN13 and DR14 suggests that the Setaria ESB1 ortholog plays a role in a variety of conditions related to water status. The B100 haplotype for this region produces a decrease in Mo as compared to the A10 allele, which is consistent with the relationship between the WT and the esb1 allele seen in A. thaliana. Given the central role played by the casparian strip in water homeostasis, this gene is a good candidate for explaining the coincidence of WUE and ionomic QTL. The translocation of the short arm of rye chromosome 1 from the cultivar Petkus into the long arm of wheat chromosome 1B confers improved tolerance to several abiotic and biotic stresses. Although several genes for resistance to biotic stresses are no longer effective, the1RS.1BL translocation is still widely used because of its beneficial effects on grain yield and improved abiotic stress tolerance . We have previously shown that the presence of a short segment of wheat 1BS chromosome from cultivar Pavon in the distal region of the 1RS translocation was associated with reduced grain yield, biomass, and canopy water status relative to near-isogenic lines carrying the complete 1RS chromosome arm . Carbon isotope discrimination data showed that the lines with the complete 1RS chromosome arm achieve higher yields and better water status through increased access to water throughout the season, rather than through water conservation . A subsequent field study showed that the improved water status of the isogenic lines with the 1RS chromosome was associated with enhanced root density below 20 cm relative to the lines with the 1RSRW chromosome .
Changes in root architecture in the field were correlated with drastic changes in root development in hydroponic growth systems, where the 1RSRW line showed a regulated arrest of the seminal root apical meristem ∼2 wk after germination. By the same time, the 1RSRW plants displayed altered gradients of reactive oxygen species in the root tips and emergence of lateral roots close to the RAM . In this study, we performed exome captures for 1RS, 1RSRW, and its parental lines T-9 and 1B+40 . We show that, as a result of a distal inversion between 1RS and 1BS chromosome arms, T-9 and 1B+40 have duplicated 1BS and 1RS orthologous regions in opposite orientations and that a crossover between these chromosomes resulted in a duplicated 1RS region colinear to the inserted 1BS segment in 1RSRW. Using these genetic stocks, we demonstrate that the dosage of the genes in the duplicated region plays an important role in the regulation of the seminal root growth. We also describe a radiation mutant with a deletion in the inserted 1BS segment and the adjacent 1RS region that restored long roots, confirming the importance of the dosage of the genes in this region on root development. Finally, we identified 38 genes within this deletion and used published RNA-sequencing data and annotation to discuss their potential as candidates for the genes regulating seminal root elongation in wheat.Previous field studies demonstrated that cultivar Hahn carrying the standard 1RS.1BL translocation had longer roots, better access to water, and significantly higher grain yields than isogenic Hahn lines carrying the 1RSRW chromosome . Hydroponic studies confirmed that 2 wk after germination, the roots in Hahn-1RSRW showed a significant reduction in the elongation rate, altered gradients of reactive oxygen species, and the emergence of lateral roots close to the RAM . This earlier reduction in root growth rates in 1RSRW relative to 1RS was also observed in this study, even in experiments that showed variable overall root growth responses . We initially assumed that the 4.8 Mb 1BS segment in the 1RSRW chromosome arm was the result of a homologous recombination event between the overlapping 1BS segments of lines T-9 and 1B+40 and that, therefore, the 1BS wheat genes have replaced the orthologous 1RS rye genes.Given the known positive effect of the 1RS translocation on drought tolerance in wheat, we hypothesized that the lost 1RS genes were the cause of shorter roots in 1RSRW. However, the exome capture sequencing of 1RS and 1RSRW demonstrated that both the 1BS and its orthologous 1RS segment were still present in 1RSRW, disproving our original hypothesis.
Our second hypothesis was that wheat genes present in the 4.8-Mb 1BS segment inserted in 1RSRW could be responsible for the shorter roots. However, the characterization of the Hahn-T-18 line,nft vertical farming which carries a 17-Mb distal 1BS segment and has no identifiable duplications, provided evidence against this hypothesis. The roots of T-18 were slightly longer than those in 1RS at the initiation of the measurements but showed no significant differences in their root growth rates after that day . When the 1BS segment was combined with the 1RS segment in the Hahn-T-21 and Hahn-1B+40, the roots were significantly longer than the roots of 1RSRW and slightly, but not significantly, shorter than the roots in the control 1RS line . Taken together, these results provided conclusive evidence that the presence of the wheat genes in the 1BS segment alone was not responsible for the short roots 1RSRW and disproved our second hypothesis. Our third, and still current, hypothesis, is that the change in gene dosage generated by the duplications of the 1BS and 1RS colinear regions was responsible for the arrest in the seminal root growth. The lack of differences in root growth rate between T-18 and 1RS between 9 and 28 d suggest that the genes in the 1BS segment are not responsible for the reduced growth rate in 1RSRW during the same period . The 1BS-1RS duplication in T-21 and 1B+40 resulted only in a minor decrease in growth rate relative to 1RS and their final root lengths were significantly longer than in 1RSRW . As T-21 tended to be shorter than 1B+40 in both experiments, we cannot rule out the possibility that their different proximal regions may contribute to modulate the effect of the 2R+2B duplication on root length. These results suggest that adding duplicated 1BS genes has a smaller effect on seminal root growth than adding more copies of the 1RS orthologues. The stronger effect of the 1RS segment was evident in plants heterozygous for the 1RSRW chromosome , which showed seminal root length intermediate to that of 1RS and 1RSRW . Based on this result, we hypothesize that the duplication of the 1RS region in 1RSRW is the main driver for shorter roots in this line, but we do not entirely discard the idea that the genes in the 1BS segment may also contribute to the reduced root growth when combined with additional 1RS orthologues. The dosage hypothesis was reinforced by the hydroponic experiments with the radiation-mutants 1RSWW-del-8 and 1RSWW-del-10 back crossed independently to both to Hahn- 1RSRW and Hahn-1RS. In the hydroponic experiments using the back cross lines segregating for the deletions and 1RSRW, the roots of the deletion lines were significantly longer than those of the sister lines carrying at least one 1RSRW chromosome .
By contrast, in the lines segregating for the deletions and the 1RS chromosome, we observed no significant differences in root length between the homozygous deletions and their sister lines carrying at least one 1RS chromosome . The four consecutive back crosses of 1RSWW-del-8 and 1RSWW-del-10 into 1RSRW and 1RS minimized the chances of a possibly confounding effect of independent deletionsin other chromosomes of the radiation mutants. However, they did not rule out the possibility of a confounding effect of a linked deletion in 1RS. Using the exome capture, we did find a linked missing 1RS region corresponding to the orthologous rye region replaced by the proximal wheat segment in homozygotes for the 1RSWW chromosome. We have previously shown that the proximal wheat segment has no effect on root length and confirmed this result in the hydroponic experiments presented in this study . The exome capture data also allowed us to determine the length of the 1RS deleted segment in the deletion lines and to establish that the 1BS and 1RS deletions include mostly orthologous genes . Therefore, the homozygous 1RSWW-del-8 and 1RSWW-del-10 lines are expected to lose two gene copies in 1BS and two in 1RS, changing the gene dosage from 4R+2B to 2R. This hypothesis explains the identical seminal root size observed in the 1RS and the homozygous deletion lines . One limitation of the exome capture assays is that they are closed systems and some genes are not included, which resulted in annotated genes with no reads. We eliminated those genes for the analysis used to delimit the borders of the 1RS–1BS recombination events or of the duplicated 1RS region . This likely resulted in a slight overestimate of the size of the candidate gene regions and the number of potential candidate genes.Once we established conservative borders of the 1BS and 1RS deleted regions in 1RSRW-del-8/10, we considered all the annotated genes in these regions as candidates regardless of their presence in the exome capture. The 1RSAK58 genome is very close to the 1RS present in our lines, so it probably provides a good representation of the rye candidate gene region. However, the CS RefSeq 1.1 used as 1BS reference is not identical to the 1BS Pavon segment, and therefore, we cannot rule out the possibility of genes present in Pavon that are not present in the wheat reference.