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Rather, the alleles that we would expect to find are ones that stabilize or buffer the effects of the stressful environment on the plant. Hence, in the relatively hot climate of the pot experiment the plants flowered earlier, probably as an effect of the different environmental conditions, and thus the differences between them were seen to a lesser extent than in the field. Furthermore, under these hot conditions both genotypes flowered early, ruling out a drought-escape mechanism of one allele compared to the other.

Alternatively, the earlier flowering and elongated grain filling of the wild allele may in part underlie its improved productivity. Under WL conditions, HsDry2. Cuesta-Marcos et al. Both field trials and pot experiment showed that the wild allele had no advantage over the cultivated one in vegetative or TDM production; however, it showed superiority for reproductive traits PGY and HI.

Recently, loci regulating developmental characteristics were found to be co-located with flowering-time genes, including HvCEN Maurer et al. Maurer et al. This may lead to the identification of hitherto unknown pathways related to drought tolerance. Despite the similarity in reduced PGY for the early and late WL treatments, it was quite clear than the reduction was obtained via different pathways.

As expected, while spikes per plant was significantly reduced by early WL, in the late WL treatment it was not. Total GW i. As temperatures in the greenhouse were high throughout the entire season Supplementary Fig S6 , it is reasonable to assume that all plants were under mild heat stress. Therefore, the advantage in PGY for the wild allele that was obtained mainly under WW might also reflect heat resistance.

Whereas under the WW treatment the benefit of the wild allele on PGY may be attributed to higher GN, under both the early and late WL treatments the wild allele presented advantages in GW, ripening period, and reduced senescence rate.

This indicates the importance of this QTL for future breeding of barley. Comadran et al. S7 , Table S1. However, these non-synonymous and synonymous SNP variants, respectively, were not shared with plants of the HEB family carrying introgression from the wild at this position Supplementary Fig. Moreover, it may imply that there could be causal genes other than HvCEN itself, which is locked within this chromosomal region, as was shown recently Mascher et al.

Overall, the current study provides data from large-scale genome-wide association scanning to a finer-resolution scale, and sheds some more light on the promising HsDry2. This appears to be a rare case of a wild allele with direct beneficial effects on grain yield. Finer mapping of this locus should determine whether the causal gene for these multiple differences between the wild and cultivated alleles does indeed correspond to HvCEN , or whether a nearby previously overlooked gene or genes is responsible.

Table S2. Trait distributions and heritability values under WW and WL treatments. Table S3. Pairwise correlations between traits under WW and WL treatments in the field. KP and AM supplied the plant material and genotype data. The discussions and technical assistance of Prof.

Menachem Moshelion The Hebrew University were instrumental for setting up the high-content phenotyping system. We also thank Yehudit Posen for editing the manuscript. The authors declare that they have no conflict of interest. Hormonal and metabolic regulation of source—sink relations under salinity and drought: from plant survival to crop yield stability. Biotechnology Advances 32 , 12 — Google Scholar. Breeding for yield potential and stress adaptation in cereals.

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In: Ullrich SE , ed. Barley: production, improvement, and uses. Oxford, UK : Wiley-Blackwell. Google Preview. Half a century of studying genotype by environment interactions in plant breeding experiments. Crop Science 56 , — Wild barley: a source of genes for crop improvement in the 21st century? Journal of Experimental Botany 51 , 9 — Trends in Plant Science 19 , — Determinants of barley grain yield in a wide range of Mediterranean environments.

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European Journal of Agronomy 82 , — Tester M , Langridge P. Breeding technologies to increase crop production in a changing world. All p-values are derived using permutations of 10, regions of the same size from across the genome. For Europeans and Asians, the proportion of windows with extreme values was 8. This was done in order to include several upstream SNPs that have previously been shown to exhibit associations with nicotine dependence or cocaine dependence [ 17 ].

Of note, a recent genome-wide association study found that a SNP in this region, rs, was associated with reduced risk for nicotine dependence, measured using the Fagerstrom Test for Nicotine Dependence FTND [ 18 ]. These data suggest that these nicotine dependence-associated SNPs may be undergoing balancing selection or positive selection in these two populations.

Within each of these regions, we calculated the iHS score for all SNPs for which we could unambiguously determine the chimp ancestral allele. We then compared the number of SNPs within each region with iHS values above 2 or below -2, to the 10, equally sized permutated regions that were chosen at random.

As expected, the AFR population shows few extreme values only 3. The clustering of extreme iHS values in the genic areas of this region is consistent with what is known about large-scale positive selection at this locus in the EUR population and to a lesser extent in the ASN population [ 27 ]. This demonstrates the validity of this approach for identifying genes undergoing selection.

The summary statistics are given in Table 1. None of the three populations showed a proportion of extreme iHS values that was significantly different than predicted by permutation. In addition, none of the SNPs with extreme values included any of the SNPs previously found to be associated with nicotine dependence Table 2.

Summary statistics are shown in Table 1. By contrast, in the ASN population, there were few windows of extreme iHS scores and the overall proportion was not significantly different from the negative control. Several SNPs with extreme iHS values in these populations are contained within bins previously shown to be associated with either nicotine or cocaine dependence phenotypes [ 17 , 18 ].

While there are several extreme values in AFR in the middle of this gene cluster, these values do not overlap with known SNPs related to nicotine dependence in this region. All have positive values, indicating the presence of unusually long haplotypes containing the ancestral allele suggesting that the ancestral allele, which is associated with a greater risk of nicotine dependence is being favored by selection.

It contains rs and rs, two low frequency synonymous variants in CHRNB3 that have previously been reported to be associated with lower risk for nicotine dependence [ 10 ]. The dense clustering of extreme iHS values in AFR and EUR is rarely expected under a neutral model, and is consistent with the hypothesis of the action of recent selection. Thus, in both populations, the ancestral allele associated with increased risk for nicotine dependence and decreased risk for cocaine addiction is being favored.

As it seems unlikely that risk for nicotine dependence is the phenotype undergoing selection, and because nicotinic receptors are involved in memory and learning, we hypothesized that a phenotype related to memory or learning, such as attention, might be the phenotype being selected. These tests were designed to measure aspects of perceptual organization, processing speed and verbal comprehension, respectively [ 29 ].

These data suggest a modest association between genotype at these SNPs one measure of cognitive function. Interestingly, this SNP has an r 2 of 0.

Many studies have demonstrated that risk for nicotine addiction has a genetic component. We performed two tests of selection on chromosomal regions containing the genes encoding five nicotinic receptor subunits and each of these analyses indicate that selection likely occurred at the CHRNB3-A6 locus.

This can occur in either balancing selection or ongoing positive selection. This region fulfills the criteria for a sweep laid out by Voight and colleagues [ 30 ], i. Extreme values of iHS are unlikely under simple demographic models, and thus can indicate the action of an ongoing selective sweep. Despite the fact that none of the populations had significantly different p-values from the negative control in the chromosome 8 region, a few key SNPs did have extreme values.

The extreme positive iHS value in the window including rs indicates that the haplotype containing the ancestral allele is being positively selected. As the derived allele provides protection from nicotine addiction, this suggests that it is the allele that is associated with a greater risk of nicotine dependence that is being selected.

Since highly concentrated sources of nicotine were not present in the ancestral environment, it seems likely that this phenotype of nicotine dependence would have hitchhiked along with a more beneficial phenotype. One challenge with this region is that it is approximately 1,, bp away from the centromere of chromosome 8. This could be affecting the results by some unknown mechanism. Selective pressures in our ancestral environments were likely not on addiction, but rather on behaviors that were biologically rewarding i.

Given the role of nicotine in neurological function, it is possible that, in the case of nicotine addiction, the phenotype on which natural selection was working was related to enhancements in memory or cognition.

The addiction phenotype would have hitchhiked along because it acts through the same or related mechanisms. The addiction phenotype was likely not selected against in ancestral environments because the availability and opportunity for prolonged use of purified drugs was negligible.

This test is thought to largely measure processing speed, but also, to some extent, memory. Thus, our data are consistent with the possibility that improved performance on this particular cognitive test is modestly associated with a decreased risk for nicotine dependence and that alleles of SNPs in these regions have effects on a subset of cognitive pathways best captured here by the WAIS digit symbol test.

It is possible, however, that a function other than addiction or cognition is the true phenotype undergoing natural selection at these loci. Genetic studies of nicotine addiction have identified an inverse relationship between the risk for nicotine addiction and the risk for cocaine addiction. For instance, the minor allele of rs, a missense variant in CHRNA5 , increases risk for the development of nicotine dependence, and independently decreases risk for cocaine dependence [ 15 ]. However, caution must be used when interpreting this information, given that all drugs of addiction similarly affect the dopaminergic reward pathways.

Another alternative hypothesis is that the selective pressure at this locus was on social behavior. Cocaine addiction is characterized by a dampened reward response to social interaction, meaning that it inhibits the positive emotions that accompany social interaction or feelings of belonging. A recent study demonstrated that cocaine users process social gaze joint attention on an object differently than controls, resulting in a reduced activation of the reward system during social interactions [ 31 ].

Using fMRI, these authors showed that cocaine users had decreased activation of the medial orbitofrontal cortex, a region of the brain central for reward processing. Since nicotine sensitizes the animal to the effects of cocaine, which blunts the reward of social interactions, alleles that reduced the ability of nicotine to enhance the effects of cocaine would have undergone positive selection.

In this scenario, the nicotine and cocaine dependence phenotypes are not hitchhiking with memory or learning, but rather with phenotypes protecting against antisocial and therefore maladaptive behavior. The iHS analysis of this locus did not provide evidence for selection.

This could indicate that the selective pressure exerted on this locus is older that that seen for the CHRNB3-A6 locus and as such has allowed extended haplotypes to be broken down by recombination. Here we have used two statistical tests of selection and uncovered evidence of positive selection at the nicotinic receptors on chromosome 8 chromosome Multiple drug-related phenotypes are associated with SNPs in or near these loci, however for several reasons it is unlikely that these phenotypes are the direct targets of this selective pressure.

We have proposed two possible explanations 1 phenotypes related to memory and learning and 2 phenotypes related to social behavior. We were only able to discover a modest association with memory-related phenotypes, likely due to the small sample size. We also are as of yet unable to test this second hypothesis because we do not have data in our sample for a phenotype measuring sociality. However this work is the first to explicitly describe signs of natural selection acting on loci underlying substance dependence phenotypes.

These tests have different but complementary strengths. There are many variables that contribute to how far in the past a sweep can be detected, such as how extreme the sweep was in the first place.

Both the mutation rate and the recombination rate affect it as well and vary widely across the genome making generalizations difficult. By contrast, integrated haplotype score iHS functions best for detecting sweeps in progress with alleles at intermediate frequencies, mainly in the range of or after the separation of European, Asian and African populations, during the agricultural phase of human evolution.

We utilized Genomes data for these analyses. Extreme positive values can indicate either balancing selection or population subdivision, and extreme negative values can indicate positive selection or population growth [ 33 ]. If the same skew is detected across the genome, the effect is likely due to demography, whereas if the skew is localized to a few loci, selection is more likely to be occurring. They find the mean value for Africans is slightly negative Overall, the values range from approximately -2 to 2.

After an exploratory data analysis of window size, we used a sliding window size of bp, and window increments of bp for the analysis. These values were then superimposed onto graphs of the regions. It compares the rate of haplotype decay between haplotypes carrying either the ancestral or derived allele at a given site, referred to as the core SNP. Haplotypes whose core SNP is under selection will be unusually long compared to those evolving neutrally. Long haplotypes with derived alleles are indicated by negative iHS values and those with ancestral alleles are indicated by positive iHS values.

Under neutrality, extreme scores are distributed throughout the genome, however under selection, they are clustered across the selected region [ 30 ]. The haplotype decay is calculated until the extended haplotype homozygosity EHH reaches 0.

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