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"Blake, Tom"
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Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism
Sodium (Na
) accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor
showed that
-like gene was a major gene in the QTL for salt tolerance, named
. In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the
gene in salt tolerance in barley (
). A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS) was performed. Our results showed important SNPs that are correlated with salt tolerance that mapped to a region where
ion transporter located on chromosome four. Furthermore, sodium (Na
) and potassium (K
) content analysis revealed that tolerant lines accumulate more sodium in roots and leaf sheaths, than in the sensitive ones. In contrast, sodium concentration was reduced in leaf blades of the tolerant lines under salt stress. In the absence of NaCl, the concentration of Na
and K
were the same in the roots, leaf sheaths and leaf blades between the tolerant and the sensitive lines. In order to study the molecular mechanism behind that, alleles of the
gene from five tolerant and five sensitive barley lines were cloned and sequenced. Sequence analysis did not show the presence of any polymorphism that distinguishes between the tolerant and sensitive alleles. Our real-time RT-PCR experiments, showed that the expression of
gene in roots of the tolerant line was significantly induced after challenging the plants with salt stress. In contrast, in leaf sheaths the expression was decreased after salt treatment. In sensitive lines, there was no difference in the expression of
gene in leaf sheath under control and saline conditions, while a slight increase in the expression was observed in roots after salt treatment. These results provide stronger evidence that
gene in barley play a key role in withdrawing Na
from the xylem and therefore reducing its transport to leaves. Given all that, these data support the hypothesis that
gene is responsible for Na
unloading to the xylem and controlling its distribution in the shoots, which provide new insight into the understanding of this QTL for salinity tolerance in barley.
Journal Article
Violent ends : a novel in seventeen points of view
Relates how one boy--who had friends, enjoyed reading, playing saxophone in the band, and had never been in trouble before--became a monster capable of entering his high school with a loaded gun and firing on his classmates, as told from the viewpoints of several victims. Each perspective is written by a different writer of young adult fiction.
Book
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of these tocochromanol forms in barley, seven of which were within 2 cM of sequences homologous to cloned genes associated with tocochromanol production in barley and/or other plants. These associations confirmed a prior report based on bi-parental QTL mapping. This knowledge will aid future efforts to better understand the role of tocochromanols in barley, with specific reference to abiotic stress resistance. It will also be useful in developing barley varieties with higher tocochromanol concentrations, although at current recommended daily consumption amounts, barley would not be an effective sole source of vitamin E. However, it could be an important contributor in the context of whole grains in a balanced diet.
Journal Article
Population Structure and Linkage Disequilibrium in U.S. Barley Germplasm: Implications for Association Mapping
Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgare L.), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six-row and two-row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model-based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two-row spring, two six-row spring, and two six-row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long-range LD suggestive of admixture. Genetic distance (allele-sharing) between populations varied from 0.11 (six-row spring vs. six-row spring) to 0.45 (two-row spring vs. six-row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele-sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable.
Journal Article
Mapping of QTL associated with nitrogen storage and remobilization in barley (Hordeum vulgare L.) leaves
Nitrogen uptake and metabolism are central for vegetative and reproductive plant growth. This is reflected by the fact that nitrogen can be remobilized and reused within a plant, and this process is crucial for yield in most annual crops. A population of 146 recombinant inbred barley lines (F8 and F9 plants, grown in 2000 and 2001), derived from a cross between two varieties differing markedly in grain protein concentration, was used to compare the location of QTL associated with nitrogen uptake, storage and remobilization in flag leaves relative to QTL controlling developmental parameters and grain protein accumulation. Overlaps of support intervals for such QTL were found on several chromosomes, with chromosomes 3 and 6 being especially important. For QTL on these chromosomes, alleles associated with inefficient N remobilization were associated with depressed yield and higher levels of total or soluble organic nitrogen during grain filling and vice versa; therefore, genes directly involved in N recycling or genes regulating N recycling may be located on these chromosomes. Interestingly, the most prominent QTL for grain protein concentration (on chromosome 6) did not co‐localize with QTL for nitrogen remobilization. However, QTL peaks for nitrate and soluble organic nitrogen were detected at this locus for plants grown in 2001 (but not in 2000). For these, alleles associated with low grain protein concentration were associated with higher soluble nitrogen levels in leaves during grain filling; therefore, gene(s) found at this locus might influence the nitrogen sink strength of developing barley grains.
Journal Article
Estimation of the net energy value of barley for finishing beef steers
The objective of this study was to identify barley grain characteristics measured by laboratory procedures that could be used to predict barley energy content for finishing beef steers. Twenty-eight different barley genotypes were evaluated including 18 cultivars and 10 experimental lines. Laboratory analysis of barley samples included bulk density, particle size, N, ADF, starch, and ISDMD (in situ DM disappearance after 3 h of ruminal incubation). Animal performance data (BW, DMI, ADG, steer [NE.sub.m], and [NE.sub.g] requirements) were collected from 26 feedlot experiments conducted in Montana and Idaho during a 10-yr period and were used to estimate barley [NE.sub.m] and [NE.sub.g] content. A total of 80 experimental units were available with each experimental unit being a diet mean from an individual feedlot experiment. Fifty-eight of the 80 experimental units were randomly selected and used in the development data set and the remaining 22 experimental units were used in the validation data set. Forward, backward, and stepwise selection methods were used to identify variables to be included in regression equations for [NE.sub.m] using PROC REG of SAS. Barley samples in the model development data set represented a wide range in concentrations (DM basis): N (1.6% to 2.8%), ISDMD (25.7% to 58.7%), ADF (3.6% to 8.0%), starch (44.1% to 62.4%), particle size (1,100 to 2,814 [micro]m), and bulk density (50.8 to 69.4 kg/hL). The barley grain characteristics of particle size, ISDMD, starch, and ADF were the most important variables in six successful models ([R.sup.2] = 0.48 to 0.60; P = 0.001). The six prediction equations gave mean predicted values for [NE.sub.m] ranging from 1.99 to 2.05 Mcal/kg (average 2.04 Mcal/kg; 0.45% CV). The mean actual [NE.sub.m] values from animal performance trials ranged from 1.75 to 2.48 Mcal/kg (average 2.03 Mcal/kg; 6.5% CV). The mean bias or difference in predicted vs. actual values ranged from -0.001 to 0.005 Mcal/kg. Barley [NE.sub.g] values calculated from animal performance ranged from 1.13 to 1.78 Mcal/kg (average 1.39 Mcal/kg; 8.4% CV). Average predicted barley [NE.sub.m] and [NE.sub.g] were 0.02 and 0.01 Mcal/kg less, respectively, than the 2.06 Mcal/kg [NE.sub.m] and 1.40 Mcal/kg [NE.sub.g] reported by NRC. Barley NE can be predicted from simple laboratory procedures which will aid plant breeders developing new feed varieties and nutritionists formulating finishing rations for beef cattle. Key words: barley, beef cattle, energy, feed quality, feedlot performance
Journal Article
Mapping Genes Controlling Variation in Barley Grain Protein Concentration
Grain protein concentration is an important determinant of grain quality in many crops, including wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). While high grain protein percentage might be desirable in barley destined for monogastric feed, low grain protein concentration is desirable for malt and beer production. Low grain protein concentration is associated with increased levels of malt extract and reduced problems with beer chill haze. Molecular markers were used to map and characterize the genes responsible for low, stable grain protein concentration in a recombinant inbred line population developed from a cross between ‘Karl’ (CIho 15487), a low grain protein six‐rowed barley, and ‘Lewis’ (CIho 15856), a standard two‐rowed cultivar. Three major quantitative trait loci (QTL) were identified which impacted grain protein percentage. Two of these grain protein effects appeared to result from gene action impacting flowering date. This pleiotropic relationship may be the main reason agronomically acceptable, low protein cultivars have yet to be released.
Journal Article
Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare)
The least ambiguous genetic markers are those based on completely characterized DNA sequence polymorphisms. Unfortunately, assaying allele states by allele sequencing is slow and cumbersome. The most desirable type of genetic marker would be unambiguous, inexpensive to assay and would be assayable singly or in parallel with hundreds of other markers (multiplexable). In this report we sequenced alleles at 54 barley (Hordeum vulgare ssp. vulgare) loci, 38 of which contained single-nucleotide polymorphisms (SNPs). Many of these 38 loci contained multiple polymorphisms, and a total of 112 polymorphisms were scored in five barley genotypes. The polymorphism data set was analyzed both by using the individual mutations as cladistic characters and by reducing data for each locus to haplotypes. We compared the informativeness of these two approaches by consensus tree construction and bootstrap analysis. Both approaches provided similar results. Since some of the loci sequenced contained insertion/deletion events and multiple point mutations, we thought that these multiple-mutated loci might represent old alleles that predated the divergence of barley from H. spontaneum. We evaluated sequences from a sample of H. spontaneum accessions from the Eastern Mediterranean, and observed similar alleles present in both cultivated barley and H. spontaneum, suggesting either multiple domestication events or multiple transfers of genes between barley and its wild ancestor.
Journal Article
Genetic analysis of the function of major leaf proteases in barley (Hordeum vulgare L.) nitrogen remobilization
Most of the nitrogen harvested with the seeds of annual crops is remobilized and retranslocated within the plant between anthesis and plant death. While chloroplasts contain most of the reduced nitrogen present in photosynthetically active leaf cells, the (major) pathway(s) involved in the degradation of their proteins prior to the retranslocation of the resulting amino acids are unknown. In this study, a population of 146 recombinant inbred barley lines (RIL), derived from the cross between two varieties with a highly inheritable difference in grain protein concentration, was used to map quantitative trait loci (QTL) for leaf amino-, carboxy- and endopeptidase activities relative to previously determined QTL for grain protein, leaf N storage, and remobilization. The results strongly suggested that major endopeptidases, assayed at both acidic and slightly alkaline pH values (favouring vacuolar and extravacuolar enzymes, respectively) are not instrumental in leaf N remobilization or the control of grain protein accumulation. Similarly, QTL determined for aminopeptidases (relative to QTL for N remobilization) indicated no functional role for the enzyme(s) assayed in plant N recycling. By contrast, careful evaluation of QTL data suggested that one or several carboxypeptidase isoenzymes may be involved in this physiologically and economically important process. As these proteases (in contrast to aminopeptidases) have previously been localized in vacuoles, this result appears intriguing. These data, while shedding new light on an old problem, also indicate that the described approach may prove useful in evaluating the functional roles of additional (not assayed in this study) proteolytic systems in whole-plant nitrogen recycling.
Journal Article