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The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression.

Baker K, Bayer M, Cook N, Dreißig S, Dhillon T, Russell J, Hedley PE, Morris J, Ramsay L, Colas I, Waugh R, Steffenson B, Milne I, Stephen G, Marshall D, Flavell AJ - Plant J. (2014)

Bottom Line: First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome.Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome.Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

View Article: PubMed Central - PubMed

Affiliation: University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK.

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Related in: MedlinePlus

Gene expression level and developmental specificity are independent of LR-PC region residency in barley.Expression parameters for barley genes (Y axes) are plotted against their linear order (X axes) on barley chromosome 1H. The continuous LR-PCH is shaded grey.(a) Average RNA levels (arbitrary units), taken across 15 tissue types and developmental stages (Druka et al., 2006).(b) Developmental and/or tissue specificity quotients (= data from (a) divided by their corresponding standard deviations).
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fig02: Gene expression level and developmental specificity are independent of LR-PC region residency in barley.Expression parameters for barley genes (Y axes) are plotted against their linear order (X axes) on barley chromosome 1H. The continuous LR-PCH is shaded grey.(a) Average RNA levels (arbitrary units), taken across 15 tissue types and developmental stages (Druka et al., 2006).(b) Developmental and/or tissue specificity quotients (= data from (a) divided by their corresponding standard deviations).

Mentions: The LR-PC region has been considered a repressive environment and gene expression has reported to be reduced in the LR-PC region of maize and soybean (Du et al., 2012; Gent et al., 2012). We therefore explored mRNA expression across the barley genome. Steady-state mRNA levels in 15 tissue types, covering a variety of developmental stages of cv. Morex (Druka et al., 2006), were plotted against corresponding pseudo-physical map positions (IBGSC, 2012). Averaged RNA values across all tissue types are shown for chromosome 1H as an example in Figure 2(a) and detailed expression data are in Figure S4. No difference in RNA level was observed between the genes of the LR-PC region and those from the HR region, either by chromosome or by tissue type (anova, P > 0.05).


The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression.

Baker K, Bayer M, Cook N, Dreißig S, Dhillon T, Russell J, Hedley PE, Morris J, Ramsay L, Colas I, Waugh R, Steffenson B, Milne I, Stephen G, Marshall D, Flavell AJ - Plant J. (2014)

Gene expression level and developmental specificity are independent of LR-PC region residency in barley.Expression parameters for barley genes (Y axes) are plotted against their linear order (X axes) on barley chromosome 1H. The continuous LR-PCH is shaded grey.(a) Average RNA levels (arbitrary units), taken across 15 tissue types and developmental stages (Druka et al., 2006).(b) Developmental and/or tissue specificity quotients (= data from (a) divided by their corresponding standard deviations).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4309411&req=5

fig02: Gene expression level and developmental specificity are independent of LR-PC region residency in barley.Expression parameters for barley genes (Y axes) are plotted against their linear order (X axes) on barley chromosome 1H. The continuous LR-PCH is shaded grey.(a) Average RNA levels (arbitrary units), taken across 15 tissue types and developmental stages (Druka et al., 2006).(b) Developmental and/or tissue specificity quotients (= data from (a) divided by their corresponding standard deviations).
Mentions: The LR-PC region has been considered a repressive environment and gene expression has reported to be reduced in the LR-PC region of maize and soybean (Du et al., 2012; Gent et al., 2012). We therefore explored mRNA expression across the barley genome. Steady-state mRNA levels in 15 tissue types, covering a variety of developmental stages of cv. Morex (Druka et al., 2006), were plotted against corresponding pseudo-physical map positions (IBGSC, 2012). Averaged RNA values across all tissue types are shown for chromosome 1H as an example in Figure 2(a) and detailed expression data are in Figure S4. No difference in RNA level was observed between the genes of the LR-PC region and those from the HR region, either by chromosome or by tissue type (anova, P > 0.05).

Bottom Line: First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome.Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome.Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

View Article: PubMed Central - PubMed

Affiliation: University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK.

Show MeSH
Related in: MedlinePlus