Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation

Elena Potokina, Arnis Druka, Zewei Luo, Roger Wise, Robbie Waugh, Mike Kearsey

    Research output: Contribution to journalArticle

    122 Citations (Scopus)

    Abstract

    Transcript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profile individuals from a segregating population to accurately identify robust polymorphic molecular genetic markers. We applied the method to identify more than 2000 genetic polymorphisms (transcript derived markers, TDMs) from an experiment involving two commercial varieties of barley (Hordeum vulgare; Steptoe and Morex) and their doubled-haploid progeny. With this set of TDMs, we constructed a genetic map and used it for the genome-wide eQTL analysis of about 16 000 genes in a relatively large population (n = 139). We identified 23 738 significant eQTLs at a genome-wide significance (P ≤ 0.05), affecting the expression of 12 987 genes. Over a third of these genes with expression variation have only one identified eQTL while the rest have two to six. A large proportion of the quantitatively controlled transcripts appear to be regulated by both cis and trans effects. More than half of the quantitatively controlled transcripts appear to be primarily regulated by cis eQTLs in this population. We show that although there appear to be eQTL hotspots many of these are in chromosomal regions of low recombination, such as genetic centromeres, and so have a high gene density per centimorgan. Some chromosomal regions have a significant excess of eQTL over the number expected from gene density, and many of these are biased towards eQTL for which the allele from one particular parent increases the expression level.

    Original languageEnglish
    Pages (from-to)90-101
    Number of pages12
    JournalPlant Journal
    Volume53
    Issue number1
    DOIs
    Publication statusPublished - Jan 2008

    Fingerprint

    Quantitative Trait Loci
    Hordeum
    quantitative trait loci
    barley
    Genome
    Gene Expression
    gene expression
    genome
    Genes
    genes
    Population
    Complementary RNA
    Centromere
    Haploidy
    centromeres
    doubled haploids
    Genetic Polymorphisms
    Genetic Markers
    molecular genetics
    Hordeum vulgare

    Keywords

    • Affymetrix
    • Barley
    • eQTL
    • Genetic genomics
    • Hotspots
    • Transcript derived markers

    Cite this

    Potokina, Elena ; Druka, Arnis ; Luo, Zewei ; Wise, Roger ; Waugh, Robbie ; Kearsey, Mike. / Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. In: Plant Journal. 2008 ; Vol. 53, No. 1. pp. 90-101.
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    abstract = "Transcript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profile individuals from a segregating population to accurately identify robust polymorphic molecular genetic markers. We applied the method to identify more than 2000 genetic polymorphisms (transcript derived markers, TDMs) from an experiment involving two commercial varieties of barley (Hordeum vulgare; Steptoe and Morex) and their doubled-haploid progeny. With this set of TDMs, we constructed a genetic map and used it for the genome-wide eQTL analysis of about 16 000 genes in a relatively large population (n = 139). We identified 23 738 significant eQTLs at a genome-wide significance (P ≤ 0.05), affecting the expression of 12 987 genes. Over a third of these genes with expression variation have only one identified eQTL while the rest have two to six. A large proportion of the quantitatively controlled transcripts appear to be regulated by both cis and trans effects. More than half of the quantitatively controlled transcripts appear to be primarily regulated by cis eQTLs in this population. We show that although there appear to be eQTL hotspots many of these are in chromosomal regions of low recombination, such as genetic centromeres, and so have a high gene density per centimorgan. Some chromosomal regions have a significant excess of eQTL over the number expected from gene density, and many of these are biased towards eQTL for which the allele from one particular parent increases the expression level.",
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    Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. / Potokina, Elena; Druka, Arnis; Luo, Zewei; Wise, Roger; Waugh, Robbie; Kearsey, Mike.

    In: Plant Journal, Vol. 53, No. 1, 01.2008, p. 90-101.

    Research output: Contribution to journalArticle

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    AU - Druka, Arnis

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