Genome-wide expression quantitative trait loci (eQTL) analysis in maize

<p>Abstract</p> <p>Background</p> <p>Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes.</p> <p>Results</p> <p>A hydroponics-based genetical genomics study in roots of a <it>Zea mays </it>IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene.</p> <p>Conclusions</p> <p>Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL.</p

Report of the Final External Review of the Generation Challenge Programme

Responding to a request by the Generation Challenge Program (GCP), the IEA accepted to commission and manage an independent external review of the Challenge Program (CP) one year prior the CP’s expected termination date. This review is entirely funded by the GCP. It was planned (including development of terms of reference and selection of the review team) in consultation with one of the GCP’s major donors, the European Union (EU), so as to satisfy the donor’s evaluation needs without having to conduct two separate reviews. The review team is co-led by Pammi Sachdeva with Greg Edmeades and supported by a small support team. The review of GCP started in August 2013, and the report was completed in early 2014

The Role of Regulatory Genes During Maize Domestication: Evidence From Nucleotide Polymorphism and Gene Expression

We investigated DNA sequence variation in 72 candidate genes in maize landraces and the wild ancestor of maize, teosinte. The candidate genes were chosen because they exhibit very low sequence diversity among maize inbreds and have sequence homology to known regulatory genes. We observed signatures of selection in 17 candidate genes, indicating that they were potential targets of artificial selection during domestication. In addition, 21 candidate genes were identified as potential targets of natural selection in teosinte. A comparison of the proportion of selected genes between our regulatory genes and genes unfiltered for their potential function (but also with very low sequence diversity among maize inbreds) provided some weak evidence that regulatory genes are overrepresented among selected genes. We detected no significant association between the positions of genes identified as potential targets of selection during domestication and quantitative trait loci (QTL) responsible for maize domestication traits. However, a subset of these genes, those identified by sequence homology as kinase/phosphatase genes, significantly cluster with the domestication QTL. We also analyzed expression profiles of genes in distinct maize tissues and observed that domestication genes are expressed on average at a significantly higher level than neutral genes in reproductive organs, including kernels

Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats

The genetic basis of cultivated soybean is rather narrow. This observation has been confirmed by analysis of agronomic traits among different genotypes, and more recently by the use of molecular markers. During the construction of an RFLP soybean map (Glycine soja x Glycine max) the two progenitors were analyzed with over 2,000 probes, of which 25% were polymorphic. Among the probes that revealed polymorphisms, a small proportion, about 0.5%, hybridized to regions that were highly polymorphic. Here we report the sequencing and analysis of five of these probes. Three of the five contain segments that encode leucine-rich repeat (LRR) sequence homologous to known disease resistance genes in plants. Two other probes are relatively AT-rich and contain segments of (A)n/(T)n. DNA segments corresponding to one of the probes (A45-10) were amplified from nine soybean genotypes. Partial sequencing of these amplicons suggests that deletions and/or insertions are responsible for the extensive polymorphism observed. We propose that genes encoding LRR proteins and simple sequence repeat region prone to slippage are some of the most hypervariable regions of the soybean genome.<br>A base genética da soja cultivada é relativamente estreita. Essa observação foi confirmada por análises de características agronômicas entre diferentes genótipos e, mais recentemente, pelo uso de marcadores moleculares. Durante a construção de um mapa de RFLP da soja (Glycine soja x Glycine max), os dois progenitores foram analisados com mais de 2000 sondas, das quais 25% eram polimórficas. Entre as sondas que revelaram polimorfismos, uma pequena proporção, cerca de 0,5%, hibridizou com regiões que eram altamente polimórficas. Neste trabalho, são apresentados o seqüenciamento e análise de cinco dessas sondas. Três dessas sondas contêm segmentos que codificam repetições ricas em leucina que são homólogas a genes de resistência a doenças já conhecidos em plantas. As duas outras sondas são relativamente ricas em AT e contêm segmentos do tipo (A)n/(T)n. Segmentos de DNA correspondentes a uma das sondas (A45-10) foram amplificados a partir de nove genótipos de soja. Seqüenciamento parcial desses amplicons sugere que deleções e/ou inserções são responsáveis pelo extensivo polimorfismo observado. Nós propomos que os genes que codificam proteínas com repetições ricas em leucina e regiões de seqüências repetidas simples, que são passíveis do fenômeno de slippage (deslizamento), estão entre as regiões mais variáveis do genoma da soja

Co-expression of two groups of genes (<i>HvCesA9</i>, <i>HvCobra1</i>, <i>HvCslF6</i>, and <i>HvChitinase</i>, <i>HvGT1</i>) identified by GWAS as putatively linked to culm cellulose content with <i>HvCesA</i> genes known to be involved in primary and secondary cell wall development.

<p>Transcript abundance across a range of tissues shown in fragment per kilobase of exon per million fragments mapped (FPKM) for group 1, primary cell wall including <i>HvCesA1</i>, <i>HvCesA2</i>, and <i>HvCesA6</i> (A) for reference, and group 2, secondary cell wall including <i>HvCesA4</i>, <i>HvCesA7</i> and <i>HvCesA8</i> for reference (B). Abbreviations for tissues/ developmental stages as follows; EMB = Embryo tissues (germinating), ROO = Root (10cm seedlings), LEA = Shoot (10cm seedlings), INF1 = Inflorescence (0.5cm), INF2 = Inflorescence (1–1.5cm), NOD = Tillers (3rd internode), CAR5 = Grain (5 Days Post Anthesis—DPA), CAR15 = Grain (15 DPA), ETI = Etiolated (10 day seedlings), LEM = Lemma (6 weeks Days After Planting—DAP), LOD = Lodicule (42 DAP), PAL = Palea (42 DAP), EPI = Epidermis (28 DAP), RAC = Rachis (35 DAP), ROO2 = Root (28 DAP seedling), SEN = Senescing leaf (63 DAP).</p

Phenotypic data used to carry out a genome wide association study (GWAS).

<p>(A) Mean culm cellulose content for 2-row and 6 row spring barley accessions by breeding program. (B) Mean culm cellulose content for all lines to illustrate the distribution of this trait in the barley CAP programs included in this analysis.</p

Regions of the barley genome identified by GWAS as having significant associations with cellulose content.

<p>This table includes just pop 3 and 5 as these were the two subpopulatons in which significant association with culm cellulose content were identified. Significant (−log10 p ≥ 3) marker-trait associations which pass the False Discovery Rate (FDR) adjusted p value threshold of ≤ 0.05 are indicated by *,</p><p>≤ 0.01 are indicated by **,</p><p>and ≤ 0.001 are indicated by ***</p><p>R-squared values for each marker are also included. The marker name and location for the SNP with the highest lod score is provided for each QTL. Germplasm included in the analysis was a subset of 2-rowed and 6- rowed spring accessions from the Barley CAP project. Subpopulations, referred to here as “Pop”, are those determined by STRUCTURE analysis based on degree of shared genetic ancestry. Barley Gene ID (MLOC), Morex Contig, 3^rd internode FPKM—fragments per kilobase of exon per million fragments mapped from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130890#pone.0130890.ref039" target="_blank">39</a>] are provided for each candidate gene identified under each peak where information is available. Four different versions of the barley map were used to provide information for each locus: 9K i-Select [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130890#pone.0130890.ref035" target="_blank">35</a>], Barley Genome Zipper [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130890#pone.0130890.ref037" target="_blank">37</a>], POPSEQ [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130890#pone.0130890.ref038" target="_blank">38</a>] and the IBSC [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130890#pone.0130890.ref039" target="_blank">39</a>]. Question marks indicate where no obvious candidate was identified for particular regions based on the available annotations.</p><p>Regions of the barley genome identified by GWAS as having significant associations with cellulose content.</p