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Towards the genetic architecture of seed lipid biosynthesis and accumulation in Arabidopsis thaliana

We report the quantitative genetic analysis of seed oil quality and quantity in six Arabidopsis thaliana recombinant inbred populations, in which the parent accessions were from diverse geographical origins, and were selected on the basis of variation for seed oil content and lipid composition. Although most of the biochemical steps involved in lipid biosynthesis are known and the key genes have been identified, the regulation of the processes that results in the final oil composition and total amount is not understood. By using physically anchored markers it was possible to compare results across populations. A total of 219 quantitative trait loci (QTLs) were identified, of which 81 were significant at P<0.001. Some of these colocalise with QTLs identified previously, but many novel QTLs were also identified. The results highlight the importance of studying traits in multiple populations, which will lead to a better understanding of the contribution that natural variation makes to the genetic architecture of a phenotype.

C M O’Neill1, C Morgan1, C Hattori1, M Brennan2, U Rosas3, H Tschoep4, P X Deng1, D Baker1, R Wells1 and I Bancroft1

  1. 1Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, UK
  2. 2Monsanto Company, St Louis, MO, USA
  3. 3Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
  4. 4SESVANDERHAVE NV/SA, Tienen, Belgium

Heredity (2012) 108, 115–123 Full paper here.

Fusion–fission experiments in Aphidius: evolutionary split without isolation in response to environmental bimodality

Studying host-based divergence naturally maintained by a balance between selection and gene flow can provide valuable insights into genetic underpinnings of host adaptation and ecological speciation in parasites. Selection-gene flow balance is often postulated in sympatric host races, but direct experimental evidence is scarce. In this study, we present such evidence obtained in host races of Aphidius ervi, an important hymenopteran agent of biological control of aphids in agriculture, using a novel fusion–fission method of gene flow perturbation. In our study, between-race genetic divergence was obliterated by means of advanced hybridisation, followed by a multi-generation exposure of the resulting genetically uniform hybrid swarm to a two-host environment. This fusion–fission procedure was implemented under two contrasting regimes of between-host gene flow in two replicated experiments involving different racial pairs. Host-based genetic fission in response to environmental bimodality occurred in both experiments in as little as six generations of divergent adaptation despite continuous gene flow. We demonstrate that fission recovery of host-based divergence evolved faster and hybridisation-induced linkage disequilibrium decayed slower under restricted (6.7%) compared with unrestricted gene flow, directly pointing at a balance between gene flow and divergent selection. We also show, in four separate tests, that random drift had no or little role in the observed genetic split. Rates and patterns of fission divergence differed between racial pairs. Comparative linkage analysis of these differences is currently under way to test for the role of genomic architecture of adaptation in ecology-driven divergent evolution.

I Emelianov1, A Hernandes-Lopez1, M Torrence1 and N Watts1

1Plant and Invertebrate Ecology, Rothamsted Research, Harpenden Herts, UK

Correspondence: Dr I Emelianov, Plant and Invertebrate Ecology, Rothamsted Research, West Common, Harpenden Herts, AL5 2JQ, UK.

Heredity (2011) 106, 798–807 Full paper here.

Kin assortment in juvenile shoals in wild guppy populations

Grouping provides many potential benefits to individuals in terms of foraging and anti-predator protection. However, it has been suggested that individuals could gain additional benefits in terms of indirect fitness by grouping with kin. Surprisingly, the genetic composition of wild fish shoals and the importance of kin-associated shoaling remain poorly understood. The Trinidadian guppy (Poecilia reticulata) has life history traits that might promote kin structure of shoals such as internal fertilisation and small brood size in contrast to many other fish species. Even though previous studies did not find any indication of kin structure in shoals of adult guppies, it is possible that related juveniles remain together in shoals, partly because of lower mobility and because the advantages of kin association may change with age. Using 10 microsatellite markers, we conducted a genetic analysis on 40 shoals from four populations. Pair-wise relatedness was inferred using a modified version of the software package COLONY and permutation tests were conducted to test the hypothesis that kin occur together in juvenile shoals more often than expected by chance. The frequency of sib dyads among juveniles within shoals was significantly larger than that between shoals in two high predation populations but not in two low predation populations. This finding contributes to the understanding of factors underlying shoal composition and highlights the potential of recent methodological advances for detecting such relationships.

C Piyapong1,2, R K Butlin3, J J Faria2, K J Scruton2, J Wang4 and J Krause2,5

  1. 1Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham, Thailand
  2. 2Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
  3. 3Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
  4. 4Institute of Zoology, Regent’s Park, London, UK
  5. 5Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Biology and Ecology of Fishes, Müggelseedamm 310, Berlin, Germany

Correspondence: Dr C Piyapong, Department of Biology, Faculty of Science, Mahasarakham University, Khamrieng Campus, Mahasarakham 44150, Thailand. E-mail

Heredity (2011) 106, 749–756 Full paper here.


SynGAP isoforms exert opposing effects on synaptic strength

A.C. McMahon,M.W. Barnett,T.S. O’Leary,P.N. Stoney,M.O. Collins,S. Papadia,J.S. Choudhary,N.H. Komiyama,S.G.N. Grant,G.E. Hardingham,D.J.A. Wyllie & P.C. Kind

Nature Communications, June 2012

Alternative promoter usage and alternative splicing enable diversification of the transcriptome. Here we demonstrate that the function of Synaptic GTPase-Activating Protein (SynGAP), a key synaptic protein, is determined by the combination of its amino-terminal sequence with its carboxy-terminal sequence. 5′ rapid amplification of cDNA ends and primer extension show that different N-terminal protein sequences arise through alternative promoter usage that are regulated by synaptic activity and postnatal age. Heterogeneity in C-terminal protein sequence arises through alternative splicing. Overexpression of SynGAP α1 versus α2 C-termini-containing proteins in hippocampal neurons has opposing effects on synaptic strength, decreasing and increasing miniature excitatory synaptic currents amplitude/frequency, respectively. The magnitude of this C-terminal-dependent effect is modulated by the N-terminal peptide sequence. This is the first demonstration that activity-dependent alternative promoter usage can change the function of a synaptic protein at excitatory synapses. Furthermore, the direction and degree of synaptic modulation exerted by different protein isoforms from a single gene locus is dependent on the combination of differential promoter usage and alternative splicing.

Full paper here.

Barley (Hordeum vulgare L.) is among the world’s earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 ‘high-confidence’ genes with homology support from other plant genomes.

Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

Read the full paper here.

Pediatric Research

Sex Differences in the Ovine Fetal Cortisol Response to Stress

This study tested the hypothesis that the sexually dimorphic adrenocortical response to stress is already established before birth. Chronically instrumented late gestation pregnant sheep carrying 16 male and 15 female age-matched singleton fetuses were subjected to an acute episode of hypoxic stress. Maternal and fetal blood gases, adrenocorticotrophic hormone (ACTH), and cortisol were measured. In addition, six male and six female fetuses received the ACTH analog, Synacthen, and plasma cortisol was measured. During hypoxic stress, the increment in plasma cortisol was 2-fold greater in male versus females fetuses (30.6 ± 3.2 versus 14.3 ± 2.0 ng/mL; p < 0.001) mediated, in part, by greater adrenocortical sensitivity to ACTH. The data support the hypothesis tested and show that sex-specific differences in the cortisol stress response are present before birth with the output of cortisol being much greater in male than in female fetuses.

Dino A Giussani1,*, Andrew J W Fletcher1 and David S Gardner1,**

1Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom

Correspondence: Dino A. Giussani, Ph.D., Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom; e-mail:

*D.A.G. is a Royal Society-Wolfson Research Merit Award holder. This work was supported by the British Heart Foundation, The BBSRC, The Sir Jules Thorn Trust, The Lister Institute, and The Sir Isaac Newton Trust.

**D.S.G. is currently at The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RA, United Kingdom.

Pediatric Research (2011) 69, 118–122 Full paper here.

The EMBO Journal

Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis

In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.

Steffen Vanneste1,2,7, Frederik Coppens1,2,7, EunKyoung Lee3, Tyler J Donner4, Zidian Xie5, Gert Van Isterdael1,2, Stijn Dhondt1,2, Freya De Winter1,2, Bert De Rybel1,2,8, Marnik Vuylsteke1,2, Lieven De Veylder1,2, Jiří Friml1,2, Dirk Inzé1,2, Erich Grotewold5, Enrico Scarpella4, Fred Sack3, Gerrit T S Beemster1,2,6 and Tom Beeckman1,2

  1. Department of Plant Systems Biology, VIB, Ghent, Belgium
  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
  3. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
  4. Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
  5. Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, OH, USA
  6. Department of Biology, University of Antwerp, Antwerp, Belgium

The EMBO Journal (2011) 30, 3430 – 3441. Full paper here.

TAG – Theoretical and Applied Genetics

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences.

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.

P. K. Sabadin, M. Malosetti, M. P. Boer, F. D. Tardin, F. G. Santos, C. T. Guimarães, R. L. Gomide, C. L. T. Andrade, P. E. P. Albuquerque and F. F. Caniato, et al.