Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy.
Theoretical and Applied Genetics (Impact Factor: 3.79). 03/2012; 125(1):171-84. DOI: 10.1007/s00122-012-1824-8
Source: PubMed


Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

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    • "The geographical distribution of neutral genetic diversity in barley has been the focus of a number of studies . Clear geographic clustering of European landrace barley has been shown, both on a continental scale ( Jones et al., 2011, Pasam et al., 2014) and in certain regions, such as Spain (Yahiaoui et al., 2008), Sardinia (Rodriguez et al., 2012), and Fennoscandia (Leino and Hagenblad, 2010; Forsberg et al., 2015). This suggests limited geneflow , which would facilitate the evolution of local adaption in response to climatic differences. "
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    ABSTRACT: Barley landraces from Northern Europe form genetically distinct latitudinal groups, suggesting that adaption plays an important role in the geographical distribution of genetic diversity. Here, we investigate how Northern European barley landraces relate to landraces from other parts of Europe and whether candidate genes for climate adaption can be identified. For this purpose, 27 barley landraces, available as century-old seed specimens, were genotyped with a 384 single nucleotide polymorphism (SNP) assay. Landraces from the Nordic countries formed a genetically distinct group relative to landraces from Central and Southern Europe. Polymorphic positions in the flowering time genes HvCO1, HvFT1, Ppd-H1, and VRN1- H1 were genotyped. The previously known allele distribution of Ppd-H1 with the responsive allele present in the South and the nonresponsive allele in the North was confirmed. The other three genes were more variable in Central and Southern Europe compared to the North and neither of the flowering time genes showed any geographically correlated variation within the Nordic countries. Allelic frequencies from the 384 SNP set were correlated with climatic variables. This allowed us to identify five SNPs putatively associated with length of growth season, and two SNPs putatively associated with precipitation. The results show how historical crop specimens can be used to study how genetic variation has been geographically distributed and the genetics of adaption.
    Crop Science 10/2015; 55(november–december 2015):2766-2776. DOI:10.2135/cropsci2015.02.0119 · 1.58 Impact Factor
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    • "human Herpes simplex virus) (1). At high packaging densities, DNA–DNA interactions are mediated mainly by electrostatic and hydration forces (2–5); the latter arising from the structuring of water molecules on the macromolecular surface. These interactions are observed to result in a spacing that ranges ∼15–20 Å in distance (6), corresponding to 3–4 water layers at each DNA surface. "
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    ABSTRACT: The DNA structure in phage capsids is determined by DNA-DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage λ capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging.
    Nucleic Acids Research 02/2013; 41(8). DOI:10.1093/nar/gkt137 · 9.11 Impact Factor
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    • "Alvarez et al. (2005) use the term metapopulations to describe how landrace populations within a defined geographical or morphological frame share and exchange genetic material. Genetic diversity studies of barley landraces in Sardinia (Papa et al., 1998; Rodriguez et al., 2012) and Ethiopia (Demissie et al. 1998) concluded that landraces in these areas were influenced by frequent seed exchange, resulting in high within-population diversity and differentiation between populations that was sometimes difficult to detect. In our case, some metapopulations could be suggested, for example, extant and historical peas from Jämtland and the historical peas in Dalarna and Bohuslän. "
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    ABSTRACT: Landrace crops are formed by local adaptation, genetic drift and gene flow through seed exchange. In reverse, the study of genetic structure between landrace populations can reveal the effects of these forces over time. We present here the analysis of genetic diversity in 40 Swedish field pea (Pisum sativum L.) populations, either available as historical seed samples from the late nineteenth century or as extant gene bank accessions assembled in the late twentieth century. The historical material shows constant high levels of within-population diversity, whereas the extant accessions show varying, and overall lower, levels of within-population diversity. Structure and principal component analysis cluster most accessions, both extant and historical, in groups after geographical origin. County-wise analyses of the accessions show that the genetic diversity of the historical accessions is largely overlapping. In contrast, most extant accessions show signs of genetic drift. They harbor a subset of the alleles found in the historical accessions and are more differentiated from each other. These results reflect how, historically present metapopulations have been preserved during the twentieth century, although as genetically isolated populations.Heredity advance online publication, 21 November 2012; doi:10.1038/hdy.2012.93.
    Heredity 11/2012; 110(4). DOI:10.1038/hdy.2012.93 · 3.81 Impact Factor
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