We analyzed the complete genome sequence of Arabidopsis thaliana and sequence data from 83 genes in the outcrossing A. lyrata, to better understand the role of gene expression on the strength of natural selection on synonymous and replacement sites in Arabidopsis. From data on tRNA gene abundance, we find a good concordance between codon preferences and the relative abundance of isoaccepting tRNAs in the complete A. thaliana genome, consistent with models of translational selection. Both EST-based and new quantitative measures of gene expression (MPSS) suggest that codon preferences derived from information on tRNA abundance are more strongly associated with gene expression than those obtained from multivariate analysis, which provides further support for the hypothesis that codon bias in Arabidopsis is under selection mediated by tRNA abundance. Consistent with previous results, analysis of protein evolution reveals a significant correlation between gene expression level and amino acid substitution rate. Analysis by MPSS estimates of gene expression suggests that this effect is primarily the result of a correlation between the number of tissues in which a gene is expressed and the rate of amino acid substitution, which indicates that the degree of tissue specialization may be an important determinant of the rate of protein evolution in Arabidopsis.

We investigated DNA sequence diversity for loci on chromosomes 1 and 2 in six natural populations of Arabidopsis lyrata and tested for the role of natural selection in structuring genomewide patterns of variability, specifically examining the effects of recombination rate on levels of silent polymorphism. In contrast with theoretical predictions from models of genetic hitchhiking, maximum-likelihood-based analyses of diversity and divergence do not suggest reduction of diversity in the region of suppressed recombination near the centromere of chromosome 1, except in a single population from Russia, in which the pericentromeric region may have undergone a local selective sweep or demographic process that reduced variability. We discuss various possibilities that might explain why nucleotide diversity in most A. lyrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region.

Barley is one of the world's most important crops providing food and related products for millions of people.

10 Abstract The genetic basis of several different 11 components of resistance to Rhynchosporium secalis 12 in barley was investigated in a mapping population 13 derived from a cross between winter and spring 14 barley types. 34Rhynchosporum secalis (Oudem) J.J. Davis, the 35 pathogen that causes 'rhynchosporium', 'barley leaf 36 blotch ' or 'scald', in Hordeum vulgare L. (barley). is 37 one of the most economically important barley 38 pathogens worldwide, particularly in cool humid 39 environments, causing reductions in both yield and 40 grain quality (Zhan et al. 2008). Average yield losses 41 (from Canada) have been estimated at 5-10% (Tur-42 kington et al. 1998), though losses of up to 40% have 43 been reported under conditions favourable for the 44 disease (Xi et al. 2000). Mapping studies have located 45 a number of major resistance (R) genes and quanti-46 tative trait loci (QTL) affecting expression of resis-47 tance to R. secalis; these are predominantly located 48 on barley chromosomes 2H, 3H and 7H (Zhan et al. 49 2008). Whilst current control strategies in the UK 50 frequently include a fungicide treatment, commercial 51 cultivars with good levels of resistance, probably due ; it has been the main winter barley malting culti-166 var grown by farmers over this period. It was initially 167 rated as having a good resistance to R. secalis,b e i n g 168 rated '8', on a 1-9 scale of increasing host resistance as 169 described in the recommended list protocols (www. 170 hgca.com). Leonie originally had the best rating of '9,' 171 but its resistance rating had declined to '5.9' by 2010 172 (www.hgca.com). Cv Cocktail was first recommended 173 for cultivation in the UK in 2003 and was formerly an 174 accepted spring barley malting cultivar in the UK. It 175 does not possess either of the two R genes for resistance 176 to R. secalis found in current UK spring barley cultivars 177 and had a moderate resistance rating of '5' when first 178 recommended, which had increased slightly to '5.9' in 179 the 2010 recommended list (www.hgca.com). 180 WB05-13 was bred to combine the resistance to 181 R.secalis and BaYMV-1 of Leonie with the accepted 182 malting quality attributes of Pearl; thus progeny from 183 its cross with Cocktail are expected to segregate for 184 resistance to R. secalis and to BaYMV-1 as well as 185 for the sdw1 dwarfing gene found in Cocktail. In 186 addition, WB05-13 has the Vrs1.t allele at the VRS1 187 locus on chromosome 2H and the mapping popula-188 tion therefore also segregates for the deficiens ear 189 type. Over 800 individual plants were derived from 190 microspore culture of the F 1 progeny; 550 lines were 191 fertile and produced sufficient seed for a field 192 multiplication plot that was sown at the James Hutton 44Author Proof (2007/2008 and 2008/2009) at the 271 James Hutton Institute rhynchosporium disease nurs-272 ery (Table 1). Cocktail, Leonie and Pearl together 273 with seven other controls were included in the trial to 274 give a trial with 200 entries. Field trials were...

Hybridization is an important evolutionary factor in the diversification of many plant and animal species. Of particular interest is that historical hybridization resulting in the origin of new species or introgressants has occurred between species now geographically separated by great distances. Here, we report that Senecio massaicus, a tetraploid species native to Morocco and the Canary Islands, contains genetic material of two distinct, geographically separated lineages: a Mediterranean lineage and a mainly southern African lineage. A time-calibrated internal transcribed spacer phylogeny indicates that the hybridization event took place up to 6.18 Ma. Because the southern African lineage has never been recorded from Morocco or the Canary Islands, we hypothesize that it reached this area in the distant past, but never became permanently established. Interestingly, the southern African lineage includes S. inaequidens, a highly invasive species that has recently become widespread throughout Europe and was introduced at the end of the 19th century as a 'wool alien'. Our results suggest that this more recent invasion of Europe by S. inaequidens represents the second arrival of this lineage into the region.