SummaryFaba bean (Vicia faba L.) is a globally important nitrogen‐fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence‐based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2‐cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40‐1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5′ end of the gene.

Background: The floral dip method of transformation by immersion of inflorescences in a suspension of Agrobacterium is the method of choice for Arabidopsis transformation. The presence of a marker, usually antibiotic-or herbicide-resistance, allows identification of transformed seedlings from untransformed seedlings. Seedling selection is a lengthy process which does not always lead to easily identifiable transformants. Selection for kanamycin-, phosphinothricin-and hygromycin B-resistance commonly takes 7-10 d and high seedling density and fungal contamination may result in failure to recover transformants.

The clustered organization of Hox genes provides a powerful opportunity to examine gene gain and loss in evolution because physical linkage is a key diagnostic feature which allows homology to be established unambiguously. Furthermore, Hox genes play a key role in determination of axial and appendicular skeletal morphology and may be a key component of the evolution of diverse metazoan body forms. Despite suggestions that changes in Hox gene number played a role in evolution of metazoan body plans, there has been a general lack of evidence for such variation amongst gnathostomes (or indeed any vertebrate) and it has therefore been widely assumed that differential regulation may be the key element in all vertebrate Hox evolution. We have studied the Hox gene clusters of a teleost fish, Fugu rubripes, to test the possibility that Hox organization may have varied since the origin of jawed vertebrates. We have identified four Hox complexes in Fugu and found an unprecedented degree of variation when compared with tetrapod clusters. Our data show that: Fugu clusters are widely variant with respect to length; at least nine genes have been lost; there is a new group-2 paralogue; and pseudo-gene remnants of group-1 and group-3 paralogues were found in the Hoxc complex, when compared with the present mammalian clusters. We show that gene loss after duplication of the prototypical vertebrate Hox clusters is a key feature of both tetrapod and fish evolution.

Developing seedlings of the Arabidopsis gun1 (genomes uncoupled1) mutant, which is defective in retrograde plastid-to-nucleus signalling, show several previously unrecognized mutant phenotypes. gun1 seedlings accumulated less anthocyanin than wild-type seedlings when grown in the presence of 2% (w/v) sucrose, due to lower amounts of transcripts of early anthocyanin biosynthesis genes in gun1. Norflurazon and lincomycin, which induce retrograde signalling, further decreased the anthocyanin content of sucrose-treated seedlings, and altered the temporal pattern of anthocyanin accumulation. Lincomycin treatment altered the spatial pattern of sucrose-induced anthocyanin accumulation, suggesting that plastids provide information for the regulation of anthocyanin biosynthesis in Arabidopsis seedlings. The temporal pattern of accumulation of LHCB1 transcripts differed between wild-type and gun1 seedlings, and gun1 seedlings were more sensitive to sucrose suppression of LHCB1 transcript accumulation than wild-type seedlings. Growth and development of gun1 seedlings was more sensitive to exogenous 2% sucrose than wild-type seedlings and, in the presence of lincomycin, cotyledon expansion was enhanced in gun1 seedlings compared to the wild type. gun1 seedlings were more sensitive than wild-type seedlings to the inhibition of seedling growth and development by abscisic acid. These observations clearly implicate GUN1 and plastid signalling in the regulation of seedling development and anthocyanin biosynthesis, and indicate a complex interplay between sucrose and plastid signalling pathways.

We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all displayed on a searchable, publicly available web site at http://fugu.hgmp.mrc.ac.uk/. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, covering 30%-50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole genome analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight times less DNA but a similar gene repertoire, is ideally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. We have made some estimation of the syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from short, unedited Fugu genomic sequences. Comparative DNA sequence analyses are an essential tool in the functional interpretation of complex vertebrate genomes. This project highlights the utility of using the Fugu genome in this kind of study.Despite massive investment in genome mapping and DNA sequencing over the last 10 years, large-scale sequencing of vertebrate genomes has been initiated only very recently. This is partly because the initial emphasis has been on developing mapping, sequencing, and assembly technologies and partly because sequence-ready contigs of large regions of the human genome have not been available. Many valuable lessons have been learned-at no small expense-from the bacterial, yeast, and, in particular, the Caenorhabditis elegans projects. It is also clear, however, that mammalian genomes may present additional problems relating to the generation of cloned DNA from some regions, sequence assembly of highly repetitive DNA, and the large size of the genomes involved.To interpret much of the data, comparative sequencing of genomic regions from other vertebrates will be necessary. The identification of conserved sequences across species has always been a key technique in the identification of genes. In addition, sequence comparison in invertebrate projects has identified many genes by sequence similarity and in many cases has allowed speculation on function. Now that the resolution of genomes is approaching the single base pair, powerful analytical methods need to be used to define the many elements-both coding and noncoding-that are contained within the human genome.Despite the need for comparison, there is little investment in other vertebrate sequencing projects at this time. Small regions of conserved synteny within the mouse genome have been pinpointed for complete genomic sequencing, and this will provide an opportunity to compare not only precise orders of genes but also regions in and around the coding sequence itself. This should lead to the identification of other con...