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This study describes efforts to define and protect traditional knowledge and the associated issues of access to genetic resources, from the negotiation of the Convention on Biological Diveristy through to the Declaration of Rights of Indigenous Peoples and the Nagoya Protocol.

Bread wheat ( Triticum aestivum ) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop. Sequencing of the hexaploid bread wheat genome shows that it is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. The bread — and barley — of life Two groups in this issue report the compilation and analysis of the genome sequences of major cereal crops — bread wheat and barley — providing important resources for future crop improvement. Bread wheat accounts for one-fifth of the calories consumed by humankind. It has a very large and complex hexaploid genome of 17 Gigabases. Michael Bevan and colleagues have analysed the genome using 454 pyrosequencing and compared it with diploid ancestral and progenitor genomes. The authors discovered significant loss of gene family members upon polyploidization and domestication, and expansion of gene classes that may be associated with crop productivity. Barley is one of the earliest domesticated plant crops. Although diploid, it has a very large genome of 5.1 Gigabases. Nils Stein and colleagues describe a physical map anchored to a high-resolution genetic map, on top of which they have overlaid a deep whole-genome shotgun assembly, cDNA and RNA-seq data to provide the first in-depth genome-wide survey of the barley genome.

Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana , especially the MAGIC genetic reference population descended from these accessions. Variation between Arabidopsis strains The genomes and transcriptomes of 18 natural Arabidopsis thaliana strains have been compared with that of Col-0, the most widely used A. thaliana wild type that was sequenced as part of the Arabidopsis Genome Initiative. The comparison has been used to create a comprehensive overview of genetic variability in this classic 'laboratory' plant. Each individual genome was compared with every other individual genome in a 'many-to-many' approach, which maximizes the capture of gene variations.

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

A gene that is present in phosphate-deficiency-tolerant rice but absent from modern rice varieties is characterized and named phosphorus-starvation tolerance 1 ( PSTOL1 ); overexpression of PSTOL1 in rice species that naturally lack this gene confers tolerance to low phosphorus conditions, a finding that may have implications for agricultural productivity in rice-growing countries. Rice tolerant to low-phosphate soils Rice is a staple crop for much of Asia. Rice yields in the region are low, however, with limited availability of phosphorous fertilizers and the susceptibility of rain-fed cultivation systems to climate variation among the problems. In this study, Sigrid Heuer and colleagues report the characterization of a gene called phosphorus-starvation tolerance 1 ( PSTOL1 ), which confers tolerance to phosphorus deficiency. The gene is present in the traditional rice variety Kasalath but absent from the rice reference genome and other phosphorus-starvation-intolerant modern varieties. PSTOL1 is shown to act as an enhancer of early root growth, thereby enabling plants to acquire more phosphorus and other nutrients. Introduction of this gene into locally adapted rice varieties should enhance productivity under low-phosphorus conditions. As an essential macroelement for all living cells, phosphorus is indispensable in agricultural production systems. Natural phosphorus reserves are limited 1 , and it is therefore important to develop phosphorus-efficient crops. A major quantitative trait locus for phosphorus-deficiency tolerance, Pup1 , was identified in the traditional aus -type rice variety Kasalath about a decade ago 2 , 3 . However, its functional mechanism remained elusive 4 , 5 until the locus was sequenced, showing the presence of a Pup1 -specific protein kinase gene 6 , which we have named phosphorus-starvation tolerance 1 ( PSTOL1 ). This gene is absent from the rice reference genome and other phosphorus-starvation-intolerant modern varieties 7 , 8 . Here we show that overexpression of PSTOL1 in such varieties significantly enhances grain yield in phosphorus-deficient soil. Further analyses show that PSTOL1 acts as an enhancer of early root growth, thereby enabling plants to acquire more phosphorus and other nutrients. The absence of PSTOL1 and other genes—for example, the submergence-tolerance gene SUB1A —from modern rice varieties underlines the importance of conserving and exploring traditional germplasm. Introgression of this quantitative trait locus into locally adapted rice varieties in Asia and Africa is expected to considerably enhance productivity under low phosphorus conditions.

A genetic study of natural variation in potato tuberization onset, an important phenotype for breeding potatoes adapted to different global day lengths, has revealed a role for StCDF1 , a member of the DOF family of transcription factors. Potatoes take northerly route Potatoes were introduced into Europe from the Andes in the sixteenth century. In South America the plants had adapted to form tubers under short-day conditions, so one of the first traits likely to have been selected by growers would have been for tuber production in the long days of spring and summer encountered in northern latitudes. Christian Bachem and colleagues have cloned the gene responsible for early tuberization under long-day conditions. It encodes a DOF transcription factor that acts as a mediator between the circadian clock and the StSP6A tuberization signal. The natural allelic variation of this protein is sufficient for it to have been the basis of the domestication of the potato in latitudes where there is large summer/winter day-length variation. Breeding programmes selecting for further variants could take potatoes into new geographic regions. Potato ( Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors 1 and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal 2 . We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world’s most important food crops. This annual plant originates from the Andean regions of South America 3 . Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type 4 is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.

Sex determination in plants leads to the development of unisexual flowers from an originally bisexual floral meristem. This mechanism results in the enhancement of outcrossing and promotes genetic variability, the consequences of which are advantageous to the evolution of a species. In melon, sexual forms are controlled by identity of the alleles at the andromonoecious (a) and gynoecious (g) loci. We previously showed that the a gene encodes an ethylene biosynthesis enzyme, mACS-7, that represses stamen development in female flowers. Here we show that the transition from male to female flowers in gynoecious lines results from epigenetic changes in the promoter of a transcription factor, CmWIP1. This natural and heritable epigenetic change resulted from the insertion of a transposon, which is required for initiation and maintenance of the spreading of DNA methylation to the CmWIP1 promoter. Expression of CmWIP1 leads to carpel abortion, resulting in the development of unisexual male flowers. Moreover, we show that CmWIP1 indirectly represses the expression of the andromonoecious gene, CmACS-7, to allow tamen development. Together our data indicate a model in which CmACS-7 and CmWIP1 interact to control the development of male, female and hermaphrodite flowers in melon.

Plants defend themselves against attack by natural enemies, and these defenses vary widely across populations. However, whether communities of natural enemies are a sufficiently potent force to maintain polymorphisms in defensive traits is largely unknown. Here, we exploit the genetic resources of Arabidopsis thaliana, coupled with 39 years of field data on aphid abundance, to (i) demonstrate that geographic patterns in a polymorphic defense locus (GS-ELONG) are strongly correlated with changes in the relative abundance of two specialist aphids; and (ii) demonstrate differential selection by the two aphids on GS-ELONG, using a multigeneration selection experiment. We thereby show a causal link between variation in abundance of the two specialist aphids and the geographic pattern at GS-ELONG, which highlights the potency of natural enemies as selective forces.

Wheat was domesticated about 10,000 years ago and has since spread worldwide to become one of the major crops. Its adaptability to diverse environments and end uses is surprising given the diversity bottlenecks expected from recent domestication and polyploid speciation events. Wheat compensates for these bottlenecks by capturing part of the genetic diversity of its progenitors and by generating new diversity at a relatively fast pace. Frequent gene deletions and disruptions generated by a fast replacement rate of repetitive sequences are buffered by the polyploid nature of wheat, resulting in subtle dosage effects on which selection can operate.

When plants go halves: haploids made easy Haploid plants, inheriting chromosomes from one parent only, have important advantages in genetic research but also crucially in plant breeding, where they are used to create instant homozygous diploid lines, circumventing many generations of inbreeding. Maruthachalam Ravi and Simon Chan have now developed a simple method for producing haploid Arabidopsis thaliana via seeds that can be readily extended to crop plants. Previously haploid production involved tissue culture or genome elimination in wide crosses, and many species are intractable to these methods. The new technique involves engineering a single protein, the centromere-specific histone CENH3, to create strains whose genome is eliminated from the zygote after crossing to wild type. This generates haploid plants with chromosomes from the wild-type parent only. CENH3 plays a universal role at eukaryote centromeres, so in principle this should be transferable to all plant species. Making haploid plants — which inherit chromosomes from only one parent — is useful for genetic research and also, crucially, for plant breeding. A new method for generating haploid Arabidopsis plants is now described, involving the manipulation of a single centromeric protein, CENH3. When cenh3 null plants are crossed with wild-type plants, the mutant chromosomes are eliminated, producing haploid progeny. Production of haploid plants that inherit chromosomes from only one parent can greatly accelerate plant breeding 1 , 2 , 3 . Haploids generated from a heterozygous individual and converted to diploid create instant homozygous lines, bypassing generations of inbreeding. Two methods are generally used to produce haploids. First, cultured gametophyte cells may be regenerated into haploid plants 4 , but many species and genotypes are recalcitrant to this process 2 , 5 . Second, haploids can be induced from rare interspecific crosses, in which one parental genome is eliminated after fertilization 6 , 7 , 8 , 9 , 10 , 11 . The molecular basis for genome elimination is not understood, but one theory posits that centromeres from the two parent species interact unequally with the mitotic spindle, causing selective chromosome loss 12 , 13 , 14 . Here we show that haploid Arabidopsis thaliana plants can be easily generated through seeds by manipulating a single centromere protein, the centromere-specific histone CENH3 (called CENP-A in human). When cenh3 null mutants expressing altered CENH3 proteins are crossed to wild type, chromosomes from the mutant are eliminated, producing haploid progeny. Haploids are spontaneously converted into fertile diploids through meiotic non-reduction, allowing their genotype to be perpetuated. Maternal and paternal haploids can be generated through reciprocal crosses. We have also exploited centromere-mediated genome elimination to convert a natural tetraploid Arabidopsis into a diploid, reducing its ploidy to simplify breeding. As CENH3 is universal in eukaryotes, our method may be extended to produce haploids in any plant species.