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Xavier Argout and colleagues report the draft genome of Theobroma cacao, the tropical crop that is the source of chocolate. The sequence assembly covers approximately 80% of the genome.
The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genus, as the cultivated strawberry (Fragaria × ananassa) is an octoploid where F. vesca is predicted to be a subgenome donor.
Jason Carroll and colleagues report that the forkhead protein FOXA1 is an important determinant of estrogen receptor binding and show that expression of FOXA1 in non–breast cancer cells is sufficient to confer estrogen receptor binding and response to endocrine treatment.
Yoshiya Kawaguchi and colleagues show that a Sox9-positive progenitor pool located in the epithelia of the biliary and pancreatic ducts of adult mice serves as a continuous source of intestinal cells, hepatocytes and pancreatic acinar cells, identifying a shared pathway underlying the cellular renewal of these adult endodermal organs.
Ken Ong and colleagues report meta-analysis of 32 genome-wide association studies for age at menarche. They identify 30 loci newly associated with age at menarche, including four that were previously associated with BMI.
Nona Sotoodehnia and colleagues report a meta-analysis of 14 genome-wide association studies for QRS interval, an electrocardiogram measurement of cardiac ventricular conduction. They identify 22 loci associated with QRS duration.
Genetic variants at the FTO gene are associated with obesity in humans. Now, Roger Cox and colleagues analyze mice globally overexpressing Fto and show that increased Fto expression leads to obesity in mice.
Jun Wang and colleagues report whole-genome resequencing of 17 wild and 14 cultivated soybean accessions. They characterize population structure, patterns of linkage disequilibrium and selection in soybeans.
Michael Weber and colleagues present profiles of DNA methylation during early development of the mouse embryonic lineage in vivo. They profile 10% of the mouse genome covering all known gene promoters. They show that DNA methylation is targeted to specific gene promoters and is required to maintain gene repression.
Kamal Chowdhury and colleagues show that the microRNA-212/132 family is necessary for mouse mammary gland development. microRNA-212 and microRNA-132 are required in the mammary stroma, not the epithelium.
Thomas Brutnell and colleagues report RNA-Seq analysis of the maize leaf transcriptome during stages of leaf development. They identify dynamic changes in gene expression during the progression of leaf development.
Tatsuhiko Tsunoda and Hidewaki Nakagawa report the genome sequence of a Japanese male individual generated with high-throughput sequencing technology. Their analyses reveal a number of novel single nucleotide variants, insertions, deletions and other variants.
Bin Han and colleagues performed low-coverage sequencing of 517 rice landraces and constructed a high-density haplotype map of the rice genome. They have used this resource to carry out genome-wide association studies for 14 agronomic traits and identify 80 loci with strong association signals.
Ruth Loos and colleagues report results of a large genome-wide association study for body mass index. They identify 18 new loci associated with this trait, some of which map near key hypothalamic regulators of energy balance.
Cecilia Lindgren and colleagues report results of a large-scale genome-wide association study for waist-to-hip ratio, a measure of body fat distribution. They identify 13 new loci associated with this trait, several of which show stronger effects in women than in men.
Friedhelm Hildebrandt and colleagues combine homozygosity mapping with candidate exome capture and high-throughput sequencing to identify SDCCAG8 mutations as the cause of a retinal-renal ciliopathy. They further show that SDCCAG8 localizes to centrioles and that its depletion causes renal cysts and cell polarity defects.
Vamsi Mootha and colleagues report high-throughput targeted sequencing of 103 candidate genes in 103 individuals with human mitochondrial complex I deficiency. They identify two genes newly associated with complex I deficiency and are able to provide genetic diagnoses in 22% of their previously unsolved cases.
Riccardo Velasco and colleagues report the genome sequence of the 'Golden Delicious' domesticated apple. These data shed new insight into the genomic events that preceded the origin of this crop.
Evan Eichler and colleagues identify a large, complex structural polymorphism at 16p12.1 in a region previously associated with neurocognitive disease. They further show that the region has experienced dynamic structural evolution in primates and that disease-associated microdeletions arise on the more common human haplotype.
Thomas Bugge and colleagues report that the matriptase protease initiates an epidermal kallikrein proteolytic cascade in mice lacking Spink5, which encodes the serine protease inhibitor LEKTI. Loss of matriptase rescued some features of excessive proteolytic degradation of corneodesmosomes and inflammatory activation in LEKTI-deficient mice, which are a model of human Netherton syndrome.