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Fanjiang Kong, Zhixi Tian, Xingliang Hou, Baohui Liu and colleagues report the cloning and functional characterization of J, the locus underlying the long-juvenile (LJ) trait that has enabled tropical cultivation of soybean. They show that J, an ortholog of Arabidopsis ELF3, downregulates the expression of E1, thereby promoting flowering under short-day conditions.
Huda Zoghbi and colleagues report that loss of the ATXN1–CIC protein complex in the developing mouse forebrain results in hyperactivity and defects in learning and memory. Loss of Cic in specific brain regions causes social interaction defects, and patients with de novo CIC mutations present signs of hyperactivity, autism spectrum disorder and intellectual disability.
Xianlong Zhang, Keith Lindsey and colleagues report a population genomic analysis of Upland cotton (Gossypium hirsutum) that identifies 93 potential domestication-sweep regions and 19 candidate loci for fiber-quality-related traits. Their analysis provides evidence for asymmetric subgenome selection for long white fibers in cultivated cotton.
Amalio Telenti, Craig Venter and colleagues report common, low-frequency and rare variants associated with blood metabolite levels using whole-genome sequencing and comprehensive metabolite profiling in 1,960 individuals. They identify 246 metabolites whose levels are associated with genetic variation at 101 loci.
Melanie Bahlo and colleagues perform the first genome-wide association analysis for macular telangiectasia type 2. They identify three significant loci and report on a potential connection to the glycine/serine metabolism pathway.
Grant Stewart, Andrew Jackson, Christopher Mathew, Fowzan Alkuraya and colleagues identify a novel replication fork protein, DONSON, which is important for maintaining genome stability. Mutations in DONSON cause microcephalic dwarfism and lead to stalled replication forks and DNA damage.
Evan Eichler and colleagues use single-molecule molecular-inversion probes to sequence the coding and splicing regions of 208 candidate genes in more than 11,730 individuals with neurodevelopmental disorders. They report 91 genes with an excess of de novo or private disruptive mutations, identify 25 genes showing a bias for autism versus intellectual disability, and highlight a network associated with high-functioning autism.
Eileen Furlong, Oliver Stegle and colleagues quantify transcriptional start site (TSS) usage across 81 Drosophila lines, identifying genetic variants that affect transcript levels or the distribution of the TSS within a promoter. Using single-cell measurements, they show that variants modulating promoter shape often increase expression noise.
Louise Wain, Ian Hall, Martin Tobin and colleagues report genome-wide association analyses of lung function, identifying 43 new signals associated with one or more lung function traits. A genetic risk score derived from these results was significantly associated with risk for chronic obstructive pulmonary disease in independent populations.
David Page and colleagues report the sequence of the chicken W sex chromosome and compare ancestral W-linked genes across bird species. They find that the W chromosome did not acquire genes expressed exclusively in reproductive tissue, but retained genes through selection to maintain appropriate dosage levels of broadly expressed genes.
Mark Caulfield, Paul Elliott and colleagues use data from the UK Biobank to perform genome-wide association analysis for blood pressure traits. They identify and validate 107 novel loci and highlight new biological pathways for potential therapeutic intervention for hypertension.
Howard Chang and colleagues use allele-specific ATAC–seq to profile active regulatory DNA across the genome in mouse embryonic stem cells and neural progenitor cells. They find that monoallelic DNA accessibility across autosomes is pervasive, developmentally programmed and composed of several patterns.
Andrew Feinberg, Christine Iacobuzio-Donahue and colleagues describe the epigenomic reprogramming that occurs during pancreatic cancer progression. They also show that hematogenous metastases co-evolve a dependence on the oxidative branch of the pentose phosphate pathway (oxPPP) and that oxPPP inhibition reverses chromatin reprogramming and blocks tumorigenic potential.
Ashlee Earl and colleagues analyze whole-genome sequences from 5,310 Mycobacterium tuberculosis isolates from five continents. They find that resistance to isoniazid arises before rifampicin resistance across all of the lineages, geographical regions and time periods.
Christine Iacobuzio-Donahue and colleagues report a detailed analysis of whole-genome sequencing data from primary and metastatic tumors in four patients with pancreatic cancer. They find that in each patient primary tumors and metastases have identical mutations in known driver genes.
Michael Talkowski, David FitzPatrick, Erica Davis and colleagues report rare inherited or de novo missense variants in SMCHD1 in arhinia patients. Some of the same mutations in SMCHD1 are known to cause a phenotypically distinct muscular dystrophy disorder, FSHD2, and the distinct clinical features of the two disorders suggests that additional genes interact with SMCHD1 to cause arhinia.
Carl Anderson, Jeffrey Barrett and colleagues use whole-genome sequencing and imputation to explore the genetic architecture of inflammatory bowel disease. They identify a low-frequency missense variant in ADCY7 that doubles risk of ulcerative colitis and detect a burden of very rare, damaging missense variants in known Crohn's disease risk genes.