查看更多>>摘要：The multiparent advanced generation intercross(MAGIC)population is characterized with great potentials in power and resolution of quantitative trait locus(QTL)mapping,but single nucleotide polymorphism(SNP)-based GWAS does not fully reach its potential.In this study,a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice.A total of44 000 genes showed functional polymorphisms among eight parents,including frameshift variations or premature stop codon variations,which provides the potential to map almost all genes of the MAGIC population.Principal component analysis results showed that the MAGIC population had a weak population structure.A high-density bin map of 24 414 bins was constructed.Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development.SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date,including 14 known heading date genes.The mapping resolution of genes is dependent on genetic effects with offset distances of＜55 kb for major effect genes and＜123 kb for moderate effect genes.Four causal variants and noncoding structure variants were identified to be associated with heading date.Three to four types of alleles with strong,intermediate,weak,and no genetic effects were identified from eight parents,providing flexibility for the improvement of rice heading date.In most cases,japonica rice carries weak alleles,and indica rice carries strong alleles and nonfunctional alleles.These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs,and its use is encouraged for mapping genes and mining favorable alleles for breeding.
查看更多>>摘要：The prefrontal cortex(PFC)is essential for higher-level cognitive functions.How epigenetic dynamics participates in PFC development and aging is largely unknown.Here,we profiled epigenomic landscapes of rhesus monkey PFCs from prenatal to aging stages.The dynamics of chromatin states,including higher-order chromatin structure,chromatin interaction and histone modifications are coordinated to regulate stage-specific gene transcription,participating in distinct processes of neurodevelopment.Dramatic changes of epigenetic signals occur around the birth stage.Notably,genes involved in neuronal cell differentiation and layer specification are pre-configured by bivalent promoters.We identified a cis-regulatory module and the transcription factors(TFs)associated with basal radial glia development,which was associated with large brain size in primates.These TFs include GLI3,CREB5 and SOX9.Interestingly,the genes associated with the basal radial glia(bRG)-associated cis-element module,such as SRY and SOX9,are enriched in sex differentiation.Schizophrenia-associated single nucleotide polymorphisms are more enriched in super enhancers(SEs)than typical enhancers,suggesting that SEs play an important role in neural network wiring.A cis-regulatory element of DBN1 is identified,which is critical for neuronal cell proliferation and synaptic neuron differentiation.Notably,the loss of distal chromatin interaction and H3K27me3 signal are hallmarks of PFC aging,which are associated with abnormal expression of aging-related genes and transposon activation,respectively.Collectively,our findings shed light on epigenetic mechanisms underlying primate brain development and aging.
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