http://ibi.zju.edu.cn/software/qtlnetwork.

A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

Light and gibberellins (GAs) antagonistically regulate hypocotyl elongation in plants. It has been demonstrated that DELLAs, which are negative regulators of GA signalling, inhibit phytochrome-interacting factors 3 and 4 (PIF3 and PIF4) by sequestering their DNA-recognition domains. However, it is unclear whether there are other mechanisms of regulatory crosstalk between DELLAs and PIFs. Here, we demonstrate that DELLAs negatively regulate the abundance of four PIF proteins through the ubiquitin–proteasome system. Reduction of PIF3 protein abundance by DELLAs correlates closely with reduced hypocotyl elongation. Both sequestration and degradation of PIF3 by DELLAs contribute to a reduction in PIF3 binding to its target genes. Thus, we show that promotion of PIF degradation by DELLAs is required to coordinate light and GA signals, and the dual regulation of transcription factors by DELLAs by both sequestration and degradation may be a general mechanism.

Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the function of DE-ETIOLATED1 (DET1), a repressor of photomorphogenesis, is disrupted. However, the mechanism by which DET1 represses photomorphogenesis remains unclear. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genetic analysis showed that each pif single mutant could enhance the det1-1 phenotype, and ectopic expression of each PIF in det1-1 partially suppressed the det1-1 phenotype, based on hypocotyl elongation and cotyledon opening angles observed in darkness. Genomic analysis also revealed that DET1 may modulate the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. The observed interaction and regulation between DET1 and PIFs not only reveal how DET1 represses photomorphogenesis, but also suggest a possible mechanism by which two groups of photomorphogenic repressors, CONSTITUTIVE PHOTOMORPHOGENESIS/ DET/FUSCA and PIFs, work in concert to repress photomorphogenesis in darkness.