SNP discovery by high-throughput sequencing in soybean

<p>Abstract</p> <p>Background</p> <p>With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology.</p> <p>Results</p> <p>A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp.</p> <p>Conclusions</p> <p>We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops.</p

Demystifying Compiler Unstable Feature Usage and Impacts in the Rust Ecosystem

Rust programming language is gaining popularity rapidly in building reliable and secure systems due to its security guarantees and outstanding performance. To provide extra functionalities, the Rust compiler introduces Rust unstable features (RUF) to extend compiler functionality, syntax, and standard library support. However, these features are unstable and may get removed, introducing compilation failures to dependent packages. Even worse, their impacts propagate through transitive dependencies, causing large-scale failures in the whole ecosystem. Although RUF is widely used in Rust, previous research has primarily concentrated on Rust code safety, with the usage and impacts of RUF from the Rust compiler remaining unexplored. Therefore, we aim to bridge this gap by systematically analyzing the RUF usage and impacts in the Rust ecosystem. We propose novel techniques for extracting RUF precisely, and to assess its impact on the entire ecosystem quantitatively, we accurately resolve package dependencies. We have analyzed the whole Rust ecosystem with 590K package versions and 140M transitive dependencies. Our study shows that the Rust ecosystem uses 1000 different RUF, and at most 44% of package versions are affected by RUF, causing compiling failures for at most 12%. To mitigate wide RUF impacts, we further design and implement a RUF-compilation-failure recovery tool that can recover up to 90% of the failure. We believe our techniques, findings, and tools can help to stabilize the Rust compiler, ultimately enhancing the security and reliability of the Rust ecosystem.Comment: Published in ICSE'2024 Conference: https://conf.researchr.org/details/icse-2024/icse-2024-research-track/6/Demystifying-Compiler-Unstable-Feature-Usage-and-Impacts-in-the-Rust-Ecosystem. Project webiste: https://sites.google.com/view/ruf-study/home. Released Source Code Zonodo: https://zenodo.org/records/828937

Omega-3 Polyunsaturated Fatty Acids Protect Neural Progenitor Cells against Oxidative Injury

The omega-3 polyunsaturated fatty acids (ω-3 PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), derived mainly from fish oil, play important roles in brain development and neuroplasticity. Here, we reported that application of ω-3 PUFAs significantly protected mouse neural progenitor cells (NPCs) against H2O2-induced oxidative injury. We also isolated NPCs from transgenic mice expressing the Caenorhabditis elegans fat-1 gene. The fat-1 gene, which is absent in mammals, can add a double bond into an unsaturated fatty acid hydrocarbon chain and convert ω-6 to ω-3 fatty acids. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining showed that a marked decrease in apoptotic cells was found in fat-1 NPCs after oxidative injury with H2O2 as compared with wild-type NPCs. Quantitative RT-PCR and Western blot analysis demonstrated a much higher expression of nuclear factor erythroid 2-related factor 2 (Nrf2), a master transcriptional factor for antioxidant genes, in fat-1 NPCs. The results of the study provide evidence that ω-3 PUFAs resist oxidative injury to NPCs

Efficacy and safety of anterior transposition of the ulnar nerve for distal humerus fractures: A systematic review and meta-analysis

BackgroundThis systematic review and meta-analysis was performed to summarize available evidence of anterior transposition of the ulnar nerve for patients with distal humerus fractures.Materials and MethodsThe databases were searched from PubMed, Cochrane, Embase, Scopus, Web of Science, Chinese National Knowledge Infrastructure (CNKI), Chongqing VIP Database (VIP), and Wan Fang Database up to June 2022. The clinical outcome included operation time, fracture healing time, hospital stays, elbow joint function, and ulnar neuritis rate. Statistical analysis was performed with Review Manager 5.3 (Cochrane Collaboration).ResultsA total of 17 studies were included (8 RCTs and 9 retrospective studies), and 1280 patients were analyzed. The results of this meta-analysis showed anterior transposition group had longer operation time (MD = 20.35 min, 95%CI: 12.56–28.14, P &lt; 0.00001). There was no significant difference in fracture healing time (SMD = −0.50, 95%CI: −1.50–0.50, P = 0.33), hospital stays (MD = −1.23 days, 95%CI: −2.72–−0.27, P = 0.11), blood loss (MD = 2.66 ml, 95%CI: −2.45–7.76, P = 0.31), and ulnar neuritis rate (OR = 1.23, 95%CI: 0.63–2.42, P = 0.54) between two groups. Finally, elbow joint motion, elbow joint function, fracture nonunion, and post-operative infection (P &gt; 0.05) between two groups were not significantly statistic difference.ConclusionThis meta-analysis showed that anterior transposition group is not superior to non-transposition group for patients with distal humerus fractures without ulnar nerve injury. On the contrary, non-transposition group have shorter operation time than that of anterior transposition group. Non-transposition group did not increase the post-operative ulnar neuritis rate. Therefore, both anterior transposition group and non- transposition group are the treatment options for patients with distal humerus fractures without ulnar nerve injury. Besides, these findings need to be further verified by multi-center, double-blind, and large sample RCTs

Arabidopsis CPR5 Independently Regulates Seed Germination and Postgermination Arrest of Development through LOX Pathway and ABA Signaling

The phytohormone abscisic acid (ABA) and the lipoxygenases (LOXs) pathway play important roles in seed germination and seedling growth and development. Here, we reported on the functional characterization of Arabidopsis CPR5 in the ABA signaling and LOX pathways. The cpr5 mutant was hypersensitive to ABA in the seed germination, cotyledon greening and root growth, whereas transgenic plants overexpressing CPR5 were insensitive. Genetic analysis demonstrated that CPR5 gene may be located downstream of the ABI1 in the ABA signaling pathway. However, the cpr5 mutant showed an ABA independent drought-resistant phenotype. It was also found that the cpr5 mutant was hypersensitive to NDGA and NDGA treatment aggravated the ABA-induced delay in the seed germination and cotyledon greening. Taken together, these results suggest that the CPR5 plays a regulatory role in the regulation of seed germination and early seedling growth through ABA and LOX pathways independently