Trade-offs of Linear Mixed Models in Genome-Wide Association Studies

Genome-wide association analysis study on host resistance against the Aeromonas veronii of largemouth bass Micropterus salmoides

Largemouth bass (Micropterus salmoides) has become one of the most important freshwater economic fish farmed almost all over China in recent years. At the same time, the increasing outbreaks of diseases in its aquaculture process have caused substantial economic losses to this industry. However, at present, the genetic basis of disease resistance, including resistance against Aeromonas veronii infection, in largemouth bass is very limited. Therefore, a genome-wide association study (GWAS) on host resistance against the A. veronii of largemouth bass was conducted in the present study. A total of 627 largemouth bass were artificially challenged by A. veronii, among which 160 of the earliest deaths and 173 of the final survivals were genotyped. A total of 3076 high-quality SNPs were used for further analysis employing two analysis models, of which six shared SNPs were finally identified as significant molecular markers with the explaining phenotypic variance ranging from 2.28 % to 8.95 %. Furthermore, seven candidate genes were identified, including one gene, T-cell surface antigen CD2, which is directly involved in T cell activation and the cellular immune response. Additionally, the other identified genes play roles in critical processes such as cell survival, inflammatory responses, and signal transduction. This study lays a genetic foundation for research on largemouth bass disease resistance and studies related to A. veronii. It also contributes significantly to the future development of the commercial production of largemouth bass.

Tumor suppressor p53 modulates activity-dependent synapse strengthening, autism-like behavior and hippocampus-dependent learning

Synaptic potentiation underlies various forms of behavior and depends on modulation by multiple activity-dependent transcription factors to coordinate the expression of genes necessary for sustaining synaptic transmission. Our current study identified the tumor suppressor p53 as a novel transcription factor involved in this process. We first revealed that p53 could be elevated upon chemically induced long-term potentiation (cLTP) in cultured primary neurons. By knocking down p53 in neurons, we further showed that p53 is required for cLTP-induced elevation of surface GluA1 and GluA2 subunits of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR). Because LTP is one of the principal plasticity mechanisms underlying behaviors, we employed forebrain-specific knockdown of p53 to evaluate the role of p53 in behavior. Our results showed that, while knocking down p53 in mice does not alter locomotion or anxiety-like behavior, it significantly promotes repetitive behavior and reduces sociability in mice of both sexes. In addition, knocking down p53 also impairs hippocampal LTP and hippocampus-dependent learning and memory. Most importantly, these learning-associated defects are more pronounced in male mice than in female mice, suggesting a sex-specific role of p53 in these behaviors. Using RNA sequencing (RNAseq) to identify p53-associated genes in the hippocampus, we showed that knocking down p53 up- or down-regulates multiple genes with known functions in synaptic plasticity and neurodevelopment. Altogether, our study suggests p53 as an activity-dependent transcription factor that mediates the surface expression of AMPAR, permits hippocampal synaptic plasticity, represses autism-like behavior, and promotes hippocampus-dependent learning and memory.