Identification of epistasis loci underlying rice flowering time by controlling population stratification and polygenic effect.

Flowering time is an important agronomic trait, attributed by multiple genes, gene-gene interactions and environmental factors. Population stratification and polygenic effects might confound genetic effects of the causal loci underlying this complex trait. We proposed a two-step approach for detecting epistasis interactions underlying rice flowering time by accounting population structure and polygenic effects. Simulation studies showed that the approach used in this study performs better than classical and PC-linear approaches in terms of powers and false discovery rates in the case of population stratification and polygenic effects. Whole genome epistasis analyses identified 589 putative genetic interactions for flowering time. Eighteen of these interactions are located within 10 kilobases of regions of known protein-protein interactions. Thirty-seven SNPs near to twenty-five genes involve in rice or/and Arabidopsis (orthologue) flowering pathway. Bioinformatics analysis showed that 66.55% pairwise genes of the identified interactions (392 out of the 589 interactions) have similarity in various genomic features. Moreover, significant numbers of detected epistatic genes have high expression in different floral tissues. Our findings highlight the importance of epistasis analysis by controlling population stratification and polygenic effect and provided novel insights into the genetic architecture of rice flowering which could assist breeding programmes.

Neutrophil sphingosine 1-phosphate and lysophosphatidic acid receptors in pneumonia.

The phospholipids sphingosine 1-phosphate (S1P) and lysophosphatidic acid (LPA) act via transmembrane receptors S1P 1-5 and LPA 1-3, respectively. Both have been implicated in inflammatory responses. S1P and LPA receptor profiles on neutrophils of patients with pneumonia compared with healthy subjects were determined by PCR and Western blotting. Chemotaxis studies were performed to assess functional differences. S1P or LPA receptors were immunoprecipitated from neutrophils to assess receptor heterodimerization with CXCR1, an IL-8 receptor, by Western blotting. Receptors S1P 1, 4, and 5 and LPA 2 were expressed on neutrophils from both subject groups, but S1P 3 and LPA 1 receptor expression was mainly confined to neutrophils of patients with pneumonia. Chemotaxis of neutrophils from patients with pneumonia compared with control subjects was significantly increased in response to S1P and LPA. Pretreatment with S1P or LPA reduced IL-8-induced neutrophil chemotaxis and transcriptional expression of the CXCR1 receptor. Receptors S1P 3 and 4 and LPA 1 formed constitutive heterodimers with CXCR1. LPA treatment reduced the amount of LPA 1/CXCR1 heterodimer. Therefore, profiles of S1P and LPA receptors differ between neutrophils of patients with pneumonia and control subjects, with consequences for neutrophil function.