Evolutionary Force And Functional Characterization Of Livestock Reproductive Axis And Growth Axis Genes

In this study, we detected positive selection with reproductive axis and growth axis genes.Growth axis genes are extracted from literatures of which topic is about animal growth and repeoduction, some reproductive axis genes come form a pig repduction gene database, ReCGiP.A maximum likelihood method in codeml program is used to investigate evolution pressure of coding sequences, the excess of non-synonymous to synonymous nucleodite substitution rates per site indicate positive selection. GO and DAVID tools are used to annotate and visualize posotive selection gene function that decected in animal reproductive and growth axis, and gave a comprehensive understanding the biological meaning behind these positive selection genes. We also build a gene-to-gene co-citation netwoek for growth axis genes to study the relationship between gene network and gene evolutionary pressure. In this study we identify some SNPs in ZP2and ZP4by sequencing. The coalescent model in DetSel and LOSITAN software are used to investgate the molecular adaptation in ZP2and ZP4, besides statistical test in Tajima’D, Fu and Li’s D*, Fu and Li’s H*and Fu’s Fs.The main results of this study are:(1)311reprodutive axis genes are collected and45genes are subjected to positive selection, and722growth axis genes are collected and46genes are under positive selection. The positive genes function in reproductive axis are involved in (a) astrocyte different and activation;(b) positive regulation of protein metabolic process and (c) regulation of MAP kinase activity and positive selection genes in growth genes are related with (a) cell locomotion, including cell death, cycle, proliferation, communication;(b) metabolic, including phosphate metabolic process, protein modication process, triglyceride catabolic process;(c) activity, including protein kinase activity, catalytic activity, transferase activity, growth factors activity most of biological process were positive regulation.(2) We find a weak negative correlation between gene evolutionary pressure and gene location, and this suggests that gene location may constraint gene function. (3) We identify7SNPs in ZP2, and these mutation sites are under neutrual evolution and none of them are significantly affectet the litter size in pigs. There are27SNPs dectected in ZP4, T2950C is subjected positive selection but not is associat with litter size in swine, A268T is significantly associated with litter size but under neutral evolution.(4) LF is subjected to positive selection, Further study find that the positive selection sites are either located in the LF-bacteria binding region or the peptides of LFcin and LFampin, indicating that the selection pressure is related to LF-bacteria interaction.This study suggest that:Positive selection genes in reproduction axis and growth axis may be candidate gene in animal reproduction and growth study. Statical test could be used to identify sites or domains under positive selection express that function important (like study in chapter5), but it should be carfully investaged (T2950C was under potive selection but not associated with litter size in swine) in lab.