Explanation The Genome-wide Association Study Of Agronomic Traits In Rice By Pathway-based Analysis

Rice (Oryza sativa L.) is one of the staple food of more than half the world’s population. However, although rice production has exceeded 7 billion, much of the population growth rate is greater than the rice yield, according to current state to meet the needs of the population growth until 2050 Rice production must increase by 24% than it is now. In addition to the yield need to improve, the rice quality is also very important it is one of the factors that impact of rice-eating population health. Maintenance of genetic diversity in rice landraces for rice quality and yield breeding significant improvement. On the other hand, With the rapid development and widely used of the sequencing technology and GWAS in rice breeding tant made more abundant resource data, currently how to find useful data from these resources, is a research hot. In this study, our use the 14 local rice agronomic traits GWAS data for materials, which offer by xuehui Huang who national center for gene research, institute of plant physiology and ecology, shanghai institutes for biological sciences, Chinese academy of sciences, shanghai, china. Our according to PBA analysis theory, analysis rice agronomic traits associated pathway by PlantGSEA and GSEA analysis tools. Depth discussions rice various agronomic traits associated pathway lay the foundation for quality improvement and breeding of rice.1. GSEA analysis detected totally 103 pathways are associated with the 14 rice agronomic traits, in which the plastid pathway associated with Days to heading, drought tolerance, gelatinization temperature, grain length, Grain shattering, grain weight, grain width, hull color, leaf angle, pericarp color, splikelet number, tiller number but amylose content. Plastid, cytoplasmic membrane-bounded vesicle, membrane, mitochondrion, Plant hormone signal transduction, Proteasome, Protein processing in endoplasmic reticulum, Spliceosome, Endocytosis, Ubiquitin mediated proteolysis, Brassinosteroid biosynthesis, Phenylalanine metabolism, Plant-pathogen interaction, Ribosome total of 14 pathway associated with 7 or passages 7 rice agronomic traits. Glycosaminoglycan degradation, Sphingolipid metabolism, zinc ion binding, Thiamine metabolism... total of 35 pathway associated with only one rice agronomic traits, these rice agronomic traits were apiculus color, Days to heading, drought tolerance, gelatinization temperature, grain length, Grain shattering, grain weight, grain width, hull color, leaf angle, pericarp color, splikelet number, tiller number.2. PlantGSEA software analysis detected a total of 340 pathway associated with 14 rice agronomic traits. Including cellular component, biological process, molecular function, metabolic process, primary metabolic, process, cellular process, macromolecule metabolic process, cellular macromolecule metabolic process in which total 8 pathway associated wich 14 agronomic traits; RNA binding, DNA binding, gene expression... total of 66 pathway associated with 7 or passages 7 rice agronomic traits. Chemical homeostasis, KEGG valine leucine and isoleucine degradation, transcription regulator activity, petide deformylase activity, aerobic respiration, exopeptidase activity... in which total 205 pathway associated wich only one rice agronomic traits. In addition, our detection that rice quality agronomic traits associated with DNA binding, cytoplasmic membrane-bounded vesicle, mitochondria pathway and so on; rice yield agronomic traits associated with Valine, leucine and isoleucine degradation, Arginine and proline metabolism, nucleoprotein, transmembrane protein, transcription factor and so on; rice morphological character agronomic traits associated with membrane, nucleus pathway and so on; rice tinge agronomic traits associated with Phenylalanine metabolism, Phenylpropanoid biosynthesis, Pyruvate metabolism, Ribosome biogenesis in eukaryotes, RNA transport, membrane, zinc ion binding, intracellular, oxidative phosphorylation and so on; rice physiologic agronomic traits associated with Circadian rhythm and so on.