Genetic Dissection Of Combining Ability And Heterosis Of Rice Agronomic Traits Based On Pathway Analysis

The agronomic traits of rice include plant height,panicle length,tillers per plant,filled grains per panicle,1000-grain weight.Deep dissection of agronomic traits is a method of improving the yield of rice.With the development of high-throughput sequencing technology,the completion of rice genome sequencing has become an important turning point in rice breeding.In present study,under North Carolina design II,we constructed the test cross population,according to the principle of pathway analysis and using PlantGSEA software,the GWAS data of 9 agronomic traits including yield traits were used to analyze the phenotype,combining ability and heterosis based on pathway.The results show that:(1)The number of pathways associated with the filled grains per panicle of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA)and test cross population of original phenotype(TC)was 1,37 and 4,respectively.These pathways contains biological regulation and gene expression regulation.The flo-2 gene regulating rice grain size was included in TC dataset.(2)The number of pathways associated with the 1000-grain weight of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA)and test cross population of original phenotype(TC)was 7,1 and 4,respectively.These pathways contain cysteine and methionine metabolism.Both GCA and TC datasets contain GS3 genes for grain size.V and TC datasets contain SaM gene affecting grain weight,glycine,serine and threonine metabolism pathway.(3)The number of pathways associated with the main panicle length of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA)and test cross population of original phenotype(TC)was 76,25 and 26,respectively,These pathways contain SNARE-related vesicle movement pathway.(4)The number of pathways associated with the primary branch of main panicle of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA),test cross population of original phenotype(TC)and test cross population of heterosis over better of parents(BP)was 76,25,26 and 19,respectively.These pathwaysinclude sequence-specific DNA binding transcription factor activity and DNA-dependent transcription pathway.The OsAP2-39 gene,which controls the interaction between abscisic acid and gibberellin,is contained in the V dataset.(5)The number of pathways associated with the plant height of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA)and test cross population of original phenotype(TC)was 3,41 and 50,respectively.These pathways include ATP binding and macromolecular metabolic processes.The nd1 gene controlling plant height dwarfing was found in GCA and TC.(6))The number of pathways associated with the secondary branch of main panicle of trait in paternal population of general combining ability(GCA)and test cross population of original phenotype(TC)was 55 and 54,respectively.These pathways contain DNA-dependent transcription.(7)The number of pathways associated with the spikelet per panicle of trait in paternal population of original phenotype(V),paternal population of general combining ability(GCA),test cross population of original phenotype(TC)and test cross population of heterosis over better of parents(BP)was 21,54,76 and 4,respectively.These pathways include pollen recognition and pollen-pistil interaction.(8)The number of pathways associated with the tillers per plant of trait in paternal population of original phenotype(V),test cross population of original phenotype(TC)and test cross population of heterosis over better of parents(BP)was 5,3 and 10,respectively.These pathways include hydrolase activity.(9)The number of pathways associated with the yield of trait in paternal population of general combining ability(GCA),test cross population of original phenotype(TC)was 34 and 49 respectively.These pathways include purine nucleoside binding pathway,indicating that purine nucleoside binding would affect grain weight per plant.A biological process is a complex network regulation process,which is regulated by genome rather than single gene.In order to obtain excellent traits,high combining ability and heterosis,we can study from related pathways of a certain trait,find related genes of regulating the pathway.In this study,on the basis of geneset,utilization of pathway analysis is a new idea for obtaining heterosis and improving general combining ability of rice.