Allelic Diversity Of ZmPAP21,A Candidate Gene For Low-Phosphorus Tolerance In Maize

Pi deficiency is an important factor limiting the yield of corn.Plants acquire phosphorus mainly in the form of phosphate(Pi),the concentration of which is often the limit for plant uptake.Plants have developed complex root morphology,physiology,biochemistry and molecular adaptation mechanisms to conserve and remobilize internal Pi and to enhance Pi acquisition to secure them against Pi deficiency over a long period of time,which is called PSR(phosphate starvation response).Purple acid phosphatase(PAP),secreted by plant root,plays an important role in PSR.PAP,which is the member of the metallophosphoesterase family,was produced and excreted to mobilize inorganic phosphorus(Pi)from organic compounds for plants,Meanwhile,involved in the balance of phosphorus in plants.There contains a large number of excellent Low-phosphorus tolerance allelic variations in our abundant corn germplasm resources.Identifying these functionally alleles contributes to both understanding molecular mechanism of low-phosphorus tolerance and developing functional markers,thus improving low-phosphorus tolerance of maize new germplasm and hybrids by marker-assisted selection(MAS).The association analysis is a bridge between structural genomics and phenotypics.Therefore,the association analysis that based on candidate genes becomes an effective way to discover the functional allelic variants related to phenotypic variation.In this study,we chose GRMZM5G831009,that positioned within the range of consensus QTLs related to low-phosphorus tolerance as our candidate gene,who then was named as ZmPAP21 due to it’s homologous gene AtPAP21 in Arabidopsis.An association Group,consist of 209 inbred lines come from across the country,with a wide range of genetic diversity was analyzed for the sequence diversity and linkage disequilibrium of ZmPAP21.The result is considered to lay a foundation for the candidate-based association and mining low-phosphorus allelic variation and developing functional markers.The result were as below:(1)ZmPAP21,located on the tenth chromosomes of maize,owns 5 exons and 4 introns.The total length of the coding region is 1399bp,which includes 5 acid phosphatase family conservative region:GDXG,GDXXY,GNH(D/E),VXXH,and GHXH(the bolds represent bases that connected with metal)(2)we finally get 209 ZMPAP21 sequences from all 209 inbred lines.The polymorphism analysis of the 209 ZMPAP21 sequences showed that a total number of 41polymorphic sites were detected in the gene region.Including 45 SNPs(every 47bp to detect one)and 6 Indels(every 356bp to detect one).There 18 polymorphic sites in gene coding region.Including 15 SNPs and 3 Indels.6 of the 15 SNPs were synonymous mutations.1 of the 3 Indels have caused a frameshift mutation,which make translation beforehand.(3)The linkage disequilibrium analysis of ZmPAP21 shows that there was strong linkage disequilibrium within 500bp.Linkage disequilibrium within gene regions was in rapid decline around 1100bp(R2=0.1).According to the linkage disequilibrium structure of ZmPAP21,209 sequences were divided into nine haplotypes,two of which were rare haplotypes.(4)We compared the the haplotype analysis results with population structure and genetic relationship analysis(K=2)results that based on whole genome SNP,found that,although,some inbred lines belong to the same haplotype,their blood relationship is far.The reason for this maybe:on the one hand,the result of this experiment is only based on analysis of single gene SNP and Indel,the number of markers is small.On the other hand,may also be long-term artificial selection and the large variation of the gene.(5)According to sequence polymorphisms,we made the phylogenetic tree of ZmPAP21 gene.The result shows that 6 inbred lines(Jiao51、Nan09530、Dan598、SH15、LJS-1、08WSC187)were furthest with other inbred lines of genetic distance.