Association Mapping For Nitrogen-use Efficiency In Rice(Oryza Sativa L.)

In recent rice production,the excessive use of nitrogen fertilizers resulted in a large number of nitrogen loss,and led to the pollution of the environment.It is necessary to search for varieties harboring the genescontroling nitrogen-use efficiency.Nitrogen-use efficiency(NUE)is inherently complex,governed by multiple genetic and environmental factors in rice.In this study,157 pairs of simple sequence repeat(SSR)markers and 11 pairs of single nucleotidepolymorphism(SNP)markers were applied to assess genetic diversity and population structure of a natural population consisting of 184 rice varieties from different regions.We analyzed the association between markers and the related traits of 184 varieties using general linear model method and mix linear model methods in software of TASSEL.By developing SNP markers in the most significant QTL and consulting an RNA-seq database,we searched for genes related to NUE.The main results areas follows:1.In the population containing 184 rice varieties,nitrogen-use efficiency related traits was measured,plant height under low N,panicle number under low N,grain length under low N,plant height ratio of low N/normal N,panicle number ratio of low N/normal N and grain length ratio of low N/normal N,all of these traits phenotypic variation were large.2.A total of 852 alleles were detected in the 184 accessions by using 157 molecular markers,with an average of 5.43 alleles per locus.The genetic diversity averaged 0.6392 ranging from 0.1413(RM6451_Chr1)to 0.9094(RM8277_Chr3).The Polymorphic information content(PIC)had a mean of 0.5776 ranging from 0.1313(RM6451_Chr1)to 0.9024(RM8277_Chr3).3.Seven subpopulations were found in the population constituted of 184 rice varieties,by using Structure2.3.4 H-W balance analysis method.The number of varieties containedfrom subpopulation 1 to subpopulation 7 were 25,33,12,27,67,6 and 12,respectively.4.Through the GLM and MLM models detected a total of 47 SSR markers associated with nitrogen-use efficiency(P?0.01).Including 19 loci significantly associated with plant height under low N,including 7 loci significantly related with plant height ratio of low N/normal N,including 14 loci significantly associated with panicle number under low N,including 7 loci significantly related with panicle number ratio of low N/normal N,including 4 loci significantly associated with grain length under low N,including 7 loci significantly related with grain length ratio of low N/normal N.5.From the associated loci with plant height ratio of low N/normal N,panicle number ratio of low N/normal N,grain length ratio of low N/normal N,to identify elite alleles and their typical carrier materials.For the PHR traits,at the QTLassociated with markerRM5639,the ninth allele(RM5639-9)showedthe largest phenotypic effect(19.60%)and was supposedas an elite allele.It could be found in cultivar Yunxiangjing only.For the TNR traits,at the QTL associated with markerW2,the allele(W2-3)showedthe largest phenotypic effect(14.20%),and was supposedas an elite allele that presented in seven cultivars including the typical cultivar Taducan.For the GLR traits,at the QTL associated with markerRM518,the allele(RM518-1)that existed in two cultivars including typical Hunheti showedthe largest phenotypic effect(19.20%).6.Using SNP markers to increase significant associated loci RM5748 3Mb region marker density.From SNP database screened 5 intragenic SNPs and 6 intergenic SNPs to develop SNP markers.The result show that the eighth SNP loci most significant associated with plant height ratio low N/normal N,predicting near the site there may be have a gene control of nitrogen-use efficiency.7.Using RNA-seq database screen the differentially expressed gene in flanking region around RM5748.LOC_Os03g19420,encoding nicotianamine synthase,showed differentially expression levels under low N condition and normal N resupply,may play a role in the nitrogen-use efficiency.