SNP And Association Analysis Of Two Wood Property Genes Of Catalpa Fargesii Bur.

Catalpa fargesii Bur, Bignoniaceae, is an endemic tree in China and well known byits precious timber. It mainly distributed in basins near rivers like Weishui, Fenhe, YellowRiver and in Qinling Mountain area. The breeding study of C. fargesii mainly focuses onmethods, resource collection, cultivar selection, etc., however, barely bases on molecularlevel. In this study, sucrose synthase gene and p-coumarate3-hydroxylase gene wereisolated using a combination of single nucleotide polymorphism and association analysismethods.1) Sucrose synthase gene (SUS) is a key gene in cellulose synthesis pathway. In thisexperiment, the cloned CfSUS cDNA was2887bp in length with an open reading frame(ORF) of2418bp, which encoding805amino acid. DNA of CfSUS5067bp in length weregained after obtaining the introns, in which, coding region was divided into12paragraphsby11introns. The genomic sequences of CfSUS in93C. fargesii clones were aligned,compared and analyzed. Then a total of135single nucleotide polymorphisms (SNPs) weredetected in CfSUS. The numbers of SNPs appeared in exons, introns, non-coding regionswere76,53,6and the frequencies were1/32,1/19,1/9respectively.5inserts and7missings were detected, involving44loci, among which there were1time occurring inexon,10in intron on and1in3’UTR. The range of Indels length was1~15bp. Nucleotidepolymorphism was0.01841. In coding region, there were19silent mutations and57Non-synonymous mutations. Among the135SNPs, there was one third position mutation(T/C/A), while the rest were second-class mutations which contained84transformationsand50transversions. The association analysis of48common SNPs among the135SNPsand9material characters showed that: there were8markers loci significantly associatedwith the average diameter while3significantly associated with string to the centraldiameter; Only two genotypes were detected on the eight loci associated with the averagediameter, of which corresponding phenotype showed base bias; Three genotypes weredetected on three loci associated with string to central diameter, phenotypic types arecharacterized by a homozygous genotype corresponding phenotype is higher than the othertype homozygous genotype phenotypethe, both corresponding phenotype is higher thanhybrid genotype corresponding phenotype. 2) P-coumarate3-hydroxylase gene (hereinafter referred to as C3H) is a key gene inlignin synthesis pathway. In this experiment, the cloned CfC3H cDNA was1825bp inlength and contained an open reading frame (ORF) of1530bp and encoded509aminoacids. DNA of CfC3H3511bp in length were gained after obtaining the introns, in which,coding region was divided into3paragraphs by2introns. The genomic sequence ofCfC3H in88C. fargesii clones were compared and analyzed. Then a total of163singlenucleotide polymorphisms (SNPs) were detected in CfC3H. The numbers of SNPsappearing in5’UTR, exons, introns,3’UTR were4,55,94,10and the frequencies were1/11,1/36,1/6,1/13respectively.45Indels were detected on152sites. Nucleotidepolymorphism was0.00307. In coding region, there were15silent mutations and44Non-synonymous mutations. In the163SNPs, there were157diallele which contained104ttransformations and53transversions, and the rate of Convert/transversion was1.96. Theassociation analysis of17common SNPs in the163SNPs and9material charactersshowed that: there was only one locus associated with siphonopore rate significantly,which was on exon1with two alleles C and G on it and3genotypes detected. Thesiphonopore rates of the three genotypes of marker loci were different, arranging asfollows: CC>GG>CG.