The Variation And Genetic Stability Of Chloroplast Genome Of Loblolly Pine(Pinus Taeda L.)

In order to understand the variation and identify the parentage model of chloroplast genome of loblolly pine,chloroplast genome of the 54 individuals from the second generation breeding population and 45 offspring individuals from a 9×5 tester design??were compared,results are as follows:1.After sequencing and control the quality of chloroplast genome,the sequence was compared with the referenced sequence?registration: NC₀21440.1?in NCBI database.81 SNPs loci were found,which unevenly distribute between 3990 bp to 119714bp?the referenced chloroplast is 121530bp?.2.The sequences of 32 SNPs with variation rate of more than 5% were annotated from the 54 individuals of the second generation breeding population,of which 14 SNPs were in the gene interval and 18 SNPs were in 9 genes.9 SNPs were detected in the gene ycf1,accounting for 11.11% of the total SNP site and 50% of the SNP sites of gene.The gene ycf2 has 3 SNPs,accounting for 3.70% of total SNP and 16.67% of SNP of genes.There were 1 SNP in the gene trnG-GCC,atpH,rpoC1,rps11,rpl2,rrn23,and chlN,respectively.3.23 pairs of specific primers were designed according to SNP sites with a variation frequency of more than 5%.Using the 23 primer pairs to amplificated the 45 individuals and their parents of the tester design.,the product was sequenced and 19 SNPs were detected and compared by using software MAGE.It was found that all the female parent were inconsistent to the offspring with the SNP haploid.Based on 19 SNPs,the male parent N4 is exactly the same as the seven progeny individuals,and there are two SNPs difference with the other two.W03 is consistent with only one progeny,and five of the progeny are consistent.Male parent 222 is not consistent with the offspring,but the five 222 ramets are consistent with each other,and the nine children are the same.The 7 ramets of S1 are consistent,different from the progeny,and 8 progeny are consistent.It is confirmed that the chloroplast of Pinus taeda is not a matrilineal inheritance.4.The phylogenetic trees were constructed using Neighbor Joining method or Maximum Linlihood method based on 19 SNPs and MEGA software.Individuals from different male parent can differentiate,as the same as the results of SNPs comparison.In the three phylogenetic trees,the results of the circle tree are more intuitive.5.The optimal result of this study was that all SNPs were consistent between the male parent ramets and the progeny.But the actual results are a little different from our assumptions.However,based on uniformity of 7 progeny and their male parent N4 in 19 SNPs,all or most offspring of male parent of W03,222 and S1 are consistent,but different from the mother parents,it was preliminarily confirmed that the chloroplasts are in paternal inheritance.In order to obtain the sufficient evidence,subsequent tests shall be validated using materials with clear parental relationship under strict control conditions.