A Taxonomic Study On Kernel-Using Apricot Using Morphological Traits,Chloroplast Genome And Nuclear Genome SSR

Kernel-using apricot is an ecological and economic species native to the China,it is one of the six woody grain and oil species,also known as "iron banker".Comparing with other apricot,Kernel-using apricot has extremely strong adaptability,high yield,high nutritional and economic vaules,and has a highly potential for the development and utilization.The taxonomic status of Kernel-using apricot is still being debated,which significantly hindered the breeding of Kernel-using apricot and limited the industrialization of genetic resources.In this study,Kernel-using apricot and two Armeniaca taxa(Prunus armeniaea L.and Prunus sibirica L.)were selected to analysis the taxonomic status of Kernel-using apricot based on morphological traits,Chloroplast(cp)genome,and nuclear SSRs.The main results are included as follows:1.The genetic diversity analysis of morphological characteristics showed that there was a high variation in leaf,flower,fruit,stone and nucleolus of Kernel-using apricot,P.armeniaea and P.sibirica.The fruit weight variation coefficient was the highest(0.72),whereas,the leaf shape index was smallest(0.05),which indicated the genetic diversity of Kernel-using apricot,P.armeniaea and P.sibirica resources in china was relatively abundant.Comprehensive analysis suggested that P.armeniaea was the highest level of genetic diversity,followed by P.sibirica and Kernel-using apricot.2.The cp genome sequence of Kernel-using apricot,P.armeniaea and P.sibirica showed that the cp genome of P.sibirica was the largest(158224 bp),followed by the Kernel-using apricot(157994 bp)and P.armeniaea(157951 bp),which resulted from the sequence diversity of LSC and SSC.The cp genome structure and content were similar to those of typical angiosperm cp genomes with a pair of IRs separated by an SSC regionand an LSC region,and contained 129 unique genes,including 85 protein-coding genes,36 transfer RNA(t RNAs),and eight ribosomal RNA(r RNAs).No rearrangements were observed in the Kernel-using apricot,P.armeniaea and P.sibirica,which was consist with the cp genomes of Prunus persica,Prunus pseudocerasus and Nicotiana tabacum.The variation of SSRs,SNP,indel and IR/SC border were identified in the Kernel-using apricot,P.armeniaea and P.sibirica cp genome,which could be used for studying the germplasm identification,population structure,and phylogenetics of Armeniaca.3.The genetic diversity revealed by nuclear SSR,the rusults indicated a high level of genetic diversity(He=0.85,I=2.20)was obtained in Kernel-using apricot,P.armeniaea and P.sibirica,and the highest degree of genetic diversity occurred in P.armeniaea(He=0.76,I=1.64),fllowed by P.sibirica(He=0.76,I=1.59)and Kernel-using apricot(He=0.72,I=1.45).The genetic differentiation values(FST)and gene flow(Nm)was estimated between 0.07-0.12 and 2.17-3.18,respectively.Molecular variance(AMOVA)analysis revealed that there were12.41% genetic variation among taxa,87.59% genetic variation within texon.4.The single factor analysis of variance and principal component analysis showed that almost morphological characteristics of Kernel-using apricot was larger than that of P.sibirica,whereas,less than that of P.armeniaea.There were 27 characteristics,including leaf length,leaf width,and petiole length etc.,between Kernel-using apricot and P.sibirica show highly significant or significant differences,and 17 characteristics,including mesocarp split,fruit length,and fruit width etc.,between Kernel-using apricot and P.armeniaea show highly significant or significant differences.Cluster analysis was performed based on morphological characteristics,which showed that Kernel-using apricot was closed to P.armeniaea.5.Most of SSR,SNP and indel of Kernel-using apricot,P.armeniaea and P.sibirica were identified in non-coding region cp genome,including 43 cp SSR from both Kernel-using apricot and P.sibirica,53 cp SSR from both Kernel-using apricot and P.armeniaea,683 SNP from both Kernel-using apricot vs P.sibirica,346 SNP from both Kernel-using apricot vs P.armeniaea,22 and 66 indel from Kernel-using apricot vs P.armeniaea and Kernel-using apricot vs P.sibirica,respectively.Seventy-seven protein coding genes were used for phylogenetic inference,supporting a sister relationship between Kernel-using apricot and P.armeniaea.Therefore,our results indicated that Kernel-using apricot closed to P.armeniaea based on both coding and non-coding genes of cp genome.6.The analysis of Structure,UPGMA,NJ and PCo A were performed based on nuclear SSR showed Kernel-using apricot was closed to P.armeniaea.There was a simlarly genetic background between Kernel-using apricot and North China region(Hebei,Shanxi),Northwest China region(Shaanxi),Northeast China region(Liaoning)and East China region(Shandong).In summary,Kernel-using apricot was closed to P.armeniaea,where some stability differences were found in both of them.In our study,according to the morphological traits,cp genome,nulcear SSR,and the concept of subspecies and varieties,Kernel-using apricot should be classfied into a variety of P.armeniaea.