| Caragana intermedia,a species of Caragana Fabr.,Leguminosae and perennial xerophytism shrub growing on fixed and semi-fixed dunes where the altitude ranges from 900m to 2400m,widely distributes in north and northwest China.It plays critical roles in soil and water conservation,and is valuable as forage,medicine and environmental afforestation.Revealing the genetic background of C.intermedia provides theoretical basis for breeding materials selection,analysis of system evolution,reasonable utilization of resources and better ' protection strategies'formulation.Molecular marker is a powerful tool to study genetic structures,directly reflecting the genetic differences between group and individual at DNA level.Based on SSR markers independently developed from the C.intermedia transcriptome data under drought stress,in this paper,C.intermedia samples from ten different regions in central Inner Mongolia were collected and the genetic diversity was analyzed.The results are as following:1.Based on SSR markers developed from the C.intermedia transcriptome under drought stress:Altogether 404 SSR markers were found which were distributing in 349 Unigenes,with an occurrence frequency of 14.78%.The most abundant motif type is dinucleotide,which accounts for 64.90%of the total SSRs;Then comes the trinucleotide,with a frequency of 33.70%.The dominant motifs of dinucleotide are mainly AG/CT and GA/TC,accounting for 29.45%of the total SSRs;the trinucleotide motifs are mainly AAG/CTT,accounting for 5.69%of the total SSRs.Seventy-six pairs of primers were designed and synthesized,among them,54 pairs of primers produced clear bands.Seven pairs of good primers which are with perfect polymorphism and repeatability and are also suitable for C.korshinskii were finally selected.The number of alleles amplified from each pairs of primers ranges from 3 to 8,with an average of 5.The variation of observed heterozygosity in each site is from 0.108 to 0.398,with an average of 0.251,and the variation of expected heterozygosity ranges from 0.105 to 0.495,which averages 0.268.2.Genetic diversity analysis of populations:The genetic diversity of 10 populations were analyzed based on the selected 7 pairs of polymorphic primers.The results show that genetic diversity index are respectively NA = 2.547,NE= 1.424,HE=0.261 and I = 0.445.Genetic diversity of 10 populations was evaluated by the integration of the genetic diversity index of NE,HE and I.The conclusion is that the overall genetic diversity of the population is low,the highest population is BL,the lowest is the population SZ.According to NE,HE and I,the genetic diversity of population from high to low in turn is BL,LC,HY,HL,DG,WN,GY,MA,WC and SZ.3.Genetic differentiation analysis of populations:The genetic distance among populations ranges from 0.0027 to 0.0722,and the range of genetic identity is from 0.9304 to 0.9973.According to the genetic identity,UPGMA clustering the population finds that most of the populations are divided into two catageries of C.intermedia and C.korshinskii,but there are some overlapping phenomenon among the populations.The average inbreeding coefficient(Fis)of the population is 0.143,which indicates that there are obvious inbreeding phenomena in the population;the gene degree of differentiation(Fst)was from 0.036 to 0.164,with an average of 0.065,indicating that populations have moderate genetic differentiation.The gene flow(Nm)was high,with an average of 3.589,leading to a small genetic variation among populations.Analyzing the genetic distance and geographical distance of the population finds that there is no significant relationship between the two groups(R2 = 0.023,R2 = 0,0201);Molecular variance analysis(AMOVA)indicates that the variation mainly occurs between individuals within the population.All the analyses above show that the genetic diversity of the tested materials is low,which may be caused by the close sampling distance of the population or much human beings intervention,more genetic communication and obvious inbreeding phenomenon. |
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