Study On Genetic Diversity Of Chinese Fir Based On SLAF-seq Technology

Chinese fir[Cunninghamia lanceolata(Lamb.)Hook]is mainly distributed in the southarea of Qinling,Huaihe and north mountain area of Vietnam.It is the advanced species in the Taxodiaceae and one of the commercial forest in the south of China.The diversity level of geographic population about Chinese fir is comparative low,and the genetic differentiation is significant in the population.However,there are little researches about its dynamic change,distribution feature,origin and so on,and the researches,which are concerned on how to project and recover the Chinese fir population,are still insufficient.In order to achieve the following purposes,such as showing genetic relationship,gene exchange,Genetic diversity and evolutionary relationship among geographic populations,speculating its evolution history and so on,104 germplasm resources selected in 8 geographic populations are used to analyze the genetic diversity and genetic evolution of the Chinese fir population by the SLAF-seq technology.The conclusions are as follow:(1)First,we use the SLAF-seq technology to analyze the genetic evolution of the selected germplasm resources.The sequencing depth is 17.18X,610008 SLAF labels are developed and 808697 SNPs are obtained.According to the integrity and filtering by MAF,there are 193591 high consistency groups SNPs.After evolution analysis,104 germplasm resources are divided into two subgroups,i.e.,subgroup 1 and subgroup 2,and the resources are classified by the geographical origin.The phylogenetic tree analysis agrees with the population structure analysis.The genetic distance among different populations are larger than it in one population.The AMOVA results suggest that 14.403%of 104 molecular variations are obtained in different population and 83.089%are obtained in one population.(2)The linkage disequilibrium exists in the 193591 high consistency groups SNPs and the value of r2 is between 0.8 and 1.0.The genetic diversity existsin the 104 germplasm resources and the effective number of alleles(Ne)is between 1.105 and 2.0,The average value is 1.413.The expected heterozygous number(He)is between 0.095 and 0.505 and the average value is 0.266.The observed heterozygous number(Ho)is between 0 and 0.990,and the average value is 0.127.The Nei’s diversity index is between 0.095 and 0.505,and the average value is 0.268.The Shannon’s information index is between 0.199and 0.693,and the average value is 0.425.(3)According to the population structure analysis and phylogenetic analysis,connecting with geological environment change and fossil vegetation data since the Tertiary period,we speculate that Chinese fir evolution in 8 geographic populations is spread from Nanling areas and extends around it,and the Sichuan basin may be a shelter of climate change in the Tertiary period.Because of the closure of basin environment,the relatively large differentiation formed.(4)In the conservation of genetic resources of Chinese fir,only when the germplasm resources with relatively distant relationship are selected as the hybrid parents,it is possible to produce offspring with good performance.When the genetic basis is narrow,we can choose the germplasm resources,which the genetic diversity is high in this study,to conduct genetic improvement.Thus,the results of this study can be effectively applied to the breeding of Chinese fir genetic resources.The overall LD level of the selected geographic populations was high,which was helpful for the subsequent association analysis and the discovery of favorable genes.We can use the results of research to protect plasm resources of Chinese fir and make genetic improvement.The high linkage disequilibrium can be used to genetic correlation analysis and gene mining.