Genetic Diversity Of Wild And Cultivated Populations Revealed By SSR Markers In Castanea Henryi

Castanea henryi(Skam)Rehd.et Wils.is a famous woody and fruit tree species in southern China.The cultivation has a long history,and a number of cultivars have been formed.In order to carry out effective breeding,we must first understand its genetic diversity.In this study,genomic and transcriptome SSR markers were generated by high-throughput sequencing.These SSRs were used to analyze the genetic diversity of wild and cultivated populations,which will provide great significance to the protection and breeding of gene resources..The main conclusions are as follows:1.In the 2,051,475 sequences from the SSR enriched library 2,117,345 SSRs are searched,and the number of SSRs in the composite form is 640,155.The GC content of C.henryi was 35.8%,and the SSR content of the dinucleotide was the most repeating unit,accounting for 73.22% of the total,followed by trinucleotide(12.61%),single nucleotide(12.56%),and tetranucleotide(1.33%).The dominant repeating unit of single nucleotide,dinucleotide and trinucleotide are A/T,AC/GT,AAG/CTT,respectively..Ten pairs of stable,high codominance and polymorphism genomic SSR primers were obtained.2.Transcriptome sequencing was performed on the root,stem,leaf,female flower,male flower and fruit tissue of the excellent variety "Jianou No.1".Unigene analysis was performed and 176,928 Unigenes were obtained.The NR database annotated 45,036 Unigenes(44.23%),and the most information was obtained.The KEGG database obtained the least information,and only 6695 Unigenes were annotated.Unigene has been annotated to 5,422 in all databases,accounting for only 3.06%.The 35,972 pairs of SSR primers were searched,and the distribution frequency was 20.33%.Among them,21,762 single-base repeats accounted for 60.50%,followed by dinucleotides(24.83%),trinucleotides(13.69%),and tetranucleotides(0.86%).Six pairs of EST-SSR primers with good stability,high codominance and polymorphism were obtained.3.Genetic diversity analysis of wild and cultivated populations was carried out using the developed genomic and transcriptome SSR.The 10 pairs of genomic SSRs were mainly distributed at 107-370 bp,and the 6 pairs of transcriptome SSRs were mainly distributed at 100-328 bp.The combined analysis of genomic and transcriptome SSR showed that the population observed allele was 2.375-5.875,the effective allele was 1.749-3.843,the Shannon information index was 0.607-1.433,and the expected heterozygosity was 0.384-0.710.The population genetic diversity(Ht)was 0.742,the genetic diversity(Hs)in the population was 0.596,the gene differentiation coefficient(Fst)was 0.196,and the gene flow is 0.039.Cluster analysis was carried out,and he 12 populations were divided into 4 categories.The first category included JY and JT,the second category includes JC,the third category includes LS and JJ,and the fourth category includes GY,LP,HN,JS,TNKS,TN and HY.