Characteristics Of SSR And SNP In I. Dichotoma And I. Domestica Using RAD Sequencing

The materials were purple-flowered I.dichotoma,yellow-flowered I.dichotoma,white-flowered I.dichotoma,I.domestica.They were sequenced by RAD sequencing.The characteristics of SNP and SSR were analyzed by SNP and SSR sites identified after sequencing.The development of SSR markers and SNP markers provided the basis for bioinformatics.Through SSR analysising,some SSR primers were designed to develop polymorphic molecular markers that could be used in the genus Iris for further study.It laid the foundation in developing markers for the Iris.The main findings are as follows:1.SSR analysising was performed on three colours of I.dichotoma and I.domestica.A total of 16012 SSRs were identified.The redults showed that the types of mononucleotide repeats were the most,accounting for 33.18% of the total SSR,and the mainly length was 10-20 bp.Except for purple-flowered I.dichotoma,accounting for32.19% of the total SSR,and the mainly length was 15-21 bp.The average of the total SSRs was 29.25% in dinucleotide repeats,and 13-26 bp in length.In purple-flowered I.dichotoma,the dinucleotide repeat was 1676(31.77%).The number of trinucleotide repeats was 1607(30.46%).In the three colours of I.dichotoma,the types of repeat motifs was mononucleotide,T and A were the main types;CT and GA were the main types in dinucleotide repeat types,followed by TC and AG,TA,AT,TG;GCA and GAA were the main types in trinucleotide repeat types.In I.domestica,the types of repeat motifs was mononucleotide,A and T were the main type;in the dinucleotide repeat type,GA and CT are the main types,followed by AG,TC,AT,and TA;in trinucleotide repeat types,GAA and GCA were the main types.2.SNP analysising of the four materials identified a total of 31014 SNPs.Among these four materials,the SNP heterozygosity ranged from 3.34% to 10.50%.It showed that the SNP heterozygosity was relatively low,which indicated that the homogenicity of the genome was high.The SNPs of the four materials were transition and transversion,and the transition was significantly higher than that of the transversion,the occurrence frequency of C/T was high.3.Through RAD sequencing,homology comparisons were performed on the tags obtained from the four materials.After comparison,the proportion of homology between the purple-flowered I.dichotoma and white-flowered I.dichotoma reached 80.18%,which was similar to the yellow-flowered I.dichotoma.The proportion of homology reached81.32%,and the proportion of homology with I.domestica reached 54.47%.The homology of white-flowered I.dichotoma with the yellow-flowered I.dichotoma reached 81.34%,and the homology with I.domestica reached 55.86%.The proportion of the homology of yellow-flowered I.dichotoma and I.domestica reached 54.87%.After homology comparison,it was found that there was a high proportion of homology between purple-flowered I.dichotoma,yellow-flowered I.dichotoma and white-flowered I.dichotoma.4.By screening and amplifying 51 pairs of primers,4 pairs of effective primers were screened from the primers,and then 4 pairs of primers were detected in 43 samples of Iris.The results were as follows: The amplification results of primer No.7 showed that different bands were amplified in I.dichotoma,I.domestica,I.mandshurica,I.ruthenica,I.tigridia,I.ventricosa,I.ensata,and I.halophila.No bands were amplified in I.laevigate,I.typhifolias was the same bands as that of I.germanica.In the amplification results of No.19 primers,I.dichotoma,I.domestica,I.laevigate,I.ensata,and I.halophila were amplified different bands.Among them,the same bands were amplified from I.laevigate,I.ensata,and I.halophila.Only differential bands of I.domestica were amplified in primer No.28,in the amplification results of primer No.40,there were significant differences among the bands amplified in I.dichotoma,I.domestica,I.typhifolia,I.germanica,I.mandshurica,I.ruthenica,I.tigridia,I.laevigate.The same bands were amplified from I.ventricosa and I.laevigate,and the other same bands were amplified from I.ensata and I.halophila.5.In this experiment,31014 SNPs and 16012 SSRs were identified from I.dichotoma and I.domestica by using RAD-seq,which laid the foundation for the development of molecular markers in further study,which shows that RAD-seq could be applied to the genus Iris.