Guangdong nongye kexue (Feb 2022)
Analysis of SSR and SNP Loci in Agrotis segetum Based on Transcriptome Sequencing
Abstract
【Objective】Based on transcriptome dataset of Agrotis segetum, the SSR and SNP loci were analyzed.【Method】Total RNA of A. segetum was extracted and the transcriptomes were sequenced with Illumina sequencing platform. SSR and SNP information in total unigene sequences were separately analyzed by MISA and GATK.【Result】In the study, the A. segetum tra nscriptome database contained 66 469 unigene sequences. MISA was used to search the Unigene sequences and 4 438 SSR loci were obtained, which were distributed on 4 048 Unigene sequences, accounting for 6.09% of the total sequences. Mononucleotide and trinucleotide repeats accounted for 54.73% and 29.29% of the total repeats, respectively. The A/T motifs were the dominant microsatellite loci of A. segetum SSR. SSR motifs contained 4 to 24 repeats, with 5 repetitions (21.67%) as the dominant repetitions. The length of SSR loci sequence ranged from 12 bp to 127 bp, including 3 493 moderately polymorphic loci and 820 highly polymorphic loci. GATK was used to search SNP loci in Unigene sequence, and 371 148 SNP loci were successfully searched, inculding 237 619 conversion types and 133 529 transversion types. C/T accounted for 18.61% of the total SNP sites, with the highest ratio, followed by G/A accounting for 18.28%, and all of which belonged to conversion types. The ratio of conversion type (64.02%) was significantly higher than that of transversion type (35.98%).【Conclusion】The SSR loci in the transcriptome database of A. segetum have higher distribution frequency, more species and richer polymorphism; and the conversion type is the main type of SNP variation, which can provide a very important scientific basis for future studies on the genetic structure and differentiation, genetic evolution, migratory rule and integrated control of A. segetum population.
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