Journal of Dalian Ocean University  2024, Vol. 39 Issue (1): 48-56 DOI: 10.16535/j.cnki.dlhyxb.2023-164 |
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| SSR, SNP and InDel locus characteristics analysis in Gymnocypris eckloni based on transcriptome sequencing |
| HE Caixia，LI Changzhong，JIN Wenjie，BAO Changhong，JIAN Shenglong，LI Zhaonan，WANG Linan，YAN Qingchun，WANG Zhenji，WANG Guojie，CHEN Yanxia*
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| 1.College of Ecological and Environmental Engineering，Qinghai University，Xining 810016，China；2.Qinghai Fisheries Technology Extension Center，Xining 810012，China |
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Abstract In order to utilize molecular markers for large-scale development and marker-assisted selection in breeding of Gymnocypris eckloni, the transcriptome was sequenced by Illumina Novaseq 2000 platform, and the SSR, SNP and InDel loci were analyzed using MISA and GATK3 software in gill, kidney, and liver of G.eckloni, after total RNA extraction and cDNA library construction. The results showed that a total of 128 727 SSR were found in 486 221 Unigenes, with a frequency of 26.47% and an average of one SSR per 3.76 kb; There were six repeat types in G.eckloni SSR, among which mononucleotide and dinucleotide were dominant, accounting for 46.53% and 42.45% of the total number of SSR loci, respectively. The total number of repeat motif types was 77, among which the frequency of the two motifs, A/T and AC/GT, were the most frequent, and they were the dominant repeat motifs in the SSRs of G.eckloni; Among all the repeats, the number of repeats between 5 and 15 was the largest, accounting for 87.52% of all SSR loci. In addition, 399 080 SNP loci were obtained by GATK3 software, and the transitions types were more than the transversion types, accounting for 56.29% and 43.71% of the total SNPs, respectively. The distribution frequency of A/G was slightly higher than C/T in the transition type, while the frequency of A/T was the highest and that of C/G was the lowest in the transversion type. The analysis showed that a total of 254 065 InDel loci were identified from the transcriptome of G.eckloni, with an average of one InDel locus per 1 903 bp. The largest number of unigenes was found in both SNP and InDel loci, and the unigenes containing one locus of SNP and InDel were the largest. The SSR, SNP and InDel loci were shown to be abundant in the transcriptome of G.eckloni, and the findings will be of great value for the identification of germplasm resources, population genetics and conservation management of the G.eckloni in the future.
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Published: 13 March 2024
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