Development of whole-genome simple sequence repeat markers in Proto-salanx chinensis and their test in different ecological populations
Krait software was used to analyze the distribution characteristics of perfect microsatellites in the whole genome of Protosalanx chinensis, which was published in 2020 with a higher degree of splicing, and to develop polymorphic microsatellite DNA (also known as simple sequence repeat) markers. The...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Zhejiang University Press
2023-06-01
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| Series: | 浙江大学学报. 农业与生命科学版 |
| Subjects: | |
| Online Access: | https://www.academax.com/doi/10.3785/j.issn.1008-9209.2022.04.191 |
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| Summary: | Krait software was used to analyze the distribution characteristics of perfect microsatellites in the whole genome of Protosalanx chinensis, which was published in 2020 with a higher degree of splicing, and to develop polymorphic microsatellite DNA (also known as simple sequence repeat) markers. The results showed that a total of 587 554 perfect microsatellite loci were obtained in the whole genome of P. chinensis, with a total sequence length of 11 803 017 bp, accounting for 2.53% of the whole genome length. Among six repeat types of microsatellites, the number of dinucleotide was the largest (401 585, accounting for 68.35%). In the 99 pairs of primers designed for microsatellite loci, 39 were polymorphic. Among them, 14 microsatellite markers with favorable polymorphism were selected to test one representative population selected from each of the migratory, landlocked, and introduced populations. The results indicated that 14 microsatellite markers with favorable polymorphism could achieve effective amplification in the three representative populations. The genetic diversity and genetic structure of the three populations were analyzed, and it was found that the migratory population (Chongming Island population) had abundant genetic variation (the mean expected heterozygosity is 0.614, and the mean polymorphism information content is 0.576), which could be clustered into a genetic group different from the freshwater populations [including Taihu Lake population (landlocked) and Lianhuan Lake population (introduced)], and there were large genetic distance and extremely high level of genetic differentiation level between them [the genetic differentiation index (F<sub>st</sub>) is higher than 0.25, P＜0.05]. The genetic variations between the two freshwater populations (Taihu Lake and Lianhuan Lake populations) were relatively scarce and the genetic distance between them was small. Although there was significant genetic differentiation between them, the genetic differentiation level was relatively low (F<sub>st</sub>=0.102, P＜0.05). These results indicate that the migratory population has potential conservation value of germplasm resource, which provide basis for the development of microsatellite markers and construction of genetic maps, and furthermore provide references for the subsequent evaluation of large-scale population germplasm resources of P. chinensis. |
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| ISSN: | 1008-9209 2097-5155 |