Abstract: In order to accelerate the research process of marker-assisted selection (MAS) in breeding of tapertail anchovy (Coilianasus), the brain transcriptome sequencing was carried out in 12 individuals of 2 years old including 6 females and 6 males of cultured tapertail anchovy, respectively. The MISA software was used to mining expressed sequence tag-simple sequence repeats (EST-SSRs) from unigenes in the brain transcriptome of tapertail anchovy, and large-scale development of polymorphic EST-SSRs was carried out by SSRMMD tool. The genetic diversity of three cultured populations of tapertail anchovy was studied based on the selected polymorphic EST-SSR markers. Results showed that 95 905 EST-SSRs were identified from 143 374 unigenes in the brain transcriptome of female tapertail anchovy, and 88 774 EST-SSRs were identified from 135 215 unigenes in the brain transcriptome of male tapertail anchovy, with the maximal number of di-nucleotide EST-SSRs, and decreasing trend of the number of the other nucleotide EST-SSRs, accompanied by an increase in the number of repeat base. The dominant repeating units were found to be A/T in mononucleotide, dinucleotide and trinucleotide EST-SSRs, AC/GT in dinucleotide and AGG/CCT in trinucleotide EST-SSRs. Twenty EST-SSRs sequences from 1 082 polymorphic EST-SSRs were randomly selected to design specific PCR amplification primers, in order to evaluate their validity and polymorphism. Eighteen pairs of primers were proved to have better polymorphism and were used to evaluate the genetic diversity of three cultured tapertail anchovy populations in different years (2018, 2019 and 2020). The tapertail anchovy had average values of 0.445 2 in observed heterozygosity (Ho), 0.485 4 in expected heterozygosity (He) and 0.485 4 in polymorphic information content (PIC) in the three cultured populations, which proved that the genetic variation of cultured tapertail anchovy was still abundant. The finding indicated that these polymorphic EST-SRRs developed from the brain transcriptome data were applied to germplasm resource evaluation of the cultured population in different years and further genetic breeding research of tapertail anchovy.
于爱清, 施永海, 徐嘉波. 长江刀鲚脑转录组多态性EST-SSRs的规模化开发与利用[J]. 大连海洋大学学报, 2023, 38(2): 196-205.
YU Aiqing, SHI Yonghai, XU Jiabo. Development and application of polymorphic EST-SSRs Markers in cultured tapertail anchovy (Coilia nasus) based on brain transcriptome dataset. Journal of Dalian Ocean University, 2023, 38(2): 196-205.
2023, Vol. 38 
