Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream<italic style="font-style: italic"> Acanthopagrus latus</italic>

Jin ZHANG; Jinmei LIU; Chong HAN; Cheng PENG; Yong LI; Junhong XIA; Yong ZHANG; Shuisheng LI; Haoran LIN

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Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus

Biology | Updated：2024-10-12

- Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus
- Journal of Oceanology and Limnology Vol. 41, Issue 3, Pages: 1073-1083(2023)
- Affiliations：
  
  1.State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
  2.Zhuhai Modern Agriculture Development Center, Zhuhai 519000, China
  3.Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Author bio：
  
  lshuish@mail.sysu.edu.cn
- Funds：
- DOI：
  CLC：
- Received：24 September 2021，
  
  Published：01 May 2023
- Accepted：
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ZHANG Jin,LIU Jinmei,HAN Chong,et al.Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus[J].Journal of Oceanology and Limnology,2023,41(03):1073-1083.
DOI：

ZHANG Jin,LIU Jinmei,HAN Chong,et al.Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus[J].Journal of Oceanology and Limnology,2023,41(03):1073-1083. DOI：

摘要

Abstract

Yellowfin seabream

Acanthopagrus latus

is an important economic fish in Chinese coastal areas. Given its narrow distribution and overfishing

the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction. We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream. A total of 68 086 unigenes were obtained

with an N50 of 3 391 bp on average length of 2 933 bp. A total number of 50 593 expressed sequence tags linked to simple sequence repeats (EST-SSR) were identified

among them dinucleotide repeats (40.6%) and AC/GT motifs (38.5%) were the most frequent. Of the 190 EST-SSRs for which PCR primer pairs were designed

150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism. The alleles per locus ranged 6‍‍‍–‍50 on averag

e of 25.3. The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953

respectively. The polymorphic index content (PIC) values of each locus ranged 0.587‍‍‍–‍0.966 on average of 0.851. Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation

the Fangchenggang (FCG) population in Guangxi Province had the highest mean observed heterozygosity (

) value (0.786)

whereas the Zhangzhou (ZZ) population in Fujian Province had the lowest (0.678). The pairwise fixation index (

) values indicated significant population differentiation among six yellowfin seabream populations. This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation

population genetics

and breeding studies of yellowfin seabream in South China.

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references

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Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus

DOI：

摘要

Abstract

关键词

Keywords

references