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Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris .

Authors :
Yang YC
Chu PY
Chen CC
Yang WC
Hsu TH
Gong HY
Liao IC
Huang CW
Source :
Animals : an open access journal from MDPI [Animals (Basel)] 2024 Jun 05; Vol. 14 (11). Date of Electronic Publication: 2024 Jun 05.
Publication Year :
2024

Abstract

The Pacific blue shrimp ( Litopenaeus stylirostris ) is a premium product in the international seafood market. However, intensified farming has increased disease incidence and reduced genetic diversity. In this study, we developed a transcriptome database for L. stylirostris and mined microsatellite markers to analyze their genetic diversity. Using the Illumina HiSeq 4000 platform, we identified 53,263 unigenes from muscle, hepatopancreas, the intestine, and lymphoid tissues. Microsatellite analysis identified 36,415 markers from 18,657 unigenes, predominantly dinucleotide repeats. Functional annotation highlighted key disease resistance pathways and enriched categories. The screening and PCR testing of 42 transcriptome-based and 58 literature-based markers identified 40 with successful amplification. The genotyping of 200 broodstock samples revealed that N a, H <subscript>o</subscript> , H <subscript>e</subscript> , PIC, and F <subscript>IS</subscript> values were 3, 0.54 ± 0.05, 0.43 ± 0.09, 0.41 ± 0.22, and 0.17 ± 0.27, respectively, indicating moderate genetic variability and significant inbreeding. Four universal microsatellite markers (CL1472.Contig13, CL517.Contig2, Unigene5692, and Unigene7147) were identified for precise diversity analysis in Pacific blue, Pacific white ( Litopenaeus vannamei ), and black tiger shrimps ( Penaeus monodon ). The transcriptome database supports the development of markers and functional gene analysis for selective breeding programs. Our findings underscore the need for an appropriate genetic management system to mitigate inbreeding depression, reduce disease susceptibility, and preserve genetic diversity in farmed shrimp populations.

Details

Language :
English
ISSN :
2076-2615
Volume :
14
Issue :
11
Database :
MEDLINE
Journal :
Animals : an open access journal from MDPI
Publication Type :
Academic Journal
Accession number :
38891732
Full Text :
https://doi.org/10.3390/ani14111685