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Yang YC, Chu PY, Chen CC, Yang WC, Hsu TH, Gong HY, Liao IC, Huang CW. Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris. Animals (Basel) 2024; 14:1685. [PMID: 38891732 PMCID: PMC11171113 DOI: 10.3390/ani14111685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
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 Na, Ho, He, PIC, and FIS 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.
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Affiliation(s)
- Ya-Chi Yang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Che-Chun Chen
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Academia Sinica Road, Sec. 2, Nankang, Taipei 11529, Taiwan;
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - I Chiu Liao
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
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Mondal D, Chakrabarty U, Dutta S, Mallik A, Mandal N. Identification and characterization of novel microRNAs in disease-resistant and disease-susceptible Penaeus monodon. FISH & SHELLFISH IMMUNOLOGY 2021; 119:347-372. [PMID: 33961994 DOI: 10.1016/j.fsi.2021.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs), known as a translational regulator, are evolutionary conserved, small, and noncoding RNA. They have played a vital role in disease biology through the host-virus-miRNA-interaction. In this study, novel miRNAs of naturally occurring, virus-free disease-resistant and disease-susceptible Penaeus monodon were identified and characterized. In disease-susceptible samples, 45 homologous mature miRNAs and 28 homologous precursor miRNAs were identified. In disease-resistant samples, 52 homologous mature miRNAs and 87 homologous precursor miRNAs were identified. In disease-susceptible samples, 33 novel mature miRNAs and 33 novel precursor miRNAs were identified. In disease-resistant samples, 523 novel mature miRNAs and 141 novel precursor miRNAs were identified. Differential expression study revealed the up-regulated and down-regulated miRNAs in disease-resistant and disease-susceptible P. monodon. Gene ontology pathway of known and novel miRNAs revealed that P. monodon miRNAs might have a potential and specific role in signal transduction, cell-to-cell signaling, innate immune response and defense response to different pathogens.
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Affiliation(s)
- Debabrata Mondal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, West Bengal, India
| | - Usri Chakrabarty
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, West Bengal, India
| | - Sourav Dutta
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, West Bengal, India
| | - Ajoy Mallik
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, West Bengal, India; Department of Zoology, Dinabandhu Mahavidyalaya, North 24 Parganas, Bongaon, West Bengal, India
| | - Nripendranath Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, West Bengal, India.
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