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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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Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
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Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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