Yang Ya-Chi, Chu Pei-Yun, Chen Che-Chun, Yang Wen-Chin, Hsu Te-Hua, Gong Hong-Yi, Liao I Chiu, Huang Chang-Wen
Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan.
Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Academia Sinica Road, Sec. 2, Nankang, Taipei 11529, Taiwan.
Animals (Basel). 2024 Jun 5;14(11):1685. doi: 10.3390/ani14111685.
The Pacific blue shrimp () 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 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 a, , , PIC, and 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 (), and black tiger shrimps (). 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.
太平洋蓝虾（）是国际海鲜市场上的优质产品。然而，集约化养殖增加了疾病发生率并降低了遗传多样性。在本研究中，我们开发了一个太平洋蓝虾的转录组数据库，并挖掘微卫星标记以分析其遗传多样性。利用Illumina HiSeq 4000平台，我们从肌肉、肝胰腺、肠道和淋巴组织中鉴定出53263个单基因。微卫星分析从18657个单基因中鉴定出36415个标记，主要为二核苷酸重复序列。功能注释突出了关键的抗病途径和富集类别。对42个基于转录组的标记和58个基于文献的标记进行筛选和PCR检测，鉴定出40个扩增成功的标记。对200个亲虾样本进行基因分型，结果显示a、、、PIC和值分别为3、0.54±0.05、0.43±0.09、0.41±0.22和0.17±0.27，表明遗传变异性中等且存在显著的近亲繁殖。鉴定出四个通用微卫星标记（CL1472.Contig13、CL517.Contig2、Unigene5692和Unigene7147），用于太平洋蓝虾、太平洋白虾（）和黑虎虾的精确多样性分析。该转录组数据库支持为选择性育种计划开发标记和功能基因分析。我们的研究结果强调需要一个适当的遗传管理系统，以减轻近亲繁殖衰退、降低疾病易感性并保护养殖虾种群的遗传多样性。
