长毛对虾(Penaeus penicillatus)SNP标记开发及亲子鉴定技术研究

长毛对虾是我国南方沿海地区的重要经济虾类。近年来,由于过度捕捞、病害频发以及海洋环境恶化,长毛对虾的自然资源量大幅减少。为补充自然资源,改善种群结构,1980年我国开始对长毛对虾开展增殖放流工作。然而,增殖放流的效果如何,目前尚缺乏有效的评估手段。以长毛对虾为实验材料,通过对其基因组进行de novo测序和重测序开发SNP (single nucleotide polymorphism)标记,最终建立长毛对虾的亲子鉴定技术。具体研究结果如下:长毛对虾基因组大小为1 335.76 Mb GC (guanine cytosine)含量为40.86%,N50为1 221 bp;以组装的长毛对虾基因组为参考基因组通过重测序进行SNP挖掘,共获得12 579 780个原始SNP位点,经筛选,优化及模型选择,最终建立了基于192个SNP标记的长毛对虾亲子鉴定技术,亲子鉴定成功率为100%(95%的置信度)。研究结果可为下一步长毛对虾增殖放流效果评估提供参考。

DEVELOPMENT OF SNP MARKERS AND PARENTAGE ASSIGNMENT TECHNIQUES IN PENAEUS PENICILLATUS

Penaeus penicillatus is an essential marine economic shrimp in the southeastern coastal regions of China. Wild populations of P. penicillatus have declined dramatically in recent years due to overfishing, marine environmental pollution, and other causes. Since 1980, China has initiated numerous stock-enhancing programs for P. penicillatus to replenish natural resources and improve population structure. However, no efficient evaluation method is available at present. SNP (single nucleotide polymorphism) markers were developed by De novo genome sequencing and resequencing in P. penicillatus, and parentage assignment techniques were established for P. penicillatus. Results show that the genome size of P. penicillatus is 1 335.76 Mb, GC (guanine cytosine) content is 40.86%, and the assembly of the genome contigs N50 reaches 1 221 bp. The whole-genome sequencing and SNP marker discovery were performed using the assembled P. penicillatus genome as the reference genome, yielding a total of 12 579 780 original SNP markers. Through screening, optimization, and model selection, a parentage assignment technique was developed for P. penicillatus based on 192 SNP markers, by which a parentage assignment rate of 100% with 95% confidence was achieved. This study offered a reference for future evaluation on the stock-enhancing effects for P. penicillatus.