Centre for Sustainable Tropical Fisheries & Aquaculture, and the College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
ARC Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.
Sci Rep. 2017 Sep 4;7(1):10360. doi: 10.1038/s41598-017-10515-7.
The Pacific whiteleg shrimp, Litopenaeus vannamei, is the most farmed aquaculture species worldwide with global production exceeding 3 million tonnes annually. Litopenaeus vannamei has been the focus of many selective breeding programs aiming to improve growth and disease resistance. However, these have been based primarily on phenotypic measurements and omit potential gains by integrating genetic selection into existing breeding programs. Such integration of genetic information has been hindered by the limited available genomic resources, background genetic parameters and knowledge on the genetic architecture of commercial traits for L. vannamei. This study describes the development of a comprehensive set of genomic gene-based resources including the identification and validation of 234,452 putative single nucleotide polymorphisms in-silico, of which 8,967 high value SNPs were incorporated into a commercially available Illumina Infinium ShrimpLD-24 v1.0 genotyping array. A framework genetic linkage map was constructed and combined with locus ordering by disequilibrium methodology to generate an integrated genetic map containing 4,817 SNPs, which spanned a total of 4552.5 cM and covered an estimated 98.12% of the genome. These gene-based genomic resources will not only be valuable for identifying regions underlying important L. vannamei traits, but also as a foundational resource in comparative and genome assembly activities.
太平洋白对虾（Litopenaeus vannamei）是全球养殖量最大的水产养殖品种，年总产量超过 300 万吨。Litopenaeus vannamei 一直是许多选择性育种计划的重点，旨在提高其生长速度和疾病抵抗力。然而，这些计划主要基于表型测量，忽略了通过将遗传选择纳入现有育种计划来获得的潜在收益。这种遗传信息的整合受到有限的可用基因组资源、背景遗传参数以及对商业性状遗传结构的了解的阻碍。本研究描述了一组综合基因组基因资源的开发，包括在计算机中鉴定和验证 234452 个推定的单核苷酸多态性，其中 8967 个高价值 SNP 被纳入商业可用的 Illumina Infinium ShrimpLD-24 v1.0 基因分型阵列。构建了一个框架遗传连锁图谱，并结合不平衡方法进行基因座排序，生成了一个包含 4817 个 SNP 的综合遗传图谱，总长度为 4552.5cM，覆盖了基因组的估计 98.12%。这些基于基因的基因组资源不仅对鉴定重要的 Litopenaeus vannamei 性状的相关区域非常有价值，而且还可以作为比较和基因组组装活动的基础资源。
