A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei

Abstract 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

Genomics, molecular epidemiology and diagnostics of infectious hypodermal and hematopoietic necrosis virus

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is one of the major viral pathogens of penaeid shrimps worldwide, which has resulted in severe mortalities of up to 90 % in cultured Penaeus (Litopenaeus) stylirostris from Hawaii and hence designated Penaeus stylirostris densovirus (PstDNV). IHHNV is distributed in shrimp culture facilities worldwide. It causes large economic loss to the shrimp farming industry. Our knowledge about the natural reservoirs of IHHNV is still scarce. Recent studies suggest that there is sufficient sequence variation among the isolates from different locations in Asia, suggesting multiple geographical strains of the virus. Four complete genomes and several partial sequences of the virus are available in the GenBank. Complete genome information would be useful for assessing the specificity of diagnostics for viruses from different geographical areas. Comparisons of complete genome sequences will help us gain insights into point mutations that can affect virulence of the virus. In addition, because of unavailability of shrimp cell lines for culturing IHHNV in vitro, quantification of virus is difficult. The recent progress in research regarding clinical signs, geographical distribution, complete genome sequence and genetic variation, transmission has made it possible to obtain information on IHHNV. A comprehensive understanding of IHHNV infection process, pathogenesis, structural proteins and replication is essential for developing prevention measures. To date, no effective prophylactic measure for IHHNV infection is available for shrimp to reduce its impact. This review provides an overview of key issues regarding IHHNV infection and disease in commercially important shrimp species

Mollusc harvesting in the Pre - European contact Pacific Islands: investigating resilience and sustainability

Mollusc shells, which are often quite numerous in archaeological sites throughout the Pacific Islands, offer good proxies for assessing environmental change as well as human impact. Documented changes in species size, richness, and abundance have often been interpreted as evidence of resource abuse by shellfish gatherers. While this may be valid in some cases, archaeologists need to consider other variables to explain change (or stability) in shell distribution. A better understanding of ecological and biological (life history) characteristics associated with shell midden deposits, as well as greater awareness of ethnographic and ethnoarchaeological data on the interaction between people and varieties of marine resources, may result in a reinterpretation of past human behavior. A growing interest in indigenous resource management among contemporary Pacific Island communities has led some archaeologists to seek tangible evidence of community resilience and sustainable use of resources in the past. This chapter draws primarily from direct observations and semi-structured interviews among mollusc gatherers in Kiribati, eastern Micronesia, and examines selected case studies of archaeological shell deposits from the Pacific Islands that could shed new light on marine resource management to complement the more widespread research conclusions that depict human impact in largely negative terms