Genotyping Services

Overview

Benchmark Genetics now provides the global aquaculture industry with cost-effective genotyping solutions optimized for a range of applications and species. Our team has designed and commercialized genotyping technologies for a variety of consolidated and emerging species, with marker densities suited for the different needs of our clients. Harnessing our major internal genotyping volumes and experience, we can offer world-leading prices and quality. As part of our portfolio, we also offer fully customized genotyping tools designed to help our clients achieve the best outcome for their breeding programs.

Cost-Effective Genotyping

We provide a full genotyping service at market-leading prices, from tissue sample to quality-controlled data. Clients simply ship small tissue samples from their animals according to a simple protocol, and we take care of the DNA extraction, the genotyping tool purchase, and the genotyping service. We have extensive experience in this process from several years and hundreds of thousands of samples, meaning our process is streamlined, accurate, and efficient. We include quality-control analysis of the genotype data, and can provide further support with application of the data towards clients’ selective breeding programs through our Benchmark Genetic Services team.

High Density Genotyping

20 – 70K SNPs

We offer high density genotyping for most of the major global aquaculture species using highly accurate and well-established SNP array technology. This SNP marker density is suitable for genomic selection, genome-wide association studies, population diversity and structure analysis, and parentage assignment. We have off-the-shelf solutions for the following species, and can offer potential clients a trial of our tools to ensure they meet their needs.

  • Whiteleg Shrimp (P. vannamai)
  • Atlantic Salmon (S. salar)
  • Nile Tilapia (O. niloticus)
  • Rainbow Trout (O. mykiss)
  • European Seabass (D. labrax)
  • Gilthead Seabream (S. aurata)
  • Arctic Char (S. alpinus)
  • Channel Catfish (I. punctatus)
  • Coho Salmon (O. kisutch)
  • Pacific Oyster (C. gigas)
  • European Flat Oyster (O. edulis)
  • Tambaqui (C. macropomum)
  • Pacu (P. brachypomus)
  • Coral (Acropora spp.)

For other species, please contact us to discuss.

Medium Density Genotyping

2 – 7K SNPs

For developing and promising species we offer panels in densities between 2 000 and 7 000 SNPs, they provide a platform for simple marker-assisted and genomic selection, along with parental assignment, genetic diversity analyses, etc. Avaliable or in development for the following species:

  • Whiteleg Shrimp (P. vannamai)
  • Atlantic Salmon (S. salar)
  • Coho Salmon (O. kisutch)
  • Nile tilapia (O. niloticus)
  • Rainbow Trout (O. mykiss)
  • European Seabass (D. labrax)
  • Gilthead Seabream (S. aurata)
  • Artic Char (S. alpinus)
  • Channel Catfish (I. punctatus)
  • Pacific Oyster (C. gigas)
  • European Flat Oyster (O. edulis)
  • Tambaqui (C. macropomum)
  • Pacu (P. brachypomus)
  • Coral (Acropora spp.)
  • Tiger Prawn (P. monodon)
  • Barramundi (L. calcarifer)
  • Turbot (S. maximus)
  • Sengalese Sole (S. senegalensis)
  • Rohu (L. rohita)
  • Meagre (A. regius)

Currently in development: Atlantic Halibut (H. hippoglossus), Red Snapper (L. campechanus), African Catfish (C. gariepinus), Abalone (H. midae), Common Sole (S. Solea), and Yellowtail Kingfish (S. lalandi). 

For other species, please contact us to discuss.

Genes

Low Density Genotyping

1 – 500 SNPs

We offer low density genotyping solutions for a wide range of species at highly competitive prices. The two main services we offer are:

  1. Multiplex SNP panels: these are low density panels specifically designed for a species or strain, and are used for parentage assignment, genetic diversity, or genetic structure analysis.
  2. Single SNP assays: these are targeted assays for one or more specific SNPs in the genome of your species of interest. These can be used for marker-assisted selection for major quantitative trait loci (QTL), or sex determination in certain species.
Genetic Services Products - lead image

Custom Array Design

Our team have world-leading expertise in genotyping tool design and application, having done so for some of the most widely-used arrays on the market. We offer array design and subsequent genotyping services for new species, or specific arrays tailored to clients’ target populations. This can cover low, medium, and high density genotyping. Due to our very high volume of genotyping, we also offer this service at market-leading prices. We welcome collaboration and will work to provide the optimum solution for our partners and clients.

Integrated Services

The genotyping and array design services described here is an integral component of offerings from Benchmark’s Genetics Services division, formerly Akvaforsk Genetics. This strategic integration solidifies our leading position as provider of technical support related to design, implementation, and operation of broodstock management and breeding programs to the global aquaculture sector. Leveraging unparalleled track record, which spans approximately 40 programs for more than 20 species including salmonids, freshwater and marine fish, shrimp, and mollusks, we have extensive experience. The extension of our services to include genotyping and array design, complemented by downstream analyses of genomic data, solidifies Benchmark Genetics as a one-stop destination for all pertinent genetic services for effective improvement of aquaculture species.

Clients can place their trust in Benchmark Genetics, benefiting from our extensive track record and unparalleled experience, making us the preferred partner for all genetic services in aquaculture.

Dr. Ross Houston

Director of Genetics and Innovation

Ross Houston leads Benchmark Genetics’ global breeding programs for Atlantic salmon and whiteleg shrimp. He also leads R&D activities, with a particular focus on applications of current and emerging technologies, including SNP array development, reproductive technologies, and gene editing. Ross is Chair of Benchmark Innovation Board and has over 20 years of experience in applied genetics research in aquaculture breeding, with more than 115 scientific publications.

Dr. Agustin Barria

Senior Geneticist

Agustin works with our clients to design, assess, optimize, and support their breeding programs. He has over a decade of experience in animal breeding and genomics as well as the use and development of genomic tools in aquaculture. As such, Agustin also works closely with Benchmark Genetics’ Molecular Genetics team. He has extensive experience in using high-density genomic data for genetic population studies and quantitative genetics. His track record includes spearheading genomic strategies within the Nile tilapia GIFT program, and augmenting resistance to Tilapia Lake Virus. Agustin holds a PhD in Aquaculture and Genetics from the University of Chile. He has (co)authored over 40 scientific publications.

Dr. Morten Rye

Director of External Services and International Strategies

Heading Benchmark Genetics’ External Services Team, Morten leads Benchmark Genetics’ pursuit of international commercial partnerships and coordinates our technical deliveries to external clients. Morten holds 35+ years in aquaculture genetics with extensive management experience in R&D and program operations. His expertise spans more than 20 species, and he has made significant contributions to genetic research and breeding programs for marine and freshwater fish, shrimp, and molluscs globally. Holding a 1992 PhD in Animal Breeding and Genetics from the Norwegian University of Agriculture, Morten has (co)authored 80+ scientific papers and several book chapters focused on applied genetics and selection in aquaculture.

Dr. Maria Nayfa

Senior Geneticist

Maria works with our clients to support and design practical and tailor-made solutions for assessing, managing, improving, and establishing their breeding programs. With over a decade of experience in aquaculture and genomics, Maria has worked closely with collaborators on projects in five continents, and more than ten countries and species. She holds a PhD in Aquaculture and Genetics from James Cook University, Australia and has an extensive background in animal breeding and genomics, population genetics, and quantitative genomics. She has (co)authored over 15 scientific publications, book chapters, and government reports.

Dr. Carolina Peñaloza

Lead, Molecular Genetics

Carolina is the Lead of Benchmarks Molecular Genetics program, where she is responsible for developing cost-effective genotyping solutions for a variety of aquaculture species. She is an aquaculture geneticist with over 10 years of experience who has designed some of the most successful SNP arrays in the field. Together with her team, she keeps Benchmark at the forefront of efficient genotyping. Carolina holds a MPhil and PhD from the University of Edinburgh, Scotland. She has (co)authored over 30 scientific publications and government reports.

Adrian Antonsen

Geneticist

Adrian works with our clients on the support, design, and practical implementation of cost-effective integrated breeding programs tailored to generate significant genetic improvements within commercial growing operations. He joined Benchmark Genetics in 2021 and has since been involved in the design and support of successful breeding programs for over 10 different species all over the world. Adrian holds a MS in Biotechnology from the Norwegian University of Science and Technology and has strong background in biotechnology, genetics, and bioinformatics.

Dr. Shernae Woolley

Geneticist, Molecular Genetics

Shernae is part of Benchmark’s Molecular Genetics program where she plays a key role in developing and optimising genotyping solutions for several aquatic species. Her role includes R&D activities with a focus on broad molecular genetic applications. She is a molecular geneticist who brings her extensive experience in terrestrial livestock genomics to aquaculture. As part of an expert team, she helps keep Benchmark at the forefront of genetic applications. Shernae holds a PhD from the University of Sydney, Australia and has (co)authored several scientific publications.

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