How genomics enables a more sustainable, cost-efficient shrimp production

BREEDING WITH GENOMIC PRECISION

Aquaculture is one of the fastest-growing food production industries worldwide. Under pressure from a growing population, a duty to improve animal welfare, and to reduce the environmental impact of food production, aquaculture must continuously develop new and innovative techniques and tools to overcome these current and oncoming challenges and meet the economic, environmental, and welfare expectations from the industry, regulators, and consumers.

Blue and red particles DNA helix.

Shrimp production, like other aquaculture activities, faces implicit risks that depend on interrelated biological, environmental, management, technological, regulatory, and economic elements. For example, white spot syndrome virus disease still causes multibillion annual US$ losses for shrimp farmers all around the world. The disease spreads quickly and preventive measures for contagion have proven ineffective. Therefore, traits such as improved disease resistance, general robustness in handling, and fast growth reducing the risk are crucial to the production and are increasingly gaining relevance as the industry advances.

At Benchmark Genetics we breed shrimp using the best technology available in Genetics and Genomics, optimizing the gains in key health, production, and commercial traits, ensuring that our animals are capable of very high performance with the best health and welfare.

Breeding methodologies

Family selection

This method compares families for different traits that are important in commercial production, allowing breeders to accurately identify families with specific genetic advantages. Family selection is an effective way of minimizing the levels of inbreeding, as we are in control of the pedigrees of each family.

Family-based selective breeding programs are traditionally based on performance recordings of the selected candidates and their siblings to predict the genetic merit of the candidates. Henderson’s mixed model equations are used in the best linear unbiased prediction (BLUP) of individual breeding values (EBVs) utilizing an animal model that uses the numerator (pedigree-based) relationship matrix (A). These methods proved to be highly successful to improve many quantitative traits with moderate to high genetic variation and heritability and are key for the selection of traits that must be measured in dead animals such as carcass quality.

Selection of best breeding candidates on a molecular level:

Individual selection

In traits such as growth, where the phenotypes are easily measured on breeding candidates, individuals can be efficiently selected based on their performance. In recent years new genomic methods have been developed to identify the best breeders based on DNA sequence by genotyping. By understanding which genotypes (often using SNPs — single nucleotide polymorphisms representing a difference in a single DNA building block, called a nucleotide) are associated with excellent performance in each trait, it is possible to screen populations for the best performing offspring.

In some traits, where single SNPs are associated with a large amount of variation (often described as QTLs — Quantitative Trait Loci), individuals can be selected on a small number of SNPs. In both cases, genotyping has improved the effectiveness of selection by more accurately identifying the individuals with improved performance.

QTL – Quantitative Trait Loci

A QTL is a position or regions of the genetic sequence (genome) at which genetic variation is associated with a particular quantitative trait associated with a significant amount of variation of such trait. It is often identified using one or a small number of SNPs. The SNPs are genetic markers for the QTL and can be used in a particular form of selection known as marker-assisted selection (MAS).


In Atlantic salmon, a significant QTL has been identified for resistance to the IPN virus, which accounts for over 80% of the genetic variation in resistance. SNP markers for this QTL are used to identify and breed from resistant individuals in the nucleus and for commercial egg production, reducing the number of outbreaks of IPN.

Although in many traits most of the variation is accounted for by several genes, making Genomic Selection more effective, geneticists continue the research to identify significant QTLs for other traits.

The use of genetic markers can dramatically improve both genetic gain and selection accuracy. These markers assisted selection (MAS) schemes are optimal when the markers or QTL explain a large proportion of the total variance of the trait, as in the case of the QTL for resistance to IPN in Atlantic salmon. However, many quantitative traits are polygenic where phenotypic variation (e.g., resistance to disease) is explained by multiple genes which all of them combined can explain the genetic variance, and MAS will not be very effective for such traits.

Genomic Selection

As mentioned before, in most traits, genetic variation is controlled by a large number of genes, each with a small effect (Polygenic traits). For these traits, Genomic Selection (GS) is a more comprehensive methodology, better adapted and more effective than MAS in identifying individuals for breeding. Using advanced genetic methods, we can successfully select parent animals with the most suitable genes for commercial offspring production.

In the last years, with the exponential growth in DNA sequence technologies, it is now possible to look at hundreds of thousands of SNPs located in the whole genome.  Genomic selection (GS) is a method that uses the information from thousands of SNPs across the genome combined with phenotypic data to predict the genomic breeding values (GEBVs) of all genotyped individuals (even without phenotype records). This method has proven to increase the accuracy of selection compared with the traditional pedigree-based prediction of breeding values.

This approach considers all markers when estimating the breeding value of the candidate, without the need to surpass a significance threshold for association with a particular trait of interest as happens with the QTLs.  When the effects of the markers across the entire genome are estimated, these effects can be used to select individuals lacking phenotypes. As such, in the case of disease resistance, there would be fewer requirements for challenge testing of siblings for diseases of economic importance.

Molecular markers provide a new source of information, which is the DNA fingerprint of the individual against a given trait, and will give higher accuracy when predicting EBVs. Thus, selection response will be potentially higher in traits in which the accuracy is low, i.e., traits with low heritability or traits that cannot be measured in the selection candidate, such as disease resistance 

Genomics and Molecular DNA tools have a wide range of applications, not just in shrimp, salmon, and tilapia breeding, but also in livestock selection and a variety of human-related research, such as the exome sequencing in humans to predict diseases.


Some may be familiar with the use of molecular markers to identify human ancestry, which through a simple DNA test reveals a person’s unique ethnic background and matches them with newfound relatives.

Advantages of genomics in breeding

  • Improves the accuracy of predicted breeding values and selection of candidates
  • Opportunity to select candidates within and between families based on their individual genomic breeding values. This is particularly important for carcass quality traits, sex limited traits and diseases traits, because the candidates get only average family breeding values in traditional selection methods
  • Reduces the inbreeding coefficient allowing breeders to keep a wider genetic diversity in the breeding population (Indirectly due to individual vs family selection)

Technology transfer from Salmon to shrimp

Benchmark Genetics is a world leader in breeding and genetics for several aquaculture species, operating 5 in-house programs for Atlantic salmon, tilapia, and P Vannamei shrimp, with extensive experience from 30 applied breeding programs covering 20 species in 16 countries.
Making use of modern breeding technologies such as QTL and Genomic Selection, improved disease resistance, faster growth, and better yield are driving forces in our selective breeding programs — resulting in cost-effective production and higher economic returns for hatcheries and farmers.

Salmon breeding programs in Norway started in the late 1970s, 20 years ahead of shrimp breeding programs in the US and Latin America. After decades of experience, constant development, and innovation, Benchmark’s salmon breeding programs have reached a leading position with over 40% of the global production powered by our genetics.

Benchmark has mastered this technology in salmon and is transferring and implementing it, along with its team of experts’ knowledge and experience, to its P Vannamei shrimp breeding program. Although the technology is key to this success, the experience and know-how in aquaculture breeding programs give Benchmark a strategic advantage over its competitors, which have recently begun to implement it.

BENCHMARK’S GLOBAL PRESENCE.
See a video of Benchmark’s Elite Multiplication Centre in Fellsmere, Florida, the USA.

If you want to know more about how Benchmark Genetics uses genomics to enable cost-efficient, sustainable aquaculture, please contact: Chung Mai – Sales Manager Asia Benchmark Genetics Shrimp
+84 914 578 687  
 chung.m@bmkgenetics.com

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