GenomResist: Genomic selection for improved disease resistance of shrimp

In a previous collaborative project with the Central Institutes for Freshwater and Brackishwater Aquaculture in India, Nofima discovered markers in the genetic code (DNA sequence) associated with resistance to white spot syndrome virus in tiger shrimp. White spot syndrome virus has a severe impact on shrimp production around the world. The aim of this project was to extend the previous project to implement "genomic selection" to improve disease resistance and to transfer marker technologies to other important shrimp species grown around the world. The bulk of world production has recently changed from tiger to white shrimp. We have sequenced most of the genes in white shrimp and compared the genomes of the two species. Families of white shrimp produced by partner Syaqua were challenged with the disease and genotyped for the markers associated with white spot resistance in our previous project, and we have found that one of the genes associated with viral resistance in tiger shrimp also affects viral resistance in white shrimp. Information about the DNA code from across the entire shrimp genome has been used to choose which animals should be bred in order to improve the disease resistance of the next generation of partner Benchmark Genetics Colombia's white shrimp for production. An evaluation of the accuracy and rate of genetic improvement using these new technologies and methods was made, the genetic variation for resistance to white spot syndrome virus detected using this technology was found to be high and genomic selection was found to improve the rate of survival with challenge to white spot syndrome virus from 38% in randomly selected shrimp to 51% after one generation of genomic selection. A manuscript has been drafted describing these results. Genomic selection was therefore demonstrated to have a significant and large (15%) effect on average group survival. Due to the large variation in survival present and relative high heritability detected, further selection would be expected to produce high genetic gains. Shrimp selected for disease resistance will be distributed to hatcheries and knowledge about genomic selection is being broadly disseminated through publications and workshops. We have demonstrated that selective breeding using these new technologies and methods can be effectively implemented to improve the ability to resist this disease. Commercial operators and small farming communities will benefit, and the production of shrimp will be made more reliable and profitable from the dissemination of seedstock that is selected for white spot virus resistance in this way.

Outcome: One quantitative trait locus (QTL) was detected both in white-leg shrimp and tiger shrimp. One generation of genomic selection improved WSSV resistance by 15%. Fifty white-leg shrimp SNPs corresponding to tiger shrimp QTL positions were identified. 10,273 new SNPs were identified and 18,643 were used for genomic selection. Impact: One generation of genomic selection resulted in 15% higher WSSV resistance making shrimp more robust and farmers less affected by production losses. Genomic heritability was high. There is large potential to make further genetic improvement using genomic selection. Plans were made to distribute improved stock around the world. Uptake will reduce the need for antibiotics, reduce consumption of antibiotics by people, profit pond holders and increase food security. We have developed expertise in the application of genomic technologies and we have drafted a relatively high impact publication.

In our recent collaboration with India we discovered gene markers associated with resistance to Aeromonas hydrophila and white spot syndrome virus (WSSV) in rohu carp and tiger shrimp respectively. These diseases impact carp and shrimp production in India and around the world. If selection using these markers can be effectively implemented, small farming communities would benefit and India would gain an advantage in the production of these important food species. The bulk of production in India has recently changed from tiger to white shrimp. The aim of this proposal is to transfer marker technologies to other important shrimp species in India (vannamei shrimp) and to validate and extend the findings from our last project, to implement genomic selection to improve shrimp disease resistance. Evenly spaced single nucleotide polymorphisms will be selected from across the vannamei genome, including markers mapping to corresponding areas as QTL identified by our last study. Fifty families will be bred, some offspring will be used as a "training population" for estimating disease resistance allele substitution effects at each locus, the rest will be used as candidates for breeding. Identity by descent genomic selection will be applied to create an experimental line. A separate control line will be created without genomic selection for comparison. An evaluation of genetic progress will be made, and advice provided on the incorporation of other traits. This project will also evaluate whether loci associated with WSSV resistance in tiger shrimp are similar in white shrimp. White shrimp will be sequenced to identify polymorphisms in the same genes marking loci affecting WSSV resistance in tiger shrimp. Families challenged with WSSV will be genotyped to find markers associated with disease resistance in white shrimp. Shrimp selected for disease resistance will be distributed to hatcheries around the world and knowledge about genomic selection will be broadly disseminated through publications and workshops.