GENOMIC SELECTION FOR DISEASE RESISTANCE TO THE COPEPOD Lernanthropus kroyeri IN EUROPEAN SEABASS USING THE MEDFISH SNP-ARRAY AND SELECTED LOW-DENSITY SNP PANELS

Oikonomou, S.1,2, Kazlari Z.1, Papanna K.3, Manousaki T.2, Loukovitis D.1,4, Dimitroglou A.3, Kottaras L.3, Gourzioti E.3, Pagonis C.3, Kostandis A.3, Papaharisis L.3, Tsigenopoulos C. S.2, and Chatziplis, D.1 1

Lab. of Agrobiotechnology and Inspection of Agricultural Products, Dept. of Agriculture, International Hellenic University, Greece. 2Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Greece. 3Nireus Aquaculture SA, Greece. 4Research Institute of Animal Science, ELGO, Greece.


SUMMARY

The copepod Lernanthropus kroyeri is a host-specific parasite affecting the gills of the European seabass. Based on a multi-trait pedigree analysis with growth traits, the heritability of parasite count of the fish was previously estimated to be 0.28 (n=2,425, Papapetrou et al., 2021), while when a selected sub-sample of infected fish (985) was genotyped using the MedFish array (Peñaloza et al., 2020), the univariate heritability of parasite count was estimated 0.75, using a Pedigree Relationship Matrix (PRM), and 0.71 using a Genomic Relationship Matrix (GRM). A GWAS was performed for parasite count and growth and based on the results, we constructed two low-density panels (SNP–panel 1 and SNP–panel 2) from selected numbers of SNPs i.e., 1960 and 2907 using as criteria the p-value from the GWAS analysis (p-value<0.01 and <0.05, respectively). Estimated Breeding Values (EBVs) were estimated using BLUP and Genomic Estimated Breeding Values (GEBVs) were calculated using GBLUP for the three SNP panels (MedFish array, SNP–panel 1 &2), with BLUPF90. Each time, 20% of the population was selected randomly and its phenotypes were masked, thus, the breeding values (EBVs & GEBVs) were estimated using the information from 80% of the total fish. This process was performed 20 times and the correlation between the predicted values and phenotypes was estimated. A One-way ANOVA with repeated measurements was performed among the four groups showing a significant difference (p-value<0.01) among the four genetic evaluation procedures. Finally, the use of pedigree showed the lowest correlation, while the use of SNP–panel 2 provided the highest prediction followed by the SNP–panel 1. Additive genetic variance estimates are higher in selected samples, independently of the estimation method (PRM or GRM). The results indicate that small and carefully chosen SNP panels could potentially be utilized in cases of multi-trait genomic evaluation with alternative genotype-by-sequencing methodologies to reduce genotyping cost.

References:

Papapetrou, M., et al. (2021). On the trail of detecting genetic (co)variation between resistance to parasite infections (Diplectanum aequans and Lernanthropus kroyeri) and growth in European seabass (Dicentrarchus labrax). Aquac. Reports 20, 100767. Peñaloza, C., et al. (2021). Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata). Genomics, 113, 2097-2107.




COMPARISON BETWEEN PEDIGREE AND GENOMIC PREDICTIONS USING THE MEDFISH SNP-ARRAY AND SELECTED LOW-DENSITY SNP PANELS FOR BODY WEIGHT IN EUROPEAN SEABASS

S. Oikonomou1,2*, Z. Kazlari1, K. Papanna3, T. Manousaki2, D. Loukovitis1,4, A. Dimitroglou3,5, L. Kottaras3, E. Gourzioti3, C. Pagonis3, A. Kostandis3, L. Papaharisis3, C. S. Tsigenopoulos2, D. Chatziplis1

1. Lab. of Agrobiotechnology and Inspection of Agricultural Products, Dept. of Agriculture International Hellenic University, Greece
2. Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) Hellenic Centre for Marine Research (HCMR), Greece
3. Nireus Aquaculture SA, Greece
4. Research Institute of Animal Science, ELGO, Greece
5. Agricultural University of Athens, Department of Animal Science, Greece

Email: valiaekonomou@hotmail.com


Introduction:

Genomic selection can improve the selection accuracy and reduce the generation interval. However, pedigree selection has been utilized for growth and body weight in commercial aquaculture breeding programs because of the increased cost of genotyping. Thus, in the present study an effort was made to develop a reduced, low-cost SNP panel to be utilized for genomic selection purposes for production traits (i.e., growth, body weight) and disease/parasite resistance (i.e., parasite count). The aim of the study is to compare the pedigree and genomic predictions using the 30K MedFISH array (Peñaloza et al., 2020) and selected low-density SNP panels for body weight in European seabass (Dicentrarchus labrax).


Materials and Methods

For this purpose, a selected sub-sample of 985 fish, from the total of 1,576 fish, infested with Lernanthropus kroyeri, was genotyped using the MedFISH array. Two GWAS were performed, one for growth in the sea cage and the other one for the final weight at the end of the experimental period (Oikonomou et al. 2022a, in press) and from these the significantly associated SNPs with the trait of interest (p-value<0.05) were selected. Further, a multitrait GWAS using different growth at different periods in the sea cage was performed and significantly associated SNPs (p-value<0.01) were selected. Based on the above criteria, 1,715 SNPs related to growth were finally selected.

Furthermore, a GWAS was performed for resistance to Lernanthropus kroyeri (parasite count, PC) (Oikonomou et al. 2022a, in press). Two low-density panels (SNP–panel 1 and SNP–panel 2) were constructed using two selected groups of SNPs as criteria, according to their p-value from the GWAS (p-value<0.01 and <0.05, respectively). Then, 245 and 1,192 SNPs associated to parasite resistance (GWAS for parasite resistance), were included in the SNP-panel 1 and SNP-panel 2, respectively. Τhose SNP panels were enriched with the 1,715 SNPs related to growth. Thus, two reduced density SNP – panels, which included 1,960 SNPs (named as SNP-panel 1) and 2,907 SNPs (named as SNP – panel 2) were constructed

Estimated Breeding Values (EBVs) for the final body weight were calculated using Best Linear Unbiased Prediction (BLUP) and Genomic Estimated Breeding Values (GEBVs) for the final body weight were assessed using Genomic-BLUP (GBLUP) for the three SNP panels (30K MedFISH array, SNP–panel 1 & 2), using BLUPF90. Each time, 20% of the population was selected randomly and its phenotypes were masked (216 fish), thus, the breeding values (EBVs or GEBVs) were estimated using the information from 80% of the total fish. This process was performed 20 times and the correlation between the predicted values for the final body weight and phenotypes was calculated in the validation group. A one-way ANOVA with repeated measurements was performed among the four groups (SNP–panel 1, SNP–panel 2, 30K MedFISH array and pedigree).


Results

In the validation group, the use of pedigree showed the lowest correlation coefficient (0.38) followed by the 30K MedFISH array (0.41), while the use of SNP–panel 1 (1,960 SNPs) provided the highest prediction (0.70) followed by the SNP–panel 2 (2,907 SNPs) in which the estimate was 0.66 (Figure 1). Moreover, a statistically significant difference (p-value<0.01) among the four genetic evaluation procedures was found. The post-hoc analyses with a Bonferroni adjustment were performed and revealed that there was a statistically significant difference between each pair.

diagram

Discussion

When, selecting for disease resistance (parasite count) instead of body weight, the SNP – panel 2 provided the highest estimate (0.81) followed by the SNP – panel 1 (0.75) (Oikonomou et al. 2022b) while selecting for body weight the SNP- panel 1 provided the highest estimation (0.70). Regardless of the selection trait (disease resistance or body weight), higher correlation coefficient was established using small, selected SNP panels compared to the 30K MedFISH array.

Furthermore, higher correlation coefficient was found when using genomic information (30K MedFISH array and SNP- panel 1& 2) than when using pedigree relationship matrix. These findings indicate that small and cleverly selected SNP panels, such as SNP – panel 1 and 2 could potentially be utilized in cases of multi-trait genomic evaluation, and in some cases, can provide better predictions especially when parts of phenotypic information is missing.

Reference

  1. Peñaloza C, Manousaki T, Franch R, et al., 2021. Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata). Genomics, 113, 2096-2107.
  2. Oikonomou S., Kazlari Z., Papapetrou M., et al. 2022a. Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass, in press.
  3. Oikonomou, S., Kazlari Z., Papanna K., et al. 2022b. Genomic selection for disease resistance to the copepod lernanthropus kroyeri in european seabass using the medfish snparray and selected low-density snp panels. In 6th Genomics in Aquaculture (GIA), Symposium, (4-6 May, Granada, Spain).