Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement

Abstract

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (< 3). SNP data were also used to assess the feasibility of genomic selection for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosome 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. Genomic selection was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 – 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that genomic selection will likely be a viable option for improvement of survival in extreme low salinity.

Evaluating a short vs. long-term progeny test and investigating physiology associated with survival in extreme low salinity for the eastern oyster Crassostrea virginica

“…A short-term (2 month) and long-term (6 month) challenge at extreme low salinity (< 3) were conducted to investigate the effect of challenge duration and temperature on oyster extreme low salinity survival. Similar to results from previous extreme low salinity challenges (McCarty et al, 2022(McCarty et al, , 2020, mortality varied among families in the two challenges and narrow-sense heritability estimates were moderate and significantly different from zero. Family mortality was highly correlated between the short-term and long-term challenges, suggesting that an extreme low salinity challenge at a single high temperature (27°C) captures similar mortality trends as the more realistic, 6-month challenge where temperature was adjusted daily to mimic the natural, seasonal variation in temperature experienced from spring to fall.…”

“…Mortality peaked after 6 weeks at 27°C in the short-term challenge (experimental conditions more comparable to previous low salinity challenges: constant temperature of 27°C and 1-2 month exposure duration), while peak mortality (experimental day with the most mortality) occurred 10-12 days after exposure using >80 mm adults in previous studies (McCarty et al, 2020(McCarty et al, , 2022. The delay in mortality observed during the short-term challenge in this study suggests that smaller and younger oysters (< 40 mm, 1-yr old) are more tolerant to a salinity <3 and temperature 27°C than larger oysters (> 80mm, 2 and 3-yrs old; McCarty et al, 2020McCarty et al, , 2022. These results support previous literature suggesting that mortality at specific temperatures and salinities is size-class dependent, where smaller oysters have a higher tolerance to low salinity and high temperature compared to larger 30 oysters (> 75 mm) (La Peyre et al, 2013;Lowe et al, 2017;McCarty et al, 2020;Rybovich et al, 2016).…”

Evaluating a short vs. long-term progeny test and investigating physiology associated with survival in extreme low salinity for the eastern oyster Crassostrea virginica

“…A short-term (2 month) and long-term (6 month) challenge at extreme low salinity (< 3) were conducted to investigate the effect of challenge duration and temperature on oyster extreme low salinity survival. Similar to results from previous extreme low salinity challenges (McCarty et al, 2022(McCarty et al, , 2020, mortality varied among families in the two challenges and narrow-sense heritability estimates were moderate and significantly different from zero. Family mortality was highly correlated between the short-term and long-term challenges, suggesting that an extreme low salinity challenge at a single high temperature (27°C) captures similar mortality trends as the more realistic, 6-month challenge where temperature was adjusted daily to mimic the natural, seasonal variation in temperature experienced from spring to fall.…”

“…Mortality peaked after 6 weeks at 27°C in the short-term challenge (experimental conditions more comparable to previous low salinity challenges: constant temperature of 27°C and 1-2 month exposure duration), while peak mortality (experimental day with the most mortality) occurred 10-12 days after exposure using >80 mm adults in previous studies (McCarty et al, 2020(McCarty et al, , 2022. The delay in mortality observed during the short-term challenge in this study suggests that smaller and younger oysters (< 40 mm, 1-yr old) are more tolerant to a salinity <3 and temperature 27°C than larger oysters (> 80mm, 2 and 3-yrs old; McCarty et al, 2020McCarty et al, , 2022. These results support previous literature suggesting that mortality at specific temperatures and salinities is size-class dependent, where smaller oysters have a higher tolerance to low salinity and high temperature compared to larger 30 oysters (> 75 mm) (La Peyre et al, 2013;Lowe et al, 2017;McCarty et al, 2020;Rybovich et al, 2016).…”

Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens

“…At the genomic level, we found enriched pathways associated with osmoregulation, including transmembrane and calcium ion transport, consistent with prior gene expression results under low salinity stress (Eierman & Hare, 2014;Maynard et al, 2018). Additional enrichment of ion binding, membrane transport, and DNA/RNA replication and repair pathways suggests that salinity adaptation is controlled by many genes of small effect, in accordance with previous QTL data on low salinity survival (McCarty et al, 2022). We note that GO analyses are limited by incomplete annotation and biased toward genes with clear functional hypotheses (Tiffin & Ross-Ibarra, 2014) and an expectation of few large-effect loci when many traits are polygenic (Rausher & Delph, 2015;Rockman, 2012).…”

Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout

“…Our results showed that genomic prediction for TLE would lead to a relative increase of ~ 11% for GS accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. However, only a few studies investigated selection accuracy for environmental stress-related traits such as heat tolerance in Pacific abalone (Haliotis discus hannai) (Liu et al, 2022) and salinity tolerance in eastern oyster (Crassostrea virginica) (McCarty et al, 2022) or growth-related traits under chronic thermal stress in rainbow trout (Yoshida and Yáñez, 2022). Still, both genomic prediction accuracies and relative increase in accuracy in comparison to PBLUP were in a similar range as in this study.…”

Evaluating a short vs. long-term progeny test and investigating physiology associated with survival in extreme low salinity for the eastern oyster Crassostrea virginica

“…A short-term (2 month) and long-term (6 month) challenge at extreme low salinity (< 3) were conducted to investigate the effect of challenge duration and temperature on oyster extreme low salinity survival. Similar to results from previous extreme low salinity challenges (McCarty et al, 2022(McCarty et al, , 2020, mortality varied among families in the two challenges and narrow-sense heritability estimates were moderate and significantly different from zero. Family mortality was highly correlated between the short-term and long-term challenges, suggesting that an extreme low salinity challenge at a single high temperature (27°C) captures similar mortality trends as the more realistic, 6-month challenge where temperature was adjusted daily to mimic the natural, seasonal variation in temperature experienced from spring to fall.…”

“…Mortality peaked after 6 weeks at 27°C in the short-term challenge (experimental conditions more comparable to previous low salinity challenges: constant temperature of 27°C and 1-2 month exposure duration), while peak mortality (experimental day with the most mortality) occurred 10-12 days after exposure using >80 mm adults in previous studies (McCarty et al, 2020(McCarty et al, , 2022. The delay in mortality observed during the short-term challenge in this study suggests that smaller and younger oysters (< 40 mm, 1-yr old) are more tolerant to a salinity <3 and temperature 27°C than larger oysters (> 80mm, 2 and 3-yrs old; McCarty et al, 2020McCarty et al, , 2022. These results support previous literature suggesting that mortality at specific temperatures and salinities is size-class dependent, where smaller oysters have a higher tolerance to low salinity and high temperature compared to larger 30 oysters (> 75 mm) (La Peyre et al, 2013;Lowe et al, 2017;McCarty et al, 2020;Rybovich et al, 2016).…”

Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens

“…At the genomic level, we found enriched pathways associated with osmoregulation, including transmembrane and calcium ion transport, consistent with prior gene expression results under low salinity stress (Eierman & Hare, 2014;Maynard et al, 2018). Additional enrichment of ion binding, membrane transport, and DNA/RNA replication and repair pathways suggests that salinity adaptation is controlled by many genes of small effect, in accordance with previous QTL data on low salinity survival (McCarty et al, 2022). We note that GO analyses are limited by incomplete annotation and biased toward genes with clear functional hypotheses (Tiffin & Ross-Ibarra, 2014) and an expectation of few large-effect loci when many traits are polygenic (Rausher & Delph, 2015;Rockman, 2012).…”

Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout

“…Our results showed that genomic prediction for TLE would lead to a relative increase of ~ 11% for GS accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. However, only a few studies investigated selection accuracy for environmental stress-related traits such as heat tolerance in Pacific abalone (Haliotis discus hannai) (Liu et al, 2022) and salinity tolerance in eastern oyster (Crassostrea virginica) (McCarty et al, 2022) or growth-related traits under chronic thermal stress in rainbow trout (Yoshida and Yáñez, 2022). Still, both genomic prediction accuracies and relative increase in accuracy in comparison to PBLUP were in a similar range as in this study.…”

Evaluating a short vs. long-term progeny test and investigating physiology associated with survival in extreme low salinity for the eastern oyster Crassostrea virginica

“…A short-term (2 month) and long-term (6 month) challenge at extreme low salinity (< 3) were conducted to investigate the effect of challenge duration and temperature on oyster extreme low salinity survival. Similar to results from previous extreme low salinity challenges (McCarty et al, 2022(McCarty et al, , 2020, mortality varied among families in the two challenges and narrow-sense heritability estimates were moderate and significantly different from zero. Family mortality was highly correlated between the short-term and long-term challenges, suggesting that an extreme low salinity challenge at a single high temperature (27°C) captures similar mortality trends as the more realistic, 6-month challenge where temperature was adjusted daily to mimic the natural, seasonal variation in temperature experienced from spring to fall.…”

“…Mortality peaked after 6 weeks at 27°C in the short-term challenge (experimental conditions more comparable to previous low salinity challenges: constant temperature of 27°C and 1-2 month exposure duration), while peak mortality (experimental day with the most mortality) occurred 10-12 days after exposure using >80 mm adults in previous studies (McCarty et al, 2020(McCarty et al, , 2022. The delay in mortality observed during the short-term challenge in this study suggests that smaller and younger oysters (< 40 mm, 1-yr old) are more tolerant to a salinity <3 and temperature 27°C than larger oysters (> 80mm, 2 and 3-yrs old; McCarty et al, 2020McCarty et al, , 2022. These results support previous literature suggesting that mortality at specific temperatures and salinities is size-class dependent, where smaller oysters have a higher tolerance to low salinity and high temperature compared to larger 30 oysters (> 75 mm) (La Peyre et al, 2013;Lowe et al, 2017;McCarty et al, 2020;Rybovich et al, 2016).…”

Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens

“…At the genomic level, we found enriched pathways associated with osmoregulation, including transmembrane and calcium ion transport, consistent with prior gene expression results under low salinity stress (Eierman & Hare, 2014;Maynard et al, 2018). Additional enrichment of ion binding, membrane transport, and DNA/RNA replication and repair pathways suggests that salinity adaptation is controlled by many genes of small effect, in accordance with previous QTL data on low salinity survival (McCarty et al, 2022). We note that GO analyses are limited by incomplete annotation and biased toward genes with clear functional hypotheses (Tiffin & Ross-Ibarra, 2014) and an expectation of few large-effect loci when many traits are polygenic (Rausher & Delph, 2015;Rockman, 2012).…”

Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout

“…Our results showed that genomic prediction for TLE would lead to a relative increase of ~ 11% for GS accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. However, only a few studies investigated selection accuracy for environmental stress-related traits such as heat tolerance in Pacific abalone (Haliotis discus hannai) (Liu et al, 2022) and salinity tolerance in eastern oyster (Crassostrea virginica) (McCarty et al, 2022) or growth-related traits under chronic thermal stress in rainbow trout (Yoshida and Yáñez, 2022). Still, both genomic prediction accuracies and relative increase in accuracy in comparison to PBLUP were in a similar range as in this study.…”