Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica

Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica)

“…This strategy of SNP discovery generated a panel of markers that is representative of the genetic variation present across multiple locations and thus should be applicable to Eastern oysters originating from diverse populations in Canada. Given that we focused on populations at the northern range limit of C. virginica , our SNP chip complements that which was recently published for US populations ( Guo et al 2023 ). Indeed, the genetic composition between Canadian populations and populations further south may differ substantially, as a north-south genetic break has been observed on the Eastern Scotian Shelf for other marine species distributed along the Northwestern Atlantic coast ( Stanley et al 2018 , Lehnert et al .…”

“…Null alleles result in an excess of homozygotes and have been associated with apparent non-Mendelian segregation observed at microsatellite loci developed for C. virginica ( Reece et al . 2004 ) and were implicated as a major source of MIEs in a SNP panel designed for the same species ( Guo et al . 2023 ).…”

“…A validated panel of 58 SNPs was previously released, primarily for use in parentage analysis and studies of population structure ( Thongda et al 2018 ). More recently, high-density SNP arrays were published for C. virginica in the United States ( Guo et al 2023 ). The potential of genomic selection in oysters is well established; thus, the availability of genomic tools could have enormous positive impacts on the Eastern oyster aquaculture industry.…”

A common garden experiment supports a genetic component underlying the increased resilience of common cockle (Cerastoderma edule) to the parasite Marteilia cochillia

“…We also observed significant heterozygote deficit in samples from both stocks ( F IS = 0.316 and 0.326 in affected and naïve stocks, respectively) (Tables S3 and S4; Figure 4). Positive F IS values have been commonly reported in mollusks (Pino‐Querido et al, 2015) and specifically in common cockle (Vera et al, 2022), and have been mostly attributed to the presence of null alleles related to the high nucleotide polymorphisms reported in this group (Guo et al, 2023; Zhan et al, 2009). However, F IS values in our study were significantly higher than those previously reported in shellfish beds from Galicia (average F IS = 0.104; Vera et al, 2023) and could be either related to the mixing of different cohorts originated from small number of contributors when obtaining progenies at hatchery (Wahlund effect) or to the particular high heterozygote deficit detected at specific loci, such as CE2, CE11, CE25, CE50, CE51, CE52, and CE53 (Figure S4).…”

Genetic improvement of oysters: Current status, challenges, and prospects

“…Some genome‐wide association studies (GWAS) were carried out and identified SNPs linked to disease resistance, 91,195,223 low salinity tolerance, 196 nutrient traits, 224 shell growth, shell shape traits, 225 and so on. The development of SNP arrays for oysters raises the opportunity to test GS strategies for polygenic traits (Table 4), such as those SNP arrays recently developed for C. gigas , 211,227,228 O. edulis , 226,228 C. ariakensis , 229 and C. virginica 230,231 . The potential for using GS to advance breeding has been evaluated in several studies (Table 5), such as low salinity survival for C. virginica , 196 morphometric traits, edibility traits, and disease traits for C. angulata , 233 growth, meat content, and colour traits for C. gigas , 211,232 and resistance to O. herpesvirus for C. gigas 91 .…”