Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Abstract

The Pacific oyster, Crassostrea gigas , is an important aquaculture shellfish around the world with great economic and ecological value. Selective breeding programs have been carried out globally to improve production and performance traits, while genomic signatures of artificial selection remain largely unexplored. In China, we performed selective breeding of C . gigas for over a decade, leading to production of several fast‐growing strains. In the present study, we conducted whole‐genome resequencing of 20 oysters from two fast‐growing strains that have been successively selected for 10 generations, and 20 oysters from the two corresponding wild populations. Sequencing depth of >10× was achieved for each sample, leading to identification of over 12.20 million SNPs. The population structures investigated with three independent methods (principal component analysis, phylogenetic tree, and structure) suggested distinct patterns among selected and wild oyster populations. Assessment of the linkage disequilibrium (LD) decay clearly indicated the changes in genetic diversity during selection. Fixation index ( F st ) combined with cross‐population composite likelihood ratio (XP‐CLR) allowed for identification of 768 and 664 selective sweeps (encompassing 1042 and 872 genes) tightly linked to selection in the two fast‐growing strains. KEGG enrichment and functional analyses revealed that 33 genes are important for growth regulation, which act as key components of various signaling pathways with close connection and further take part in regulating the process of cell cycle. This work provides valuable information for the understanding of genomic signatures for long‐term selective breeding and will also be important for growth study and genome‐assisted breeding of the Pacific oyster in the future.

A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae

“…By exploiting a new flat oyster genome, we demonstrated that nearly all consistent outliers are located on OE‐C8, spanning a region of 29.44 Mb and that half of the suggestive ones also mapped at OE‐C8, but population data suggest that this region could span 33.83 Mb, nearly half of OE‐C8. Previous studies suggested quick dropping of LD with physical distance in molluscs, especially in the wild, associated with their typical large effective population sizes (Gutiérrez et al, 2017; Hu et al, 2021; Vera et al, 2022; Zhong et al, 2017). In edible cockle ( Cerastoderma edule ), a species with an overlapping distribution and similar life‐history features to flat oyster, Vera et al (2022) detected a maximum r 2 of 0.05, which was significant at distances below 50 kb.…”

“…(Di et al, 2015;Gallaga-Maldonado et al, 2020;Maynard et al, 2016), sometimes involving specific immune genes, such as the histocompatibility complex (MHC; Kekäläinen et al, 2009;Penn et al, 2002). It is important to note that the term resistance applied until now in this and previous studies related to bonamiosis infection is rather inaccurate, as the response to the parasite may be related both to resistance against infection and the ability to survive once infected (tolerance) (Holbrook et al, 2021) in the wild, associated with their typical large effective population sizes (Gutiérrez et al, 2017;Hu et al, 2021;Vera et al, 2022;Zhong et al, 2017). In edible cockle (Cerastoderma edule), a species with an overlapping distribution and similar life-history features to flat oyster, Vera et al (2022) detected a maximum r 2 of 0.05, which was significant at distances below 50 kb.…”

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

“…Furthermore, conserved synteny and chromosomal architecture against an independently assembled flat oyster genome assembly (Boutet et al, 2022), coupled with the general high congruency of the assembled super-scaffolds with linkage groups, further confirmed the global quality of our assembly. Expansions to gene families involved in stress responses during bivalve evolution may reflect adaptation to a filter-feeding sessile lifestyle in a hostile environment (Guo et al, 2018; Regan et al, 2021; Hu et al, 2022). Past work has revealed expansions in gene families encoding heat shock proteins, as well as families involved in apoptosis inhibition and innate immunity, including C-type lectins and C1q complement domain containing proteins.…”

Revealing Selection in Breeding and Genetic Characteristics of Economically Important Traits of New Species of Apostichopus Japonicas Based on Genome Resequencing and GWAS Analysis

“…It is worth noting that, strictly speaking, the CN population is not a wild population, but has been subjected to unintentional artificial selection. Therefore, irrespective of whether we are referring to the AY-1 population or the CN population, the LD attenuation distance is shorter than that of other domesticated aquatic animals (For example, Crassostrea Gigas, Nile Tilapia, Large Yellow Croaker, scallop) (Cádiz et al, 2020;Hu et al, 2022;Kon et al, 2021;Wang et al, 2021). Therefore, we speculate that the gene recombination frequency and genetic diversity of the current cultured A. japonicas populations in China are generally high.…”