Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources

Abstract

Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b‐RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (FST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.

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

“…(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.…”

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

“…Moreover, a broad color diversity exists in this species across its full distribution range underpinned by a substantial genetic variation, as the high heritabilities estimated in our study demonstrate, so its putative adaptive role should deserve further studies. Interestingly, the C13 color associated QTL overlaps with a genomic region in the same chromosome which showed very consistent signals of divergent selection in the whole Northeast Atlantic and in the Northern Region (above the Ushant Front), including several outliers above the neutral background and highly significant linkage disequilibrium suggestive of selective sweeping 20 .…”

“…These methods, including Restriction-site Associated DNA (RAD) sequencing 13 and its derivations, ddRAD 14 , 2b-RAD 15 or SLAF 16 , have been successfully used for high-throughput genotyping in many aquaculture species 17 , including several important commercial molluscs 18 . GBS methods have been recently applied to understand adaptive variation of common cockle from Northeast Atlantic, and consistent signals of adaptive variation were detected both at microgeographic (dd-RAD; 19 ) and macrogeographic (2b-RAD; 20 ) scales. GBS have facilitated the construction of high-resolution linkage maps 21 – 23 , which are important tools for genome scaffolding and assembly 24 and have aided to disentangle the genetic basis of relevant evolutionary or productive traits through quantitative trait locus (QTL) screening 25 , 26 .…”

The broad shell colour variation in common cockle (Cerastoderma edule) from Northeast Atlantic relies on a major QTL revealed by GWAS using a new high-density genetic map

“…Moreover, a broad colour pattern diversity exist in this species across its full distribution range and, importantly, with a substantial underlying genetic variation, as the high heritabilities estimated in our study demonstrate, so its putative adaptive role should deserved further studies. Interestingly, the C13 colour associated QTL overlaps with a genomic region in the same chromosome which showed very consistent signals of divergent selection, including several outliers above the neutral background and highly significant linkage disequilibrium suggestive of selective sweeping (Vera et al, 2022).…”

“…These methods, including Restriction-site Associated DNA (RAD) sequencing (Baird et al, 2008) and its derivations, ddRAD (Peterson et al, 2012), 2b-RAD (Wang et al, 2012) or SLAF (Sun et al, 2013), have been successfully used for high-density genotyping in many aquaculture species (Robledo et al, 2018), including several important commercial molluscs (Gomes dos Santos et al, 2020). GBS methods have been recently applied to understand adaptive variation of common cockle from Northeast Atlantic, and consistent signals of adaptive variation were detected both at microgeographic (dd-RAD; Coscia et al, 2020) and macrogeographic (2b-RAD; Vera et al, 2022) scales. GBS have facilitated the construction of high-resolution linkage maps (Maroso et al, 2018; Dong et al, 2019; de la Herrán et al, 2022), which are important tools for genome scaffolding and assembly (Fierst, 2015), and have aided to disentangle the genetic basis of relevant evolutionary or productive traits through quantitative trait locus (QTL) screening (Aslam et al, 2020; Yin & Hedgecock, 2021).…”