A Genome-Wide Association Study Identifies the Genomic Region Associated with Shell Color in Yesso Scallop, Patinopecten yessoensis

Abstract

The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform. A total of 322,332,684 high-quality reads were obtained, and the average sequencing depth was 18.4×. One genomic region on chromosome 11 that included 239 single-nucleotide polymorphisms (SNPs) was identified as significantly associated with shell color. After verification by high-resolution melting in another population, two SNPs were selected as specific loci for reddish-orange shell color. These two SNPs could be used to improve the selective breeding progress of true-breeding strains with complete reddish-orange scallops. In addition, within the significantly associated genomic region, candidate genes were identified using marker sequences to search the draft genome of Yesso scallop. Three genes (LDLR, FRIS, and FRIY) with known functions in carotenoid metabolism were identified. Further study using high-performance liquid chromatography proved that the relative level of carotenoids in the reddish-orange shells was 40 times higher than that in the brown shells. These results suggested that the accumulation of carotenoids contributes to the formation of reddish-orange shells.

Colour in bivalve shells: Using resonance Raman spectroscopy to compare pigments at different phylogenetic levels

“…It seems likely that the polyenes in molluscan shell pigments are based on carotenoid precursors, which are known to colour soft tissues and are correlated with colour in shells . As most animals are incapable of producing carotenoids de novo, molluscan carotenoids are likely to be dietary in origin, whereas some modifications may be genetically controlled .…”

“…There have been a growing number of studies in the last decade investigating the pigments responsible for molluscan shell colour and the genes and pathways responsible for their production . Techniques used to distinguish pigments in shells have included high‐performance liquid chromatography, mass spectrometry, and UV‐visible spectrophotometry, but difficulties in some studies have arisen from the low concentrations of pigments .…”

A preliminary identification of genomic loci for body colour variation in the sea cucumberApostichopus japonicus

“…Those results showed that 2b‐RAD sequencing is robust for SNP marker discovery and in combination with GWAS provide an effective tool for gene mapping in A. japonicus . The high efficiency of 2b‐RAD sequencing and GWAS was also demonstrated in mapping genomic regions for shell colour in the Yesso Scallop, Patinopecten yessoensis (Zhao et al, ).…”

Attempted use of an uncommon bay scallop color morph for tracking the contribution of restoration efforts to population recovery

“…This color morph is uncommon in New York as well as in other native bay scallop populations, with observed frequencies of 1.5% in Connecticut (Stiles et al ) and ≤1.5% in Nantucket, Massachusetts (S. Tettelbach, personal observation). Shell color in some molluscan species has been shown to be heritable, but in others it may also vary due to environmental influences (Williams ; Zhao et al ). In bay scallops, shell color and pattern have been shown to be genetically determined (Kraeuter et al ; Adamkewicz & Castagna ; Qin et al ; Teng et al ); this is also true for other scallop species (Wolff & Garrido ; Zheng et al ; Zhao et al ), with color likely related to the deposition of different pigments, for example, melanin (Sun et al ).…”

“…Shell color in some molluscan species has been shown to be heritable, but in others it may also vary due to environmental influences (Williams ; Zhao et al ). In bay scallops, shell color and pattern have been shown to be genetically determined (Kraeuter et al ; Adamkewicz & Castagna ; Qin et al ; Teng et al ); this is also true for other scallop species (Wolff & Garrido ; Zheng et al ; Zhao et al ), with color likely related to the deposition of different pigments, for example, melanin (Sun et al ). Through self‐crosses of A. irradians , which are simultaneous hermaphrodites, Adamkewicz and Castagna () concluded that the background shell color is determined by a single gene, with rarer yellow or orange colors being dominant to white; more diverse overlying patterns and pattern colors, which may almost completely obscure the underlying background color (Elek ; Elek & Adamkewicz ), are under control of 1 or more additional genes.…”