A Genome-Wide Association Study Identifies Candidate Genes Associated With Shell Color in Bay Scallop Argopecten irradians irradians

Abstract

Molluscan shell color has consistently drawn attention for its abundant diversity and commercial use in shellfish breeding projects. Recently, two new strains of bay scallop (Argopecten irradians irradians) with different shell colors as marked phenotypic traits have been artificially bred to improve their economic values; however, the inheritance mechanism of their shell pigmentation is still unclear. In this study, a genome-wide association study (GWAS) was conducted to determine the genetic basis of shell color in bay scallops utilizing 29,036 high-quality single-nucleotide polymorphisms (SNPs) derived from 80 purple-red (PP) and 80 black-brown (BP) shell color individuals. The result of the GWAS showed that 469 SNPs (p <1.72E−6) significantly associated with shell color were mainly distributed in chromosome 7. The top three SNPs (i.e., chr7-12764003, chr7-13213864, and chr7-11899306) are located in the genic region of G-protein-coupled receptor-like 101 (GRL101), polyketide synthase 1 (PKS1), and phosphoinositide phospholipase C (PLC1), which have been widely reported to be involved in pigmentation. Successfully, the top three SNPs were verified in another non-breeding bay scallop population. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses obtained 38 GO terms covering 297 genes and aggregating pathways involving 252 annotated genes. Specifically, the expression profiles of the top three identified candidate genes were detected in mantles of PP and BP individuals by real-time quantitative reverse transcription PCR. The significantly higher expression levels of GRL101 (6.43-fold) and PLC1 (6.48-fold) in PP, and PKS1 (12.02-fold) in BP implied that GRL101 and PLC1 potentially functioned in PP shell coloration, and black pigmentation in BP might be principally regulated by PKS1. Our data provide valuable information for deciphering the phenotype differences of shell color in the bay scallop.

Genome-wide association and transcriptome studies reveal the segregation mechanism of mantle markings in three-way cross hybrid abalone

“…Most of the significant SNPs associated with mantle color were primarily allocated to chromosome 15 of three-way cross abalone. Similarity to the bay scallop, most of the significant SNPs associated with shell color were primarily allocated to chromosome 7 (Zhu et al, 2021). In the Yesso scallop, the major SNPs associated with shell color are located on chromosome 11 (Zhao et al, 2017), and almost all the significant…”

A Chitin-Binding Protein Ultra-highly expressed in the Outer Fold of Mantle is Related to Shell Colour in Pacific Oyster Crassostrea gigas

“…The central mantle is involved in the calcification and thickening of the shell, such as inhibiting CaCO3 crystal and regulating the growth of epithelial cells and Ca 2+ ; the mantle edge contains a large number of conchiolin proteins prompting the shell to grow outward and participating in shell periostraca formation 18,39,41,42 . Shell colour is also correlated with the colour of the mantle edge 13,22,43,44 contains a large number of genes and genetic locus related to shell colour 8,[45][46][47][48] . The mantle edge has outer, middle and inner folds 49,50 .…”

Cloning, Characterization, and Expression Prolife Analysis of Tyrosinase Genes: Insights into Black Shell Formation in Cyclina sinensis

“…At present, the characteristics of nutrition, disease resistance, growth, shell color, and other traits can be used to determine specifc molecular markers to screen out superior species of C. sinensis [6]. Among those characteristics, shell color has been widely studied in regards to its molecular inheritance [7]. Te polymorphism of shell color is afected by genes, the environment, food, and other factors.…”