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.
Highlights
The shell of mollusks with diverse forms and alternative colors has always appealed to consumers and scientists (Comfort, 1950)
After quality filtering, a set of 29,036 qualified single-nucleotide polymorphisms (SNPs) were successfully assigned to the 16 chromosomes of bay scallop and used for
Annotation results showed that the top three SNPs were located in three genes, including G-protein-coupled receptor-like 101 (GRL101), polyketide synthase 1 (PKS1), and PLC1, which were further selected for comparing their expression differences in mantles between PP and brown shell color population (BP) individuals
Summary
The shell of mollusks with diverse forms and alternative colors has always appealed to consumers and scientists (Comfort, 1950). Investigation in Pacific oyster, Crassostrea gigas, demonstrated that shell pigmentation is controlled by two genetic loci, with one responsible for the secretion of pigments and the other responsible for the distribution mode of pigmentation (Xu et al, 2019). The same method was exerted in two extreme color phenotypes of Yesso scallop, Patinopecten yessoensis, and 25 significantly differential expression genes were identified for unraveling shell color differences (Sun et al, 2016). These researches provided pivotal loci/genes responsible for the formation of shell coloration and served as candidate markers for mollusks breeding projects
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
