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

• Published in: Marine biotechnology (New York, N.Y.) Vol. 19; no. 3; pp. 301 - 309
• Main Authors: Zhao, Liang, Li, Yangping, Li, Yajuan, Yu, Jiachen, Liao, Huan, Wang, Shuyue, Lv, Jia, Liang, Jun, Huang, Xiaoting, Bao, Zhenmin
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-06-2017; Springer Nature B.V
• Subjects: Animal Shells - chemistry; Animals; Aquaculture; Biomedical and Life Sciences; Breeding; Carotenoids; Carotenoids - genetics; Chromosome 11; Chromosomes; Color; Colour; Economics; Engineering; Freshwater & Marine Ecology; Fruits; Gene sequencing; Genes; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; High performance liquid chromatography; High resolution; Libraries; Life Sciences; Liquid chromatography; Marine molluscs; Melting; Metabolism; Microbiology; Original Article; Patinopecten yessoensis; Pectinidae - chemistry; Pectinidae - genetics; Polymorphism; Polymorphism, Single Nucleotide; Population genetics; Scallops; Selective breeding; Sequence Analysis, DNA; Shellfish; Shells; Single-nucleotide polymorphism; Visual perception; Zoology; Yesso scallop; Candidate gene; GWAS; SNP; Carotenoid; Shell color
• ISSN: 1436-2228; 1436-2236
• DOI: 10.1007/s10126-017-9751-y

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.