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

Marine Biotechnology
Liang ZhaoZhenmin Bao

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 sequen...Continue Reading

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Citations

May 17, 2018·Marine Biotechnology·Fei SunGen Hua Yue
Mar 14, 2019·Marine Biotechnology·Bi Jun LiJun Hong Xia
Jan 4, 2021·Current Opinion in Genetics & Development·Suzanne V Saenko, Menno Schilthuizen
Feb 15, 2020·International Journal of Biological Macromolecules·Yuying SunJiquan Zhang

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Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

R
BLASTN
Plink
Perl script
qqman

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