Identification Of Genes And SNPs Associated With Carotenoids Accumulation In Yesso Scallop (Patinopecten Yessoensis)

Carotenoids which function as retinoid (vitamin A) precursors andantioxidants, are obtained from the diet and cannot be synthesized de novo inanimals. Yesso scallop (Patinopecten yessoensis, Jay,1857) is importantaquaculture species in China. The new variety “Haida Golden Scallop”developed from this species is enriched in carotenoids compared with thenormal ones, providing a good studying model for the mechanism underlyingcarotenoid absorption, transformation and metabolism in animals. In this study,we cloned the Stearoyl-CoA desaturase (SCD) gene from P. yessoensis, and foundthe expression differences of this gene between “Haida Golden Scallop” andnormal P. yessoensis. Further genome-wide association study (GWAS) identifiedSNPs (single nucleotide polymorphisms) which showed significant gentotypedifferences between “Haida Golden Scallop” and normal P. yessoensis. This studywill provide important information to our understanding of the molecularmechanism of carotenoids accumulation in P. yessoensis and candidate geneticloci for scallop breeding aiming at improving carotenoid content.1Cloning of Yesso scallop SCD gene (PySCD) and analysis of the expressiondifference of this gene between normal scallop and “Haida golden scallop”The PySCD gene had4exons and3introns and a full-length cDNA of2559bpcontains a990bp open reading frame (ORF) encoding329amino acids. Thepredicted protein of PySCD had4transmembrane domain and3histidine-boxmotifs which was the characteristic feature of PySCD gene family. Several putativebinding sites for transcription factors, including sterol-regulatory element binding protein (SREBP) binding sites, CCAAT recognition sites and retinoic acidX receptor (RXR) binding sites were present in the5’ flanking region. Meanwhile,a minisatellite DNA with unit length of37bp and repeat number of25was foundat5kp upstream of the transcription initiation site.Expression levels of PySCD during the developmental stages (fertilized eggs,blastulae, gastrulae, D-shaped larvae, and veliger larvae) and in adult tissues(mantle, gill, gonad, kidney, striated muscle, and digestive gland) were analyzedusing real-time qRT-PCR (quantitative reverse transcription PCR). PySCDtranscripts were detected in all of the developmental stages sampled withsignificantly higher expression levels in the newly fertilized eggs and veligerlarvae than in those of other stages. In adult scallops, PySCD were detected in allthe sampled tissues, and digestive gland, gonad and striated muscle exhibitedsignificantly higher expression levels of PySCD than other tissues. A comparisonof PySCD expression showed that significantly more PySCD transcripts weredetected in “Haida golden scallop” than normal scallop in veliger larvae. In adulttissues, significantly higher expression level of PySCD was found in the digestivegland, striated muscle, and gonad of “Haida golden scallop” than that in thecorresponding tissues of normal Yesso scallops. The higher expression level ofPySCD in “Haida golden scallop” than that in ordinary yesso scallop implied thathigh expression of PySCD maight promote the carotenoids accumulation and thecarotenoids accumulation in “Haida golden scallop” maight be related with lipidmetabolism.2Identification of SNPs associated with carotenoids accumulation in Yessoscallop using GWASGWAS was proformed in12“Haida golden scallops” and12normal scallopsusing2b-rad protocol to identify SNPs associated with carotenoids accumulation.A total of6G base pairs and172,875,615reads (40-fold sequencing coverage)were produced by sequencing the2b-rad libraries, and then287,909tags which contained89,221SNPs were obtained. Sixty of these SNPs exhibited significantgenotype frequencies between “Haida golden scallop” and normal yesso scallop,and8of them were further verified in other two different population groups.The8SNPs which showed significantly difference genotype frequenciesbetween “Haida Golden scallop” and normal yesso scallop were furtherannotated based on the genome sequences of Yesso scallop. Nighty nine geneswere found around these SNPs, which were mapped to Kyoto Encyclopedia ofGenes and Genomes (KEGG) pathways including lipid metabolism, signaltransduction and immune system. Further functional analysis of these genescould deepen our understanding of the molecular mechanism underlyingcarotenoid accumulation in “Haida golden scallop”.