Identification of Single-Locus PCR-Based Markers Linked to Shell Background Color in the Pacific Oyster (Crassostrea gigas)

Abstract

A number of Pacific oyster (Crassostrea gigas) with golden shell background color were obtained which show great potential to develop a niche market. To improve the selective breeding progress of true-breeding strains with complete golden oysters, research was conducted to identify genetic markers linked to the shell color locus. An F1-segregating population was obtained by crossing two oysters with golden shell and white shell. Genomic DNA from eight progenies with golden shell and eight progenies with white shell were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly linked to shell color across the segregating population. The seven AFLP markers were all derived from the golden dam and mapped onto a single linkage group flanking the shell color locus. In conversion of the AFLPs into single-locus PCR-based markers, a sequence-characterized amplified region (SCAR) marker, named SCARJ8-2, a single nucleotide polymorphism (SNP) marker, named SNPL2-4, and a simple sequence repeat (SSR) marker, named SSRO11-2, were obtained. These markers obtained in this study will be useful for marker-assisted selection of the Pacific oyster.

Identification of a microsatellite marker that is completely linked to shell colour in small abalone,Haliotis diversicolor

“…In Pacific abalone, new bluish-coloured (B-type) and orange-coloured (O-type) individuals were discovered and segregation data indicate that the bluishand orange-coloured variants were heritable (Kobayashi, Kawahara & Hasekura 2004;Liu et al 2009). Shell colour variation in various marine species is determined by simple genetic patterns (Adamkewicz & Castagna 1988;Wada & Komaru 1990;Liu et al 2009;Ge et al 2015).…”

“…Molluscan shell colour is mainly determined by genetic factors and is affected by environmental factors such as diet, salinity, light and substratum (Mitton 1977;Gruneberg 1979;Gray 1994;Ekendahl & Johannesson 1997;Ekendahl 1998;Sokolova & Berger 2000;Zou, Zhang, Guo, Zhu, Li & Jiang 2014). In general, shell colour variation determination is under a relatively simple genetic mechanism, as has been found in mussel (Mytilus edulis L.), clam (Mercenaria mercenaria), pearl oyster (Pinctada fucata martensii) and Pacific oyster (Chanley 1961;Newkirk 1980;Wada & Komaru 1990;Ge, Li, Yu & Kong 2015). In Pacific abalone, the O-type and G-type (dark-brown or green) shell colours are under genetic control by a single locus with a recessive o (for orange shell) allele and a dominant G (for dark-brown or green shell) allele (Liu, Wu, Zhao, Zhang & Guo 2009).…”

“…In addition, several microsatellite markers in small abalone have been reported. The identification of molecular markers linked to shell colour could be helpful in discriminating homozygous and heterozygous orange individuals and therefore significantly reduce the cost of producing breeding lines and significantly accelerate the breeding programme (Ge et al 2015). In this study, we screened 308 microsatellite markers for their association to shell colour using the DNA pooling approach.…”

Biotechnologies from Marine Bivalves

“…Different from the DNA microarray analysis, high-throughput sequencing can lead to gene discovery and to the validation of population genetics markers for breeding programmes. The identification of single nucleotide polymorphisms (SNPs, codominant-inherited molecular features very abundant in animal genomes) in bivalves is just a preliminary step, before starting to validate their association with valuable quantitatively inherited traits or with stress-responsive genes, and to proceed with fine linkage mapping and population genetics analyses (Coppe et al 2012;Ge et al 2015;Nie et al 2015;Dong et al 2016;Fan et al 2016;Wang et al 2016a, b;Qi et al 2017;Gutierrez et al 2017;Azéma et al 2017).…”

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

“…Pacific oysters exhibited distinct shell colors (golden, white, and black) and the shell pigmentation has been considered as a quantitative trait that is controlled by many genes with small-effects [ 15 ]. Quantitative trait locus (QTL) for shell pigmentation and background coloration have been established with amplified fragment length polymorphism (AFLP) makers [ 16 – 17 ], which will facilitate our explore to the genetic mechanisms of shell coloration in the C . gigas .…”