A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

Abstract

Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13∶1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.

Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

“…Using randomly selected individuals or all individuals of a family as mapping population, the identified QTLs are usually evenly distributed across the linkage groups [23], [61]. To identify QTLs, the family structure is extremely important in the experimental design.…”

Development of Molecular Resources for an Intertidal Clam, Sinonovacula constricta, Using 454 Transcriptome Sequencing

“…To date, there have been few studies on QTLs affecting growth-related traits in shellfish. QTL analyses in several aquaculture species such, as salmonids [3], tilapia [4], sea bass [5], [6], oyster [7], clam [8], and scallop [9], [10], have demonstrated the feasibility of genetic analysis using molecular markers. High-density genetic linkage maps are required for QTL analysis.…”

High-resolution linkage and quantitative trait locus mapping using an interspecific cross between Argopecten irradians irradians (♀) and A. purpuratus (♂)

“…Taking advantage of 2b-RAD method, high-resolution genetic linkage maps were constructed for the bay and Peruvian scallops by cost-effectively genotyping a full-sibling family of 152 scallops. The mapping density of the bay scallop was 0.32 cM with a 97.7% coverage, surpassing the resolution of all the previously constructed genetic maps (Li et al 2012;Qin et al 2007a, b;Wang et al 2007). The linkage map for the Peruvian scallops constructed in this study is the first one for this species, with a resolution of 0.51 cM and a mapping coverage of 98.9%.…”

“…Limited by the number of developed markers and high-throughput genotyping platforms, genetic studies in scallops lack progress in uncovering the molecular mechanisms underlying various commercial traits. Most of the previously constructed genetic maps in scallops were with relatively low resolutions, limiting the sensitivity and accuracy in determining quantitative trait genes (Li et al 2005(Li et al , 2012Wang et al , 2005Wang et al , 2007Zhan et al 2009). Recent development of genotyping by sequencing (GBS) technologies has allowed high-throughput and efficient genotyping (Elshire et al 2011;Narum et al 2013;Poland and Rife 2012).…”