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

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.

海湾扇贝（Argopecten irradians）是中国经济价值最为重要的水产养殖物种之一。本研究利用包含两个类回交杂种家系的作图群体，针对海湾扇贝的两个亚种（A. i. irradians与A. i. concentricus）构建了基于微卫星（microsatellite）的整合遗传连锁图谱。本研究共将161个微卫星标记与1个表型（壳色）标记定位至16个连锁群（LGs），该数目与海湾扇贝的单倍体染色体数一致。雌性与雄性的性别特异图谱长度分别为779.2 cM与781.6 cM，而性别平均图谱总长度为849.3 cM。整合图谱的平均分辨率为5.9 cM/位点，预估覆盖度达81.3%。分离偏倚标记在杂交亲本中占比更高，提示分离偏倚可能源于两个海湾扇贝亚种基因组间的种间相互作用。双亲共有连锁标记的雌雄重组率整体为1.13∶1，且两个家系的不同亲本间重组率也存在显著差异。本研究测定了壳长（SL）、壳高（SH）、壳宽（SW）与总重量（TW）4个体型相关性状，用于数量性状位点（QTL）分析。最终在5个连锁群上检测到3个显著QTL与6个提示性QTL。在3个显著QTL中，2个（qSW-10与qTW-10，分别调控壳宽与总重量）定位于LG10上标记AiAD121附近的同一区域，分别解释20.5%与27.7%的表型变异；剩余1个显著QTL（qSH-7，调控壳高）定位于LG7，可解释15.8%的表型变异。6个提示性QTL则分布于4个不同的连锁群上。本研究构建的遗传连锁图谱与体型相关QTL，可为海湾扇贝的标记辅助选择（MAS）提供理论支撑。