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

Abstract

The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS).

Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction

“…Other studies have reported heritability estimates for weight ranging from 0.1 to 0.5 in C. gigas ( Hedgecock et al, 1991 ; Sheridan, 1997 ; Langdon et al, 2003 ; Evans and Langdon, 2006 ). Our results are consistent with heritability estimates described for shell measurements, e.g., Li et al (2011) reported values of 0.149–0.402 for SH in C. gigas at 12 months of age, while Kong et al (2015) described estimates of 0.49 for SH and 0.36 for SL, and Xu et al (2017) reported heritability values of 0.18 for SH and 0.25 for SL. These results imply that growth can potentially be improved by selective breeding.…”

“…Global production of this species reached ∼0.6 M tones in 2016 ( FAO, 2018 ). Given its importance, several selective breeding programs based on family and mass selection have been conducted for the improvement of economically important traits such as body weight, growth rate, survival and yield ( Langdon et al, 2003 ; Evans and Langdon, 2006 ; Li et al, 2011 ; de Melo et al, 2016 ), showing an improvement of the target traits after 1–5 generations. As with other aquaculture species, the recent development of genomic tools opens up the possibility for incorporating genetic markers into breeding programs via genomic selection, resulting in improved selection accuracy and genetic gain ( Goddard and Hayes, 2007 ).…”

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp ( Hypophthalmichehys nobilis )

“…This present genetic map also significantly improved our previous linkage map (Zhu et al, 2014) by both resolution and accuracy, which would be useful for QTL mapping and identification of potential genes for growth in bighead carp. Genetic linkage maps with more markers may have a larger map size, but other factors such as chromosome interferences may also affect the size of a genetic linkage map (Li and He, 2014;Sun and Liang, 2004). The total length of this new linkage map shorter than the previous map may be because different chromosome interferences derived from interspecific hybridization (Zhu et al, 2014) and intraspecific cross (this study).…”

Applications of genotyping by sequencing in aquaculture breeding and genetics

“…In addition, RAD‐like techniques have been very popular for marker discovery and QTL mapping in bivalve shellfish including Chinese scallop ( Argopecten irradians ; Jiao et al . ), Akoya pearl oyster ( Pinctata fucata ; Li & He ; Shi et al . ), variously coloured abalone ( Haliotis diversicolor ; Ren et al .…”