Quantitative trait loci and genetic association analysis reveals insights into complex pearl quality traits in donor silver-lipped pearl oysters

• This work describes the first QTL and genetic associations for pearl quality traits.
• We present nine putative QTL and 25 marker associations for pearl quality traits.
• We offer novel insights into the genetic architecture of pearl quality traits.
• One major genomic region was identified with a strong influence on pearl colour.
• These preliminary QTL and genetic associations should encourage further studies.

Pearl oysters are commercially farmed for their gemstone quality pearls worldwide and are an important animal model for understanding bivalve biology. However, despite their economic and scientific significance, limited quantitative genetic studies have been undertaken to identify genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). Over the last decade, pearling industries worldwide have shown strong interest in genetic stock improvement aiming to increase the production of high quality ‘South Sea’ pearls. However, before genetic breeding programmes can be initiated, the genetic architecture of such traits needs to be elucidated. This study investigates the genetic architecture of complex pearl quality traits (pearl size, weight, surface complexion and colour) and presents the first putative quantitative trait loci (QTL) and genetic associations to these commercially important pearl quality traits.To identify QTL and genetic associations to pearl quality traits, a total of 2114 pearl grading records were recorded over 342 pearl oysters. Utilising these phenotypic records, this study provides strong evidence that pearl quality traits have a low to moderate additive genetic component (h2 from 0.14 to 0.34) and supports previous quantitative genetic studies that these traits are polygenic in nature. A total of nine putative QTL and 25 marker associations for pearl colour, one QTL for pearl surface complexion and three genetic associations to pearl size and weight were identified using 11 half-sib families. The majority of QTL and genetic associations were detected for pearl colour whereby the most prominent QTL were located within a 2 cM interval on LG10. QTL in this region were mapped for four out of five sub-categories of pearl colour and explained from 32% to 46.1% of the phenotypic variation observed in pearl colour. Segregation in multiple families provides further support that genes localised to this region have significant effects on pearl colour.The segregation of these preliminary QTL and detection of genetic associations provide insights into the genetic architecture of pearl quality traits and will direct further research into the establishment of genetic breeding programmes for pearl quality within the Pinctada maxima pearling industry.