The common pearl oyster, Pinctada fucata (Gould), is the most important species that is cultured for production of marine pearls in China. Heavy mortality and the decline of pearl quality have resulted in a breeding programme being established in recent years. In this study, we conducted selective breeding for the second generation of pearl oyster P. fucata (JCS‐2) by mass selection for shell height (SH) with a selection intensity of 1.614, and analysed the growth of the selected line (JCS‐2) and the non‐selected control line (JCC) during a 1‐year grow‐out period. The results show that the selected line grew faster than the control one in the SH and total weight (TW) (P<0.05), and there were higher proportion of larger sized oysters. Coefficient of variation for SH of JCS‐2 was smaller than that of JCC. The current genetic gains and realized heritability for JCS‐2 averaged 16.03 ± 4.79% and 0.713 ± 0.208 at 3–15 months of age respectively. The findings indicated the selection response to faster growth for SH is markedly effective in the second generation, and there was a high correlated response of TW when selecting for SH.

Pearl oysters have been found to secrete nacre and form pearls with good quality and significant commercial interest. However, the transcriptomic and genomic resources for pearl oysters are still limited. To improve this situation, transcriptome sequencing was conducted from four species of pearl oysters with Illumina HiSeq™ 2000. There were four gigabase-scale transcriptomes for four species of pearl oysters, ∼26.3 million reads with ∼2.37 gigabase base pairs (Gbp) in Pinctada fucata, ∼26.5 million reads with ∼2.39 Gbp in Pinctada margaritifera, ∼27.0 million reads with ∼2.43 Gbp in Pinctada maxima, and ∼25.9 million reads with ∼2.33 Gbp in Pteria penguin, respectively. After sequence assembly and blastx alignment, the numbers of annotated unigenes ≥200 bp were 33,882 in P. fucata, 30,666 in P. margaritifera, 26,420 in P. maxima, and 29,928 in P. penguin. Based on these annotated unigenes among four species of pearl oysters, CDSs were extracted and predicted and furthermore, analyses of GO and KEGG assignments were performed. In addition, 60 putative genes of growth factors and their receptors from four species of pearl oysters were predicted. This study established an excellent resource for gene discovery and expression in pearl oysters, but also offered a significant platform for functional genomics and comparative genomic studies for mollusks.