Large-Scale Development of Gene-Associated Single-Nucleotide Polymorphism Markers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies

• Published in: DNA Research
• Main Authors: Jiao, Wenqian, Fu, Xiaoteng, Li, Jinqin, Li, Ling, Feng, Liying, Lv, Jia, Zhang, Lu, Wang, Xiaojian, Li, Yangping, Hou, Rui, Zhang, Lingling, Hu, Xiaoli, Wang, Shi, Bao, Zhenmin
• Format: Text
• Language: English
• Published: Oxford University Press 2014
• Subjects: Full Papers; Pacific; Pacific oyster
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989488; http://www.ncbi.nlm.nih.gov/pubmed/24277739; https://doi.org/10.1093/dnares/dst048

Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among subfamilies of Pectinidae. Gene annotations were available for 73% of the markers, and 65% could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible for scallop growth regulation, and provided markers for further genetic improvement of C. farreri in breeding programmes.