title: Large-scale development of gene-associated single-nucleotide polymorphism markers for molluscan population genomic, comparative genomic, and genome-wide association studies.
abstract: 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.
authors.affiliation: Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
authors.forename: Wenqian
authors.initials: W
authors.lastname: Jiao
authors.forename: Xiaoteng
authors.initials: X
authors.lastname: Fu
authors.forename: Jinqin
authors.initials: J
authors.lastname: Li
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.forename: Liying
authors.initials: L
authors.lastname: Feng
authors.forename: Jia
authors.initials: J
authors.lastname: Lv
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.forename: Xiaojian
authors.initials: X
authors.lastname: Wang
authors.forename: Yangping
authors.initials: Y
authors.lastname: Li
authors.forename: Rui
authors.initials: R
authors.lastname: Hou
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000235:genetics*; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D005838:Genotype; D056186:Metagenomics; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: genome-wide association (GWAS); high resolution melting (HRM); mollusca; single-nucleotide polymorphism (SNP); transcriptome