High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker

Shi, Yaohua; Wang, Shi; Gu, Zhenxin; Lv, Jia; Zhan, Xin; Yu, Chengcheng; Bao, Zhenmin; Wang, Aimin

doi:10.1016/j.aquaculture.2014.08.044

Cited by 44 publications

(34 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, we adopted the pseudo-testcross strategy to construct the first high-density SNP genetic linkage map for R. philippinarum by taking advantage of parental heterozygosity 44 . The final consensus linkage map contained 9658 markers with a resolution of 0.42 cM (Table 1), comparable with other genetic linkage maps constructed through 2b-RAD (0.39–0.41 cM) 43,45 . In this study, the average intermarker distance was 0.42 cM in the sex-average map, which is much lower than that in previous linkage maps 43,46 .…”

Section: Discussionsupporting

confidence: 55%

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Nie

Yan

Huo

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.

show abstract

Section: Discussionsupporting

confidence: 55%

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Nie

Yan

Huo

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…), Akoya pearl oyster ( Pinctata fucata ; Li & He ; Shi et al . ), variously coloured abalone ( Haliotis diversicolor ; Ren et al . ; Yesso scallop ( Patinopecten yessoensis ; Dou et al .…”

Section: Applications Of Rad Sequencing In Aquaculturementioning

confidence: 99%

Applications of genotyping by sequencing in aquaculture breeding and genetics

Robledo

Palaiokostas

Bargelloni

et al. 2017

Reviews in Aquaculture

217

172

View full text Add to dashboard Cite

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

show abstract

“…SNPs developed from functional genes may be used in association studies, which could genetically improve species. For example, some SNPs are associated with growth traits in the pearl oyster (Shi et al, 2014), and SNPs screened from the myostatin gene are associated with growth traits in the scallop and carp (Wang et al, 2010;Guo et al, 2011;Liu et al, 2012;Sun et al, 2012). All of the annotation unigenes and their SNPs may be useful for studying the commercial traits of P. fucata, such as growth, resistance, and reproduction.…”

Section: Resultsmentioning

confidence: 99%

Development of coding single nucleotide polymorphic markers in the pearl oyster Pinctada fucata based on next-generation sequencing and high-resolution melting analysis

et al. 2016

View full text Add to dashboard Cite

The pearl oyster Pinctada fucata is an important commercial marine shellfish that is cultured for producing saltwater pearls. In this study, 468 single nucleotide polymorphisms (SNPs) were screened from P. fucata transcriptome data, and 119 polymorphic SNPs were successfully isolated by a two-step small-amplicon high-resolution melting assay. Of these, 88 were annotated with BLAST in the Nr database and 90 were in the open reading frame, including 16 non-synonymous SNPs and 74 synonymous SNPs; 12 SNPs were in the 3'-untranslated region (UTR) and 1 was in the 5'-UTR. Twenty-five SNPs were randomly chosen to test the genetic diversity of 40 wild individuals from Liusha Bay, China. All of the loci had two alleles. The observed and expected heterozygosities ranged from 0.0417 to 0.6042 and from 0.2945 to 0.5053, respectively. Minor allele frequencies ranged from 0.1771 to 0.5000, and the polymorphism information content ranged from 0.2516 to 0.3750. These novel SNP markers can contribute to P. fucata genetics and breeding studies.

show abstract

High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker

Cited by 44 publications

References 39 publications

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Applications of genotyping by sequencing in aquaculture breeding and genetics

Development of coding single nucleotide polymorphic markers in the pearl oyster Pinctada fucata based on next-generation sequencing and high-resolution melting analysis

Contact Info

Product

Resources

About