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

Fan, Sigang; Wei, Jinjia; Guo, Yihui; Huang, Guiju; Yu, Dahui

doi:10.4238/gmr15049054

Cited by 3 publications

(3 citation statements)

References 33 publications

(35 reference statements)

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“…Compared to non-coding genomic markers, SNPs developed from functional genes are potentially more closely related to phenotypic variations [34,46]. In our study, 220 (85.27%) KASP markers were located in exons and altered the amino acid sequence encoded, and so could be used as functional markers.…”

Section: Kasp Markers Are Cost-effective and Powerfulmentioning

confidence: 74%

An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

Shu

Wei

et al. 2020

PLoS ONE

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Kompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510-1 and Y510-9, and generated a total of more than 38.5 billion clean base pairs. A total of 827,720 SNP loci were identified with an estimated density of 3,217 SNPs/Mb. Further, a total of 387,354 SNPs with at least 30 bp to the next most adjacent SNPs on either side were selected as resource for KASP markers. From this resource, 258 (96.27%) of 268 SNP loci were successfully transformed into KASP-SNP markers using a Roche LightCycler 480-II instrument. Among these markers, 221 (85.66%) were co-dominant markers, 220 (85.27%) were non-synonymous SNPs, and 257 (99.6%) were newly developed markers. In addition, 53 markers were applied for genotyping of 34 Brassica rapa accessions. Cluster analysis separated these 34 accessions into three clusters based on heading types. The millions of SNP loci, a large set of resource for KASP markers, as well as the newly developed KASP markers in this study may facilitate further genetic and molecular breeding studies in Brassica rapa.

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Section: Kasp Markers Are Cost-effective and Powerfulmentioning

confidence: 74%

An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

Shu

Wei

et al. 2020

PLoS ONE

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“…Different from the DNA microarray analysis, high-throughput sequencing can lead to gene discovery and to the validation of population genetics markers for breeding programmes. The identification of single nucleotide polymorphisms (SNPs, codominant-inherited molecular features very abundant in animal genomes) in bivalves is just a preliminary step, before starting to validate their association with valuable quantitatively inherited traits or with stress-responsive genes, and to proceed with fine linkage mapping and population genetics analyses (Coppe et al 2012;Ge et al 2015;Nie et al 2015;Dong et al 2016;Fan et al 2016;Wang et al 2016a, b;Qi et al 2017;Gutierrez et al 2017;Azéma et al 2017).…”

Section: Living Monitors and Source Of Versatile Biotechnological Toolsmentioning

confidence: 99%

Biotechnologies from Marine Bivalves

Venier

Gerdol

Domeneghetti

et al. 2018

Goods and Services of Marine Bivalves

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Bivalve molluscs comprise more than 9000 extant species. A number of them are traditionally farmed worldwide and are fundamental in the functioning of benthic ecosystems. The peculiarities of marine bivalves have inspired versatile biotechnological tools for coastal pollution monitoring and several new biomimetic materials. Moreover, large amounts of sequence data available for some farmed bivalve species can be used to unveil the organism's responses to environmental factors (e.g. global climate change, emergence of new infectious agents and other production problems). In bivalves, data from genomics and transcriptomics increases more quickly than data from other omics, and permit new bioinformatics inferences, real comparative genomics and the study of molecules suitable for biotechnological innovations. Bivalves (and their microorganism communities) produce a variety of bioactive peptides, proteins and metabolites. Among them, the numerous families of antimicrobial peptides identified in the Mediterranean mussel likely contribute to its vigour and could assist with the identification of molecular scaffolds for innovative pharmaceuticals, nutraceuticals and constructs suitable for other applications.

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Section: Living Monitors and Source Of Versatile Biotechnological Toolsmentioning

confidence: 99%

An introduction to assessments

2016

Acing the LLB

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

Cited by 3 publications

References 33 publications

An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

Biotechnologies from Marine Bivalves

An introduction to assessments

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