Inheritance of high-resolution melting profiles in assays targeting single nucleotide polymorphisms in protein-coding sequences of the Pacific oyster Crassostrea gigas: Implications for parentage assignment of experimental and commercial broodstocks

Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution melting (UP-HRM) marker is a useful tool for detecting of single nucleotide polymorphisms (SNPs). The objectives of this study were to develop UP-HRM markers to differentiate specific SNPs patterns on oil palm. The marker was developed and tested with Elaeis guineensis (Eg), Elaeis oleifera (Eo), Eo x Eg (hybrid), and was validated with 53 individuals of BC1F1 populations ((Eo x Eg) x Eg). Four UP-HRM markers were developed based on 2 SNPs in the stearoyl-acyl-carrier-protein 9-desaturase (EgSAD), 1 SNP in the auxin-responsive protein IAA27-like (EgIAA27), and 1 SNP in the 1-amino cyclopropane-1-carboxylate oxidase (EgACC) genes. The SNP discovery result showed that Eg was represented a reference homozygote genotype, while Eo was represented as an alternative homozygote genotype and the Eo x Eg hybrid was represented as a heterozygote genotype in all genes. The typical UP-HRM melt curve graph was successfully generated. This result was consistent with each genotype model for all four markers. The UP-HRM markers can distinguish each genotype according to the single-pass sequencing results. Furthermore, dendrogram analysis on validation divided 53 BC1F1 samples into three cluster groups.

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Identification of ryanodine receptor 1 single-nucleotide polymorphisms by high-resolution melting using the LightCycler 480 System

Analytical Biochemistry ◽

10.1016/j.ab.2007.11.019 ◽

2008 ◽

Vol 374 (2) ◽

pp. 396-404 ◽

Cited By ~ 28

Author(s):

Hilbert Grievink ◽

Kathryn M Stowell

Keyword(s):

High Resolution ◽

Single Nucleotide Polymorphisms ◽

Ryanodine Receptor ◽

High Resolution Melting ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Ryanodine Receptor 1

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High-Resolution Melting Analysis of Single Nucleotide Polymorphisms

Molecular Typing of Blood Cell Antigens - Methods in Molecular Biology ◽

10.1007/978-1-4939-2690-9_2 ◽

2015 ◽

pp. 5-27 ◽

Cited By ~ 4

Author(s):

Carol M. Bruzzone ◽

Clifford J. Steer

Keyword(s):

High Resolution ◽

Single Nucleotide Polymorphisms ◽

High Resolution Melting ◽

High Resolution Melting Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Melting Analysis

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Genotyping single-nucleotide polymorphisms of human genes involved in organophosphate detoxification by high-resolution melting

Analytical and Bioanalytical Chemistry ◽

10.1007/s00216-014-7734-7 ◽

2014 ◽

Vol 406 (21) ◽

pp. 5087-5092 ◽

Cited By ~ 4

Author(s):

Ivan Kurdyukov ◽

Gennady Rodionov ◽

Andrey Radilov ◽

Vladimir Babakov

Keyword(s):

High Resolution ◽

Single Nucleotide Polymorphisms ◽

High Resolution Melting ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Human Genes ◽

Organophosphate Detoxification

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Single nucleotide polymorphisms (SNPs) of exons 3, 4, 5 and 9 of the matrix metalloproteinase 2 (MMP-2) gene in breast carcinoma of Malaysian women using high resolution melting analysis

Pathology ◽

10.1097/01268031-200941001-00180 ◽

2009 ◽

Vol 41 ◽

pp. 74-75

Author(s):

Sabariah Abdul Rahman ◽

Chan Soon Choy ◽

Rozita Rosli ◽

Sharifah Noor Akmal Syed Hussain ◽

Noor Hisham Abdullah

Keyword(s):

High Resolution ◽

Breast Carcinoma ◽

Single Nucleotide Polymorphisms ◽

Matrix Metalloproteinase ◽

High Resolution Melting ◽

Matrix Metalloproteinase 2 ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

The Matrix ◽

Melting Analysis

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A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

GigaScience ◽

10.1093/gigascience/giab020 ◽

2021 ◽

Vol 10 (3) ◽

Cited By ~ 1

Author(s):

Carolina Peñaloza ◽

Alejandro P Gutierrez ◽

Lél Eöry ◽

Shan Wang ◽

Ximing Guo ◽

...

Keyword(s):

Crassostrea Gigas ◽

Pacific Oyster ◽

Sequence Data ◽

High Coverage ◽

Protein Coding ◽

Rolling Circle ◽

Repeat Elements ◽

Pacific Biosciences ◽

The Pacific ◽

Chromosome Level

Abstract Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.

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