Genome-wide association screening and MassARRAY for detection of high-temperature resistance-related SNPs and genes in a hybrid abalone (Haliotis discus hannai ♀ × H. fulgens ♂) based on super genotyping-by-sequencing

Zhao, Zhen; Gan, Hanling; Xu, Lin; Wang, Linyue; Yao, Yanyu; Li, Lü; Wang, Yilei; Zhang, Ziping

doi:10.1016/j.aquaculture.2023.739576

Cited by 2 publications

(5 citation statements)

References 75 publications

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“…This outlines the importance of SNP selection in assay design, as not all SNPs will be relative to a research question or ubiquitous in a species. Another example is in Li et al (2023), where TaqMan genotyping was applied to diagnose tembusu virus in ducks and astrovirus in geese [26]. In that study, the authors report success in designing an accurate diagnostic test for one or both viruses at the same time [26].…”

Section: Taqman Methodsmentioning

confidence: 99%

“…MassArray SNP genotyping is a method of genotyping that combines multiplex PCR with mass spectrometry to genotype SNPs [2,42]. This method has been applied in agricultural sciences before and functions basically as follows [43][44][45]. The method functions by designing multiple primers specific to target SNPs, performing multiplex PCR to amplify a DNA sample, and then conducting MALDI-TOF mass spectrometry to genotype the samples [2].…”

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

“…This method is limited by the number of SNPs and special equipment requirements (Agena MASSarray platform). However, it is overall a rapid, accurate genotyping method [43][44][45]. In Zhao et al (2023), to identify temperature resistance genes in abalone fish [44], the authors report repeatable and accurate genotyping for seven different SNPs that were determined to be relevant to heat resistance [44].…”

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

“…However, it is overall a rapid, accurate genotyping method [43][44][45]. In Zhao et al (2023), to identify temperature resistance genes in abalone fish [44], the authors report repeatable and accurate genotyping for seven different SNPs that were determined to be relevant to heat resistance [44]. In Ji et al ( 2023), the MassArray method was applied to identify candidate marker genes in sheep associated with litter size [45].…”

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

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Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Lawrie,

Massey

2023

Applied Biosciences

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Single Nucleotide Polymorphisms (SNPs) are variations that occur at single nucleotides in the genome and are present at an appreciable level in a population. SNPs can be linked to phenotypes of interest, for example diseases, recent adaptations, or species hybridization. They can also be used to study phylogeny and evolutionary history. Technologies that rapidly identify and catalog the presence of SNPs in a DNA sample are known as SNP genotyping panels, and they continue to undergo rapid development. Such methods have great utility across the agricultural sciences in diverse areas such as plant and animal breeding, pathogen and pesticide resistance identification, outbreak tracing, and hybridization detection. Here, we provide an overview of 14 different SNP genotyping technologies and weigh some of the pros and cons associated with each platform. This review is not comprehensive or technical, nor does it aim to be. Rather, the objective is to provide an introduction to the landscape of genotyping technologies for researchers who do not have experience with these methods. Three classes of SNP genotyping methods are Polymerase Chain Reaction (PCR)-based (nine different methods), microarray-based (one method), and Next-Generation Sequencing (NGS)-based (four different methods). We discuss how each genotyping class is suited for different niches; PCR-based has a low SNP count and high sample number, microarray-based has a very high SNP count and a moderate sample number, and Next-Generation Sequencing-based has a moderate SNP count and moderate number of samples. Included are basics about how the methods function and example use cases of each method. Additionally, we introduce and discuss the potential for the MinION sequencer in SNP genotyping. For each technology, we provide insights into cost, equipment needs, labor costs, experimental complexity, data output complexity, and accessibility. These considerations address the feasibility of deploying the technologies in an agricultural science environment.

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Section: Taqman Methodsmentioning

confidence: 99%

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

Section: Massarray Snp Genotyping Systemmentioning

confidence: 99%

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Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Lawrie,

Massey

2023

Applied Biosciences

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“…Carotenoids serve as potent antioxidants in aquatic creatures, bolstering their resistance to temperature fluctuations [14].In addition, with an increasingly challenging environment and rising temperatures [15], an abalone's heat tolerance becomes a vital metric in its farming. The recent introduction of the heat adhesion duration (HAD) method, which measures abalone adhesive capacity, offers a high-throughput evaluation [16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Comparative Responses of Orange-Foot and Common-Foot Haliotis gigantea to Carotenoid-Enriched Diets: Survival, Heat Tolerance, and Bacterial Resistance

Ke,

Liu,

Zeng

et al. 2024

Animals

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Carotenoids, known to enhance survival, heat tolerance, and bacterial resistance, play an essential role in the nutrition of economically important aquatic animals. This study specifically examined their impact as feed additives on the abalone Haliotis gigantea. We prepared 13 compound feeds with varying levels of astaxanthin, zeaxanthin, and β-carotene, and administered them to both common-footed and orange-footed H. gigantea. The survival rate of H. gigantea was about 70–80%, with no significant differences in survival observed among the various carotenoid-supplemented feeding groups or when compared with the control group, nor between orange-footed and common-footed individuals. In heat attachment duration experiments, orange-foot abalones exhibited longer attachment durations with certain concentrations of astaxanthin and zeaxanthin, whereas common-foot abalones showed extended durations with astaxanthin, zeaxanthin, and β-carotene, indicating that common-foot abalones might benefit more from these carotenoids. Additionally, our results showed similar patterns and levels of Vibrio harveyi AP37 resistance in both orange-footed and common-footed H. gigantea, suggesting a uniform response to carotenoid supplementation in their bacterial defense mechanisms. This study suggests the potential benefits of carotenoid supplementation in H. gigantea and contributes to the theoretical basis for developing high-quality artificial compound feeds.

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Genome-wide association screening and MassARRAY for detection of high-temperature resistance-related SNPs and genes in a hybrid abalone (Haliotis discus hannai ♀ × H. fulgens ♂) based on super genotyping-by-sequencing

Cited by 2 publications

References 75 publications

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Comparative Responses of Orange-Foot and Common-Foot Haliotis gigantea to Carotenoid-Enriched Diets: Survival, Heat Tolerance, and Bacterial Resistance

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