Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng, Zhuoying; Yang, Yang; Wang, Xi; Wu, Lina; Hua, Sijie; Zhang, Hanfei; Meng, Zining

doi:10.3390/genes12071042

Cited by 23 publications

(17 citation statements)

References 81 publications

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“…In this study, the chip was employed to conduct a clustering analysis of 60 Langshan roosters with documented pedigree information. The results showed that all siblings were accurately clustered, which is consistent with previous findings [30]. Collectively, these results indicate that the chip developed in this study holds great potential for genetic research on local chicken populations.…”

Section: Discussionsupporting

confidence: 91%

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Animal Research and One Health

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Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid‐phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high‐quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome‐wide association study of broilers, resulting in the identification of several growth‐ and meat quality‐related loci. Therefore, the newly developed chip is efficient, cost‐effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.

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Section: Discussionsupporting

confidence: 91%

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Animal Research and One Health

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“…The two different datasets may have differences in data resolution and therefore this may account for some of the differences in the results. However, studies evaluating the performance of SNPs versus microsatellites found high power to resolve relatedness and parentage when using 100-500 SNPs, and results between the two types of data were highly congruent (Flanagan and Jones 2019;Premachandra et al 2019;Weng et al 2021). Despite the congruence of the two datasets, we note that there may be inherent variation in their results due to the differences in genetic approach, thus care should be taken when comparing them.…”

Section: Shifts In Reproductive Behaviourmentioning

confidence: 68%

Genetics reveals shifts in reproductive behaviour of the invasive bird parasite Philornis downsi collected from Darwin’s finch nests

et al. 2022

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Due to novel or dynamic fluctuations in environmental conditions and resources, host and parasite relationships can be subject to diverse selection pressures that may lead to significant changes during and after invasion of a parasite. Genomic analyses are useful for elucidating evolutionary processes in invasive parasites following their arrival to a new area and host. Philornis downsi (Diptera: Muscidae), the avian vampire fly, was introduced to the Galápagos Islands circa 1964 and has since spread across the archipelago, feeding on the blood of developing nestlings of endemic land birds. Since its discovery, there have been significant changes to the dynamics of P. downsi and its novel hosts, such as shifting mortality rates and changing oviposition behaviour, however no temporal genetic studies have been conducted. We collected P. downsi from nests and traps from a single island population over a 14-year period, and genotyped flies at 469 single nucleotide polymorphisms (SNPs) using restriction-site associated DNA sequencing (RADSeq). Despite significant genetic differentiation (FST) between years, there was no evidence for genetic clustering within or across four sampling years between 2006 and 2020, suggesting a lack of population isolation. Sibship reconstructions from P. downsi collected from 10 Darwin’s finch nests sampled in 2020 showed evidence for shifts in reproductive behaviour compared to a similar genetic analysis conducted in 2004–2006. Compared with this previous study, females mated with fewer males, individual females oviposited fewer offspring per nest, but more unique females oviposited per nest. These findings are important to consider within reproductive control techniques, and have fitness implications for both parasite evolution and host fitness.

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“…Nevertheless, the tested markers proved to be more helpful than those used for parentage analysis in the wild boar ( S. scrofa ) [ 62 ] and goat ( Capra hircus ) [ 63 ] populations. However, the evaluation of the microsatellite markers used for the pedigree analysis in plateau pika ( Ochotona curzoniae ) [ 64 ] and giant grouper ( Epinephelus lanceolatus ) [ 65 ] showed better values than those obtained by us. This is further proof that the YWLL46 should be removed, because this marker underestimates the values in every analysis.…”

Section: Discussionmentioning

confidence: 92%

Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Podbielska

Piórkowska

Szmatoła

2021

Animals

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This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Cited by 23 publications

References 81 publications

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Genetics reveals shifts in reproductive behaviour of the invasive bird parasite Philornis downsi collected from Darwin’s finch nests

Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

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