A 50K SNP array reveals genetic structure for bald eagles (Haliaeetus leucocephalus)

Judkins, Megan E.; Couger, Brian; Warren, Wesley C.; Bussche, Ronald A. Van Den

doi:10.1007/s10592-019-01216-x

Cited by 11 publications

(13 citation statements)

References 42 publications

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“…These numbers compare favorably with similar studies of non-model organisms ( e.g. , Lundregan et al 2018 ; Kim et al 2018 ; Judkins et al 2020 ). Overall, no relationship was found between the call rate per sample and DNA concentration, in contrast to Hagen et al (2013) who reported that failed samples had significantly lower DNA concentrations than successful ones.…”

Section: Discussionsupporting

confidence: 79%

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony

Humble

Paijmans

Forcada

et al. 2020

G3 Genes|Genomes|Genetics

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High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such "cryptic relatedness" within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.

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Section: Discussionsupporting

confidence: 79%

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony

Humble

Paijmans

Forcada

et al. 2020

G3 Genes|Genomes|Genetics

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“…The total success rate of 94.31% across all breeds, and the segregating rate of 86.02% in DSN, was high in comparison to other described works with the Affymetrix technology, varying, for example, from a calling rate of 46.16% in the Atlantic salmon [ 39 ], 74.81% in water buffalo [ 40 ], to 90.48% in the bald eagle [ 37 ]. The decision to use SNPs that were informative on the Illumina BovineSNP50 was straightforward not only because these SNPs were successfully called but also because these SNPs, which are common on both chips, allow the joint analysis of animals genotyped with the Illumina BovineSNP50 and the DSN200k SNP chip.…”

Section: Discussionmentioning

confidence: 81%

“…Generally, the in silico conversion, physical or genetic distance between markers, and allele frequencies are the main selection motives [ 31 – 34 ]. Nevertheless, a similar approach prioritizing high impact and/or rare variants, and candidate variants to important traits as we implemented was also used for the catfish 250 k array [ 35 ], GeneSeek Genomic Profiler™ F250 chip [ 36 ], and 50 k Axiom bald eagle SNP chip [ 37 ]. In our case, we were able to select informative variants in DSN and keep a uniform distribution across the genome in DSN including variants targeting all haplotype blocks longer than 5 kb, whereof most were even longer than 1 kb.…”

Section: Discussionmentioning

confidence: 99%

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

et al. 2021

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Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

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“…In contrast, only a handful of medium‐high density SNP chips have been designed for noncommercial wild species such as house sparrow (Hagen et al, 2013; Lundregan et al, 2018), great tit (van Bers et al, 2012; Kim et al, 2018), polar bear (Malenfant et al, 2015), flycatcher (Kawakami et al, 2014), fur seal (Humble et al, 2020), Florida scrub‐jay (Chen et al, 2016) and bald eagle (Judkins et al, 2020). These SNP chips for wild species generate a quantity of genomic data that can be used, for example, to infer relatedness (Humble et al, 2020) and population structure (Hagen et al, 2013; Judkins et al, 2020; Malenfant et al, 2015; Viengkone et al, 2016), analyse the genomic architecture of traits (Duntsch et al, 2020; Husby et al, 2015; Kim et al, 2018; Laine et al, 2019; Lundregan et al, 2018; Santure et al, 2013, 2015; Silva et al, 2017), characterise copy number variants in the genome (da Silva et al, 2018; Kim et al, 2018) and investigate the genomic landscape of linkage and linkage disequilibrium (Hagen et al, 2020; Kawakami et al, 2014; van Oers et al, 2014). SNP chips developed for model organisms or agricultural systems have also been utilised to address evolutionary, ecological, and conservation questions.…”

Section: Introductionmentioning

confidence: 99%

“…Medium (~thousands to tens of thousands of loci) and high (~hundreds of thousands of loci) density SNP chips have been routinely developed for commercial species, often with a focus on enabling production gains from genome wide association studies, genomic selection and prediction (https://www.illum ina.com/areas -of-inter est/agrig enomi cs/plant -anima l-genom ics/genot yping.html). In contrast, only a handful of medium-high density SNP chips have been designed for noncommercial wild species such as house sparrow (Hagen et al, 2013;Lundregan et al, 2018), great tit (van Bers et al, 2012;Kim et al, 2018), polar bear (Malenfant et al, 2015), flycatcher (Kawakami et al, 2014), fur seal (Humble et al, 2020), Florida scrubjay (Chen et al, 2016) and bald eagle (Judkins et al, 2020). These SNP chips for wild species generate a quantity of genomic data that can be used, for example, to infer relatedness (Humble et al, 2020) and population structure (Hagen et al, 2013;Judkins et al, 2020;Malenfant et al, 2015;Viengkone et al, 2016), analyse the genomic architecture of traits (Duntsch et al, 2020;Husby et al, 2015;Kim et al, 2018;Laine et al, 2019;Lundregan et al, 2018;Santure et al, 2013Santure et al, , 2015Silva et al, 2017), characterise copy number variants in the genome (da Silva et al, 2018;Kim et al, 2018) and investigate the genomic landscape of linkage and linkage disequilibrium (Hagen et al, 2020;Kawakami et al, 2014;van Oers et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi

Lee

Millar

Brekke

et al. 2021

Molecular Ecology Resources

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Next‐generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost‐effective identification of genome‐wide variation. Single nucleotide polymorphism (SNP) arrays, or “SNP chips”, enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction‐aided digest sequencing (RAD‐seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low‐coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD‐seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost‐effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.

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A 50K SNP array reveals genetic structure for bald eagles (Haliaeetus leucocephalus)

Cited by 11 publications

References 42 publications

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi

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