Targeted Genome-wide SNP Genotyping in Feral Horses Using Non-invasive Fecal Swabs

Overview

Journal Conserv Genet Resour

Publisher Springer

Date 2022 Jun 8

PMID 35673611

Authors

Stefan Gavriliuc

Salman Reza

Chanwoori Jeong

Fitsum Getachew

Philip D McLoughlin

Jocelyn Poissant

Affiliations

Soon will be listed here.

Abstract

Supplementary Information: The online version contains supplementary material available at 10.1007/s12686-022-01259-2.

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References

Chiou K, Bergey C . Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces. Sci Rep. 2018; 8(1):1975. PMC: 5792461. DOI: 10.1038/s41598-018-20427-9. View

Shafer A, Wolf J, Alves P, Bergstrom L, Bruford M, Brannstrom I . Genomics and the challenging translation into conservation practice. Trends Ecol Evol. 2014; 30(2):78-87. DOI: 10.1016/j.tree.2014.11.009. View

Mengulluoglu D, Fickel J, Hofer H, Forster D . Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species: Caucasian lynx as a case species. PLoS One. 2019; 14(5):e0216549. PMC: 6510455. DOI: 10.1371/journal.pone.0216549. View

Li H . A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27(21):2987-93. PMC: 3198575. DOI: 10.1093/bioinformatics/btr509. View

Allendorf F . Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol. 2016; 26(2):420-430. DOI: 10.1111/mec.13948. View

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

Kim J, Santure A, Barton H, Quinn J, Cole E, Visser M . A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol Ecol Resour. 2018; 18(4):877-891. DOI: 10.1111/1755-0998.12778. View

Saber A, Hiltermann T, Kok K, Terpstra M, de Lange K, Timens W . Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors. Carcinogenesis. 2016; 38(2):144-151. DOI: 10.1093/carcin/bgw128. View

Carlson C, Smith J, Stanaway I, Rieder M, Nickerson D . Direct detection of null alleles in SNP genotyping data. Hum Mol Genet. 2006; 15(12):1931-7. DOI: 10.1093/hmg/ddl115. View

10.

Nairismagi M, Tan J, Lim J, Nagarajan S, Ng C, Rajasegaran V . JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma. Leukemia. 2016; 30(6):1311-9. PMC: 4895162. DOI: 10.1038/leu.2016.13. View

11.

Kim S, Misra A . SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng. 2007; 9:289-320. DOI: 10.1146/annurev.bioeng.9.060906.152037. View

12.

Carroll E, Bruford M, DeWoody J, Leroy G, Strand A, Waits L . Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl. 2018; 11(7):1094-1119. PMC: 6050181. DOI: 10.1111/eva.12600. View

13.

Scolnick J, Dimon M, Wang I, Huelga S, Amorese D . An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples. PLoS One. 2015; 10(7):e0128916. PMC: 4488430. DOI: 10.1371/journal.pone.0128916. View

14.

King S, Schoenecker K, Fike J, Oyler-McCance S . Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for noninvasive sampling. Ecol Evol. 2018; 8(8):4053-4064. PMC: 5916305. DOI: 10.1002/ece3.3956. View

15.

Latorre-Cardenas M, Gutierrez-Rodriguez C, Lance S . Isolation and characterization of 13 microsatellite loci for the Neotropical otter, Lontra longicaudis, by next generation sequencing. Mol Biol Rep. 2019; 47(1):731-736. DOI: 10.1007/s11033-019-05165-z. View

16.

White L, Fontsere C, Lizano E, Hughes D, Angedakin S, Arandjelovic M . A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Mol Ecol Resour. 2019; 19(3):609-622. DOI: 10.1111/1755-0998.12993. View

17.

Regan C, Medill S, Poissant J, McLoughlin P . Causes and consequences of an unusually male-biased adult sex ratio in an unmanaged feral horse population. J Anim Ecol. 2020; 89(12):2909-2921. DOI: 10.1111/1365-2656.13349. View

18.

Gold S, Regan C, McLoughlin P, Gilleard J, Wilson A, Poissant J . Quantitative genetics of gastrointestinal strongyle burden and associated body condition in feral horses. Int J Parasitol Parasites Wildl. 2019; 9:104-111. PMC: 6462499. DOI: 10.1016/j.ijppaw.2019.03.010. View

19.

Hagen I, Billing A, Ronning B, Pedersen S, Parn H, Slate J . The easy road to genome-wide medium density SNP screening in a non-model species: development and application of a 10 K SNP-chip for the house sparrow (Passer domesticus). Mol Ecol Resour. 2013; 13(3):429-39. DOI: 10.1111/1755-0998.12088. View

20.

Wade C, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F . Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009; 326(5954):865-7. PMC: 3785132. DOI: 10.1126/science.1178158. View