Low-coverage whole-genome sequencing in livestock species for individual traceability and parentage testing
Casellas Vidal, Joaquim (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Martín de Hijas-Villalba, Melani (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Vázquez-Gómez, Marta (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Id-Lahoucine, Samir (Animal and Veterinary Science Group. Scotland's Rural College)

Date:	2021
Abstract:	Procedures for genetic traceability of animal products and parentage testing mainly focus on microsatellites or SNPs panels. Nevertheless, current availability of high-throughput sequencing technologies must be considered as an appealing alternative. This research focused on the evaluation of low-coverage whole-genome sequencing for traceability and paternity testing purposes, within a context of evidential statistics. Analyses were performed on a simulation basis and assumed individuals with 30 100-Mb/100-cM chromosome pairs and ~1,000,000 polymorphic SNPs per chromosome. Ten independent populations were simulated under recombination and mutation with effective populations size 100 (generations 1-1000), 10,000 (generation 1001) and 25,000 (generation 1002), and this last generation was retained for analytical purposes. Appropriate both traceability and paternity tests were developed and evaluated on different high-throughput sequencing scenarios accounting for genome coverage depth (0. 01×, 0. 05×, 0. 1× and 0. 5×), length of base-pair reads (100, 1000 and 10,000 bp), and sequencing error rate (0%, 1% and 10%). Assuming true sequencing error rates and genotypic frequencies, 0. 05× genome coverage depth guaranteed 100% sensitivity and specificity for traceability and paternity tests (n = 1000). Same results were obtained when sequencing error rate was arbitrarily set to 0, or the maximum value assumed during simulation (i. e. , 1%). In a similar way, uncertainly about genotypic frecuencies did not impair sensitivity under 0. 05× genome coverage, although it reduced specificity for paternity tests up to 85. 2%. These results highlighted low-coverage whole-genome sequencing as a promising tool for the livestock and food industry with both technological and (maybe) economic advantages.
Grants:	Ministerio de Economía y Competitividad BES-2017-080596 Ministerio de Economía y Competitividad CGL2016-80155- R
Note:	Altres ajuts: acords transformatius de la UAB
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Evidential statistics ; Paternity ; Sequencing ; Simulation ; Traceability
Published in:	Livestock Science, Vol. 251 (september 2021) , p. 104629, ISSN 1878-0490

DOI: 10.1016/j.livsci.2021.104629

8 p, 1.8 MB

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