Low-coverage whole-genome sequencing in livestock species for individual traceability and parentage testing

Joaquim Casellas*, Melani Martín de Hijas-Villalba, Marta Vázquez-Gómez, Samir Id-Lahoucine

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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 to 1,000), 10,000 (generation 1,001) and 25,000 (generation 1,002), 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, 1,000 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 = 1,000). Same results were obtained when sequencing error rate was arbitrarily set to 0, or the 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.
Original languageEnglish
Article number104629
JournalLivestock Science
Early online date17 Jul 2021
DOIs
Publication statusFirst published - 17 Jul 2021

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