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Communication Dans Un Congrès Année : 2022

RNA-SEQ data for reliable SNP detection and genotype calling in livestock species: interest for coding variant characterization and cis-regulation analysis by allele-specific expression

Thierry Burlot
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Résumé

In addition to their common usages for studying gene expression, RNA-seq data that have accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and tools for whole exome sequencing are unavailable. These SNPs detected in expressed regions can be used to characterize variants affecting protein functions, and to study cis-regulated genes by analyzing allele-specific expression (ASE). However, gene expression can be highly variable, and filters for SNP detection using the popular GATK tool are not yet standardized, making SNP detection and genotype calling by RNA-seq a challenging endeavor. We compared SNP calling results on two independent chicken populations (n = 15 & n = 8) for which both RNA-seq and DNA-seq data was available for the same samples. The RNA-seq SNP detection was performed with GATK RNA-seq specific suggested filters. We showed that, in expressed regions, 91% of SNPs detected by RNA-seq were also detected by DNA-seq (at 20X coverage); we characterized the remaining 9% SNPs. We then studied the impact of two factors (genotype (GT) call-rate and read number supporting the GT) on the concordance of genotypes detected by DNA-seq versus RNA-seq and proposed thresholds for them that led to a 95% concordance. Applying these filters to 744 RNA-seq samples collected on 10 chicken populations, we found 9.9M SNPs in total, with on average 560,000 SNPs per population with a GT call rate ≥ 50% and 340,000 with a MAF ≥10%. We then showed that, such RNA-seq data can be used for i) detecting SNPs with a severe predicted impact on proteins, despite their rarity in each population (more than 17,000 SNPs), and ii) studying, on a large scale, cis-regulations of gene expression by using the ASE approach:in particular we showed that on average 80% of protein-coding and 70% of long non-coding genes with an expression level ≥ 1TPM could be analyzed for ASE. Finally, we illustrated the possibility to perform population genetic analysis using such SNPs detected exclusively in expressed regions, as an alternative set to the standard low- or high-density SNP genotyping arrays. This work shows that RNA-seq data can be used with good confidence to detect SNPs and associated GT within various populations and used them for different types of analysis.

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Dates et versions

hal-04132375 , version 1 (19-06-2023)

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  • HAL Id : hal-04132375 , version 1

Citer

Frédéric Jehl, Fabien Degalez, Maria Bernard, Frédéric Lecerf, Laetitia Lagoutte, et al.. RNA-SEQ data for reliable SNP detection and genotype calling in livestock species: interest for coding variant characterization and cis-regulation analysis by allele-specific expression. 26. World's Poultry Congress (WPC), Aug 2022, Paris, France. pp.405. ⟨hal-04132375⟩
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