Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues

AbstractHybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their ability to outcompete the native parent. It is crucial to understand the mechanisms that drive these transgressive hybrid traits to diagnose and develop strategies to manage hybrid populations. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 40% (6/15) able to tolerate temperatures greater than either parent. We quantified the genomic response of each individual to discover and compare thermal abatement strategies. We found that CTS and BTS have strikingly different numbers and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. We evaluated transgressive and variable phenotypes by uncovering regulatory mechanisms that give rise to these unique traits. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms of the parental lineages. We found that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting that BTS-biased expression confers improved thermal tolerance. We discuss the implications of these findings with respect to ongoing management of CTS in the face of future climate change.

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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