Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Abstract Background Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Results Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). Conclusions The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.

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Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish

BMC Genomics ◽

10.1186/1471-2164-14-929 ◽

2013 ◽

Vol 14 (1) ◽

pp. 929 ◽

Cited By ~ 53

Author(s):

Ruijia Wang ◽

Luyang Sun ◽

Lisui Bao ◽

Jiaren Zhang ◽

Yanliang Jiang ◽

...

Keyword(s):

Disease Resistance ◽

Candidate Genes ◽

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Positional Candidate ◽

Allele Specific ◽

Enteric Septicemia

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Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF

Journal of Applied Genetics ◽

10.1007/s13353-019-00485-z ◽

2019 ◽

Vol 60 (1) ◽

pp. 97-101 ◽

Cited By ~ 2

Author(s):

Monika Stachowiak ◽

Krzysztof Flisikowski

Keyword(s):

Skeletal Muscle ◽

Lipid Metabolism ◽

Candidate Genes ◽

Allelic Imbalance ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific

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Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

10.1101/2021.09.27.462036 ◽

2021 ◽

Author(s):

Caroline K. Hu ◽

Ryan A. York ◽

Hillery C. Metz ◽

Nicole L. Bedford ◽

Hunter B. Fraser ◽

...

Keyword(s):

Gene Expression ◽

Candidate Genes ◽

Sister Species ◽

Behavioral Context ◽

Specific Expression ◽

Allele Specific Expression ◽

Regulatory Changes ◽

Allele Specific ◽

Burrowing Behavior ◽

Regulated Gene Expression

SummaryHow evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed in some behaviors of recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution.

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Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and gene level

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765202120191453 ◽

2021 ◽

Vol 93 (3) ◽

Author(s):

SHEIDA VARKOOHI ◽

MOHAMMAD HOSSEIN BANABAZI ◽

MOJGAN GHSEMI-SIAB

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Gene Level ◽

Allele Specific

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Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

Scientific Reports ◽

10.1038/s41598-021-86782-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jennifer Jessica Bruscadin ◽

Marcela Maria de Souza ◽

Karina Santos de Oliveira ◽

Marina Ibelli Pereira Rocha ◽

Juliana Afonso ◽

...

Keyword(s):

Transcription Factor ◽

Expression Pattern ◽

Binding Sites ◽

Sequence Similarity ◽

Bos Indicus ◽

Meat Tenderness ◽

Nucleotide Polymorphisms ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific

AbstractSingle nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.

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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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