Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Baazaoui, Imen; Bedhiaf-Romdhani, Sonia; Mastrangelo, Salvatore; Ciani, Elena

doi:10.1016/j.animal.2021.100193

Cited by 30 publications

(39 citation statements)

References 40 publications

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“…Notably, the most stratified SVs in these two regions are among the top selective variants indicated by both SVs and SNPs. The most differentiated SV cluster are located at IBH region which has also reported as a candidate selective region affecting fat tail trait 53, 54 . Notably, six highly differentiated SVs including one de novo SV were identified in the IBH selective region (Fig.…”

Section: Resultsmentioning

confidence: 96%

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Gong

Zhang

et al. 2021

Preprint

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Structural variations (SVs) are a major contributor of genetic diversity and phenotypic variations, however their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep breeds using PacBio HiFi sequencing. We then constructed an ovine graph pan-genome and demonstrated its advantage in discovering 142,593 biallelic SVs (Insertions and deletions), 7,028 divergent alleles and 13,419 multiallelic variations with high accuracy and sensitivity. To link the SVs to genotypes, we genotyped the SVs in 687 resequenced individuals of domestic and wild sheep using a graph-based approach and identified numerous population-stratified variants, of which expression-associated SVs were detected by integrating RNA-seq data. Taking the varying sheep tail morphology as example, we located a putative causative insertion in HOXB13 gene responsible for the long tail and reported multiple large SVs associated with the fat tail. Beyond generating a benchmark resource for ovine structural variants, our study also highlighted that the population genetics analysis based on graph pan-genome rather than reference genome will greatly benefit the animal genetic research.

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Section: Resultsmentioning

confidence: 96%

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Gong

Zhang

et al. 2021

Preprint

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“…Many studies have attempted to identify the candidate gene associated with tail fat and understand the underlying mechanisms of fat deposition ( Ahbara et al, 2018 ; Amane et al, 2020 ; Baazaoui et al, 2021 ; Bakhtiarizadeh & Alamouti, 2020 ; Dong et al, 2020 ; Han et al, 2021 ; Li et al, 2018a ; Mastrangelo et al, 2019a ; Mastrangelo et al, 2019b ; Moioli, Pilla & Ciani, 2015 ; Moradi et al, 2012 ; Wei et al, 2015 ; Xu et al, 2017 ; Yuan et al, 2017 ; Zhang et al, 2019 ; Zhao et al, 2020 ; Zhi et al, 2018 ; Zhu et al, 2016 ). Previous studies suggested that microRNAs ( Miao et al, 2015a ; Pan et al, 2018 ), lncRNAs ( Bakhtiarizadeh & Salami, 2019 ; He et al, 2020 ) and mRNAs ( Bakhtiarizadeh et al, 2019 ; Kang et al, 2017a ; Miao et al, 2015b ; Wang et al, 2014 ) may regulate tail fat deposition in sheep.…”

Section: Introductionmentioning

confidence: 99%

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

Yuan

Sun

et al. 2021

PeerJ

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Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

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“…The bone morphogenetic protein 2 (BMP2) gene (chromosome 13) was highlighted as a highly potential causative when fat-tailed and thin-tailed sheep breeds were genomically compared (Moioli et al 2015;Pan et al 2019;Baazaoui et al 2021). Within its first exon, studies have reported a possible missense mutation (Chr13:48462350C>T; Oar_v3.1; Ala>Val); however, this single nucleotide mutation lacked a complete association within different tail phenotypic patterns (Moioli et al 2015;Pan et al 2019).…”

Section: Bmp2 As a Potential Candidate Gene For The Sheep Fattail Phenotypementioning

confidence: 99%

“…2019; Baazaoui et␣al . 2021). Within its first exon, studies have reported a possible missense mutation (Chr13:48462350C>T; Oar_v3.1; Ala>Val); however, this single nucleotide mutation lacked a complete association within different tail phenotypic patterns (Moioli et␣al .…”

Section: Telling the Tale Of Tail In Sheep: Genomic Insightsmentioning

confidence: 99%

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

et al. 2021

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Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation (s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.

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Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Cited by 30 publications

References 40 publications

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

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