Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Li, Xin; Yang, Ji Hyun; Shen, Min; Xie, Xinglong; Liu, Guangjian; Xu, Yaxi; Lv, Feng‐Hua; Yang, Hua; Yang, Yonglin; Liu, Changbin; Zhou, Ping; Wan, Pengcheng; Zhang, Yunsheng; Gao, Lei; Yang, Jingquan; Pi, Wen-Hui; Ren, Yan-Ling; Shen, Zhiqiang; Wang, Zhen; Deng, Juan; Xu, Song-Song; Salehian-Dehkordi, Hosein; Hehua, EEr; Esmailizadeh, Ali; Dehghani-Qanatqestani, Mostafa; Štěpánek, Ondřej; Weimann, Christina; Erhardt, G.; Amane, Agraw; Mwacharo, Joram M.; Han, Jianlin; Hanotte, Olivier; Lenstra, Johannes A.; Kantanen, Juha; Coltman, David W.; Kijas, James W.; Bruford, Michael William; Kathiravan, P.; Wang, Xinhua; Li, Menghua

doi:10.1038/s41467-020-16485-1

Cited by 177 publications

(215 citation statements)

References 77 publications

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“…A total of 74,692 common sites for 126 accessions (Additional file 3 : Table S22) were overlapped and used to determined the validation rate. The validation rate for 126 accessions was 98.14–99.71% with a high total validation rate 99.18%, showing a low false positive rate (0.82%) of SNPs in this study, which was comparable with the validation rates reported from other studies about maize and sheep resequencing efforts [ 82 , 106 ].…”

Section: Methodssupporting

confidence: 89%

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Guan

et al. 2021

Genome Biol

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Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. Results Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. Conclusions Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

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Section: Methodssupporting

confidence: 89%

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Guan

et al. 2021

Genome Biol

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“…3b, Additional file 5: Table S5). According to the previous report, in which the authors identified differentially expressed genes (DEGs) in samples of tail fat between thin-and fat-tailed sheep breeds, here we also found two up-regulated (PDGFD and IRF2BP2) and one down-regulated ASE genes (TEN1) in samples of tail fat, by comparing these two breeds [15]. IRF2BP2 gene is located in the quantitative trait loci (QTL) which is related to tail fat deposition, and TEN1 gene was considered to be associated with tail fat weight trait in Hulun Buir sheep [49].…”

Section: Analysis Of Ase Genes In Adipose Tissuesupporting

confidence: 78%

“…Seven (BCO2, BIN1, IRF2BP2, LRRC2, LOC101118164, LOC101104530 and SFRP1 genes) and six (PDGFD, PPDPF, PM20D1, PPM1K, PPA2 and TUBA8 genes) ASE genes were selected in thin-and fat-tailed sheep, respectively. Among these ASE genes, LRRC2 gene was identified as the important gene which were thought to be associated with meat production traits at chromosomewise significance level in sheep [49], while PDGFD gene was considered to be a primary causal gene for fat deposition in the tails of sheep [15]. A total of nine and seven ASE SNPs were found in LRRC2 and PDGFD genes, respectively, majority of these ASE SNPs located in 3'-UTR region of their respective genes.…”

Section: Discussionmentioning

confidence: 99%

“…5a). As a member of the platelet derived growth factor (PDGF), PDGFD gene plays an important role in regulation of adipocyte function and its expression is closely related to the fat deposition in sheep tail [15,52]. From eight samples of adipose tissue, seven ASE SNPs were found in PDGFD gene.…”

Section: Investigation Of Ase Genes Located In the Selected Regionsmentioning

confidence: 99%

“…These studies have proposed candidate genes, such as MSL1, PFKFB4, TRDN,FBF1,SETD7 and GRM1 [7,8]. On the other side, genomic scan for detecting regions associated with fat deposition were also performed in several sheep breeds [9][10][11][12][13][14][15][16][17]. However, the molecular mechanisms underlying gene expression related to such economically important traits remained mostly unexplored.…”

Section: Introductionmentioning

confidence: 99%

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Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Shao¹,

He²,

Pan³

et al. 2020

Preprint

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Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

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Research progress and applications of genome‐wide association study in farm animals

Tan

Fahey

et al. 2023

Animal Research and One Health

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Exploring the genetic loci underlying economic traits is foundational for innovation in modern animal breeding technology. Genome‐wide association studies (GWAS) have been valid and commonly used tools to dissect the genomic variants associated with phenotypes for the past ∼20 years and have contributed to our understanding of genetic and molecular bases of various traits. Here, we comprehensively review the recent research progress on GWAS methods. We highlight the methodological advancements enabled by the combination of new proteome, transcriptome, epigenome, and metagenome information and multi‐omics analysis algorithms. The advances in GWAS investigations of chickens, pigs, cattle, and other animals during the last 5 years are also described. Finally, we discuss the current applications of GWAS in cutting‐edge breeding technologies and overall future perspectives of the post‐GWAS era.

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Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Cited by 177 publications

References 77 publications

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Research progress and applications of genome‐wide association study in farm animals

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